abaqus_batch

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Submitting Abaqus Jobs to Batch System: abaqus_batch

A script is available for submitting Abaqus jobs to the PBS batch queues on the SGI/Altix system at NCSA, 
or PBS batch queues on EMt64/linux cluster at NCSA. The script is at /usr/apps/csm/scripts/abaqus_batch.

When the script is invoked with the option --help, it prints a list of its options and exits:

 [smith@forge scripts]$ /usr/apps/csm/forge_scr/abaqus_batch --help
   
ABAQUS 6.11-1 --- EMT64
________________________________________

usage: /usr/apps/csm/forge_scr/abaqus_batch job_name [options]

For complete information, see 
 http://www.ncsa.uiuc.edu/UserInfo/Resources/Software/CSM/abaqus_batch.html

This script submits an Abaqus/Standard job to the batch system.  
options:
  --help             # display options and exit
  --dryrun           # Check arguments and exit

  --input file       # input file (default is job_name.inp)
  --user_sub file    # compile and link user supplied Fortran subroutines
  --lib library      # link with the given library (or libraries)
  --datacheck        # datachecking (no runs)
  --double           # double precision executable for Abaqus/Explicit
  --restart file     # use restart file from earlier Abaqus run 
  --globalmodel file # global model's results file with NO .fil extension
  --datafile file    # reads input from external data file
  --datafile2 file2.tar   # transferes and untars file.tar archive to batch host.
                     #(file.tar should archive all nonstandard external files)
  --fil file         # reads data from previous result file (*.fil file)

  --wall time         # wall clock time in minutes; default is 60 mins
  --mem mem          # Abaqus/Standard memory in Mbytes; default is 5000 Mb
  --pbs_mem pbs_mem  # (on Ember only) PBS job memory in Mbytes; default is 2000 Mb
  --np np            # number of processors; default is 1
  --mpi_domain       # Explicit Only use domain decomposition mpi solver
  --no_copy_back     # suppress copying of output files to submit directory;
                     # (output files can still be retrieved from UniTree)
  --mail             # to receive email after job completes
  --proj proj_name   # to charge SU-s to a different then default project
  --append_env       # appends your .env file to the local .env file on batch host

examples:
  abaqus_batch eb33rms7 --wall 40 --mem 3500 --pbs_mem 7000 --np 24

  abaqus_batch m3 --datacheck

  abaqus_batch m3 --input m3v5 --user_sub m3.f --lib scs --wall 120 --mem 1000

  abaqus_batch m3 --input m3v6 --restart m3v5r4 --wall 160 --mem 1500 --np 2

  abaqus_batch m3 --input m3v6 --fil mrv5 --wall 160 --mem 2500 --mail

  abaqus_batch m3 --input m3v7 --wall 220 --mem 1200 --np 3 --no_copy_back 

  abaqus_batch m3 --input m3v7 --wall 220 --mem 1200 --globalmodel c2004g --proj abc
 
  abaqus_batch m3 --input shake2 --wall 100 --mem 400 --datafile force.amp

  abaqus_batch m3 --input shake2 --wall 100 --mem 400 --datafile force.amp --datafile2 file2.tar

 

In normal use, the script prints a summary of requested options and submits a batch job. The 
batch job runs Abaqus/Standard or Abaqus/Explicit , creates a gzipped tar file with the user's input files and any 
Abaqus output files, and then uploads the tar file to the mass storage system. In addition, all 
Abaqus output files are copied to the directory where abaqus_batch was invoked. Email is 
sent to the user if the batch job fails.

Stdout and stderr from the execution of Abaqus/Standard(Explicit) are redirected to a single file. The name of the file has the form jobname.log, where jobname is the job name that appears on the abaqus_batch command line.

A typical invocation is shown below with an input deck and a user subroutine, "llq" or ("bjobs" on tun/linux) command is
is excuted to check if job is queued.

  co-login1% ls
  t2.inp mysub.f
  co-login1% /usr/apps/csm/scripts/abaqus_batch t2 --wall 20 --mem 1500 --user_sub mysub.f

  ABAQUS 6.10-2  --- SGI/Altix 

  SUMMARY OF COMMAND LINE ARGUMENTS, DEFAULTS
  job name:       t2
  input file: /u/ncsa/skoric/abq/t2.inp
  number of processors: 1
  submitting a job to the batch queuing system
  estimated cpu time: 20 minute(s)
  estimated memory usage: 1500 Mbyte(s)
  compiling and linking Fortran subroutines in file /u/ncsa/skoric/abq/mysub.f

  
  output files will be copied back to the submit directory
   (a tar file of the output files will also be found on UniTree 
    in your UniTree directory ~/abaqus_batch/)

For complete information, see
http://www.ncsa.uiuc.edu/UserInfo/Resources/Software/CSM/abaqus_batch.html

To check the status of your batch jobs type qstat -u your_login .

Abaqus 6.10 sometimes overallocates memory on ember.
To avoid termination of your job due to excessive memory usage,
use --pbs_mem option on ember in addition to --mem option.
--pbs_mem value should be 50% to 100% more then --mem value . This option is not available on abe.

Please keep in mind that batch jobs are killed by the batch system, if they use more wall
time than they request. Check the output files to find out how 
much wall clock time and memory your jobs use, and plan walll clock time and memory requests for 
future jobs accordingly. Use datacheck option in interactive run, or --datacheck option in batch to
check for necessary memory requirements for your run.

All the files are regularly purged from scratch, and it might happen that your large input files 
are purged even before your job starts executing from batch (while it is still pending in 
batch). To prevent this, submit your large inputs from your home directory and use 
--no_copy_back option to suppress copying back large outputs to your home directory. Your 
tarred outputs can be still found on UniTree in your home UniTree directory ~/abaqus_batch/.

The tar file that's uploaded to the mass storage system at the end of each job is placed in
~/abaqus_batch in the user's mass storage system home directory. Uploaded tar files have 
names of the form jobid.tar.gz, where jobid is the 4(or 5)digit job-id assigned by the batch 
system.

--fil  result_file_name     If your job reads data from a previous results file (*.fil), then this option just copies *.fil file to the directory on the execution host where your job will be running. This is not fil option from interactive execution procedure. Use this option in batch only if you are reading results files from previous runs.

--datafile  data_file_name     Similar to --fil, this option copy to the batch host an external file that your job reads from (things like amplitude, node, or element data).

--globalmodel  global_model_results_file    This option specifies the name of the global model's results file from which the results are to be interpolated to drive a submodel analysis. This option is required whenever the *SUBMODEL or *BOUNDARY SUBMODEL option is in the input file.

--datafile2 file.tar Use this option if there are many non standard Abaqus files that need to be copied to the batch host.
You must tar all non standard files into an archive first. Please see FAQ #13.

 This script does not have any options for interactive use of Abaqus.