.gitignore

@@ -7,7 +7,6 @@
 # Icon must end with two \r
 Icon
 
-
 # Thumbnails
 ._*
 
@@ -38,23 +37,3 @@ Temporary Items
 # Local History for Visual Studio Code
 .history/
 
-# local files
-
-spool/qmaster/jobs
-spool/qmaster/job_scripts
-spool/qmaster/messages*
-spool/qmaster/qmaster.pid
-spool/qmaster/heartbeat
-spool/qmaster/arseqnum
-spool/qmaster/advance_reservations
-spool/qmaster/jobseqnum
-spool/qmaster/zombies
-spool/gaia
-spool/minos11
-spool/minos12
-spool/minos13
-spool/minos14
-spool/minos15
-spool/minos26
-spool/minos27
-spool/qmaster/users

README.md

@@ -1,3 +1,3 @@
 # gridengine
 
-Scripts and configuration files to manage the gridengine software running int the Geophysics cluster.
+Scripts to manage the gridengine software

bin/suspend.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/ksh
-
+# $Id: suspend.sh 365 2013-11-18 09:58:17Z kasper $
 # This script should be added as the SUSPEND_METHOD in the
 # queue definition with a $job_pid, $job_id, and $job_owner arguments.
 # e.g. script.sh $job_pid $job_id $job_owner

bin/term.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/ksh
-# $Id: SGETerm.sh 364 2013-11-18 09:55:05Z kasper $
+# $Id: term.sh 364 2013-11-18 09:55:05Z kasper $
 # This script should be added as the TERMINATE_METHOD in the
 # queue definition with $job_pid, $job_id, $job_owner, and interval arguments.
 # e.g.  script.sh $job_pid $job_id $job_owner 90

examples/drmaa/example.c

@@ -1,211 +0,0 @@
-/*___INFO__MARK_BEGIN__*/
-/*************************************************************************
- * 
- *  The Contents of this file are made available subject to the terms of
- *  the Sun Industry Standards Source License Version 1.2
- * 
- *  Sun Microsystems Inc., March, 2001
- * 
- * 
- *  Sun Industry Standards Source License Version 1.2
- *  =================================================
- *  The contents of this file are subject to the Sun Industry Standards
- *  Source License Version 1.2 (the "License"); You may not use this file
- *  except in compliance with the License. You may obtain a copy of the
- *  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
- * 
- *  Software provided under this License is provided on an "AS IS" basis,
- *  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
- *  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
- *  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
- *  See the License for the specific provisions governing your rights and
- *  obligations concerning the Software.
- * 
- *   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
- * 
- *   Copyright: 2001 by Sun Microsystems, Inc.
- * 
- *   All Rights Reserved.
- * 
- ************************************************************************/
-/*___INFO__MARK_END__*/
-#include <stdio.h>
-#include <unistd.h>
-#include <string.h>
-
-#include "drmaa.h"
-
-#define JOB_CHUNK 8
-#define NBULKS 3
-
-static drmaa_job_template_t *create_job_template(const char *job_path, int seconds, int as_bulk_job);
-
-int main(int argc, char *argv[])
-{
-   char diagnosis[DRMAA_ERROR_STRING_BUFFER];
-   const char *all_jobids[NBULKS*JOB_CHUNK + JOB_CHUNK+1];
-   char jobid[100];
-   int drmaa_errno, i, pos = 0;
-   const char *job_path;
-   drmaa_job_template_t *jt;
-  
-   if (argc<2) {
-      fprintf(stderr, "usage: example <path-to-job>\n");
-      return 1;
-   }
-   job_path = argv[1];
-
-   if (drmaa_init(NULL, diagnosis, sizeof(diagnosis)-1) != DRMAA_ERRNO_SUCCESS) {
-      fprintf(stderr, "drmaa_init() failed: %s\n", diagnosis);
-      return 1;
-   }
-
-   /*
-    *   submit some bulk jobs
-    */
-   if (!(jt = create_job_template(job_path, 5, 1))) {
-      fprintf(stderr, "create_job_template() failed\n");
-      return 1;
-   }
-   for (i=0; i<NBULKS; i++) {
-      drmaa_job_ids_t *jobids;
-      int j;
-
-      while ((drmaa_errno=drmaa_run_bulk_jobs(&jobids, jt, 1, JOB_CHUNK, 1, diagnosis,
-                 sizeof(diagnosis)-1))==DRMAA_ERRNO_DRM_COMMUNICATION_FAILURE) {
-         fprintf(stderr, "drmaa_run_bulk_jobs() failed - retry: %s %s\n", diagnosis, drmaa_strerror(drmaa_errno));
-         sleep(1);
-      } 
-      if (drmaa_errno != DRMAA_ERRNO_SUCCESS) {
-         fprintf(stderr, "drmaa_run_bulk_jobs() failed: %s %s\n", diagnosis, drmaa_strerror(drmaa_errno));
-         return 1;
-      }
-
-      printf("submitted bulk job with jobids:\n");
-      for (j=0; j<JOB_CHUNK; j++) {
-         drmaa_get_next_job_id(jobids, jobid, sizeof(jobid)-1);
-         all_jobids[pos++] = strdup(jobid);
-         printf("\t \"%s\"\n", jobid);
-      } 
-      drmaa_release_job_ids(jobids);
-   }
-   drmaa_delete_job_template(jt, NULL, 0);
-
-   /*
-    *   submit some sequential jobs
-    */
-   if (!(jt = create_job_template(job_path, 5, 0))) {
-      fprintf(stderr, "create_sleeper_job_template() failed\n");
-      return 1;
-   }
-   for (i=0; i<JOB_CHUNK; i++) {
-      while ((drmaa_errno=drmaa_run_job(jobid, sizeof(jobid)-1, jt, diagnosis,
-               sizeof(diagnosis)-1)) == DRMAA_ERRNO_DRM_COMMUNICATION_FAILURE) {
-         fprintf(stderr, "drmaa_run_job() failed - retry: %s\n", diagnosis);
-         sleep(1);
-      }
-      if (drmaa_errno != DRMAA_ERRNO_SUCCESS) {
-         fprintf(stderr, "drmaa_run_job() failed: %s\n", diagnosis);
-         return 1;
-      }
-      printf("\t \"%s\"\n", jobid);
-      all_jobids[pos++] = strdup(jobid);
-   }
-
-   /* set string array end mark */
-   all_jobids[pos] = NULL;
-
-   drmaa_delete_job_template(jt, NULL, 0);
-
-   /*
-    *   synchronize with all jobs
-    */
-   drmaa_errno = drmaa_synchronize(all_jobids, DRMAA_TIMEOUT_WAIT_FOREVER, 0, diagnosis, sizeof(diagnosis)-1);
-   if (drmaa_errno != DRMAA_ERRNO_SUCCESS) {
-      fprintf(stderr, "drmaa_synchronize(DRMAA_JOB_IDS_SESSION_ALL, dispose) failed: %s\n", diagnosis);
-      return 1;
-   }
-   printf("synchronized with all jobs\n");
-
-   /*
-    *   wait all those jobs
-    */
-   for (pos=0; pos<NBULKS*JOB_CHUNK + JOB_CHUNK; pos++) {
-      int stat;
-      int aborted, exited, exit_status, signaled;
-
-      drmaa_errno = drmaa_wait(all_jobids[pos], jobid, sizeof(jobid)-1, 
-         &stat, DRMAA_TIMEOUT_WAIT_FOREVER, NULL, diagnosis, sizeof(diagnosis)-1);
-
-      if (drmaa_errno != DRMAA_ERRNO_SUCCESS) {
-         fprintf(stderr, "drmaa_wait(%s) failed: %s\n", all_jobids[pos], diagnosis);
-         return 1;
-      }
-
-      /*
-       * report how job finished 
-       */
-      drmaa_wifaborted(&aborted, stat, NULL, 0);
-      if (aborted)
-         printf("job \"%s\" never ran\n", all_jobids[pos]);
-      else {
-         drmaa_wifexited(&exited, stat, NULL, 0);
-         if (exited) {
-            drmaa_wexitstatus(&exit_status, stat, NULL, 0);
-            printf("job \"%s\" finished regularly with exit status %d\n", 
-                  all_jobids[pos], exit_status);
-         } else {
-            drmaa_wifsignaled(&signaled, stat, NULL, 0);
-            if (signaled) {
-               char termsig[DRMAA_SIGNAL_BUFFER+1];
-               drmaa_wtermsig(termsig, DRMAA_SIGNAL_BUFFER, stat, NULL, 0);
-               printf("job \"%s\" finished due to signal %s\n", 
-                  all_jobids[pos], termsig);
-            } else
-               printf("job \"%s\" finished with unclear conditions\n", 
-                  all_jobids[pos]);
-         }
-      }
-   }
-
-   if (drmaa_exit(diagnosis, sizeof(diagnosis)-1) != DRMAA_ERRNO_SUCCESS) {
-      fprintf(stderr, "drmaa_exit() failed: %s\n", diagnosis);
-      return 1;
-   }
-   
-  return 0;
-}
-
-
-static drmaa_job_template_t *create_job_template(const char *job_path, int seconds, int as_bulk_job)
-{
-   const char *job_argv[2];
-   drmaa_job_template_t *jt = NULL;
-   char buffer[100];
-
-   if (drmaa_allocate_job_template(&jt, NULL, 0)!=DRMAA_ERRNO_SUCCESS)
-      return NULL;
-
-   /* run in users home directory */
-   drmaa_set_attribute(jt, DRMAA_WD, DRMAA_PLACEHOLDER_HD, NULL, 0);
-
-   /* the job to be run */
-   drmaa_set_attribute(jt, DRMAA_REMOTE_COMMAND, job_path, NULL, 0);
-
-   /* the job's arguments */
-   sprintf(buffer, "%d", seconds);
-   job_argv[0] = buffer; 
-   job_argv[1] = NULL;
-   drmaa_set_vector_attribute(jt, DRMAA_V_ARGV, job_argv, NULL, 0);
-
-   /* join output/error file */
-   drmaa_set_attribute(jt, DRMAA_JOIN_FILES, "y", NULL, 0);
-
-   /* path for output */
-   if (!as_bulk_job)
-      drmaa_set_attribute(jt, DRMAA_OUTPUT_PATH, ":"DRMAA_PLACEHOLDER_HD"/DRMAA_JOB", NULL, 0);
-   else
-      drmaa_set_attribute(jt, DRMAA_OUTPUT_PATH, ":"DRMAA_PLACEHOLDER_HD"/DRMAA_JOB."DRMAA_PLACEHOLDER_INCR, NULL, 0);
-
-   return jt;
-}

examples/drmaa/howto1.c

@@ -1,56 +0,0 @@
-/*___INFO__MARK_BEGIN__*/
-/*************************************************************************
- * 
- *  The Contents of this file are made available subject to the terms of
- *  the Sun Industry Standards Source License Version 1.2
- * 
- *  Sun Microsystems Inc., March, 2001
- * 
- * 
- *  Sun Industry Standards Source License Version 1.2
- *  =================================================
- *  The contents of this file are subject to the Sun Industry Standards
- *  Source License Version 1.2 (the "License"); You may not use this file
- *  except in compliance with the License. You may obtain a copy of the
- *  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
- * 
- *  Software provided under this License is provided on an "AS IS" basis,
- *  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
- *  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
- *  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
- *  See the License for the specific provisions governing your rights and
- *  obligations concerning the Software.
- * 
- *   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
- * 
- *   Copyright: 2001 by Sun Microsystems, Inc.
- * 
- *   All Rights Reserved.
- * 
- ************************************************************************/
-/*___INFO__MARK_END__*/
-#include <stdio.h>
-#include "drmaa.h"
-
-int main (int argc, char **argv) {
-   char error[DRMAA_ERROR_STRING_BUFFER];
-   int errnum = 0;
-
-   errnum = drmaa_init (NULL, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not initialize the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   printf ("DRMAA library was started successfully\n");
-   
-   errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   return 0;
-}

examples/drmaa/howto1_1.c

@@ -1,81 +0,0 @@
-/*___INFO__MARK_BEGIN__*/
-/*************************************************************************
- * 
- *  The Contents of this file are made available subject to the terms of
- *  the Sun Industry Standards Source License Version 1.2
- * 
- *  Sun Microsystems Inc., March, 2001
- * 
- * 
- *  Sun Industry Standards Source License Version 1.2
- *  =================================================
- *  The contents of this file are subject to the Sun Industry Standards
- *  Source License Version 1.2 (the "License"); You may not use this file
- *  except in compliance with the License. You may obtain a copy of the
- *  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
- * 
- *  Software provided under this License is provided on an "AS IS" basis,
- *  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
- *  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
- *  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
- *  See the License for the specific provisions governing your rights and
- *  obligations concerning the Software.
- * 
- *   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
- * 
- *   Copyright: 2001 by Sun Microsystems, Inc.
- * 
- *   All Rights Reserved.
- * 
- ************************************************************************/
-/*___INFO__MARK_END__*/
-#include <stdio.h>
-#include "drmaa.h"
-
-int main (int argc, char **argv) {
-   char error[DRMAA_ERROR_STRING_BUFFER];
-   int errnum = 0;
-   char contact[DRMAA_CONTACT_BUFFER];
-
-   errnum = drmaa_init (NULL, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not initialize the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   printf ("DRMAA library was started successfully\n");
-
-   errnum = drmaa_get_contact (contact, DRMAA_CONTACT_BUFFER, error,
-                               DRMAA_ERROR_STRING_BUFFER);
-   
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not get the contact string: %s\n", error);
-      return 1;
-   }
-
-   errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   errnum = drmaa_init (contact, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not reinitialize the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   printf ("DRMAA library was restarted successfully\n");
-
-   errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   return 0;
-}

examples/drmaa/howto2.c

@@ -1,100 +0,0 @@
-/*___INFO__MARK_BEGIN__*/
-/*************************************************************************
- * 
- *  The Contents of this file are made available subject to the terms of
- *  the Sun Industry Standards Source License Version 1.2
- * 
- *  Sun Microsystems Inc., March, 2001
- * 
- * 
- *  Sun Industry Standards Source License Version 1.2
- *  =================================================
- *  The contents of this file are subject to the Sun Industry Standards
- *  Source License Version 1.2 (the "License"); You may not use this file
- *  except in compliance with the License. You may obtain a copy of the
- *  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
- * 
- *  Software provided under this License is provided on an "AS IS" basis,
- *  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
- *  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
- *  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
- *  See the License for the specific provisions governing your rights and
- *  obligations concerning the Software.
- * 
- *   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
- * 
- *   Copyright: 2001 by Sun Microsystems, Inc.
- * 
- *   All Rights Reserved.
- * 
- ************************************************************************/
-/*___INFO__MARK_END__*/
-#include <stdio.h>
-#include "drmaa.h"
-
-int main (int argc, char **argv) {
-   char error[DRMAA_ERROR_STRING_BUFFER];
-   int errnum = 0;
-   drmaa_job_template_t *jt = NULL;
-
-   errnum = drmaa_init (NULL, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not initialize the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   errnum = drmaa_allocate_job_template (&jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not create job template: %s\n", error);
-   }
-   else {
-      errnum = drmaa_set_attribute (jt, DRMAA_REMOTE_COMMAND, "sleeper.sh",
-                                    error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         const char *args[2] = {"5", NULL};
-         
-         errnum = drmaa_set_vector_attribute (jt, DRMAA_V_ARGV, args, error,
-                                              DRMAA_ERROR_STRING_BUFFER);
-      }
-      
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         char jobid[DRMAA_JOBNAME_BUFFER];
-
-         errnum = drmaa_run_job (jobid, DRMAA_JOBNAME_BUFFER, jt, error,
-                                 DRMAA_ERROR_STRING_BUFFER);
-
-         if (errnum != DRMAA_ERRNO_SUCCESS) {
-            fprintf (stderr, "Could not submit job: %s\n", error);
-         }
-         else {
-            printf ("Your job has been submitted with id %s\n", jobid);
-         }
-      } /* else */
-
-      errnum = drmaa_delete_job_template (jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not delete job template: %s\n", error);
-      }
-   } /* else */
-
-   errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   return 0;
-}

examples/drmaa/howto2_1.c

@@ -1,105 +0,0 @@
-/*___INFO__MARK_BEGIN__*/
-/*************************************************************************
- * 
- *  The Contents of this file are made available subject to the terms of
- *  the Sun Industry Standards Source License Version 1.2
- * 
- *  Sun Microsystems Inc., March, 2001
- * 
- * 
- *  Sun Industry Standards Source License Version 1.2
- *  =================================================
- *  The contents of this file are subject to the Sun Industry Standards
- *  Source License Version 1.2 (the "License"); You may not use this file
- *  except in compliance with the License. You may obtain a copy of the
- *  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
- * 
- *  Software provided under this License is provided on an "AS IS" basis,
- *  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
- *  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
- *  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
- *  See the License for the specific provisions governing your rights and
- *  obligations concerning the Software.
- * 
- *   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
- * 
- *   Copyright: 2001 by Sun Microsystems, Inc.
- * 
- *   All Rights Reserved.
- * 
- ************************************************************************/
-/*___INFO__MARK_END__*/
-#include <stdio.h>
-#include "drmaa.h"
-
-int main (int argc, char **argv) {
-   char error[DRMAA_ERROR_STRING_BUFFER];
-   int errnum = 0;
-   drmaa_job_template_t *jt = NULL;
-
-   errnum = drmaa_init (NULL, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not initialize the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   errnum = drmaa_allocate_job_template (&jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not create job template: %s\n", error);
-   }
-   else {
-      errnum = drmaa_set_attribute (jt, DRMAA_REMOTE_COMMAND, "sleeper.sh",
-                                    error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         const char *args[2] = {"5", NULL};
-         
-         errnum = drmaa_set_vector_attribute (jt, DRMAA_V_ARGV, args, error,
-                                              DRMAA_ERROR_STRING_BUFFER);
-      }
-      
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         drmaa_job_ids_t *ids = NULL;
-
-         errnum = drmaa_run_bulk_jobs (&ids, jt, 1, 30, 2, error, DRMAA_ERROR_STRING_BUFFER);
-
-         if (errnum != DRMAA_ERRNO_SUCCESS) {
-            fprintf (stderr, "Could not submit job: %s\n", error);
-         }
-         else {
-            char jobid[DRMAA_JOBNAME_BUFFER];
-
-            while (drmaa_get_next_job_id (ids, jobid, DRMAA_JOBNAME_BUFFER) == DRMAA_ERRNO_SUCCESS) {
-               printf ("A job task has been submitted with id %s\n", jobid);
-            }
-         }
-
-         drmaa_release_job_ids (ids);
-      }
-     
-      errnum = drmaa_delete_job_template (jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not delete job template: %s\n", error);
-      }
-   } /* else */
-
-   errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   return 0;
-}

examples/drmaa/howto3.c

@@ -1,156 +0,0 @@
-/*___INFO__MARK_BEGIN__*/
-/*************************************************************************
- * 
- *  The Contents of this file are made available subject to the terms of
- *  the Sun Industry Standards Source License Version 1.2
- * 
- *  Sun Microsystems Inc., March, 2001
- * 
- * 
- *  Sun Industry Standards Source License Version 1.2
- *  =================================================
- *  The contents of this file are subject to the Sun Industry Standards
- *  Source License Version 1.2 (the "License"); You may not use this file
- *  except in compliance with the License. You may obtain a copy of the
- *  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
- * 
- *  Software provided under this License is provided on an "AS IS" basis,
- *  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
- *  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
- *  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
- *  See the License for the specific provisions governing your rights and
- *  obligations concerning the Software.
- * 
- *   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
- * 
- *   Copyright: 2001 by Sun Microsystems, Inc.
- * 
- *   All Rights Reserved.
- * 
- ************************************************************************/
-/*___INFO__MARK_END__*/
-#include <stdio.h>
-#include "drmaa.h"
-
-int main (int argc, char **argv) {
-   char error[DRMAA_ERROR_STRING_BUFFER];
-   int errnum = 0;
-   drmaa_job_template_t *jt = NULL;
-
-   errnum = drmaa_init (NULL, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not initialize the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   errnum = drmaa_allocate_job_template (&jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not create job template: %s\n", error);
-   }
-   else {
-      errnum = drmaa_set_attribute (jt, DRMAA_REMOTE_COMMAND, "sleeper.sh",
-                                   error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         const char *args[2] = {"5", NULL};
-         
-         errnum = drmaa_set_vector_attribute (jt, DRMAA_V_ARGV, args, error,
-                                              DRMAA_ERROR_STRING_BUFFER);
-      }
-      
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         char jobid[DRMAA_JOBNAME_BUFFER];
-         char jobid_out[DRMAA_JOBNAME_BUFFER];
-         int status = 0;
-         drmaa_attr_values_t *rusage = NULL;
-
-         errnum = drmaa_run_job (jobid, DRMAA_JOBNAME_BUFFER, jt, error,
-                                 DRMAA_ERROR_STRING_BUFFER);
-
-         if (errnum != DRMAA_ERRNO_SUCCESS) {
-            fprintf (stderr, "Could not submit job: %s\n", error);
-         }
-         else {
-            printf ("Your job has been submitted with id %s\n", jobid);
-            
-            errnum = drmaa_wait (jobid, jobid_out, DRMAA_JOBNAME_BUFFER, &status,
-                                 DRMAA_TIMEOUT_WAIT_FOREVER, &rusage, error,
-                                 DRMAA_ERROR_STRING_BUFFER);
-            
-            if (errnum != DRMAA_ERRNO_SUCCESS) {
-               fprintf (stderr, "Could not wait for job: %s\n", error);
-            }
-            else {
-               char usage[DRMAA_ERROR_STRING_BUFFER];
-               int aborted = 0;
-
-               drmaa_wifaborted(&aborted, status, NULL, 0);
-
-               if (aborted == 1) {
-                  printf("Job %s never ran\n", jobid);
-               }
-               else {
-                  int exited = 0;
-
-                  drmaa_wifexited(&exited, status, NULL, 0);
-
-                  if (exited == 1) {
-                     int exit_status = 0;
-
-                     drmaa_wexitstatus(&exit_status, status, NULL, 0);
-                     printf("Job %s finished regularly with exit status %d\n", jobid, exit_status);
-                  }
-                  else {
-                     int signaled = 0;
-
-                     drmaa_wifsignaled(&signaled, status, NULL, 0);
-
-                     if (signaled == 1) {
-                        char termsig[DRMAA_SIGNAL_BUFFER+1];
-
-                        drmaa_wtermsig(termsig, DRMAA_SIGNAL_BUFFER, status, NULL, 0);
-                        printf("Job %s finished due to signal %s\n", jobid, termsig);
-                     }
-                     else {
-                        printf("Job %s finished with unclear conditions\n", jobid);
-                     }
-                  } /* else */
-               } /* else */
-               
-               printf ("Job Usage:\n");
-               
-               while (drmaa_get_next_attr_value (rusage, usage, DRMAA_ERROR_STRING_BUFFER) == DRMAA_ERRNO_SUCCESS) {
-                  printf ("  %s\n", usage);
-               }
-               
-               drmaa_release_attr_values (rusage);
-            } /* else */
-         } /* else */
-      } /* else */
-
-      errnum = drmaa_delete_job_template (jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not delete job template: %s\n", error);
-      }
-   } /* else */
-
-   errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   return 0;
-}

examples/drmaa/howto3_1.c

@@ -1,116 +0,0 @@
-/*___INFO__MARK_BEGIN__*/
-/*************************************************************************
- * 
- *  The Contents of this file are made available subject to the terms of
- *  the Sun Industry Standards Source License Version 1.2
- * 
- *  Sun Microsystems Inc., March, 2001
- * 
- * 
- *  Sun Industry Standards Source License Version 1.2
- *  =================================================
- *  The contents of this file are subject to the Sun Industry Standards
- *  Source License Version 1.2 (the "License"); You may not use this file
- *  except in compliance with the License. You may obtain a copy of the
- *  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
- * 
- *  Software provided under this License is provided on an "AS IS" basis,
- *  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
- *  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
- *  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
- *  See the License for the specific provisions governing your rights and
- *  obligations concerning the Software.
- * 
- *   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
- * 
- *   Copyright: 2001 by Sun Microsystems, Inc.
- * 
- *   All Rights Reserved.
- * 
- ************************************************************************/
-/*___INFO__MARK_END__*/
-#include <stdio.h>
-#include "drmaa.h"
-
-int main (int argc, char **argv) {
-   char error[DRMAA_ERROR_STRING_BUFFER];
-   int errnum = 0;
-   drmaa_job_template_t *jt = NULL;
-
-   errnum = drmaa_init (NULL, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not initialize the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   errnum = drmaa_allocate_job_template (&jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not create job template: %s\n", error);
-   }
-   else {
-      errnum = drmaa_set_attribute (jt, DRMAA_REMOTE_COMMAND, "sleeper.sh",
-                                   error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         const char *args[2] = {"5", NULL};
-         
-         errnum = drmaa_set_vector_attribute (jt, DRMAA_V_ARGV, args, error,
-                                              DRMAA_ERROR_STRING_BUFFER);
-      }
-      
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         drmaa_job_ids_t *ids = NULL;
-
-         errnum = drmaa_run_bulk_jobs (&ids, jt, 1, 30, 2, error, DRMAA_ERROR_STRING_BUFFER);
-
-         if (errnum != DRMAA_ERRNO_SUCCESS) {
-            fprintf (stderr, "Could not submit job: %s\n", error);
-         }
-         else {
-            char jobid[DRMAA_JOBNAME_BUFFER];
-            const char *jobids[2] = {DRMAA_JOB_IDS_SESSION_ALL, NULL};
-
-            while (drmaa_get_next_job_id (ids, jobid, DRMAA_JOBNAME_BUFFER) == DRMAA_ERRNO_SUCCESS) {
-               printf ("A job task has been submitted with id %s\n", jobid);
-            }
-            
-            errnum = drmaa_synchronize (jobids, DRMAA_TIMEOUT_WAIT_FOREVER,
-                                        1, error, DRMAA_ERROR_STRING_BUFFER);
-            
-            if (errnum != DRMAA_ERRNO_SUCCESS) {
-               fprintf (stderr, "Could not wait for jobs: %s\n", error);
-            }
-            else {
-               printf ("All job tasks have finished.\n");
-            }
-         } /* else */
-
-         drmaa_release_job_ids (ids);
-      } /* else */
-
-      errnum = drmaa_delete_job_template (jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not delete job template: %s\n", error);
-      }
-   } /* else */
-
-   errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   return 0;
-}

examples/drmaa/howto3_2.c

@@ -1,182 +0,0 @@
-/*___INFO__MARK_BEGIN__*/
-/*************************************************************************
- * 
- *  The Contents of this file are made available subject to the terms of
- *  the Sun Industry Standards Source License Version 1.2
- * 
- *  Sun Microsystems Inc., March, 2001
- * 
- * 
- *  Sun Industry Standards Source License Version 1.2
- *  =================================================
- *  The contents of this file are subject to the Sun Industry Standards
- *  Source License Version 1.2 (the "License"); You may not use this file
- *  except in compliance with the License. You may obtain a copy of the
- *  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
- * 
- *  Software provided under this License is provided on an "AS IS" basis,
- *  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
- *  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
- *  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
- *  See the License for the specific provisions governing your rights and
- *  obligations concerning the Software.
- * 
- *   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
- * 
- *   Copyright: 2001 by Sun Microsystems, Inc.
- * 
- *   All Rights Reserved.
- * 
- ************************************************************************/
-/*___INFO__MARK_END__*/
-#include <stdio.h>
-#include "drmaa.h"
-
-int main (int argc, char **argv) {
-   char error[DRMAA_ERROR_STRING_BUFFER];
-   int errnum = 0;
-   drmaa_job_template_t *jt = NULL;
-
-   errnum = drmaa_init (NULL, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not initialize the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   errnum = drmaa_allocate_job_template (&jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not create job template: %s\n", error);
-   }
-   else {
-      errnum = drmaa_set_attribute (jt, DRMAA_REMOTE_COMMAND, "sleeper.sh",
-                                   error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         const char *args[2] = {"5", NULL};
-         
-         errnum = drmaa_set_vector_attribute (jt, DRMAA_V_ARGV, args, error,
-                                              DRMAA_ERROR_STRING_BUFFER);
-      }
-      
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         drmaa_job_ids_t *ids = NULL;
-         int start = 1;
-         int end = 30;
-         int step = 2;
-
-         errnum = drmaa_run_bulk_jobs (&ids, jt, start, end, step, error,
-                                       DRMAA_ERROR_STRING_BUFFER);
-
-         if (errnum != DRMAA_ERRNO_SUCCESS) {
-            fprintf (stderr, "Could not submit job: %s\n", error);
-         }
-         else {
-            char jobid[DRMAA_JOBNAME_BUFFER];
-            const char *jobids[2] = {DRMAA_JOB_IDS_SESSION_ALL, NULL};
-
-            while (drmaa_get_next_job_id (ids, jobid, DRMAA_JOBNAME_BUFFER)
-                                                     == DRMAA_ERRNO_SUCCESS) {
-               printf ("A job task has been submitted with id %s\n", jobid);
-            }
-            
-            errnum = drmaa_synchronize (jobids, DRMAA_TIMEOUT_WAIT_FOREVER,
-                                        0, error, DRMAA_ERROR_STRING_BUFFER);
-            
-            if (errnum != DRMAA_ERRNO_SUCCESS) {
-               fprintf (stderr, "Could not wait for jobs: %s\n", error);
-            }
-            else {
-               char jobid[DRMAA_JOBNAME_BUFFER];
-               int status = 0;
-               drmaa_attr_values_t *rusage = NULL;
-               int count = 0;
-               
-               for (count = start; count < end; count += step) {
-                  errnum = drmaa_wait (DRMAA_JOB_IDS_SESSION_ANY, jobid,
-                                       DRMAA_JOBNAME_BUFFER, &status,
-                                       DRMAA_TIMEOUT_WAIT_FOREVER, &rusage,
-                                       error, DRMAA_ERROR_STRING_BUFFER);
-
-                  if (errnum != DRMAA_ERRNO_SUCCESS) {
-                     fprintf (stderr, "Could not wait for job: %s\n", error);
-                  }
-                  else {
-                     char usage[DRMAA_ERROR_STRING_BUFFER];
-                     int aborted = 0;
-
-                     drmaa_wifaborted(&aborted, status, NULL, 0);
-
-                     if (aborted == 1) {
-                        printf("Job %s never ran\n", jobid);
-                     }
-                     else {
-                        int exited = 0;
-
-                        drmaa_wifexited(&exited, status, NULL, 0);
-
-                        if (exited == 1) {
-                           int exit_status = 0;
-
-                           drmaa_wexitstatus(&exit_status, status, NULL, 0);
-                           printf("Job %s finished regularly with exit status %d\n",
-                                  jobid, exit_status);
-                        }
-                        else {
-                           int signaled = 0;
-
-                           drmaa_wifsignaled(&signaled, status, NULL, 0);
-
-                           if (signaled == 1) {
-                              char termsig[DRMAA_SIGNAL_BUFFER+1];
-
-                              drmaa_wtermsig(termsig, DRMAA_SIGNAL_BUFFER, status, NULL, 0);
-                              printf("Job %s finished due to signal %s\n", jobid, termsig);
-                           }
-                           else {
-                              printf("Job %s finished with unclear conditions\n", jobid);
-                           }
-                        } /* else */
-                     } /* else */
-
-                     printf ("Job Usage:\n");
-
-                     while (drmaa_get_next_attr_value (rusage, usage, DRMAA_ERROR_STRING_BUFFER)
-                                                                          == DRMAA_ERRNO_SUCCESS) {
-                        printf ("  %s\n", usage);
-                     }
-
-                     drmaa_release_attr_values (rusage);
-                  } /* else */
-               } /* for */
-            } /* else */
-         } /* else */
-
-         drmaa_release_job_ids (ids);
-      } /* else */
-
-      errnum = drmaa_delete_job_template (jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not delete job template: %s\n", error);
-      }
-   } /* else */
-
-   errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   return 0;
-}

examples/drmaa/howto4.c

@@ -1,110 +0,0 @@
-/*___INFO__MARK_BEGIN__*/
-/*************************************************************************
- * 
- *  The Contents of this file are made available subject to the terms of
- *  the Sun Industry Standards Source License Version 1.2
- * 
- *  Sun Microsystems Inc., March, 2001
- * 
- * 
- *  Sun Industry Standards Source License Version 1.2
- *  =================================================
- *  The contents of this file are subject to the Sun Industry Standards
- *  Source License Version 1.2 (the "License"); You may not use this file
- *  except in compliance with the License. You may obtain a copy of the
- *  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
- * 
- *  Software provided under this License is provided on an "AS IS" basis,
- *  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
- *  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
- *  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
- *  See the License for the specific provisions governing your rights and
- *  obligations concerning the Software.
- * 
- *   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
- * 
- *   Copyright: 2001 by Sun Microsystems, Inc.
- * 
- *   All Rights Reserved.
- * 
- ************************************************************************/
-/*___INFO__MARK_END__*/
-#include <stdio.h>
-#include "drmaa.h"
-
-int main (int argc, char **argv) {
-   char error[DRMAA_ERROR_STRING_BUFFER];
-   int errnum = 0;
-   drmaa_job_template_t *jt = NULL;
-
-   errnum = drmaa_init (NULL, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not initialize the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   errnum = drmaa_allocate_job_template (&jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not create job template: %s\n", error);
-   }
-   else {
-      errnum = drmaa_set_attribute (jt, DRMAA_REMOTE_COMMAND, "sleeper.sh",
-                                    error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         const char *args[2] = {"60", NULL};
-         
-         errnum = drmaa_set_vector_attribute (jt, DRMAA_V_ARGV, args, error,
-                                              DRMAA_ERROR_STRING_BUFFER);
-      }
-      
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         char jobid[DRMAA_JOBNAME_BUFFER];
-
-         errnum = drmaa_run_job (jobid, DRMAA_JOBNAME_BUFFER, jt, error,
-                                 DRMAA_ERROR_STRING_BUFFER);
-
-         if (errnum != DRMAA_ERRNO_SUCCESS) {
-            fprintf (stderr, "Could not submit job: %s\n", error);
-         }
-         else {
-            printf ("Your job has been submitted with id %s\n", jobid);
-            
-            errnum = drmaa_control (jobid, DRMAA_CONTROL_TERMINATE, error,
-                                    DRMAA_ERROR_STRING_BUFFER);
-            
-            if (errnum != DRMAA_ERRNO_SUCCESS) {
-               fprintf (stderr, "Could not delete job: %s\n", error);
-            }
-            else {
-               printf ("Your job has been deleted\n");
-            }
-         }
-      } /* else */
-
-      errnum = drmaa_delete_job_template (jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not delete job template: %s\n", error);
-      }
-   } /* else */
-
-   errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   return 0;
-}

examples/drmaa/howto5.c

@@ -1,149 +0,0 @@
-/*___INFO__MARK_BEGIN__*/
-/*************************************************************************
- * 
- *  The Contents of this file are made available subject to the terms of
- *  the Sun Industry Standards Source License Version 1.2
- * 
- *  Sun Microsystems Inc., March, 2001
- * 
- * 
- *  Sun Industry Standards Source License Version 1.2
- *  =================================================
- *  The contents of this file are subject to the Sun Industry Standards
- *  Source License Version 1.2 (the "License"); You may not use this file
- *  except in compliance with the License. You may obtain a copy of the
- *  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
- * 
- *  Software provided under this License is provided on an "AS IS" basis,
- *  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
- *  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
- *  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
- *  See the License for the specific provisions governing your rights and
- *  obligations concerning the Software.
- * 
- *   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
- * 
- *   Copyright: 2001 by Sun Microsystems, Inc.
- * 
- *   All Rights Reserved.
- * 
- ************************************************************************/
-/*___INFO__MARK_END__*/
-#include <stdio.h>
-#include <unistd.h>
-#include "drmaa.h"
-
-int main (int argc, char **argv) {
-   char error[DRMAA_ERROR_STRING_BUFFER];
-   int errnum = 0;
-   drmaa_job_template_t *jt = NULL;
-
-   errnum = drmaa_init (NULL, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not initialize the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   errnum = drmaa_allocate_job_template (&jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not create job template: %s\n", error);
-   }
-   else {
-      errnum = drmaa_set_attribute (jt, DRMAA_REMOTE_COMMAND, "sleeper.sh",
-                                    error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         const char *args[2] = {"60", NULL};
-         
-         errnum = drmaa_set_vector_attribute (jt, DRMAA_V_ARGV, args, error,
-                                              DRMAA_ERROR_STRING_BUFFER);
-      }
-      
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not set attribute \"%s\": %s\n",
-                  DRMAA_REMOTE_COMMAND, error);
-      }
-      else {
-         char jobid[DRMAA_JOBNAME_BUFFER];
-
-         errnum = drmaa_run_job (jobid, DRMAA_JOBNAME_BUFFER, jt, error,
-                                 DRMAA_ERROR_STRING_BUFFER);
-
-         if (errnum != DRMAA_ERRNO_SUCCESS) {
-            fprintf (stderr, "Could not submit job: %s\n", error);
-         }
-         else {
-            int status = 0;
-            
-            printf ("Your job has been submitted with id %s\n", jobid);
-            
-            sleep (20);
-            
-            errnum = drmaa_job_ps (jobid, &status, error,
-                                   DRMAA_ERROR_STRING_BUFFER);
-            
-            if (errnum != DRMAA_ERRNO_SUCCESS) {
-               fprintf (stderr, "Could not get job' status: %s\n", error);
-            }
-            else {
-               switch (status) {
-                  case DRMAA_PS_UNDETERMINED:
-                     printf ("Job status cannot be determined\n");
-                     break;
-                  case DRMAA_PS_QUEUED_ACTIVE:
-                     printf ("Job is queued and active\n");
-                     break;
-                  case DRMAA_PS_SYSTEM_ON_HOLD:
-                     printf ("Job is queued and in system hold\n");
-                     break;
-                  case DRMAA_PS_USER_ON_HOLD:
-                     printf ("Job is queued and in user hold\n");
-                     break;
-                  case DRMAA_PS_USER_SYSTEM_ON_HOLD:
-                     printf ("Job is queued and in user and system hold\n");
-                     break;
-                  case DRMAA_PS_RUNNING:
-                     printf ("Job is running\n");
-                     break;
-                  case DRMAA_PS_SYSTEM_SUSPENDED:
-                     printf ("Job is system suspended\n");
-                     break;
-                  case DRMAA_PS_USER_SUSPENDED:
-                     printf ("Job is user suspended\n");
-                     break;
-                  case DRMAA_PS_USER_SYSTEM_SUSPENDED:
-                     printf ("Job is user and system suspended\n");
-                     break;
-                  case DRMAA_PS_DONE:
-                     printf ("Job finished normally\n");
-                     break;
-                  case DRMAA_PS_FAILED:
-                     printf ("Job finished, but failed\n");
-                     break;
-               } /* switch */
-            } /* else */
-         } /* else */
-      } /* else */
-
-      errnum = drmaa_delete_job_template (jt, error, DRMAA_ERROR_STRING_BUFFER);
-
-      if (errnum != DRMAA_ERRNO_SUCCESS) {
-         fprintf (stderr, "Could not delete job template: %s\n", error);
-      }
-   } /* else */
-
-   errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   return 0;
-}

examples/drmaa/howto6.c

@@ -1,128 +0,0 @@
-/*___INFO__MARK_BEGIN__*/
-/*************************************************************************
- * 
- *  The Contents of this file are made available subject to the terms of
- *  the Sun Industry Standards Source License Version 1.2
- * 
- *  Sun Microsystems Inc., March, 2001
- * 
- * 
- *  Sun Industry Standards Source License Version 1.2
- *  =================================================
- *  The contents of this file are subject to the Sun Industry Standards
- *  Source License Version 1.2 (the "License"); You may not use this file
- *  except in compliance with the License. You may obtain a copy of the
- *  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
- * 
- *  Software provided under this License is provided on an "AS IS" basis,
- *  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
- *  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
- *  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
- *  See the License for the specific provisions governing your rights and
- *  obligations concerning the Software.
- * 
- *   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
- * 
- *   Copyright: 2001 by Sun Microsystems, Inc.
- * 
- *   All Rights Reserved.
- * 
- ************************************************************************/
-/*___INFO__MARK_END__*/
-#include <stdio.h>
-#include "drmaa.h"
-
-int main (int argc, char **argv) {
-   char error[DRMAA_ERROR_STRING_BUFFER];
-   int errnum = 0;
-   char contact[DRMAA_CONTACT_BUFFER];
-   char drm_system[DRMAA_DRM_SYSTEM_BUFFER];
-   char drmaa_impl[DRMAA_DRM_SYSTEM_BUFFER];
-   unsigned int major = 0;
-   unsigned int minor = 0;
-      
-   errnum = drmaa_get_contact (contact, DRMAA_CONTACT_BUFFER, error,
-                               DRMAA_ERROR_STRING_BUFFER);
-   
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not get the contact string list: %s\n", error);
-   }
-   else {
-      printf ("Supported contact strings: \"%s\"\n", contact);
-   }
-
-   errnum = drmaa_get_DRM_system (drm_system, DRMAA_DRM_SYSTEM_BUFFER, error,
-                               DRMAA_ERROR_STRING_BUFFER);
-   
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not get the DRM system list: %s\n", error);
-   }
-   else {
-      printf ("Supported DRM systems: \"%s\"\n", drm_system);
-   }
-   
-   errnum = drmaa_get_DRMAA_implementation (drmaa_impl, DRMAA_DRM_SYSTEM_BUFFER,
-                                            error, DRMAA_ERROR_STRING_BUFFER);
-   
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not get the DRMAA implementation list: %s\n", error);
-   }
-   else {
-      printf ("Supported DRMAA implementations: \"%s\"\n", drmaa_impl);
-   }
-
-   errnum = drmaa_init (NULL, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not initialize the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   errnum = drmaa_get_contact (contact, DRMAA_CONTACT_BUFFER, error,
-                               DRMAA_ERROR_STRING_BUFFER);
-   
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not get the contact string: %s\n", error);
-   }
-   else {
-      printf ("Connected contact string: \"%s\"\n", contact);
-   }
-
-   errnum = drmaa_get_DRM_system (drm_system, DRMAA_CONTACT_BUFFER, error,
-                               DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not get the DRM system: %s\n", error);
-   }
-   else {
-      printf ("Connected DRM system: \"%s\"\n", drm_system);
-   }
-
-   errnum = drmaa_get_DRMAA_implementation (drmaa_impl, DRMAA_DRM_SYSTEM_BUFFER,
-                                            error, DRMAA_ERROR_STRING_BUFFER);
-   
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not get the DRMAA implementation list: %s\n", error);
-   }
-   else {
-      printf ("Supported DRMAA implementations: \"%s\"\n", drmaa_impl);
-   }
-
-   errnum = drmaa_version (&major, &minor, error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not get the DRMAA version: %s\n", error);
-   }
-   else {
-      printf ("Using DRMAA version %d.%d\n", major, minor);
-   }
-   
-   errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER);
-
-   if (errnum != DRMAA_ERRNO_SUCCESS) {
-      fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error);
-      return 1;
-   }
-
-   return 0;
-}

examples/drmaa/ruby/array.rb

@@ -1,77 +0,0 @@
-#!/usr/bin/ruby
-
-#########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2006
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#   Copyright: 2006 by Sun Microsystems, Inc.
-#
-#   All Rights Reserved.
-#
-#########################################################################
-
-require 'drmaa'
-
-class Sleeper < DRMAA::JobTemplate
-	def initialize
-		super
-		self.command = "/bin/sleep"
-		self.arg     = ["1"]
-		self.stdout  = ":/dev/null"
-		self.join    = true
-	end
-end
-
-# Two array jobs are submitted. The second array task remains in
-# hold until the predecessor task was run. Demonstrate possible 
-# use of hold/release.
-
-NTASKS = 30
-session = DRMAA::Session.new
-
-jt = Sleeper.new
-pre = session.run_bulk(jt, 1, NTASKS, 1)
-suc = session.run_bulk(jt, 1, NTASKS, 1)
-
-h = Hash.new
-for i in 0 .. NTASKS-1 do
-	h[pre[i]] = suc[i] 
-end
-
-session.wait_each{ |info|
-	job = info.job
-	if h.has_key?(job) 
-		session.release(h[job])
-	end
-
-	if info.wifexited?
-		puts job + " returned with " + info.wexitstatus.to_s
-		# info.rusage.each { |u| puts "usage " + u }
-	elsif info.wifaborted?
-		puts job + " aborted"
-	elsif info.wifsignaled?
-		puts job + " died from " + info.wtermsig
-	end
-}
-
-exit 0

examples/drmaa/ruby/attributes.rb

@@ -1,49 +0,0 @@
-#!/usr/bin/ruby
-
-#########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2006
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#   Copyright: 2006 by Sun Microsystems, Inc.
-#
-#   All Rights Reserved.
-#
-#########################################################################
-
-require 'drmaa'
-
-version = DRMAA.version
-drm = DRMAA.drm_system
-impl = DRMAA.drmaa_implementation
-contact = DRMAA.contact
-puts "DRMAA: #{drm} version #{version} impl #{impl} contact #{contact}"
-
-session = DRMAA::Session.new
-
-puts "supported DRMAA job template attributes:"
-attrs = DRMAA.attributes.each { |n| puts "   #{n}" }
-puts "supported DRMAA job template vector attributes:"
-attrs = DRMAA.vector_attributes.each { |n| puts "   #{n}" }
-
-
-exit 0

examples/drmaa/ruby/example.rb

@@ -1,70 +0,0 @@
-#!/usr/bin/ruby
-
-#########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2006
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#   Copyright: 2006 by Sun Microsystems, Inc.
-#
-#   All Rights Reserved.
-#
-#########################################################################
-
-require 'drmaa'
-
-class Sleeper < DRMAA::JobTemplate
-	def initialize
-		super
-		self.command = "/bin/sleep"
-		self.arg     = ["1"]
-		self.stdout  = ":/dev/null"
-		self.join    = true
-	end
-end
-
-version = DRMAA.version
-drm = DRMAA.drm_system
-impl = DRMAA.drmaa_implementation
-contact = DRMAA.contact
-puts "DRMAA #{drm} v #{version} impl #{impl} contact #{contact}"
-
-session = DRMAA::Session.new
-
-t = Sleeper.new
-
-jobid = session.run(t) 
-puts "job: " + jobid
-
-session.run_bulk(t, 1, 20).each { |job| 
-	puts "job: " + job 
-}
-
-session.wait_each{ |info|
-	if ! info.wifexited?
-		puts "failed: " + info.job
-	else	
-		puts info.job + " returned with " + info.wexitstatus.to_s
-	end
-}
-
-exit 0

examples/drmaa/ruby/flow/README

@@ -1,39 +0,0 @@
-== Workflow interpreter and processor
-
-   flow.rb is a utility for running job workflows in 
-   DRMAA-compliant DRM systems. Workflows are specified in 
-   flowfiles that allow expression of
-
-     * concurrent and sequential execution of sub-flows
-     * multiple runs of sub-flows with varying parameter sets
-     * actual jobs are defined in terms of DRMAA attributes
-   
-   in addition any subflow or sets of subflows can be run
-   as used with make(1) by specifying it as target.
-
-=== Job defaults
-
-   To minimize the extent of attributes necessarily
-   specified in flowfiles, flow.rb provides defaults for 
-   jobs' command path, stdout/stdin path, current working
-   directory and job name.
-
-=== Workflow verification
-
-   The -verify option can be used to print dependencies and
-   job attributes for diagnosis purposes.  To ensure each
-   workflow job can be run, a number of verifications is 
-   performed before the first job gets submitted.
-
-=== Job streaming
-
-   Large workflows are automatically run in job streaming mode
-   upon DRM saturation and a job maximum can be set in .flowrc.rb
-   to place an upper limit of jobs be kept concurrently in the
-   DRM for each workflow.
-
-=== Pre-submission plug-in
-
-   Enforcement of site-specific policies can easily be 
-   achieved through pre-submission procedures that allow
-   any job attribute to be modified freely.

examples/drmaa/ruby/flow/flow.rb

@@ -1,911 +0,0 @@
-#!/usr/bin/ruby
-
-#########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2006
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#   Copyright: 2006 by Sun Microsystems, Inc.
-#
-#   All Rights Reserved.
-#
-#########################################################################
-# TODO: 
-# - provide means to restart entire flows with failed flowjobs be rerun only
-# - support bulk jobs
-# - allow DRMAA user hold be used despite user hold be used by flow itself
-#########################################################################
-
-require 'drmaa'
-
-
-# ------------------------------------------------------------------------------------------
-# Exceptions thrown during parsing stage
-
-class ParsingFunction < ArgumentError ; end
-class ParsingFormat < ArgumentError ; end
-
-
-# ------------------------------------------------------------------------------------------
-# The FlowFunction classes represent the entities found in the flowfile.
-
-class FlowFunction
-end
-class JobsInParallel < FlowFunction
-	attr_accessor :par
-	def make(key, vars, depend, depth, select)
-		do_it = select_func?(key, vars, select)
-	
-		all_jobs = Array.new
-		@par.each { |sub| 
-			name = sub[0]
-			if do_it
-				flowprint(depth, "PARALLEL: " + name)
-			end
-			new_vars = sub[1]
-			sub_vars = vars.dup
-			if ! new_vars.nil?
-				new_vars.each_pair { |var,val| sub_vars[var] = val }
-			end
-			j = $flowfunction[name]
-			if j.nil?
-				raise ParsingFunction.new("#{key}(): flow function \"#{name}\" does not exit")
-			end
-			if do_it
-				jobs = j.make(name, sub_vars, depend, depth+1, nil)
-			else
-				jobs = j.make(name, sub_vars, depend, depth+1, select)
-			end
-			if ! jobs.nil?
-				all_jobs += jobs
-			end
-		}
-		if all_jobs.size != 0
-			return all_jobs
-		else
-			return nil
-		end
-	end
-end
-
-class JobsInSequence  < FlowFunction
-	attr_accessor :seq
-	def make(key, vars, depend, depth, select)
-		do_it = select_func?(key, vars, select)
-		first = true
-		@seq.each { |sub| 
-			name = sub[0]
-			flowprint(depth, "SEQUENTIAL: " + name) if do_it
-			new_vars = sub[1]
-			sub_vars = vars.dup
-			if ! new_vars.nil?
-				new_vars.each_pair { |var,val| sub_vars[var] = val }
-			end
-			j = $flowfunction[name]
-			if j.nil?
-				raise ParsingFunction.new("#{key}: flow function \"#{name}\" does not exit")
-			end
-			if do_it
-				depend = j.make(name, sub_vars, depend, depth+1, nil)
-			else
-				depend = j.make(name, sub_vars, depend, depth+1, select)
-			end
-		}
-		return depend
-	end
-end
-
-class RunnableJob < FlowFunction
-	attr_accessor :attrs, :njobs
-	def initialize
-		@njobs = 0
-	end
-
-	def make(key, vars, depend, depth, select)
-		@njobs += 1
-		job_key = key + "#" + @njobs.to_s
-
-		do_it = select_func?(key, vars, select)
-
-		fj_attrs = Array.new
-		@attrs.each_pair { |name,t|
-			value = substitute(t, vars)
-			fj_attrs.push([ name, value ])
-		}
-		if depend.nil?
-			f = FlowJob.new(nil, fj_attrs)
-			flowprint(depth, job_key + "(" + comma_vars(vars) + ")") if do_it
-		else 
-			f = FlowJob.new(depend.dup, fj_attrs)
-			flowprint(depth, job_key + "(" + comma_vars(vars) + ") waiting for " + comma_jobs(f.depend, ", ")) if do_it
-		end
-		fj_attrs.each { |a| flowprint(depth+1, a[0] + "=\"" + a[1] + "\"") } if do_it
-		f.presubproc(job_key)
-		f.verify(job_key)
-
-		if ! do_it
-			$not_selected += 1
-			return [ ]
-		end
-
-		$flowjob[job_key] = f
-		return [ job_key ]
-	end
-end
-
-def flowprint(depth, s)
-   return if ! $parse_only
-   (depth*3).times { putc " " } ; puts s
-end
-
-def comma_vars(vars)
-s = ""
-first = true
-vars.each_pair { |var,val|
-	if first == false
-		s += ", " 
-	else
-		first = false
-	end
-	s += var + "=" + val
-}
-return s
-end
-
-def comma_jobs(jobs, sep = ",")
-s = ""
-first = true
-jobs.each { |job|
-	if first == false
-		s += sep
-	else
-		first = false
-	end
-	s += job
-}
-return s
-end
-
-def substitute(s, vars)
-vars.each_pair { |var,val|
-	s = s.sub(var, val)
-}
-return s
-end
-
-# parses name1=value1,... into a Hash
-# used both for params and attrs
-def var_list(str)
-	vars = Hash.new
-	if ! str.nil?
-		str.strip.scan(/[^,][^,]*/) { |vardef|
-			n = vardef.strip.scan(/[^=][^=]*/)
-			vars[n[0].strip] = n[1].strip
-		}
-	end
-	return vars
-end
-
-# decide if a paricular flow call was selected as target
-def select_func?(k1, vrs1, select)
-	return true if select.nil?
-
-	k2 = select[0]
-	vrs2 = select[1]
-	if k1 != k2 or vrs1.size < vrs2.size
-		return false
-	end
-
-	vrs2.each_pair { |k,v|
-		if ! vrs1.has_key?(k) or vrs1[k] != v
-			return false
-		end
-	}
-
-	return true
-end
-
-# return name of first function
-def parse_flow(file)
-	all = nil
-	begin
-		IO::foreach(file) { |line|
-			case line
-			when /^#/
-				next
-			else
-				# crack line
-				function = line.sub(/[ ]*=.*$/, "").strip
-				val = line.sub(/^[^=]*=/, "").strip
-				if all.nil?
-					all = function
-				end
-
-				# runnable job
-				if ! val.index("{").nil?
-					r = RunnableJob.new
-					jobdef = val.scan(/[^{}][^{}]*/)[0].strip
-					r.attrs = var_list(jobdef)
-					$flowfunction[function] = r
-
-				# jobs in parallel
-				elsif ! val.index("&").nil?
-					p = JobsInParallel.new
-					p.par = Array.new
-					val.scan(/[^&][^&]*/) { |sub| p.par << parse_flowcall(sub) }
-					$flowfunction[function] = p
-
-				# jobs in sequence
-				elsif ! val.index("|").nil?
-					s = JobsInSequence.new
-					s.seq = Array.new
-					val.scan(/[^|][^|]*/) { |sub| s.seq << parse_flowcall(sub) }
-					$flowfunction[function] = s
-
-				else
-					# parsing code possibly is not yet good enoug -- sorryh
-					raise ParsingFormat.new("flow file may not have empty lines")
-				end
-			end
-		}
-	end
-	return all
-end
-
-def parse_flowcall(s)
-	jobdef = s.strip.scan(/[^()][^()]*/)
-	key = jobdef[0].strip
-	vars = var_list(jobdef[1])
-	return [ key, vars ]
-end
-
-
-# ------------------------------------------------------------------------------------------
-# At end of parsing stage there is one FlowJob for each job to be run.
-# The FlowJob also keeps state information, dependency information and 
-# job finish information.
-
-class FlowJob 
-	# configuration
-	attr_accessor :attrs, :depend
-	# state information
-	attr_accessor :jobid, :info 
-	def initialize(depend, attrs)
-		@depend = depend
-		@attrs = attrs
-	end
-	# -- verification
-	def verify(key)
-		cmd = false
-		@attrs.each { |a|
-			name = a[0]
-			value = a[1]
-			if value.index('$')
-				raise ParsingFunction.new("#{key}: #{name}=#{value} contains \"$\"")
-			end
-			case name
-			when "cmd"
-				if value.index('/') == 0
-					if ! File.executable?(value)
-						raise ParsingFunction.new("#{key}: cmd=#{value} must be executable")
-					end
-				else
-					if executable_cmd(value).nil?
-						raise ParsingFunction.new("#{key}: could't find cmd=#{value} in CMDPATH")
-					end
-				end
-				cmd = true
-			when "join", "nomail"	
-				true_or_false?(key, name, value)
-			when "args", "name", "nat", "cat", "wd", "in", "out", "err", "join", "trans", "mail"
-			else
-				# bug: must use DRMAA.get_attribute_names() to detect use of invalid attributes
-				raise ParsingFunction.new("#{key}: unknown attribute \"#{name}\"")
-			end
-		}
-		if !cmd
-			raise ParsingFunction.new("#{key}: missing mandatory attribute \"cmd\"")
-		end
-	end
-	def presubproc(job_key)
-		if defined? FlowRC.presubmit_proc
-			FlowRC.presubmit_proc(job_key, @attrs)
-		end
-	end
-	def executable_cmd(cmd)
-		path = nil
-		$CMDPATH.each { |p|
-			if File.executable?(p + "/" + cmd)
-				path = p + "/" + cmd
-				break
-			end
-		}
-		return path
-	end
-	def true_or_false?(key, name, value)
-		case value
-		when "0", "false", "no", "n"
-			return false
-		when "1", "true", "yes", "y"
-			return true
-		else
-			raise ParsingFunction.new("#{key}: \"#{name}=#{value}\" is neither \"true\" nor \"false\"")
-		end
-	end
-
-	def submit(key, predecessors)
-		if $MAX_JOBS != 0 and $jobs_in_drm == $MAX_JOBS 
-			return false
-		end
-		jt = DRMAA::JobTemplate.new
-
-      # job defaults
-		jt.name = key # flow job name
-		if $flowdir.nil?
-			jt.wd = $wd
-			jt.stdout = ":/dev/null"
-			jt.join = true
-		else
-			jt.wd = $flowdir
-			jt.stdout = ":#{$flowdir}/#{key}.o"
-			jt.stderr = ":#{$flowdir}/#{key}.e"
-			jt.join = false
-		end
-
-		native = nil
-
-		attrs.each { |a|
-			name = a[0]
-			value = a[1]
-			case name
-			when "cmd"
-				if value.index("/") == 0 
-					jt.command = value
-				else
-					jt.command = executable_cmd(value)
-				end
-			when "args"
-				jt.arg = value.split(" ")
-			when "env"
-				jt.env = value.split(",")
-			when "name"
-				jt.name = value
-			when "nat"
-				native = value
-			when "cat"	
-				jt.category = value
-			when "hold"	
-				# careful! hold is used by flow itself
-				# jt.hold = true_or_false?(key, name, value)
-			when "wd"
-				jt.wd = value
-			when "in"	
-				jt.stdin = value
-			when "out"	
-				jt.stdout = value
-			when "err"	
-				jt.stderr = value
-			when "join"	
-				jt.join = true_or_false?(key, name, value)
-			when "trans"	
-				jt.transfer = value
-
-			when "mail"
-				jt.mail = value.split(",")
-			when "nomail"	
-				jt.block_mail = true_or_false?(key, name, value)
-			end
-		}
-
-		if ! predecessors.nil?
-			if $drm_depend 
-				if native.nil?
-					jt.native = "-hold_jid " + predecessors
-				else
-					jt.native = native + " -hold_jid " + predecessors
-				end
-			else
-				jt.hold = true
-				jt.native = native unless native.nil?
-			end
-		else
-			jt.native = native unless native.nil?
-		end
-
-		begin
-			jobid = $session.run(jt)
-			$already_submitted += 1
-			$last_submission = Time.now
-			@jobid = jobid
-			if ! predecessors.nil?
-				puts "#{key} " + jobid + " submitted depending on " + predecessors
-			else
-				puts "#{key} " + jobid + " submitted"
-			end
-		rescue DRMAA::DRMAATryLater
-			STDERR.puts "... try later (#{key})"
-			return false
-		end
-		$jobs_in_drm += 1
-		return true
-	end
-
-	# true, if all predecessors done 
-	def is_due? 
-		return true if @depend.nil?
-
-		self.depend.each { |key|
-			info = $flowjob[key].info
-			if info.nil? 
-				return false # not yet finished
-			end
-			if ! info.wifexited? or info.wexitstatus != 0
-				return false # failed
-			end
-		}
-
-		return true
-	end
-
-	def can_submit 
-		# now   --> [0, jobids]
-		# later --> [1, nil]
-		# never --> [2, nil]
-		r = 0
-		jobids = nil
-		self.depend.each { |key|
-			node = $flowjob[key]
-
-			info = node.info
-			if ! info.nil?
-				if !info.wifexited? or info.wexitstatus != 0
-					return [ 2, nil] # failed
-				else
-					next # done
-				end
-			end
-
-			jobid = node.jobid
-			if jobid.nil?
-				r = 1 # predecessor not yet submitted
-			else
-				# collect jobids
-				if jobids.nil?
-					jobids = jobid
-				else
-					jobids += "," + jobid
-				end
-			end
-		}
-		if r == 1
-			return [1,nil]
-		else
-			return [0,jobids]
-		end
-	end
-end
-
-
-# ------------------------------------------------------------------------------------------
-# The functions below are used by main to run the workflow  and cause 
-# successor jobs be submitted/released once they are due.
-
-# Workflow optimization requires job be submitted in order
-# pass (1): jobs without predecessors or with all predecessors run
-# pass (2): jobs whose predecessors are submitted
-# aims is as broad as possible flow submission.
-def submit_jobs(flush)
-
-	if $flowjob.size == $already_submitted or $terminate_session
-		# STDERR.puts "all jobs submitted"
-		return true # all submitted
-	end
-
-	if ! flush 
-		if $last_submission != 0 and (Time.now - $last_submission) < $STREAMING_RETRY
-			# puts "... retry not yet reached"
-			return false # retry not yet reached
-		end
-	end
-
-	# STDERR.puts "1st pass"
-	$flowjob.each_pair { |key,fj|
-		next if ! fj.jobid.nil? # already submitted
-		next if ! fj.info.nil? # already finished
-
-		# all predecessors done 
-		next if ! fj.is_due? 
-
-		if ! fj.submit(key, nil)
-			return false # try again
-		end
-
-		if $terminate_program
-			exit 1
-		elsif $terminate_session
-			terminate()
-			return true
-		end
-	}
-
-	begin
-		# STDERR.puts "2nd pass"
-		all_submitted = true
-
-		$flowjob.each_pair { |key,fj|
-			next if ! fj.jobid.nil? # already submitted
-			next if ! fj.info.nil? # already finished
-
-			# analyze predecessors
-			status = fj.can_submit()
-			if status[0] != 0 
-				all_submitted = false if status[0] == 1 
-				next
-			end
-			predecessors = status[1]
-
-			if ! fj.submit(key, predecessors)
-				return false # try again
-			end
-
-			if $terminate_program
-				exit 1
-			elsif $terminate_session
-				terminate()
-				return true
-			end
-		}
-	end until all_submitted
-
-	return true # all submitted
-end
-
-def reap_jobs
-
-	$session.wait_each(1) { |info|
-
-		# delete workflow upon user interrupt
-		if $terminate_program
-			exit 1
-		elsif $terminate_session
-			terminate()
-		end
-
-		# nothing happend
-		if info.nil?
-			submit_jobs(false)
-			next
-		end
-		$jobs_in_drm -= 1
-
-		# interpret job finish information
-		if info.wifaborted? 
-			failed = true
-			happend = "aborted"
-			caused = "terminated"
-		elsif info.wifsignaled? 
-			failed = true
-			happend = "died from " + info.wtermsig 
-			happend += " (core dump)" if info.wcoredump?  
-			caused = "terminated"
-		elsif info.wifexited?
-			exit_status = info.wexitstatus
-			if  exit_status != 0
-				failed = true
-				happend = "exited with " + exit_status.to_s
-				caused = "terminated"
-			else
-				failed = false
-				happend = "done"
-				caused = "released"
-			end
-		end
-
-		# search flow job
-		job_key = nil
-		fjob = nil
-		$flowjob.each_pair { |k,v|
-			if v.jobid.nil?
-				next 
-			end
-			if v.jobid == info.job
-				job_key = k
-				fjob = v
-				break
-			end
-		}
-		if fjob.nil?
-			puts "missing flow job for finished job " + info.job
-			exit 1
-		end
-
-		# mark flow job as done
-		fjob.info = info
-		fjob.jobid = nil
-
-		trigger = Array.new
-		if ! $terminate_session
-			# drive conclusions
-			$flowjob.each_pair { |k,v|
-				# finished and non-blocked ones: skip 
-				next if ! v.info.nil? or v.depend.nil? or v.jobid.nil?
-				# dependend to others: skip 
-				next if ! v.depend.include?(job_key)
-				
-				if failed
-					begin
-						$session.terminate(v.jobid)
-					rescue DRMAA::DRMAAInvalidJobError
-					end
-					trigger << v.jobid
-				else
-					do_rls = true
-					v.depend.each { |k|
-						do_rls = false if $flowjob[k].info.nil?
-					}
-					if do_rls and ! $drm_depend 
-						$session.release(v.jobid)
-						trigger << v.jobid
-					end
-				end
-			}
-		end
-
-		# report what happend
-		if trigger.size == 0
-			puts "#{job_key} #{info.job} " + happend
-		else
-			puts "#{job_key} #{info.job} " + happend + " " + caused + " " + comma_jobs(trigger, ", ")
-		end
-
-		submit_jobs(false)
-	}
-end
-
-# show final statistics
-def final_report
-	nfailed = 0
-	nrun = 0
-	nnotrun = 0
-
-	rusage = Hash.new
-	$flowjob.each_pair { |k,v|
-		if v.info.nil?
-			nnotrun += 1
-			next 
-		end
-		if ! v.info.wifexited? or v.info.wexitstatus != 0
-			nfailed += 1
-		else
-			nrun += 1
-		end
-		usage = v.info.rusage
-		next if usage.nil?
-		usage.each_pair { |name,value| 
-			if $USAGE_REPORT.include?(name)
-				if ! rusage.has_key?(name)
-					rusage[name] = value.to_f
-				else
-					rusage[name] += value.to_f
-				end
-			end
-		}
-	}
-	puts "# ---- final report"
-	rusage.each_pair { |name,value|
-		printf("usage: #{name} = %-7.2f\n", value)
-	}
-	puts "run: #{nrun} failed: #{nfailed} notrun: #{nnotrun}"
-end
-
-def terminate
-	if ! $did_terminate
-		STDERR.puts "Terminate!"
-		$session.terminate
-		$did_terminate = true
-	end
-end
-
-def handle_signal
-	if ! $terminate_session 
-		$terminate_session = true
-	elsif ! $terminate_program 
-		$terminate_program = true
-	end
-end
-
-def usage(ret)
-	if ret == 0
-		out =  STDOUT
-	else
-		out = STDERR
-	end
-	out.puts "usage: flow.rb [options] workflow.ff [start]"
-	out.puts "  options: -verify         only parse and verify the flow"
-	out.puts "           -dd             use DRM dependencies"
-	out.puts "           -flowdir <path> flowdir is used as defaults"
-	out.puts "  start:   <flowcall> -->  TEST or TEST($arch=solaris)"
-	exit ret
-end
-
-# ------------------------------------------------------------------------------------------
-#    main
-
-# use defaults 
-# (1) from ./.flowrc.rb 
-# (2) from $HOME/.flowrc.rb 
-# (3) or built-in ones
-
-read_rc_file = false
-if FileTest.exist?('.flowrc.rb')
-	require '.flowrc'
-	read_rc_file = true
-elsif FileTest.exist?(ENV["HOME"] + "/.flowrc.rb")
-	require ENV["HOME"] + "/.flowrc.rb"
-	read_rc_file = true
-end
-
-if ! read_rc_file
-	$CMDPATH = Dir::getwd()
-	$STREAMING_RETRY = 5
-	$USAGE_REPORT = [ ]
-	$MAX_JOBS = 0
-else
-	$CMDPATH = FlowRC::CMDPATH
-	$STREAMING_RETRY = FlowRC::STREAMING_RETRY
-	$USAGE_REPORT = FlowRC::USAGE_REPORT
-	$MAX_JOBS = FlowRC::MAX_JOBS
-end
-
-# The flowdir is used in a number of cases to have reasonable 
-# defaults. Thus it makes some difference if flowdir was 
-# specified or not:
-# 
-# wd (drmaa_wd)
-#    The flowdir is used as jobs' default working directory.
-#    Without flowdir the current working directory is simply 
-#    used. Though each jobs' working directory can also be
-#    specified within the flowfile, but if they have to that
-#    would make them harder to read by humans.  
-#
-# out/err/join (drmaa- stdout_path/stderr_path/join)
-#    Without flowdir "/dev/null" is used as default for 'out'
-#    and 'join' is true. Reason is there were no better 
-#    default to store job output/error files than the
-#    current working directory, but if that were used
-#    it might incidentally happen that masses of job 
-#    output files are dumped in some directory. If flowdir
-#    was specified at command line it is used as default
-#    for storing job output and error separately in 
-#    $flowdir/<flowjobname>.o and $flowdir/<flowjobname>.o.
-#
-# cmd (drmaa_remote_command)
-# args (drmaa_argv)
-# env (drmaa_env)
-
-
-$parse_only = false
-$drm_depend = false
-$flowdir = nil
-
-# command line parsing
-while ARGV.length >= 2 do 
-	case ARGV[0]
-	when "-verify"
-		$parse_only = true
-		ARGV.shift
-	when "-dd"
-		$drm_depend = true
-		ARGV.shift
-	when "-flowdir"
-		ARGV.shift
-		usage(1) if $flowdir or ARGV.length < 2
-		$flowdir = ARGV[0]
-		ARGV.shift
-	when "-h", "-help"
-		usage 0
-	else
-		break
-	end
-end
-if ARGV.length >= 1
-	flowfile=ARGV.shift
-	if ! FileTest.readable?(flowfile)
-	 	STDERR.puts flowfile + " does not exit"
-	 	exit 1
-	 end
-else 
-	usage(1)
-end
-if ARGV.length == 1
-	target = parse_flowcall(ARGV.shift)
-end
-usage(1) unless ARGV.length == 0
-
-# flow parsing and verification
-begin
-	$wd = Dir::getwd
-
-	$flowfunction = Hash.new
-	all = parse_flow(flowfile)
-	j = $flowfunction[all]
-
-	$flowjob = Hash.new
-	$not_selected = 0
-	target = parse_flowcall(all) if target.nil?
-	j.make(all, vars = Hash.new, nil, 0, target)
-	if $flowjob.size == 0
-		raise ParsingFormat.new("flow start \"#{target[0]}\" does not exist in #{flowfile}")
-	end
-	puts "---+ doing #{$flowjob.size} of #{$flowjob.size+$not_selected} jobs with #{target[0]} as flow target"
-
-	STDOUT.flush
-	exit 0 if $parse_only
-rescue ParsingFunction => msg
-	STDERR.puts "Error in " + msg
-	exit 1
-rescue ParsingFormat => msg
-	STDERR.puts "Format error: " + msg
-	exit 1
-end
-
-# run the workflow
-t1 = Time.now
-begin
-	$terminate_session = $terminate_program = false
-	trap("INT") { handle_signal }
-	trap("TERM") { handle_signal }
-
-	$session = DRMAA::Session.new
-	# puts "# ----- submitting jobs" 
-	$already_submitted = $last_submission = 0
-	$jobs_in_drm = 0
-
-	# May not stop reaping before all jobs 
-	# are submitted in case of streaming.
-	first = true
-	begin
-		all_reaped = false
-		all_submitted = submit_jobs(true)
-		if first
-			# puts "# ----- reaping jobs" 
-			first = false
-		else
-			if all_submitted
-				all_reaped = true 
-			else
-				sleep $STREAMING_RETRY
-			end
-		end
-		reap_jobs()
-	end until all_reaped
-
-rescue DRMAA::DRMAAException => msg
-	puts msg
-	exit 1
-end
-
-final_report()
-
-t2 = Time.now
-printf("total: %7.1f seconds\n", t2-t1)
-exit 0

examples/drmaa/ruby/flow/samples/README

@@ -1,46 +0,0 @@
-== Sample flowfiles
-
-   The samples comprise four different flowfiles
-
-		* tiny.ff      (one single job)
-		* small.ff     (29 jobs)
-		* large.ff     (780 jobs)
-		* huge.ff      (>40000 jobs)
-
-== Sample jobs
-
-   The flow require a number of job scripts
-
-		* do_make     
-		* do_test     
-		* do_inst     
-		* do_uninst   
-		* do_final    
-		* do_report   
-
-	each of which simply does a sleep.
-
-== Pre-submission procedure
-
-   In addition a sample .flowrc.rb file can be found. Besides
-   a couple of parameters it contains a pre-submission procedure.
-
-== Assumptions according the DRM setup
-
-   Note: For running the flows it is necessary to configure 
-   the DRM in a way that 
-
-		 -q gridware.q
-		 -q irix.q
-		 -q solaris.q
-		 -q linux.q
-		 -q darwin.q
- 
-   and 
-
-       -P fast    (.flowrc.rb)
-
-   can be passed as "nat" (i.e. "drmaa_native_specification").
-
-   Yet as a matter of course the set-up requirements easily can
-   be changed, if the sample files are modified accordingly.

examples/drmaa/ruby/flow/samples/do_final

@@ -1,8 +0,0 @@
-#!/bin/sh
-me=`basename $0`
-echo "# -- args $* -- #"
-echo "# -- starting $me -- #"
-sleep 1
-ret=$?
-echo "# -- finished $me -- #"
-exit $ret

examples/drmaa/ruby/flow/samples/do_inst

@@ -1,8 +0,0 @@
-#!/bin/sh
-me=`basename $0`
-echo "# -- args $* -- #"
-echo "# -- starting $me -- #"
-sleep $1
-ret=$?
-echo "# -- finished $me -- #"
-exit $ret

examples/drmaa/ruby/flow/samples/do_make

@@ -1,8 +0,0 @@
-#!/bin/sh
-me=`basename $0`
-echo "# -- args $* -- #"
-echo "# -- starting $me -- #"
-sleep 1
-ret=$?
-echo "# -- finished $me -- #"
-exit $ret

examples/drmaa/ruby/flow/samples/do_report

@@ -1,8 +0,0 @@
-#!/bin/sh
-me=`basename $0`
-echo "# -- args $* -- #"
-echo "# -- starting $me -- #"
-sleep 1
-ret=$?
-echo "# -- finished $me -- #"
-exit $ret

examples/drmaa/ruby/flow/samples/do_test

@@ -1,8 +0,0 @@
-#!/bin/sh
-me=`basename $0`
-echo "# -- args $* -- #"
-echo "# -- starting $me -- #"
-sleep 1
-ret=$?
-echo "# -- finished $me -- #"
-exit $ret

examples/drmaa/ruby/flow/samples/do_uninst

@@ -1,8 +0,0 @@
-#!/bin/sh
-me=`basename $0`
-echo "# -- args $* -- #"
-echo "# -- starting $me -- #"
-sleep $1
-ret=$?
-echo "# -- finished $me -- #"
-exit $ret

examples/drmaa/ruby/flow/samples/huge.ff

@@ -1,36 +0,0 @@
-# ------------------------------------------------------------------------------------------
-ALL = ALLFLOWS | REPORT
-ALLFLOWS = FLOW($arch=solaris) & FLOW($arch=linux) & FLOW($arch=irix) & FLOW($arch=darwin)
-FLOW = BUILD | INST | TESTS | FINAL
-# ------------------------------------------------------------------------------------------
-BUILD = { cmd=do_make, nat=-q $arch.q, args= 5 }
-INST = { cmd=do_inst, nat=-q gridware.q, args=4 -local -bin $arch, name=I$arch }
-TESTS = SEVEN & SEVEN & SEVEN & SEVEN
-SEVEN = DAY($day=mon) & DAY($day=tue) & DAY($day=wed) & DAY($day=thu) & DAY($day=fri) & DAY($day=sat) & DAY($day=sun)
-DAY = T & T & T & T
-T = S1 & S2 & S3 & S4 & S1 & S2 & S3 & S4
-S1 = TT1 | TT2 | TT3
-S2 = TT1 | TT2 | TT3
-S3 = TT1 | TT2 | TT3
-S4 = TT1 | TT2 | TT3
-TT1 = T1 & T2 & T3 & T4
-TT2 = T1 & T2 & T3 & T4
-TT3 = T1 & T2 & T3 & T4
-TT4 = T1 & T2 & T3 & T4
-TT5 = T1 & T2 & T3 & T4
-T1 = { cmd=do_test, nat= -q $arch.q, args=1, args=$day }
-T2 = { cmd=do_test, nat= -q $arch.q, args=2, args=$day }
-T3 = { cmd=do_test, nat= -q $arch.q, args=3, args=$day }
-T4 = { cmd=do_test, nat= -q $arch.q, args=4, args=$day }
-FINAL = { cmd=do_final, nat=-q $arch.q, name=FIN$arch }
-# ------------------------------------------------------------------------------------------
-REPORT = LANG($whom=engineering) & LANG($whom=markting) & LANG($whom=sales)
-LANG = RR1($lang=ger) & RR2($lang=eng) & RR3($lang=jap)
-RR1 = R1($size=1G) | R2($size=2G) | R3($size=4G)
-RR2 = R1($size=1G) | R2($size=2G) | R3($size=4G)
-RR3 = R1($size=1G) | R2($size=2G) | R3($size=4G)
-R1 = R($format=html) & R($format=wiki) & R($format=pdf) & R($format=soffice )
-R2 = R($format=html) & R($format=wiki) & R($format=pdf) & R($format=soffice )
-R3 = R($format=html) & R($format=wiki) & R($format=pdf) & R($format=soffice )
-R = { cmd=do_report, nat=-q gridware.q, args=$lang $size $format }
-# ------------------------------------------------------------------------------------------

examples/drmaa/ruby/flow/samples/large.ff

@@ -1,21 +0,0 @@
-# ------------------------------------------------------------------------------------------
-ALL = FLOW($arch=solaris) & FLOW($arch=linux) & FLOW($arch=irix) & FLOW($arch=darwin)
-FLOW = BUILD | INST | TESTS | FINAL
-TESTS = T & T & T & T
-T = S1 & S2 & S3 & S4
-S1 = TT1 | TT2 | TT3
-S2 = TT1 | TT2 | TT3
-S3 = TT1 | TT2 | TT3
-S4 = TT1 | TT2 | TT3
-TT1 = T1 & T2 & T3 & T4
-TT2 = T1 & T2 & T3 & T4
-TT3 = T1 & T2 & T3 & T4
-# ------------------------------------------------------------------------------------------
-BUILD = { cmd=do_make, nat=-q $arch.q, args=5 }
-INST = { cmd=do_inst, nat = -q gridware.q, args=1 -local -bin $arch, name=I$arch }
-FINAL = { cmd=do_final, name=FIN$arch, args=1 }
-T1 = { cmd=do_test, nat= -q $arch.q, args=1 }
-T2 = { cmd=do_test, nat= -q $arch.q, args=2 }
-T3 = { cmd=do_test, nat= -q $arch.q, args=3 }
-T4 = { cmd=do_test, nat= -q $arch.q, args=4 }
-# ------------------------------------------------------------------------------------------

examples/drmaa/ruby/flow/samples/small.ff

@@ -1,15 +0,0 @@
-# ------------------------------------------------------------------------------------------
-ALL = ALLFLOWS | REPORT
-# ------------------------------------------------------------------------------------------
-ALLFLOWS = FLOW($arch=darwin) & FLOW($arch=linux) & FLOW($arch=irix) & FLOW($arch=solaris)
-FLOW = BUILD | INST | TESTS | FINAL
-TESTS = T1 & T2 & T3 & T4
-# ------------------------------------------------------------------------------------------
-BUILD = { cmd=do_make, nat=-q $arch.q, args=5 }
-INST = { cmd=do_inst, nat=-q gridware.q, args=1 -local -bin $arch, name=I$arch }
-FINAL = { cmd=do_uninst, nat=-q $arch.q, args=1, name=FIN$arch }
-T1 = { cmd=do_test, nat = -q $arch.q, args = 1 }
-T2 = { cmd=do_test, nat = -q $arch.q, args = 2 }
-T3 = { cmd=do_test, nat = -q $arch.q, args = 3 }
-T4 = { cmd=do_test, nat = -q $arch.q, args = 4 }
-REPORT = { cmd=do_report }

examples/drmaa/ruby/flow/samples/tiny.ff

@@ -1 +0,0 @@
-TEST = {cmd=do_test, args=-w 15}

examples/drmaa/ruby/sig.rb

@@ -1,66 +0,0 @@
-#!/usr/bin/ruby
-
-#########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2006
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#   Copyright: 2006 by Sun Microsystems, Inc.
-#
-#   All Rights Reserved.
-#
-#########################################################################
-
-require 'drmaa'
-
-if ARGV.length < 1
-	puts "usage: sig.rb <job-path> <args>"
-	exit 1
-end
-
-s = DRMAA::Session.new
-
-t = DRMAA::JobTemplate.new
-t.command = ARGV[0]
-ARGV.shift
-t.arg = ARGV
-t.stdout = ":/dev/null"
-t.join = true
-
-job = s.run(t)
-
-puts "job: " + job
-
-info = s.wait(job)
-
-if info.wifexited?
-	puts info.job + " returned with " + info.wexitstatus.to_s
-elsif info.wifsignaled?
-	if info.wcoredump?
-		puts info.job + " returned died from " + info.wtermsig.to_s + " (core dumped)"
-	else
-		puts info.job + " returned died from " + info.wtermsig.to_s 
-	end
-elsif info.wifaborted?
-	puts "aborted: " + info.job
-end
-info.rusage.each_pair { |name,value| puts "usage " + name + " " + value }

examples/drmaa/ruby/stream_and_trap.rb

@@ -1,99 +0,0 @@
-#!/usr/bin/ruby
-
-#########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2006
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#   Copyright: 2006 by Sun Microsystems, Inc.
-#
-#   All Rights Reserved.
-#
-#########################################################################
-
-
-require 'drmaa'
-
-class Sleeper < DRMAA::JobTemplate
-	def initialize
-		super
-		self.command = "/bin/sleep"
-		self.arg     = ["1"]
-		self.stdout  = ":/dev/null"
-		self.join    = true
-	end
-end
-
-
-$terminate_session = $terminate_program = false
-def handle_signal
-	if ! $terminate_session 
-		$terminate_session = true
-	elsif ! $terminate_program 
-		$terminate_program = true
-	end
-end
-trap("INT") { handle_signal }
-trap("TERM") { handle_signal }
-
-session = DRMAA::Session.new
-
-# causes DRMAA::Session:run() and DRMAA::Session:run_bulk()
-# to sleep and retry in case of DRMAA::DRMAATryAgain. 
-# That way we implement job streaming.
-session.retry = 5
-
-t = Sleeper.new
-
-jobs = Array.new
-for i in 1 .. 20 do
-	job = session.run(t)
-	puts "job: " + job
-	jobs << job
-	break if $terminate_session
-end
-for i in 1 .. 10
-	bulk = session.run_bulk(t, 1, 2)
-	bulk.each { |job| puts "job: " + job }
-	jobs += bulk
-	break if $terminate_session
-end
-
-while jobs.size > 0 do
-	info = session.wait_any(1)
-	if ! info.nil?
-		if ! info.wifexited?
-			puts "failed: " + info.job
-		else	
-			puts info.job + " returned with " + info.wexitstatus.to_s
-		end
-		jobs.delete(info.job)
-	else
-		if $terminate_program
-			jobs.clear
-		elsif $terminate_session
-			session.terminate
-		end
-	end
-end
-
-exit 0

examples/drmaa/ruby/test_all.sh

@@ -1,9 +0,0 @@
-#!/bin/sh
-./example.rb && ./array.rb && ./sig.rb /bin/sleep 1 && ./stream_and_trap.rb && ./threads.rb && ./attributes.rb
-ret=$?
-if [ $ret -ne 0 ]; then
-	echo "##### failed #####"
-else
-	echo "##### success #####"
-fi
-exit $ret

examples/drmaa/ruby/threads.rb

@@ -1,80 +0,0 @@
-#!/usr/bin/ruby
-
-#########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2006
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#   The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#   Copyright: 2006 by Sun Microsystems, Inc.
-#
-#   All Rights Reserved.
-#
-#########################################################################
-
-require 'drmaa'
-require 'thread'
-
-class Sleeper < DRMAA::JobTemplate
-	def initialize
-		super
-		self.command = "/bin/sleep"
-		self.arg     = ["1"]
-		self.stdout  = ":/dev/null"
-		self.join    = true
-	end
-end
-
-# Submit a bunch of jobs from a number of threads
-# and wait for them in main thread.
-#
-# Note: Ruby threads are not identical with operating
-# system threads.
-
-version = DRMAA.version
-drm = DRMAA.drm_system
-puts "DRMAA #{drm} v #{version}"
-
-session = DRMAA::Session.new
-t = Sleeper.new
-
-i = 0
-while i<4 do
-	Thread.start do 
-		j = 0
-		while j<20 do
-			puts "job: " + session.run(t)
-			j += 1
-		end
-	end
-	i += 1
-end
-
-session.wait_each{ |info|
-	job = info.job
-	if ! info.wifexited?
-		puts "failed: " + info.job
-	else	
-		puts info.job + " returned with " + info.wexitstatus.to_s
-	end
-}
-
-exit 0

examples/jobs/array_submitter.sh

@@ -1,106 +0,0 @@
-#!/bin/sh
-#
-#___INFO__MARK_BEGIN__
-##########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2001
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#  The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#  Copyright: 2001 by Sun Microsystems, Inc.
-#
-#  All Rights Reserved.
-#
-##########################################################################
-#___INFO__MARK_END__
-
-#
-# This sample consists of three scripts belonging toghether
-#
-#    array_submitter.sh
-#    step_A_array_submitter.sh
-#    step_B_array_submitter.sh
-#
-# The number <n> passed as an argument to the interactively started 
-# array_submitter.sh is used to specify the the size of the two array 
-# jobs step_A_array_submitter.sh/step_B_array_submitter.sh which are 
-# submitted. Each single job of array job B is not scheduled before 
-# array job A has not passed the section where qalter is used to release 
-# the succesor task. Refer to qsub(1) for more information about array
-# jobs.
-#  
-# This is a typical scenario in DCC industry where schemes like this
-# are used to control sequence of large rendering jobs.
-# Note that it is necessary that all hosts where A jobs are started
-# must be submit hosts to allow the qalter happen.
-#
-
-#$ -S /bin/sh
-
-if [ x$SGE_ROOT = x ]; then
-   SGE_ROOT=/usr/SGE
-fi
-if [ ! -d $SGE_ROOT ]; then
-   echo "error: SGE_ROOT directory $SGE_ROOT does not exist"
-   exit 1
-fi
-
-ARC=`$SGE_ROOT/util/arch`
-
-QSUB=$SGE_ROOT/bin/$ARC/qsub
-QALTER=$SGE_ROOT/bin/$ARC/qalter
-
-if [ ! -x $QSUB ]; then
-   echo "error: cannot execute qsub command under $QSUB"
-   exit 1
-fi
-
-if [ ! -x $QALTER ]; then
-   echo "error: cannot execute qalter command under $QALTER"
-   exit 1
-fi
-
-tasks=0
-
-while [ "$1" != "" ]; do
-   case "$1" in
-   [0-9]*)
-      tasks=$1
-      shift 
-      ;;
-   esac
-done
-
-if [ $tasks = 0 ]; then
-   echo "usage: array_submitter.sh <number_of_tasks>"
-   exit 1
-fi
-
-# submit step A jobarray
-jobid_a=`$QSUB -t 1-$tasks -r y -N StepA $SGE_ROOT/examples/jobs/step_A_array_submitter.sh | cut -f3 -d" "|cut -f1 -d.`
-echo "submission result: jobid_a = $jobid_a"
-
-# submit step B jobarray with hold state
-jobid_b=`$QSUB -t 1-$tasks -h -r y -N StepB $SGE_ROOT/examples/jobs/step_B_array_submitter.sh | cut -f3 -d" "|cut -f1 -d.`
-echo "submission result: jobid_b = $jobid_b"
-
-# put jobid of step B into context of step A
-$QALTER -ac succ=$jobid_b $jobid_a

examples/jobs/env-tester.sh

@@ -1,36 +0,0 @@
-#!/bin/sh
-#$ -S /bin/sh
-#___INFO__MARK_BEGIN__
-##########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2001
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#  The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#  Copyright: 2001 by Sun Microsystems, Inc.
-#
-#  All Rights Reserved.
-#
-##########################################################################
-#___INFO__MARK_END__
-echo ------------------------------------
-env
-echo ------------------------------------

examples/jobs/jobnet_submitter.sh

@@ -1,77 +0,0 @@
-#!/bin/sh
-#
-#
-#___INFO__MARK_BEGIN__
-##########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2001
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#  The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#  Copyright: 2001 by Sun Microsystems, Inc.
-#
-#  All Rights Reserved.
-#
-##########################################################################
-#___INFO__MARK_END__
-
-QSUB=$SGE_ROOT/bin/$ARC/qsub
-name_base=Net
-hold=""
-jobs=5
-
-while [ "$1" != "" ]; do
-   case "$1" in
-   -N)
-      shift 
-      name_base=$1
-      shift 
-      ;;
-   -h)
-      hold=-h
-      shift 
-      ;;
-   [0-9]*)
-      jobs=$1
-      shift 
-      ;;
-   esac
-done
-
-echo "going to submit $jobs jobs"
-
-jobid=0
-REQUEST=""
-
-i=1
-while [ $i -le $jobs ]; do
-   if [ $i -ne 1 ]; then
-      opt="-hold_jid $jobid"
-   fi
-   
-   jobid=`$QSUB $REQUEST -r y -N $name_base$i $hold $opt $SGE_ROOT/examples/jobs/sleeper.sh 10 | cut -f3 -d" "`
-   if [ $i -ne 1 ]; then
-      echo submitted job \#$i name = $name_base$i with jobid $jobid and $opt
-   else
-      echo submitted job \#$i name = $name_base$i with jobid $jobid
-   fi
-   i=`expr $i + 1`
-done

examples/jobs/matlab_script.sh

@@ -1 +0,0 @@
-../../local/examples/jobs/matlab_script.sh

examples/jobs/matlab_script.sh

@@ -0,0 +1,81 @@
+#!/bin/bash
+
+#############################################################
+# This example produces a very simple plot and              #
+# saves it as Matlab figure file and as PNG file            #
+#############################################################
+
+#############################################################
+# set qsub options                                          #
+#############################################################
+# run in low.q
+#$ -l low
+
+# request enough memory
+#$ -l h_vmem=8G,memory=8G,h_stack=8M
+
+# request 1 matlab license.
+#$ -l matlab=1
+
+# Name the job 'Matlab'
+#$ -N Matlab
+
+# send e-mail after job has finished
+# use the -M option to define your e-mail address
+# #$ -M meine-email@example.org
+#$ -m e
+
+# join stdout and stderr in one file
+#$ -j y
+
+#############################################################
+# output hostname and date (comment out if not needed)      #
+#############################################################
+echo "Runnning Matlab on host " `hostname`
+echo "Starting Matlab at " `date`
+
+#############################################################
+# launch matlab                                             #
+#############################################################
+
+# run non-interactive Matlab session
+# use no display (-nodisplay)
+# don't show splash screen at startup (-nosplash)
+# don't start the matlab desktop (-nodesktop)
+# use software opengl (-softwareopengl)
+# only use single threaded computations (limit to use of 1 core, -singleCompThread)
+# execute all matlab commands between '<< END' and matching 'END'
+
+# Don't forget to add 'exit' and 'END' after replacing
+# the commands with your own!
+
+/opt/matlab/bin/matlab -nodisplay -nosplash -nodesktop -softwareopengl -singleCompThread << END
+
+  % get environment variable JOB_ID
+  jobid=str2num(getenv('JOB_ID'));
+  if isempty(jobid)
+     jobid = 0;
+  end
+
+  % create filenames for the figure
+  filename=sprintf('matlab_figure_%d', jobid);
+
+  % create new empty figure and save figure handle
+  fh = figure();
+
+  % draw plot
+  plot(-pi:0.01:pi, sin(-pi:0.01:pi));
+
+  % save figure as matlab figure and PNG
+  saveas(fh, filename, 'fig');
+  saveas(fh, filename, 'png');
+
+  % EXIT MATLAB
+  exit;
+
+END
+
+#############################################################
+# output date (comment out if not needed)                   #
+#############################################################
+echo "Matlab finnished at " `date`

examples/jobs/pascal.sh

@@ -1,107 +0,0 @@
-#!/bin/sh
-#
-#___INFO__MARK_BEGIN__
-##########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2001
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#  The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#  Copyright: 2001 by Sun Microsystems, Inc.
-#
-#  All Rights Reserved.
-#
-##########################################################################
-#___INFO__MARK_END__
-#
-# This is a sample script to demonstrate use of job dependencies. The 
-# sample submits one job for each node in the pascal triangle: 
-#
-#                        1               depth 1
-#                       / \
-#                      1   1             depth 2
-#                     / \ / \
-#                    1   2   1           depth 3
-#                   / \ / \ / \
-#                  1   3   3   1         depth 4
-#                  
-#                  :   :   :   :
-#
-# Data exchange between jobs is done via files in jobnet_dir. 
-#
-# Usage: pascal.sh <depth of pascal triangle>
-
-jobnet_dir=$HOME/pascal_jobnet
-
-if [ $# -ne 1 ]; then
-   echo "usage: pascal.sh <depth of pascal triangle>" >&2
-   exit 1
-fi 
-n=$1
-i=1
-
-mkdir $jobnet_dir
-rm $jobnet_dir/*
-
-while [ $i -le $n ]; do
-   j=1
-   while [ $j -le $i ]; do
-      prev_line=`expr $i - 1` 
-
-      # specify own jobname
-      submit_args="-N P${i}_${j}"
-
-      if [ $j -gt 1 -a $j -lt $i ]; then
-         depend1=P${prev_line}_`expr ${j} - 1`
-         depend2=P${prev_line}_${j}
-         depend="$depend1 $depend2"
-         submit_args="$submit_args -hold_jid $depend1,$depend2"
-      elif [ $j -gt 1 ]; then
-         depend=P${prev_line}_`expr ${j} - 1`
-         submit_args="$submit_args -hold_jid $depend"
-      elif [ $j -lt $i ]; then
-         depend=P${prev_line}_${j}
-         submit_args="$submit_args -hold_jid $depend"
-      fi   
-
-      echo "qsub -j y -o $jobnet_dir $submit_args -- $jobnet_dir $depend"
-      qsub -r y -j y -o $jobnet_dir $submit_args -- $jobnet_dir $depend << EOF 
-#!/bin/sh
-#$ -S /bin/sh
-result=0
-jobnet_dir=\$1
-shift
-while [ \$# -gt 0 ]; do
-   depend=\$1
-   shift
-   to_add=\`cat \$jobnet_dir/DATA_\$depend\`
-   result=\`expr \$result + \$to_add\`
-   echo "\$REQUEST: adding \$to_add found in \$jobnet_dir/DATA_\$depend results in \$result"  
-done
-if [ \$result = 0 ]; then
-   result=1
-fi
-echo \$result > \$jobnet_dir/DATA_\$REQUEST 
-EOF
-      j=`expr $j + 1`
-   done
-   i=`expr $i + 1`
-done

examples/jobs/periodic_sleeper.sh

@@ -1 +0,0 @@
-../../local/examples/jobs/periodic_sleeper.sh

examples/jobs/periodic_sleeper.sh

@@ -0,0 +1,75 @@
+#!/bin/bash
+# This job script takes a nap for 10 seconds (or paramter $2) every 30 minutes (or paramter $1)
+
+# SGE options
+#$ -N PSleeper
+#$ -l scf=1M,mem=100M,h_vmem=100M
+#$ -q normal.q
+#$ -cwd
+
+# process args
+case "$1" in
+    -h)
+        echo "usage: $0 [-h | [-d] [T] [nap]]"
+        echo "periodically take a nap"
+        echo ""
+        echo "-h   print this help and exit"
+        echo "-d   print debug info"
+        echo "T    take a nap every T minutes (default: 30)"
+        echo "nap  take a nap for nap seconds (default: 10)"
+        exit 1
+        ;;
+    *)
+        debug=0
+        terse="-terse"
+        debug_flag=""
+        do_echo=0
+        T=30
+        nap=10
+        while (( "$#" )); do
+            case "$1" in
+                -d)
+                    debug=1
+                    terse=""
+                    debug_flag="-d"
+                    do_echo=1
+                    ;;
+                *)
+                    T=${1:-30}
+                    nap=${2:-10}
+                    break
+                    ;;
+            esac
+            shift
+        done
+        ;;
+esac
+
+# set other variables
+next=$(date -d "${T} minutes" +%Y%m%d%H%M)
+script=/opt/SGE/examples/jobs/periodic_sleeper.sh
+
+# output some informations
+if [ ${debug} -eq 1 ]; then
+    echo "T = ${T}, nap=${nap}"
+    echo "next run at ${next} (YYYYMMDDhhmm)"
+    echo "debug_flag = ${debug_flag}, do_echo = ${do_echo}"
+    echo ""
+fi
+
+# commands to run in Grid Engine
+/opt/SGE/examples/jobs/sleeper.sh ${nap} ${do_echo}
+
+# re-submit script to execute in T minutes
+jobid=$(qsub ${terse} -a ${next} ${script} ${debug_flag} ${T} ${nap})
+exit_code=$?
+if [ ${debug} -eq 1 ]; then
+    echo "${jobid}"
+fi
+if [ ${exit_code} -ne 0 ]; then
+    if [ ${debug} -eq 1 ]; then
+        echo "${jobid}"
+        echo "Ups, something went wrong, check output!"
+    fi
+    exit ${exit_code}
+fi

examples/jobs/pminiworm.sh

@@ -1,79 +0,0 @@
-#!/bin/sh
-#___INFO__MARK_BEGIN__
-##########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2001
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#  The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#  Copyright: 2001 by Sun Microsystems, Inc.
-#
-#  All Rights Reserved.
-#
-##########################################################################
-#___INFO__MARK_END__
-
-#
-#
-
-# -------------------------------------------
-# --          use Bourne shell             --
-#$ -S /bin/sh
-# --             our name                  --
-#$ -N PMiniWorm
-# -------------------------------------------
-# -- send mail if the job exits abnormally --
-#$ -m a
-# -------------------------------------------
-# --     What to redirect to where         --
-#$ -e /dev/null
-#$ -o /dev/null
-
-QSUB=$SGE_ROOT/bin/$ARC/qsub
-SLEEP=120
-
-echo using $QSUB as qsub command
-
-if [ "$1" = "" ]; then
-   arg=1
-else
-   arg=`expr $1 + 1`
-fi
-NAME=W$arch$arg
-
-# started by SGE or manually 
-if [ "$JOB_ID" = "" ]; then
-   echo "submitting $NAME"
-else
-   sleep $SLEEP
-fi
-
-# first try
-# cmd="$QSUB -N $NAME -l arch=$arch $SGE_ROOT/examples/jobs/pminiworm.sh $arg"
-cmd="$QSUB -N $NAME $SGE_ROOT/examples/jobs/pminiworm.sh $arg"
-$cmd
-
-# repeat until success 
-while [ "x$?" != "x0" ]; do
-   echo "pminiworm.sh: qsub failed - retrying .." >&2
-   sleep $SLEEP
-   $cmd
-done

examples/jobs/simple.sh

@@ -1,47 +0,0 @@
-#!/bin/sh
-#
-#
-#___INFO__MARK_BEGIN__
-##########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2001
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#  The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#  Copyright: 2001 by Sun Microsystems, Inc.
-#
-#  All Rights Reserved.
-#
-##########################################################################
-#___INFO__MARK_END__
-
-# This is a simple example of a SGE batch script
-
-# request Bourne shell as shell for job
-#$ -S /bin/sh
-
-#
-# print date and time
-date
-# Sleep for 20 seconds
-sleep 20
-# print date and time again
-date

examples/jobs/simple_conda_test.sh

@@ -1 +0,0 @@
-../../local/examples/jobs/simple_conda_test.sh

examples/jobs/simple_conda_test.sh

@@ -0,0 +1,37 @@
+#! /bin/bash
+
+#############################################################
+# This example show a list of availabel conda environments  #
+#############################################################
+
+#############################################################
+# set qsub options                                          #
+#############################################################
+# run in low.q
+#$ -l low
+
+# request enough memory
+# #$ -l h_vmem=8G,memory=8G,h_stack=8M
+
+# Name the job 'Conda-Test'
+#$ -N Conda-Test
+
+#############################################################
+# initialize conda                                          #
+#############################################################
+__conda_setup="$('/opt/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
+if [ $? -eq 0 ]; then
+	eval "$__conda_setup"
+else
+	if [ -f "/opt/anaconda3/etc/profile.d/conda.sh" ]; then
+		. "/opt/anaconda3/etc/profile.d/conda.sh"
+	else
+		export PATH="/opt/anaconda3/bin:$PATH"
+	fi
+fi
+unset __conda_setup
+
+#############################################################
+# show conda environments                                   #
+#############################################################
+conda env list

examples/jobs/sleeper.sh

@@ -1,63 +0,0 @@
-#!/bin/sh
-#
-#___INFO__MARK_BEGIN__
-##########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2001
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#  The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#  Copyright: 2001 by Sun Microsystems, Inc.
-#
-#  All Rights Reserved.
-#
-##########################################################################
-#___INFO__MARK_END__
-
-#
-# Usage: sleeper.sh [time [do_echo]]
-#        default for time is 60 seconds
-#        default for do_echo is 1 (=true)
-#
-
-# -- our name ---
-#$ -N Sleeper
-#$ -S /bin/sh
-
-
-time=60
-do_echo=1
-if [ $# -ge 1 ]; then
-   time=$1
-fi
-if [ $# -ge 2 ]; then
-   do_echo=$2
-fi
-
-if [ $do_echo -ne 0 ]; then
-   /bin/echo Here I am: `hostname`. Sleeping now at: `date`
-fi
-
-sleep $time
-
-if [ $do_echo -ne 0 ]; then
-   echo Now it is: `date`
-fi

examples/jobs/ssession.sh

@@ -1,187 +0,0 @@
-#!/bin/sh
-#$ -S /bin/sh
-#$ -pe make 1
-#$ -N SSession
-#$ -v PATH
-
-#___INFO__MARK_BEGIN__
-##########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2001
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#  The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#  Copyright: 2009 by Sun Microsystems, Inc.
-#
-#  All Rights Reserved.
-#
-##########################################################################
-#___INFO__MARK_END__
-
-
-ARCH=`$SGE_ROOT/util/arch`
-ECHO="$SGE_ROOT/utilbin/$ARCH/echo_raw -e"
-
-ssession_logging_enabled="false"       # is logging enabled?
-ssession_logfile="/tmp/ssession.log"   # logfile
-tfile="taskfile.txt"                   # default taskfile name if not other specified
-mfile=""                               # makefile name
-isource="tfile"                        # type of onput "tfile" or "mfile"
-
-ssession_show_usage() 
-{
-   echo "usage: ssession [ taskfile | -mf makefile ]"
-   echo 
-   echo "   If there is neither a taskfile nor a makefile specified then"
-   echo "   this script assumes that there is taskfile named taskfile.txt"
-   echo "   in the current working directory."
-   echo
-   echo "   taskfile    - taskfile containing the tasks to be executed in the session"
-   echo "   makefile    - makefile containing the tasks an depedency definition"
-}
-
-# add start rule to makefile
-ssession_makefile_add_all()
-{
-   taskfile=$1
-   makefile=$2
-
-   start="all:" 
-   line_i=1
-   max=`wc -l $taskfile|cut -c 1-8` 
-   while [ $line_i -le $max ]; do
-      line=`head -$line_i $taskfile | tail -1` 
-
-      start=`echo $start task${line_i}`  
-      line_i=`expr $line_i + 1`
-   done
-
-   echo $start >>$makefile
-   echo "" >>$makefile
-
-   unset makefile
-   unset start
-   unset line_i
-}
-
-# add one rule for each task in taskfile
-ssession_makefile_add_task()
-{
-   taskfile=$1
-   makefile=$2
-
-   line_i=1
-   max_lines=`wc -l $taskfile|cut -c 1-8` 
-   while [ $line_i -le $max_lines ]; do
-      command=`head -$line_i $taskfile | tail -1` 
-
-      echo "task${line_i}:" >>$makefile
-      $ECHO "\t${command}" >>$makefile
-      echo "" >>$makefile
-      line_i=`expr $line_i + 1`
-   done
-
-   unset max_lines
-   unset taskfile
-   unset makefile
-   unset line_i
-}
-
-# create the makefile
-ssession_makefile_create()
-{
-   makefile=$1
-
-   if [ -f $makefile ]; then
-      rm -f $makefile 
-      echo rm
-   fi
-   touch $makefile
-
-   unset makefile
-}
-
-# destroy the taskfile
-ssession_makefile_destroy()
-{
-   makefile=$1
-
-#   rm -f $makefile
-   unset makefile
-}
-
-# start a qmake job that executes tasks in taskfile
-ssession_start_qmake()
-{
-   makefile=$1
-
-   qmake -inherit -- -f $makefile
-}
-
-ssession_log()
-{
-   if [ $ssession_logging_enabled = true ]; then
-      echo "$@" >>$ssession_logfile
-   fi
-}
-
-if [ $# = 1 ]; then
-   if [ -f "$1" ]; then
-      tfile="$1"
-   else 
-      ssession_show_usage
-      exit
-   fi
-elif [ $# = 2 ]; then
-   if [ "$1" = "-mf" ]; then
-      mfile="$2"
-      isource="mfile"      
-   else
-      ssession_show_usage
-      exit
-   fi
-else
-   tfile="taskfile.txt"
-fi
-
-if [ "$mfile" = "" ]; then
-   if [ -d "$TMPDIR" ]; then
-      mfile="${TMPDIR}/Makefile.$$"
-   else
-      mfile="/tmp/Makefile.$$"
-   fi
-fi
-
-if [ "$isource" = "tfile" ]; then
-   ssession_log "Using taskfile \"$tfile\""
-   ssession_log "Creating makefile \"$mfile\""
-   
-   ssession_makefile_create $mfile 
-   ssession_makefile_add_all $tfile $mfile 
-   ssession_makefile_add_task $tfile $mfile 
-   ssession_start_qmake $mfile
-   ssession_makefile_destroy $mfile 
-else
-   ssession_log "Using makefile \"$mfile\""
-   
-   ssession_start_qmake $mfile
-fi
-

examples/jobs/step_A_array_submitter.sh

@@ -1,47 +0,0 @@
-#!/bin/sh
-#
-#
-#___INFO__MARK_BEGIN__
-##########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2001
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#  The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#  Copyright: 2001 by Sun Microsystems, Inc.
-#
-#  All Rights Reserved.
-#
-##########################################################################
-#___INFO__MARK_END__
-
-# request "/bin/sh" as shell for job
-#$ -S /bin/sh
-
-QSTAT=$SGE_ROOT/bin/$ARC/qstat
-QALTER=$SGE_ROOT/bin/$ARC/qalter
-
-# find out successor jobid 
-# must be set by submission script
-successor=`$QSTAT -j $JOB_ID | grep context |cut -f2 -d=`
-
-# release appropriate succesor task
-$QALTER -h U $successor.$SGE_TASK_ID

examples/jobs/step_B_array_submitter.sh

@@ -1,39 +0,0 @@
-#!/bin/sh
-#
-#
-#___INFO__MARK_BEGIN__
-##########################################################################
-#
-#  The Contents of this file are made available subject to the terms of
-#  the Sun Industry Standards Source License Version 1.2
-#
-#  Sun Microsystems Inc., March, 2001
-#
-#
-#  Sun Industry Standards Source License Version 1.2
-#  =================================================
-#  The contents of this file are subject to the Sun Industry Standards
-#  Source License Version 1.2 (the "License"); You may not use this file
-#  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
-#
-#  Software provided under this License is provided on an "AS IS" basis,
-#  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
-#  WITHOUT LIMITATION, WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS,
-#  MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE, OR NON-INFRINGING.
-#  See the License for the specific provisions governing your rights and
-#  obligations concerning the Software.
-#
-#  The Initial Developer of the Original Code is: Sun Microsystems, Inc.
-#
-#  Copyright: 2001 by Sun Microsystems, Inc.
-#
-#  All Rights Reserved.
-#
-##########################################################################
-#___INFO__MARK_END__
-
-# request "/bin/sh" as shell for job
-#$ -S /bin/sh
-
-echo $JOB_ID.$SGE_TASK_ID

flex-grid/cache

@@ -1 +0,0 @@
-/rscratch/minos19/flex_grid_cache

flex-grid/config/abaqus_licenses.conf

@@ -1,33 +0,0 @@
-<?xml version="1.0"?>
-<qlicserverConfig>
- <parameters type="overwrite">
-  <param name="lmutil">/opt/SGE/flex-grid/scripts/abaqus_lmutil</param>
-  <!-- <param name="LM_LICENSE_FILE">27000@abaqus-lizenz.rz.ruhr-uni-bochum.de</param> -->
-  <param name="LM_LICENSE_FILE">27000@vmrz0300.vm.ruhr-uni-bochum.de</param>
-  <param name="dir">/opt/SGE/flex-grid/cache</param>
-  <param name="output">qlicserver_abaqus.xml</param>
- </parameters>
-<!--
-   | Map resource names (complexes) to values (features)
-   | served by the license manager(s).
-   | Resources without a "served" attribute are considered internal
-   | Resources with type "track" are reported but not managed
-   | The urgency is how much extra weight to give to particular resources.
-   | If a 'slot' is weighted with 1000, we can give an extra 10% to
-   | a few resources. [Format: INTEGER]
-   |
-   | The resource 'limit' specifies an upper limit to prevent applications
-   | from flooding the cluster and/or prevent jobs from consuming all the
-   | available licenses. A negative limit is subtracted from the total
-   | to obtain the limit. [Format: INTEGER]
-   |
-   | Derived resources are combined from sub-elements and inherit the
-   | limits from their sub-elements.
-   |
-   | Resources that are not served and not derived are internal resources
-   + -->
- <resources type="overwrite">
-  <resource name="abaqus" served="abaqus" limit="30" type="job"/>
-  <resource name="cae" served="cae" limit="2" type="job"/>
- </resources>
-</qlicserverConfig>

flex-grid/config/comsol_licenses.conf

@@ -1,31 +0,0 @@
-<?xml version="1.0"?>
-<qlicserverConfig>
- <parameters type="overwrite">
-  <param name="lmutil">/opt/matlab/etc/glnxa64/lmutil</param>
-  <param name="LM_LICENSE_FILE">/opt/SGE/flex-grid/licenses/comsol.lic</param>
-  <param name="dir">/opt/SGE/flex-grid/cache</param>
-  <param name="output">qlicserver_comsol.xml</param>
- </parameters>
-<!--
-   | Map resource names (complexes) to values (features)
-   | served by the license manager(s).
-   | Resources without a "served" attribute are considered internal
-   | Resources with type "track" are reported but not managed
-   | The urgency is how much extra weight to give to particular resources.
-   | If a 'slot' is weighted with 1000, we can give an extra 10% to
-   | a few resources. [Format: INTEGER]
-   |
-   | The resource 'limit' specifies an upper limit to prevent applications
-   | from flooding the cluster and/or prevent jobs from consuming all the
-   | available licenses. A negative limit is subtracted from the total
-   | to obtain the limit. [Format: INTEGER]
-   |
-   | Derived resources are combined from sub-elements and inherit the
-   | limits from their sub-elements.
-   |
-   | Resources that are not served and not derived are internal resources
-   + -->
- <resources type="overwrite">
-  <resource name="comsol" served="COMSOL" type="job"/>
- </resources>
-</qlicserverConfig>

flex-grid/config/local_licenses.conf

@@ -1,36 +0,0 @@
-<?xml version="1.0"?>
-<qlicserverConfig>
- <parameters type="overwrite">
-  <param name="lmutil">/opt/matlab/etc/glnxa64/lmutil</param>
-  <param name="LM_LICENSE_FILE">/opt/SGE/flex-grid/licenses/multiphysics.lic</param>
-  <param name="dir">/opt/SGE/flex-grid/cache</param>
-  <param name="output">qlicserver_local.xml</param>
-  <param name="qhost">qhost.xml</param>
-  <param name="qstat">qstat.xml</param>
- </parameters>
-<!--
-   | Map resource names (complexes) to values (features)
-   | served by the license manager(s).
-   | Resources without a "served" attribute are considered internal
-   | Resources with type "track" are reported but not managed
-   | The urgency is how much extra weight to give to particular resources.
-   | If a 'slot' is weighted with 1000, we can give an extra 10% to
-   | a few resources. [Format: INTEGER]
-   |
-   | The resource 'limit' specifies an upper limit to prevent applications
-   | from flooding the cluster and/or prevent jobs from consuming all the
-   | available licenses. A negative limit is subtracted from the total
-   | to obtain the limit. [Format: INTEGER]
-   |
-   | Derived resources are combined from sub-elements and inherit the
-   | limits from their sub-elements.
-   |
-   | Resources that are not served and not derived are internal resources
-  resource name="hyper" served="GridWorks" type="job"
-  <resource name="matlab" served="MATLAB" type="job" limit="-2"/>
-  <resource name="signal_toolbox" served="Signal_Toolbox" type="job" limit="-2"/>
-   + -->
- <resources type="overwrite">
-  <resource name="femlab" served="COMSOL" type="track"/>
- </resources>
-</qlicserverConfig>

flex-grid/config/matlab_licenses.conf

@@ -1,32 +0,0 @@
-<?xml version="1.0"?>
-<qlicserverConfig>
- <parameters type="overwrite">
-  <param name="lmutil">/opt/matlab/etc/glnxa64/lmutil</param>
-  <param name="LM_LICENSE_FILE">/opt/SGE/flex-grid/licenses/matlab.lic</param>
-  <param name="dir">/opt/SGE/flex-grid/cache</param>
-  <param name="output">qlicserver_matlab.xml</param>
- </parameters>
-<!--
-   | Map resource names (complexes) to values (features)
-   | served by the license manager(s).
-   | Resources without a "served" attribute are considered internal
-   | Resources with type "track" are reported but not managed
-   | The urgency is how much extra weight to give to particular resources.
-   | If a 'slot' is weighted with 1000, we can give an extra 10% to
-   | a few resources. [Format: INTEGER]
-   |
-   | The resource 'limit' specifies an upper limit to prevent applications
-   | from flooding the cluster and/or prevent jobs from consuming all the
-   | available licenses. A negative limit is subtracted from the total
-   | to obtain the limit. [Format: INTEGER]
-   |
-   | Derived resources are combined from sub-elements and inherit the
-   | limits from their sub-elements.
-   |
-   | Resources that are not served and not derived are internal resources
-   + -->
- <resources type="overwrite">
-  <resource name="matlab" served="MATLAB" type="job" limit="100"/>
-  <resource name="mcc" served="Compiler" type="job" limit="100"/>
- </resources>
-</qlicserverConfig>

flex-grid/config/trelis_licenses.conf

@@ -1,31 +0,0 @@
-<?xml version="1.0"?>
-<qlicserverConfig>
- <parameters type="overwrite">
-  <param name="lmutil">/opt/matlab/etc/glnxa64/lmutil</param>
-  <param name="LM_LICENSE_FILE">/opt/SGE/flex-grid/licenses/matlab.lic</param>
-  <param name="dir">/opt/SGE/flex-grid/cache</param>
-  <param name="output">qlicserver_trelis.xml</param>
- </parameters>
-<!--
-   | Map resource names (complexes) to values (features)
-   | served by the license manager(s).
-   | Resources without a "served" attribute are considered internal
-   | Resources with type "track" are reported but not managed
-   | The urgency is how much extra weight to give to particular resources.
-   | If a 'slot' is weighted with 1000, we can give an extra 10% to
-   | a few resources. [Format: INTEGER]
-   |
-   | The resource 'limit' specifies an upper limit to prevent applications
-   | from flooding the cluster and/or prevent jobs from consuming all the
-   | available licenses. A negative limit is subtracted from the total
-   | to obtain the limit. [Format: INTEGER]
-   |
-   | Derived resources are combined from sub-elements and inherit the
-   | limits from their sub-elements.
-   |
-   | Resources that are not served and not derived are internal resources
-   + -->
- <resources type="overwrite">
-  <resource name="trelis" served="TRELIS" type="job"/>
- </resources>
-</qlicserverConfig>

flex-grid/licenses/comsol.lic

@@ -1 +0,0 @@
-/opt/comsol53a/multiphysics/license/license.dat

flex-grid/licenses/hyperworks.lic

@@ -1,2 +0,0 @@
-SERVER kamikaze 80b660b0 7788
-USE_SERVER

flex-grid/licenses/ifort.lic

@@ -1,2 +0,0 @@
-SERVER kamikaze 80b660b0 28518
-USE_SERVER

flex-grid/licenses/matlab.lic

@@ -1 +0,0 @@
-/opt/matlab/licenses/01network.lic

flex-grid/licenses/multiphysics.lic

@@ -1,2 +0,0 @@
-SERVER phaidra.geophysik.ruhr-uni-bochum.de 00163ef90680 1718
-USE_SERVER

flex-grid/scripts/GridEngine-git-config

@@ -1,221 +0,0 @@
-#!/bin/sh
-#
-# Snapshot of the current GridEngine configuration using git for the
-# backend storage and tracking mechanism.
-#
-# Should normally be called via a cronjob.
-#
-# Following Edward Dale's idea:
-# http://scompt.com/blog/archives/2009/10/13/versioned-grid-engine-configuration
-# but using git for the backend
-#
-# initialize:
-#
-# git --git-dir=$GIT_DIR init --bare --shared=world
-#
-# Note: we use Perl for inplace editing since some versions of sed have
-#       problems with this task.
-################################################################################
-################################################################################
-# CUSTOMIZE THESE SETTINGS TO MATCH YOUR REQUIREMENTS:
-
-SGE_ROOT=/opt/grid
-SGE_CELL=default
-GIT_DIR=/data/cfd/share/git-repo/gridengine-config.git
-
-#
-# END OF CUSTOMIZE SETTINGS
-################################################################################
-################################################################################
-Script=${0##.*/}
-saveScript="$SGE_ROOT/util/upgrade_modules/save_sge_config.sh"
-export SGE_ROOT SGE_CELL GIT_DIR
-
-for i in git perl
-do
-    type $i >/dev/null 2>&1 || {
-        echo "Error: $Script - no '$i' found"
-        exit 1
-    }
-done
-
-#------------------------------------------------------------------------------
-usage() {
-    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
-    cat<<USAGE
-
-usage: ${0##*/} [OPTION | GIT_COMMAND]
-options:
-  -help     display this usage
-  init      initialize git repo in $GIT_DIR
-
-pass-through git commands:
-  log       ls-files
-  show      whatchanged
-
-  Snapshot of the current GridEngine configuration using git for the
-  backend storage and tracking mechanism.
-
-* git repository stored here:
-  $GIT_DIR
-
-copyright (c) 2009-10 <Mark.Olesen@faurecia.com>
-
-USAGE
-    exit 1
-}
-#------------------------------------------------------------------------------
-# parse options
-while [ "$#" -gt 0 ]
-do
-    case "$1" in
-    ( help | -h | -help )
-        usage
-        ;;
-    ( init )
-        shift
-        if [ -d "$GIT_DIR" ]
-        then
-            echo "Error: $Script - $GIT_DIR already exists"
-            exit 1
-        else
-            git --git-dir=$GIT_DIR init --bare --shared=world $@
-            rc=$?
-
-            # add a description for gitweb
-            i="$GIT_DIR/description"
-            if [ -f "$i" -a -w "$i" ]
-            then
-                echo "snapshot of the current GridEngine configuration" > $i
-            fi
-        fi
-        exit $rc
-        ;;
-    ( log | ls-files | show | whatchanged )
-        git --git-dir=$GIT_DIR $@
-        exit $?
-        ;;
-    (*)
-        usage "unknown option/argument: '$*'"
-        ;;
-    esac
-done
-
-
-
-[ -d "$GIT_DIR" ] || {
-    echo "git repo: $GIT_DIR does not exist"
-    exit 1
-}
-
-
-i="$SGE_ROOT/$SGE_CELL/common/settings.sh"
-if [ -f "$i" -a -r "$i" ]
-then
-    . "$i"
-else
-    echo "cannot read $i"
-    exit 1
-fi
-
-[ -f "$saveScript" -a -r "$saveScript" ] || {
-    echo "cannot read $i"
-    exit 1
-}
-
-# Create a fresh empty directory
-# cannot use --tmpdir on older systems
-tmpDir=$(mktemp -d "/tmp/sgeSaveConfig.XXXXXXXXXX")
-trap "rm -rf $tmpDir 2>/dev/null; exit 0" EXIT TERM INT
-
-[ -d "$tmpDir" ] || {
-    echo "Error: temp dir '$tmpDir' does not exist"
-    exit 1
-}
-
-$saveScript $tmpDir
-
-#------------------------------------------------------------------------------
-# cleanup
-#
-(
-    cd $tmpDir || exit 1
-
-    # all operations are now in the current directory
-    GIT_WORK_TREE=.
-    export GIT_WORK_TREE
-
-    # minor error checking that the save script worked
-    if [ -f backup_date -a -r backup_date ]
-    then
-        msg=$(cat backup_date)
-    else
-        echo "cannot read backup_date - $saveScript might have failed"
-        exit 1
-    fi
-
-
-    # ignore accounting (too big)
-    rm -f cell/accounting
-
-    # ignore current users
-    rm -f users/*
-
-    # ignore current load_values for exec hosts
-    perl -i -ne '/^load_values/ or print' execution/*
-
-    # assign (consumable) complex_values to zero - otherwise we indirectly
-    # track the external license usage when qlicserver is being used
-    # also sort the complexes to avoid spurious changes
-    perl -i -p -e 'if (/^complex_values/) { chomp; ' \
-               -e 's/=\d+/=0/g; s/^(complex\S+\s+)//; ' \
-               -e '$_ = $1 . join("," => sort split /,/) . "\n" }' \
-               execution/global
-
-    #
-    # determine if the configuration changed
-    #
-    # this is fairly roundabout until we find a better way
-    needsCommit=false
-
-    if [ -n "$(git ls-files -d)" ]       # files deleted?
-    then
-        needsCommit=true
-    elif [ -n "$(git ls-files -o)" ]     # files added?
-    then
-        needsCommit=true
-    else
-        # files modified?
-        # do it the long way to ensure we also get staged modifications
-        set -- $(git status | perl -ne 's/^#\s+modified:// and print')
-
-        # changes in backup_date, jobseqnum etc alone are not enough
-        # to warrant a commit
-        while [ "$#" -ge 1 ]
-        do
-            case $1 in
-            ( arseqnum | backup_date | jobseqnum )
-                shift
-                ;;
-            (*)
-                needsCommit=true
-                break
-                ;;
-            esac
-        done
-    fi
-
-    if [ "$needsCommit" = true ]
-    then
-        # register all new files
-        git add .
-
-        # commit everything
-        git commit -a -m "$msg"
-    else
-        echo "no changes to be committed $msg"
-    fi
-)
-
-exit 0
-#------------------------------------------------------------------------------

flex-grid/scripts/abaqus_lmutil

@@ -1,5 +0,0 @@
-#!/bin/sh
-# $Id: abaqus_lmutil 180 2010-09-17 15:46:41Z kasper $
-
-/opt/abaqus/Commands/abaqus licensing lmstat -a -f abaqus -S ABAQUSLM
-/opt/abaqus/Commands/abaqus licensing lmstat -a -f cae -S ABAQUSLM

flex-grid/scripts/filter-accounting

@@ -1,124 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-use Getopt::Std qw( getopts );
-use Time::Local qw( timelocal );
-
-my ($releaseDate) = qw( 2009-10-02 );
-
-( my $Script = $0 ) =~ s{^.*/}{};
-# -------------------------------------------------------------------------
-sub usage {
-    $! = 0;    # clean exit
-    warn "@_\n" if @_;
-    die <<"USAGE";
-usage:
-    $Script [OPTION] file1 [ .. fileN ]
-
-with options:
-  -b YYYY[-MM[-DD]]
-          begin date for accounting (job end_time  > DATE 2 A.M.)
-  -e YYYY[-MM[-DD]]
-          end date for accounting   (job end_time <= DATE 2 A.M.)
-  -h      usage
-
-Extract portions of the GridEngine accounting(5) file according to the
-job end_time. For example,
-    $Script -b 2008-01-01 -e 2009 ...
-extracts the accounting for jobs that finished running in 2008.
-
-The value of 2 A.M. avoids problems that daylight savings time might
-otherwise cause.
-
-version ($releaseDate)
-copyright (c) 2009 <Mark.Olesen\@faurecia.com>
-
-Licensed and distributed under the Creative Commons
-Attribution-NonCommercial-ShareAlike 3.0 License.
-http://creativecommons.org/licenses/by-nc-sa/3.0
-USAGE
-}
-
-# -------------------------------------------------------------------------
-my %opt;
-getopts( "hb:e:", \%opt ) or usage();
-usage() if $opt{h};
-
-@ARGV or usage();
-
-for (@ARGV) {
-    -f $_ or die "no file '$_'\n";
-
-    ## handle compressed files transparently
-    if (/\.bz2$/) {
-        $_ = qq{bzip2 -dc "$_"|};
-    }
-    elsif (/\.gz$/) {
-        $_ = qq{gzip -dc "$_"|};
-    }
-}
-
-for (qw( b e )) {
-    if ( $opt{$_} ||= 0 ) {
-        my ( $yy, $mm, $dd );
-
-        if ( $opt{$_} =~ /^(\d{2,4})-(\d{1,2})-(\d{1,2})$/ ) {
-            ## YYYY-MM-DD
-            ( $yy, $mm, $dd ) = ( $1, $2, $3 );
-        }
-        elsif ( $opt{$_} =~ /^(\d{2,4})-(\d{1,2})$/ ) {
-            ## YYYY-MM
-            ( $yy, $mm ) = ( $1, $2 );
-        }
-        elsif ( $opt{$_} =~ /^(\d{2,4})$/ ) {
-            ## YYYY
-            ($yy) = ($1);
-        }
-        else {
-            usage("invalid date format: '$opt{$_}'");
-        }
-
-        # treat missing month/day as '1'
-        $mm ||= 1;
-        $dd ||= 1;
-
-        # convert from YYYY-MM-DD to epoch,
-        # start at 2am - avoid problems with daylight savings time
-        $opt{$_} = timelocal( 0, 0, 2, $dd, $mm - 1, $yy );    # month (0..11)
-    }
-}
-
-$opt{b} or $opt{e} or usage("must specify at least one of -b or -e");
-
-if ( $opt{e} and $opt{b} >= $opt{e} ) {
-    usage("-b DATE must less than -e DATE");
-}
-
-my $fileCount;
-while (<>) {
-    if (/^\s*#/) {
-        ## pass-thru comments, but only for the first file
-        print unless $fileCount;
-        next;
-    }
-
-    my ($endtime) = ( split /:/ )[10];
-
-    # only allow things that ran (endtime non-zero)
-    # and that are within the filter limits
-    if (    $endtime
-        and ( $opt{b} ? ( $endtime > $opt{b} )  : 'okay' )
-        and ( $opt{e} ? ( $endtime <= $opt{e} ) : 'okay' ) )
-    {
-        print;
-    }
-}
-continue {
-    $fileCount++ if eof;
-}
-
-__END__
-
-FORMAT - see accounting(5)
-08  submission_time
-09  start_time
-10  end_time

flex-grid/scripts/qlic

@@ -1,517 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-use Getopt::Std qw( getopts );
-use POSIX qw( );
-
-( my $Script = $0 ) =~ s{^.*/}{};
-
-my $time = time;
-my $date = POSIX::strftime( "%F %T", localtime $time );
-
-$ENV{SGE_ROOT} or die "Error $Script: \$SGE_ROOT is not set\n";
-$ENV{SGE_CELL} ||= "default";    # sge_cell
-
-my ($siteLocation) = join "/" => ( $ENV{SGE_ROOT}, $ENV{SGE_CELL}, "site" );
-
-my $config = {
-    -site   => ( $siteLocation || '' ),
-    -cache  => ( $siteLocation || '' ) . "/cache/" . "qlicserver.xml",
-    -limits => ( $siteLocation || '' ) . "/" . "qlicserver.limits",
-};
-
-# ------------------------------------------------------------------------
-# utils
-
-#
-# calculate age from an epoch value
-#
-sub age {
-    my ( $a, $b ) = @_;
-    my $diff = ( $a - $b );
-
-    my $sign = '';
-    if ( $diff < 0 ) {    # handle negatives
-        $sign = '-';
-        $diff = abs($diff);
-    }
-
-    sprintf "$sign%d:%02d:%02d",    # format into hh:mm:ss
-      ( int $diff / 3_600 ),        # hh
-      ( ( int $diff / 60 ) % 60 ),  # mm
-      ( $diff % 60 );               # ss
-}
-
-#
-# change hash references to a comma-delimited string of key=value entries
-#
-sub hashRefToString {
-    map {
-        my $ref = $_;
-        ref $ref ? map { "$_=$ref->{$_}" } sort keys %$ref : ()
-    } @_;
-}
-
-#
-# extract attrib="value" ... attrib="value"
-#
-sub parseXMLattrib {
-    my $str = shift || '';
-    my %attr;
-
-    while ($str =~ s{^\s*(\w+)=\"([^\"]*)\"}{}s
-        or $str =~ s{^\s*(\w+)=\'([^\']*)\'}{}s )
-    {
-        $attr{$1} = $2;
-    }
-
-    %attr;
-}
-
-# ------------------------------------------------------------------------
-# processing of qlicserver.xml output
-#
-package qlicCache;
-
-sub new {
-    my $caller = shift;
-    my $file   = shift;
-
-    my $self = bless {
-        ( map { $_ => {} } qw( -rc ) ),
-        ( map { $_ => '' } qw( -date -host -age ) )
-    }, $caller;
-
-    -f $file or return $self;
-
-    local $_ = do { local ( @ARGV, $/ ) = $file; <>; };
-
-    # strip out all xml comments
-    s{<!--.*?-->\s*}{}sg;
-
-    # get the header section
-    s{^(.+?)</query>}{}s or return;
-    my $header = $1;
-
-    for ($header) {
-        if (m{<host (?:\s+([^<>]*))? > \s*(.+?)\s* </host>}sx) {
-            my ( $attr, $content ) = ( $1, $2 );
-            $self->{-host} = $content;
-        }
-        if (m{<time (?:\s+([^<>]*))? > \s*(.+?)\s* </time>}sx) {
-            my ( $attr, $content ) = ( $1, $2 );
-            my %attr = main::parseXMLattrib($attr);
-
-            $self->{-age} = main::age( $time, $attr{epoch} ) if $attr{epoch};
-            $self->{-date} = $content;
-        }
-    }
-
-    # only retain the <resources> contents
-    s{^.*?<resources>}{}s and s{</resources>.*$}{}s or return;
-
-    ## process <resource .../>
-    while (s{<resource (?:\s+([^/<>]*))? />}{}sx) {
-        my ($attr) = ($1);
-        my %attr   = main::parseXMLattrib($attr);
-        my $name   = delete $attr{name};
-
-        if ( defined $name ) {
-            for ( keys %attr ) {
-                $self->{-rc}{$name}{$_} = $attr{$_} || 0;
-            }
-        }
-    }
-
-    ## process <resource ...> CONTENT </resource>
-    while (s{<resource (?:\s+([^<>]*))? > \s* (.*?) \s* </resource>}{}sx) {
-        my ( $attr, $content ) = ( $1, $2 );
-        my %attr = main::parseXMLattrib($attr);
-        my $name = delete $attr{name};
-
-        if ( defined $name ) {
-            for ( keys %attr ) {
-                $self->{-rc}{$name}{$_} = $attr{$_} || 0;
-            }
-        }
-
-        ## process <user ...> COUNT </user>
-        while ( $content =~ s{<user (?:\s+([^<>]*))? >\s*(\d+)\s*</user>}{}sx )
-        {
-            my ( $attr, $count ) = ( $1, $2 );
-            my %attr = main::parseXMLattrib($attr);
-            my $user = delete $attr{name};
-            my $host = delete $attr{host};
-
-            if ( defined $user ) {
-                if ( defined $host ) {
-                    $self->{-rc}{$name}{-where}{"$user\@$host"} = $count;
-                }
-                else {
-                    ## tag waiting with '[]'
-                    $self->{-rc}{$name}{-where}{$user} = "[$count]";
-                }
-            }
-        }
-    }
-
-    return $self;
-}
-
-sub query {
-    my $self = shift;
-    %{ $self->{-rc} };
-}
-
-sub dump {
-    use Data::Dumper;
-    print Dumper( $_[0] );
-}
-
-sub available {
-    my $self = shift;
-    sort keys %{ $self->{-rc} };
-}
-
-# ------------------------------------------------------------------------
-# processing of qlicserver.limits FILE or DIRECTORY
-#
-package qlicLimits;
-
-sub new {
-    my $caller     = shift;
-    my $diskValues = shift;
-
-    my $self = bless {}, $caller;
-
-    my $fileString;
-    if ( defined $diskValues and -f $diskValues ) {
-        $fileString = do {
-            local ( *FILE, $/ );
-
-            if ( open FILE, $diskValues ) {
-                <FILE>;
-            }
-            else {
-                undef;
-            }
-        };
-    }
-    elsif ( defined $diskValues and -d $diskValues ) {
-        local *DIR;
-        my $dir = $diskValues;
-        if ( opendir DIR, $dir ) {
-            my @files = grep { -f "$dir/$_" and -r _ } readdir DIR;
-            for my $name (@files) {
-                my $limit;
-
-                # use the last value
-                if ( open FILE, "$dir/$name" ) {
-                    $limit = ( map { /^\s*(-?\d+)\s*$/ } <FILE> )[-1];
-                }
-                defined $limit or $limit = "NONE";
-                $self->{$name} = $limit;
-            }
-        }
-    }
-
-    for ($fileString) {
-        defined or next;
-
-        # strip out all comments
-        s{<!--.*?-->\s*}{}sg;
-
-        ## process <resource .../> and <resource ...></resource>
-        while (s{<resource (?:\s+([^/<>]*))? />}{}sx
-            or s{<resource (?:\s+([^/<>]*))? >\s*</resource>}{}sx )
-        {
-            my %attr  = main::parseXMLattrib($1);
-            my $name  = delete $attr{name};
-            my $limit = delete $attr{limit};
-            if ( defined $name and defined $limit ) {
-                $self->{$name} = $limit;
-            }
-        }
-    }
-
-    return $self;
-}
-
-sub change {
-    my $caller     = shift;
-    my $diskValues = shift;
-    my @args       = @_;
-
-    @args or return;
-
-    my ( %pending, %adjusted );
-
-    for (@args) {
-        s{,}{ }g;    # comma -> space-delimited
-
-        my %h = map { /^(.+?)=(.*)$/ } split;
-        for ( keys %h ) {
-            defined $h{$_} and length $h{$_} or $h{$_} = "NONE";
-            $pending{$_} = $h{$_};
-        }
-    }
-
-    keys %pending or return;
-
-    my $user = getpwuid $<;
-    if ( defined $diskValues and -d $diskValues ) {
-        local *DIR;
-        my $dir = $diskValues;
-        if ( opendir DIR, $dir ) {
-            my @files = grep { -f "$dir/$_" and -w _ } readdir DIR;
-
-            for my $name (@files) {
-                if ( exists $pending{$name} ) {
-                    local *FILE;
-                    if ( open FILE, ">", "$dir/$name" ) {
-                        print FILE "# adjusted by $user $date\n",
-                          "$pending{$name}\n";
-                        $adjusted{$name} = delete $pending{$name};
-                    }
-                }
-            }
-        }
-    }
-
-    for ( [ "adjusted" => \%adjusted ], [ "not adjusted" => \%pending ], ) {
-        my ( $label, $href ) = @$_;
-        keys %$href or next;
-        print "$label: ",
-          join( "," => map { qq{$_=$href->{$_}} } sort keys %$href ), "\n";
-    }
-}
-
-sub output {
-    my $self = shift;
-
-    my @list = map { qq{$_=$self->{$_}} } sort keys %$self;
-
-    print "limits: ";
-    if (@list) {
-        print join( "," => @list ), "\n";
-    }
-    else {
-        print "NONE\n";
-    }
-}
-
-# ------------------------------------------------------------------------
-# main
-#
-
-package main;
-import qlicCache;
-
-# ------------------------------------------------------------------------
-sub usage {
-    $! = 0;    # clean exit
-    warn "@_\n" if @_;
-    die <<"USAGE";
-usage:
-    $Script [OPTION]
-    $Script [OPTION] resource=limit .. resource=limit
-
-with options:
-  -c FILE  alternative location for the license cache
-  -C FILE  alternative location for the license limit
-  -d       dump cache file as raw xml
-  -D       dump license cache in perl format
-  -f       display free licenses only
-  -l       list license limit
-  -q       display free licenses via qhost query
-  -u       license usage via 'lacct'
-  -U       license usage per user via 'lacct -u'
-  -w       show who/where ('[]' indicates waiting jobs)
-  -h       this help
-
-* extract / display information for the GridEngine license cache
-  $config->{-cache}
-
-* adjust / display information for the license limits
-  $config->{-limits}
-
-copyright (c) 2003-10 <Mark.Olesen\@faurecia.com>
-
-Licensed and distributed under the Creative Commons
-Attribution-NonCommercial-ShareAlike 3.0 License.
-http://creativecommons.org/licenses/by-nc-sa/3.0
-USAGE
-}
-
-# -------------------------------------------------------------------------
-my %opt;
-getopts( 'hc:C:DdflqUuw', \%opt ) or usage();
-$opt{h} and usage();
-
-if ( $opt{U} ) {
-    ## user-based usage from accounting
-    my @query = ( "lacct", "-u" );
-    exec @query;
-    exit 2;
-}
-elsif ( $opt{u} ) {
-    ## usage from accounting
-    my @query = ( "lacct", $opt{w} ? "-w" : () );
-    exec @query;
-    exit 2;
-}
-
-if ( $opt{d} ) {
-    my $file = $opt{c} || $config->{-cache};
-
-    if ( not -f $file and $file !~ m{/} ) {
-        $file = "$config->{-site}/$file";
-    }
-
-    -f $file or exit 1;
-
-    local $_ = do { local ( @ARGV, $/ ) = $file; <>; };
-
-    # do a basic check for well-formed xml
-    # this might not be the case if there is a race condition
-    # and the file has not been fully written
-
-    # check for '<?xml version="1.0"?><someTag ...' at the start
-    # and '</someTag>' at the end
-    my ($tag) = m{^<\?xml (?:\s+[^<>]*?)? \?>\s*\<(\w+)}sx;
-    unless ( $tag and m{</\Q$tag\E>\s*$} ) {
-        sleep 2;    ## wait and try again
-        $_ = do { local ( @ARGV, $/ ) = $file; <>; };
-    }
-
-    $_ ||= '';      ## avoid uninitialized
-
-    print;
-    exit;
-}
-
-if ( $opt{q} ) {
-    my %free =
-      map  { /^\s+gc:(\S+?)=(\d\S*)\s*$/ }
-      grep { /^global/ ... /^\S/ } qx{qhost -F};
-
-    $_ += 0 for values %free;
-
-    for ( sort keys %free ) {
-        my $intval = $free{$_} + 0;    # normalize as integers
-        print "$_=$intval\n";
-    }
-    exit;
-}
-
-if ( $opt{l} ) {
-    qlicLimits->new( $opt{C} || $config->{-limits} )->output();
-    exit;
-}
-
-if (@ARGV) {
-    qlicLimits->change( $opt{C} || $config->{-limits}, @ARGV );
-    exit;
-}
-
-my $info = qlicCache->new( $opt{c} || $config->{-cache} );
-$info->dump() if $opt{D};
-
-my %resources = $info->query();
-
-#
-# display free licenses
-#
-if ( $opt{f} ) {
-    for my $resource ( sort keys %resources ) {
-        my $count = $resources{$resource} || {};
-        my $free  = $count->{free}        || 0;
-        print "$resource=$free\n" if $free;
-    }
-
-    exit;
-}
-
-#
-# display who/where
-#
-if ( $opt{w} ) {
-    my ($len) = sort { $b <=> $a } map { length } keys %resources;
-    $len += 2;
-
-    my $fmt    = "%-${len}s";
-    my $indent = sprintf "\n$fmt", '';
-
-    for my $resource ( sort keys %resources ) {
-        my $count = $resources{$resource} || {};
-        my @list = hashRefToString( $count->{-where} );
-        if (@list) {
-            printf $fmt, $resource;
-            print join( $indent => @list ), "\n";
-        }
-    }
-
-    exit;
-}
-
-#
-# define table output format
-#
-my @outputList;
-
-format =
-# name      total limit extern intern wait free
-@<<<<<<<<<<< @>>>>> @>>>>> @>>>>> @>>>>> @>>>> @>>>>
-@outputList
-.
-
-#
-# display table header
-# --------------------
-{
-    my @info = qw( host age );
-    my ($len) = sort { $b <=> $a } map { length } @info;
-
-    print map {
-        my $k = sprintf "%-${len}s", $_;
-        my $v = $info->{"-$_"};
-        $v ? "$k = $v\n" : ();
-    } @info;
-
-    print "\n";
-
-    @outputList = qw( resource total limit extern intern wait free );
-
-    write;
-    s/./-/g for @outputList;
-    write;
-}
-
-#
-# display table body
-# ------------------
-for my $resource ( sort keys %resources ) {
-    my $count = $resources{$resource} || {};
-    @outputList =
-      ( $resource, @{$count}{qw( total limit extern intern waiting free )} );
-
-    my $type = $resources{$resource}{type} || 0;
-
-    # no total?
-    $_ ||= "?" for $outputList[1];
-
-    if ( $type eq "intern" ) {
-        $_ = "*" for $outputList[3];
-    }
-    elsif ( $type eq "track" ) {
-        $_ = "*" for $outputList[4];
-    }
-
-    # easy to read representation for zero
-    for (@outputList) {
-        defined $_ or $_ = '.';
-    }
-
-    write;
-}
-
-# ------------------------------------------------------------------------

flex-grid/site/qloadsensor

@@ -1,325 +0,0 @@
-#!/bin/bash
-# $Id: qloadsensor 180 2010-09-17 15:46:41Z kasper $
-#
-# qloadsensor:
-# load sensor for particular file systems and floating licenses
-#
-# NB:
-#    1) add the new complexes (via qconf -mc) for the following:
-#       * complex configurations managed in the shell script
-#           eg, 'perl -x qloadsensor'
-#       * complex consumables managed global
-#           eg, 'qlicserver -c'
-#    2) initialize the global complex consumables to be managed
-#           eg, 'qlicserver -C'
-#
-# copyright (c) 2003-10 <Mark.Olesen@faurecia.com>
-#
-# Licensed and distributed under the Creative Commons
-# Attribution-NonCommercial-ShareAlike 3.0 License.
-# http://creativecommons.org/licenses/by-nc-sa/3.0
-# -----------------------------------------------------------------------------
-
-#
-# impose default GridEngine environment + ascertain the binary architecture
-#
-# you likely don't need to adjust these values, since the loadsensor is called
-# from sge_execd, which in turn is started from /etc/init.d/n1ge and
-# these variables should be correctly exported there
-#
-[ -d "$SGE_ROOT" ] || { echo "Error: SGE_ROOT=$SGE_ROOT not found"; exit 1; }
-: ${SGE_CELL:=default}
-: ${SGE_ARCH:=`$SGE_ROOT/util/arch`}
-
-export SGE_ROOT SGE_CELL SGE_ARCH
-
-# -----------------------------------------------------------------------------
-# this script should run as the 'admin_user' registered in 'bootstrap'
-#
-if [ "$UID" -eq 0 ]
-then
-    admin_user=$(sed -ne 's/^admin_user *//p' $SGE_ROOT/$SGE_CELL/common/bootstrap)
-    : ${admin_user:=root}
-    if [ $admin_user != root -a $(echo $admin_user | tr "A-Z" "a-z") != none ]
-    then
-        exec $SGE_ROOT/utilbin/$SGE_ARCH/adminrun $admin_user $0
-    fi
-fi
-
-# <settings>
-# ========================================================================
-# now that we are the admin_user, we can source our standard settings
-#   - customize *all* settings there (eg, license server settings)
-#   - ENSURE THAT '$SGE_site' IS DEFINED !!!
-#
-for i in $SGE_ROOT/$SGE_CELL/site/environ; do [ -f $i ] && . $i; done
-
-# define (unique) cluster name if not already defined
-if [ -z "$SGE_CLUSTER_NAME" -a -r "$SGE_ROOT/$SGE_CELL/common/cluster_name" ]
-then
-    SGE_CLUSTER_NAME=$(cat $SGE_ROOT/$SGE_CELL/common/cluster_name 2>/dev/null)
-fi
-: ${SGE_CLUSTER_NAME:=default}
-export SGE_CLUSTER_NAME
-
-SGE_site="$SGE_ROOT/flex-grid/site"
-
-#
-# ========================================================================
-# </settings>
-
-###############################################################################
-###############################################################################
-# CUSTOMIZE THESE SETTINGS - iff. required
-
-qlicserver="$SGE_site/qlicserver config=$SGE_site/../config/local_licenses.conf dir=$SGE_ROOT/flex-grid/cache output=$SGE_ROOT/flex-grid/cache/qlicserver.xml qhost=qhost.xml qstat=qstat.xml"
-diskmon="$SGE_site/diskmon.pl"
-
-# END OF CUSTOMIZE SETTINGS
-###############################################################################
-###############################################################################
-
-#
-# the real (not compiled in) architecture
-#
-os_arch=`$SGE_ROOT/util/arch`
-SGE_utilbin=$SGE_ROOT/utilbin/$os_arch
-
-#
-# set some constants
-#
-HOST=$($SGE_utilbin/gethostname -aname)
-UQHOST=$(echo $HOST | cut -f1 -d.)
-SGE_qmaster=unknown; export SGE_qmaster
-
-# -----------------------------------------------------------------------------
-# act_qmaster
-#
-# extract the unqualified host name from the "act_qmaster" file
-# return this value or 'unknown' on failure
-#
-act_qmaster()
-{
-    tmp=$(cat $SGE_common/act_qmaster 2>/dev/null)
-    echo ${tmp:-unknown}
-}
-
-# -----------------------------------------------------------------------------
-# df_info
-#
-# echo the $1_{total,used,free} space on filesystem $2
-#
-# gridengine uses the suffixes
-#   'k' => blocksize 1000
-#   'K' => blocksize 1024
-#
-# return 0 if 'df' fails
-df_info()
-{
-    # 1:tag 2:mount 3:filesys 4:total 5:Used 6:Avail 7:Used% 8:Mount
-   [ -d "$2" ]    && set -- $1 $2 $( df -k -P $2 2>/dev/null | tail -1 )
-
-    #!# we could add the following check:
-    #!# [ "$2" != "$8" ] && set -- $1 $2;        # mount point mismatch?
-
-    [ "$#" -ge 6 ] || set -- $1 $2 filesystem 0 0 0
-
-    echo "$UQHOST:$1_total:$4K"
-    echo "$UQHOST:$1_used:$5K"
-
-    #if [ -w "$2" ]
-    #then
-        echo "$UQHOST:$1_free:$6K"
-    #else
-    #    echo "$UQHOST:$1_free:0"
-    #fi
-}
-
-# invariant values
-if [ -e "/proc/cpuinfo" ]
-then
-    # mips=$(awk '{if (/mips/) printf "%.0f\n", $NF}' /proc/cpuinfo | tail -1)
-    mips=$(awk 'BEGIN {mips=0} /mips/ {if ($NF > mips) mips=$NF }; END {print mips}' /proc/cpuinfo)
-else
-    mips=0
-fi
-
-unset os_name
-# extract lsb_release
-if [ -e "/usr/bin/lsb_release" ]
-then
-   os_name=$(/usr/bin/lsb_release -ircs | xargs echo | sed 's/ /_/g')
-else
-   os_name='unkown'
-fi
-: ${os_name:=NONE}
-
-# -----------------------------------------------------------------------------
-# host_info
-#
-# report host specific information about filesystems, logins,
-# special hardware extensions, etc.
-#
-host_info()
-{
-    echo "$UQHOST:arch:$os_arch"
-    echo "$UQHOST:os:$os_name"
-#   df_info	tmp	/tmp
-	df_info	scratch	/scratch
-    echo "$UQHOST:mips:$mips"
-}
-
-# -----------------------------------------------------------------------------
-# iidle_info()
-# report a machine's idle time
-#
-# parse the contents from /proc/interrupts, which looks like the following:
-#
-#            CPU0
-#   0:   23024789          XT-PIC  timer
-#   1:         13          XT-PIC  keyboard
-#   2:          0          XT-PIC  cascade
-#   5:          0          XT-PIC  usb-uhci
-#   8:          2          XT-PIC  rtc
-#   9:          0          XT-PIC  acpi
-#  10:          0          XT-PIC  ehci-hcd, usb-uhci
-#  11:   16687253          XT-PIC  eth0, usb-uhci, Intel 82801DB-ICH4, nvidia
-#  12:         20          XT-PIC  PS/2 Mouse
-#  14:      77178          XT-PIC  ide0
-#  15:          2          XT-PIC  ide1
-# NMI:          0
-# LOC:          0
-# ERR:          0
-# MIS:          0
-#
-# or,
-#
-#            CPU0       CPU1
-#   0:   12820049   12818168    IO-APIC-edge  timer
-#   1:      42889      43309    IO-APIC-edge  keyboard
-#   2:          0          0          XT-PIC  cascade
-#   8:          2          0    IO-APIC-edge  rtc
-#   9:          0          0    IO-APIC-edge  acpi
-#  12:     287235     296531    IO-APIC-edge  PS/2 Mouse
-#  14:      47423      40923    IO-APIC-edge  ide0
-#  15:          2          3    IO-APIC-edge  ide1
-#  16:    7733868    7737081   IO-APIC-level  nvidia
-#  17:        159        156   IO-APIC-level  Intel ICH 82801AA
-#  19:    2155710    2159943   IO-APIC-level  e100, usb-uhci
-# NMI:          0          0
-# LOC:   25641034   25641033
-# ERR:          0
-# MIS:          0
-#
-# Thus, we need the [-1, 1..$ncpu] fields for the following sources:
-# keyboard, Mouse, serial
-#
-# NB: adding 'usb-uhci' gives problems, since this is sometimes
-# attached to the ethernet card
-#
-# set the variable 'iidle' to the idle time (seconds) since the last call
-#
-last="0 -1";
-iidle_info()
-{
-    set -- $(
-    perl -e '
-        my @last = @ARGV;
-        @ARGV = "/proc/interrupts";
-        $_    = <>;
-
-        my $ncpu = s/\s*CPU\d+//g || 0;
-        my ( $iidle, $int, $now ) = ( 0, 0, time );
-
-        $int += $_
-          for
-          map { /\s+(keyboard|Mouse|serial)$/ ? (split)[ 1 .. $ncpu ] : (); }
-          <>;
-
-        if ( $int == $last[-1] ) {    # no interactivity since last round
-            $iidle = ( $now - $last[0] );
-        }
-        else {
-            @last = ( $now, $int );
-        }
-
-        print "$iidle @last\n";
-    ' $last
-    );
-
-    echo "$UQHOST:iidle:$1";
-
-    shift; last="$@";   # save for later
-}
-# -----------------------------------------------------------------------------
-#
-# The execd running on the qmaster queries the license server
-# The contents of 'act_qmaster' should suffice to migrate the load sensor
-# for a controlled migration.
-#
-
-while :
-do
-    read input || exit 1         # wait for input
-    [ "$input" = quit ] && exit 0
-
-    echo begin                   # begin load report
-    host_info                    # host information
-    iidle_info                   # machine's idle time
-    echo end                     # end load report
-
-    # let the license query run between load reports
-    # SGE_qmaster=`act_qmaster`    # refresh the name of the qmaster
-    # if [ "$HOST" = "$SGE_qmaster" ]
-    if [ "$HOST" = "minos19" ]
-    then
-        # $qlicserver 2>> qloadsensor.err
-        $SGE_ROOT/flex-grid/site/qlicserver config=$SGE_ROOT/flex-grid/config/local_licenses.conf output=$SGE_ROOT/flex-grid/cache/qlicserver_local.xml
-        $SGE_ROOT/flex-grid/site/qlicserver config=$SGE_ROOT/flex-grid/config/abaqus_licenses.conf timeout=60 output=$SGE_ROOT/flex-grid/cache/qlicserver_abaqus.xml
-        # $SGE_ROOT/flex-grid/site/qlicserver config=/opt/SGE/flex-grid/config/trelis_licenses.conf timeout=60 output=$SGE_ROOT/flex-grid/cache/qlicserver_trelis.xml
-        $SGE_ROOT/flex-grid/site/qlicserver config=/opt/SGE/flex-grid/config/comsol_licenses.conf timeout=60 output=$SGE_ROOT/flex-grid/cache/qlicserver_comsol.xml
-        $SGE_ROOT/flex-grid/site/qlicserver config=$SGE_ROOT/flex-grid/config/matlab_licenses.conf timeout=60 output=$SGE_ROOT/flex-grid/cache/qlicserver_matlab.xml
-	lockfile $SGE_ROOT/flex-grid/cache/qlicserver.xml.lock
-        # (sed '/<\/resources>/,$ d'  $SGE_ROOT/flex-grid/cache/qlicserver_abaqus.xml ; sed '1,/<resources>/d' $SGE_ROOT/flex-grid/cache/qlicserver_trelis.xml | grep -v qlicserver | grep -v resources ; sed '1,/<resources>/d' $SGE_ROOT/flex-grid/cache/qlicserver_local.xml | grep -v qlicserver | grep -v resources ; sed '1,/<resources>/d' $SGE_ROOT/flex-grid/cache/qlicserver_matlab.xml;) > $SGE_ROOT/flex-grid/cache/qlicserver.xml
-        # (sed '/<\/resources>/,$ d'  $SGE_ROOT/flex-grid/cache/qlicserver_abaqus.xml ; sed '1,/<resources>/d' $SGE_ROOT/flex-grid/cache/qlicserver_local.xml | grep -v qlicserver | grep -v resources ; sed '1,/<resources>/d' $SGE_ROOT/flex-grid/cache/qlicserver_matlab.xml;) > $SGE_ROOT/flex-grid/cache/qlicserver.xml
-        (sed '/<\/resources>/,$ d'  $SGE_ROOT/flex-grid/cache/qlicserver_abaqus.xml ; sed '1,/<resources>/d' $SGE_ROOT/flex-grid/cache/qlicserver_local.xml | grep -v qlicserver | grep -v resources; sed '1,/<resources>/d' $SGE_ROOT/flex-grid/cache/qlicserver_comsol.xml | grep -v qlicserver | grep -v resources ; sed '1,/<resources>/d' $SGE_ROOT/flex-grid/cache/qlicserver_matlab.xml;) > $SGE_ROOT/flex-grid/cache/qlicserver.xml
-	rm -f $SGE_ROOT/flex-grid/cache/qlicserver.xml.lock
-        # $diskmon -m 2>> qloadsensor.err
-        # force rescheduling of express jobs
-        # $SGE_site/qxprs >/dev/null 2>&1
-    # else
-        # $diskmon 2>> qloadsensor.err
-    fi
-done
-exit 0    # we never get here, but just in case
-
-#------------------------------------------------------------------------------
-# feed via 'perl -x' to extract the 'host' complex configuration
-
-#!/usr/bin/perl -w
-print <DATA>
-__DATA__
-#
-# host complex configuration
-#
-#name         shortcut  type   relop requestable consumable default  urgency
-#---------------------------------------------------------------------------
-tmp_total      tmpt     MEMORY  <=   YES         NO         0        0
-tmp_used       tmpu     MEMORY  >=   NO          NO         0        0
-tmp_free       tmpf     MEMORY  <=   YES         NO         0        0
-iidle          iidle    INT     <=   YES         NO         0        0
-mips           mips     INT     <=   YES         NO         0        0
-os             os       RESTRING ==  YES         NO         NONE     0
-abaqus                    abaqus                    DOUBLE      <=    YES         YES        0        0
-cae                       cae                       DOUBLE      <=    YES         YES        0        0
-comsol                    comsol                    DOUBLE      <=    YES         YES        0        0
-hyper                     hyper                     DOUBLE      <=    YES         YES        0        0
-ifort                     ifort                     DOUBLE      <=    YES         YES        0        0
-matlab                    matlab                    DOUBLE      <=    YES         YES        0        0
-mcc                       mcc                       DOUBLE      <=    YES         YES        0        0
-multiphysics              multiphysics              DOUBLE      <=    YES         YES        0        0
-trelis                    trelis                    DOUBLE      <=    YES         YES        0        0
-scratch_free              scratch_free              MEMORY      <=    YES         YES        0        0
-scratch_total             scratch_total             MEMORY      <=    YES         NO         0        0
-scratch_used              scratch_used              MEMORY      >=    NO          NO         0        0
-# -----------------------------------------------------------------------------

local/bin/term.sh

@@ -1,30 +0,0 @@
-#!/usr/bin/ksh
-
-# This script should be added as the TERMINATE_METHOD in the
-# queue definition with $job_pid, $job_id, $job_owner, and interval arguments.
-# e.g.  script.sh $job_pid $job_id $job_owner 90
-
-if [ -z "$4" ]
-then
-    echo "Usage: $0 \$job_pid \$job_id \$job_owner interval" 
-    exit 1
-fi
-
-#echo "Term script Running on $(hostname): $USER $1 $2 $3 $4" >> ~$3/qdel_log.log
-#echo $(pgrep -g $1) >> ~$3/qdel_log.log
-
-for sig in INT TERM KILL
-do
-    stat=$(pgrep -g $1 -u $3)
-    if [ ! -z "${stat}" ]
-    then
-        #echo "Sending SIG${sig} to $1" >> ~$3/qdel_log.log
-        /usr/bin/pkill --signal ${sig} -g $1
-        sleep $4
-    else
-        break
-    fi
-done
-
-#uncomment the following for debugging
-#echo "Job $2 killed." >> ~$3/qdel_log.log

local/examples/jobs/matlab_script.sh

@@ -1,81 +0,0 @@
-#!/bin/bash
-
-#############################################################
-# This example produces a very simple plot and              #
-# saves it as Matlab figure file and as PNG file            #
-#############################################################
-
-#############################################################
-# set qsub options                                          #
-#############################################################
-# run in low.q
-#$ -l low
-
-# request enough memory
-#$ -l h_vmem=8G,memory=8G,h_stack=8M
-
-# request 1 matlab license.
-#$ -l matlab=1
-
-# Name the job 'Matlab'
-#$ -N Matlab
-
-# send e-mail after job has finished
-# use the -M option to define your e-mail address
-# #$ -M meine-email@example.org
-#$ -m e
-
-# join stdout and stderr in one file
-#$ -j y
-
-#############################################################
-# output hostname and date (comment out if not needed)      #
-#############################################################
-echo "Runnning Matlab on host " `hostname`
-echo "Starting Matlab at " `date`
-
-#############################################################
-# launch matlab                                             #
-#############################################################
-
-# run non-interactive Matlab session
-# use no display (-nodisplay)
-# don't show splash screen at startup (-nosplash)
-# don't start the matlab desktop (-nodesktop)
-# use software opengl (-softwareopengl)
-# only use single threaded computations (limit to use of 1 core, -singleCompThread)
-# execute all matlab commands between '<< END' and matching 'END'
-
-# Don't forget to add 'exit' and 'END' after replacing
-# the commands with your own!
-
-/opt/matlab/bin/matlab -nodisplay -nosplash -nodesktop -softwareopengl -singleCompThread << END
-
-  % get environment variable JOB_ID
-  jobid=str2num(getenv('JOB_ID'));
-  if isempty(jobid)
-     jobid = 0;
-  end
-
-  % create filenames for the figure
-  filename=sprintf('matlab_figure_%d', jobid);
-
-  % create new empty figure and save figure handle
-  fh = figure();
-
-  % draw plot
-  plot(-pi:0.01:pi, sin(-pi:0.01:pi));
-
-  % save figure as matlab figure and PNG
-  saveas(fh, filename, 'fig');
-  saveas(fh, filename, 'png');
-
-  % EXIT MATLAB
-  exit;
-
-END
-
-#############################################################
-# output date (comment out if not needed)                   #
-#############################################################
-echo "Matlab finnished at " `date`

local/examples/jobs/periodic_sleeper.sh

@@ -1,75 +0,0 @@
-#!/bin/bash
-# This job script takes a nap for 10 seconds (or paramter $2) every 30 minutes (or paramter $1)
-
-# SGE options
-#$ -N PSleeper
-#$ -l scf=1M,mem=100M,h_vmem=100M
-#$ -q normal.q
-#$ -cwd
-
-# process args
-case "$1" in
-    -h)
-        echo "usage: $0 [-h | [-d] [T] [nap]]"
-        echo "periodically take a nap"
-        echo ""
-        echo "-h   print this help and exit"
-        echo "-d   print debug info"
-        echo "T    take a nap every T minutes (default: 30)"
-        echo "nap  take a nap for nap seconds (default: 10)"
-        exit 1
-        ;;
-    *)
-        debug=0
-        terse="-terse"
-        debug_flag=""
-        do_echo=0
-        T=30
-        nap=10
-        while (( "$#" )); do
-            case "$1" in
-                -d)
-                    debug=1
-                    terse=""
-                    debug_flag="-d"
-                    do_echo=1
-                    ;;
-                *)
-                    T=${1:-30}
-                    nap=${2:-10}
-                    break
-                    ;;
-            esac
-            shift
-        done
-        ;;
-esac
-
-# set other variables
-next=$(date -d "${T} minutes" +%Y%m%d%H%M)
-script=$0
-
-# output some informations
-if [ ${debug} -eq 1 ]; then
-    echo "T = ${T}, nap=${nap}"
-    echo "next run at ${next} (YYYYMMDDhhmm)"
-    echo "debug_flag = ${debug_flag}, do_echo = ${do_echo}"
-    echo ""
-fi
-
-# commands to run in Grid Engine
-${script} ${nap} ${do_echo}
-
-# re-submit script to execute in T minutes
-jobid=$(qsub ${terse} -a ${next} ${script} ${debug_flag} ${T} ${nap})
-exit_code=$?
-if [ ${debug} -eq 1 ]; then
-    echo "${jobid}"
-fi
-if [ ${exit_code} -ne 0 ]; then
-    if [ ${debug} -eq 1 ]; then
-        echo "${jobid}"
-        echo "Ups, something went wrong, check output!"
-    fi
-    exit ${exit_code}
-fi

local/examples/jobs/simple_conda_test.sh

@@ -1,45 +0,0 @@
-#! /bin/bash
-
-#############################################################
-# This example show a list of availabel conda environments  #
-#############################################################
-
-#############################################################
-# set qsub options                                          #
-#############################################################
-# run in low.q
-#$ -l low
-
-# request enough memory
-# #$ -l h_vmem=8G,memory=8G,h_stack=8M
-
-# Name the job 'Conda-Test'
-#$ -N Conda-Test
-
-# send e-mail after job has finished
-# use the -M option to define your e-mail address
-# #$ -M my-email@example.org
-#$ -m e
-
-# join stdout and stderr in one file
-#$ -j y
-
-#############################################################
-# initialize conda                                          #
-#############################################################
-__conda_setup="$('/opt/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
-if [ $? -eq 0 ]; then
-	eval "$__conda_setup"
-else
-	if [ -f "/opt/anaconda3/etc/profile.d/conda.sh" ]; then
-		. "/opt/anaconda3/etc/profile.d/conda.sh"
-	else
-		export PATH="/opt/anaconda3/bin:$PATH"
-	fi
-fi
-unset __conda_setup
-
-#############################################################
-# show conda environments                                   #
-#############################################################
-conda env list

local/pe_epilog.d/00_bin-true

@@ -1 +0,0 @@
-/bin/true

local/pe_prolog.d/00_bin-true

@@ -1 +0,0 @@
-/bin/true

local/prolog.d/00_bin-true

@@ -1 +0,0 @@
-/bin/true

local/scripts/SGESuspend.sh

@@ -1,25 +0,0 @@
-#!/usr/bin/ksh
-# $Id: SGESuspend.sh 365 2013-11-18 09:58:17Z kasper $
-# This script should be added as the SUSPEND_METHOD in the
-# queue definition with a $job_pid, $job_id, and $job_owner arguments.
-# e.g. script.sh $job_pid $job_id $job_owner
-
-if [ -z "$3" ]
-then
-    echo "Usage: $0 \$job_pid \$job_id \$job_owner"
-    exit 1
-fi
-
-stat=`pgrep -g $1`
-if [ ! -z "$stat" ]
-then
-    #echo "Sending $sig to $1" >> ~$3/qdel_log.log
-    /usr/bin/pkill --signal SIGTSTP -g $1
-else
-    echo "Process $1 not found for job $2" >> ~$3/qdel_log.log
-    echo "Unable to suspend." >> ~$3/qdel_log.log
-    exit 1
-fi
-
-#uncomment the following for debugging
-#echo "Suspending Job $2 " >> ~$3/qdel_log.log

local/scripts/epilog

@@ -1,11 +0,0 @@
-#! /bin/bash
-# $Id: epilog 181 2010-09-17 15:55:28Z kasper $
-
-## Delete the STDOUT and STDERR files (.o and .e) if they are empty
-##  ( we do not want to delete non-empty files, they may contain useful
-##    troubleshooting or debug information ... )
-##
-[ -r $SGE_STDOUT_PATH -a -f $SGE_STDOUT_PATH ] && [ ! -s $SGE_STDOUT_PATH ] && rm -f $SGE_STDOUT_PATH
-[ -r $SGE_STDERR_PATH -a -f $SGE_STDERR_PATH ] && [ ! -s $SGE_STDERR_PATH ] && rm -f $SGE_STDERR_PATH
-
-exit 0

local/scripts/pe_epilog

@@ -1 +0,0 @@
-/bin/true

local/scripts/pe_prolog

@@ -1 +0,0 @@
-/bin/true

local/scripts/prolog

@@ -1 +0,0 @@
-/bin/true

local/scripts/qlogin_wrapper

@@ -1,5 +0,0 @@
-#!/bin/sh
-# $Id: qlogin_wrapper 175 2010-09-15 15:34:28Z kasper $
-HOST=$1
-PORT=$2
-/usr/bin/ssh -XAq -p $PORT $USER@$HOST

spool/common/cluster_name

@@ -1 +0,0 @@
-geophysik

spool/common/configuration

@@ -1,56 +0,0 @@
-# Version: 8.1.9
-# 
-# DO NOT MODIFY THIS FILE MANUALLY!
-# 
-conf_name                    global
-conf_version                 43
-execd_spool_dir              /data/gridengine/spool
-mailer                       /usr/bin/mail
-xterm                        /usr/bin/xterm
-load_sensor                  /data/gridengine/flex-grid/site/qloadsensor
-prolog                       NONE
-epilog                       NONE
-shell_start_mode             posix_compliant
-login_shells                 sh,bash,ksh,csh,tcsh
-min_uid                      1000
-min_gid                      1000
-user_lists                   none
-xuser_lists                  none
-projects                     none
-xprojects                    none
-enforce_project              false
-enforce_user                 auto
-load_report_time             00:00:40
-max_unheard                  00:05:00
-reschedule_unknown           00:00:00
-loglevel                     log_warning
-administrator_mail           kasper.fischer@ruhr-uni-bochum.de
-set_token_cmd                none
-pag_cmd                      none
-token_extend_time            none
-shepherd_cmd                 none
-qmaster_params               none
-execd_params                 ENABLE_BINDING=true NOTIFY_KILL=SIGTERM ENABLE_ADDGRP_KILL=true H_MEMORYLOCKED=infinity
-reporting_params             accounting=true reporting=false flush_time=00:00:15 joblog=false sharelog=00:00:00
-finished_jobs                100
-gid_range                    20000-20999
-qlogin_command               /data/gridengine/local/scripts/qlogin_wrapper
-qlogin_daemon                /usr/sbin/sshd -i
-rlogin_command               /usr/bin/ssh -XAtq
-rlogin_daemon                /usr/sbin/sshd -i
-rsh_command                  /usr/bin/ssh -XAtq
-rsh_daemon                   /usr/sbin/sshd -i
-max_aj_instances             2000
-max_aj_tasks                 75000
-max_u_jobs                   0
-max_jobs                     0
-max_advance_reservations     20
-auto_user_oticket            100
-auto_user_fshare             100
-auto_user_default_project    none
-auto_user_delete_time        infinity
-delegated_file_staging       false
-reprioritize                 0
-jsv_url                      none
-jsv_allowed_mod              ac,h,i,e,o,j,M,N,p,w
-