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Abaqus

This document provides basic information for using ABAQUS software on the Nurion system. Therefore, it does not include instructions on how to use ABAQUS software or Nurion/Linux. For information on using Nurion/Linux, please refer to the Nurion user guide available in the technical support > guides section on the KISTI website (https://www.ksc.re.kr).

A. Important Notes for Application

  • Eligible User Groups: University/Industry (SMEs)/Research Institute users

  • For new users, when completing the application form on the KSC website, you must specify Abaqus in the 'Application to be Used' section.

  • For existing users, please apply by sending your account details, affiliation, and ID to account@ksc.re.kr.

  • If you are affiliated with an industry (SME), you must submit relevant documents (e.g., SME verification, venture company verification) to account@ksc.re.kr.

  • If your affiliation changes and you no longer belong to an eligible group, Please notify account@ksc.re.kr immediately.

B. Usage policy

  • Each user is limited to 40 CPU cores.

  • Since a limited license is shared among supercomputing users, if usage exceeds the policy limits, the job may be forcibly terminated by the administrator.

  • If you require a large number of licenses due to unavoidable circumstances, you must consult with the administrator in advance through the KISTI website (https://www.ksc.re.kr).

  • Before submitting a job, please use the "lic_check" command to check the license status through the menu selection, and then submit your job.

  • To prevent overload on the login nodes (login01~04), pre/post-processing tasks are not permitted on the login nodes. However, some pre/post-processing tasks are allowed through VDI.. (Refer to the Nurion VDI guide for details - APPENDIX 9)

  • You must use the “#PBS -A abaqus” option in the job submission script.

C. Software Installation Information

1. Installation version

  • 6.14-6, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023

2. Installation Location

  • /apps/commercial/abaqus

3. Path to the executable file

  • /apps/commercial/abaqus/Commands

D. How to run the software

1. Execution method

  • Enter the command to run the job in batch mode as follows:

Format
[command] [option]

Commands

abq6146 (6-14.6version)

abq2016hf19 (2016 version)

abq2017hf13 (2017 version)

abq2018hf5 (2018 version)

abq2019hf5 (2019 version)

abq2020hf4 (2020 version)

abq2021 (2021 version)

abq2022 (2022 version)

abq2023hf7 (2023version)

Example

(6.14-6

version)

abq6146 job=job_name [cpus=ncpus] [input=inp_file] [interactive]

abq6146 job=job_name oldjob=old_job_name

abq6146 help

abq6146 information=environment

abq6146 viewer [res=res_name]

  • Please modify the parts in blue with the job name, number of cores used, and input file name before use.

  • Interactive execution is limited to 20 minutes of CPU time.

  • For long-running calculations, jobs must be submitted using the PBS scheduler.

  • Before submitting a job, run the lic_check command to verify the license status, and then submit the job.

2. Writing a scheduler job script file

  • On the Nurion system, jobs must be submitted from the login node using the PBS scheduler.

  • Example files for using PBS on the Nurion system are available at the path below, and you can refer to them when creating your job file.

  • Example files

    • /apps/commercial/test_samples/abaqus/abaqus_v6146.sh (Performed on a single node)

    • /apps/commercial/test_samples/abaqus/abaqus_v6146_multinode.sh (Performed on multiple nodes)

※ The following example is for ABAQUS version 6.14-6 on the Nurion system.

(Performed on a single node)

#!/bin/sh

#PBS -V
#PBS -N abaqus_test # Specify the job name
#PBS -q commercial # Specify the PBS queue
#PBS -l select=1:ncpus=40:mpiprocs=40:ompthreads=1 # Specify the resources to be used
#PBS -l walltime=04:00:00 # Specify the estimated job duration (hh:mm)
#PBS –A abaqus

cd $PBS_O_WORKDIR
###### Do not edit #####
TOTAL_CPUS=$(wc -l $PBS_NODEFILE | awk '')
#####################
cp /apps/commercial/abaqus/6146/6.14-6/SMA/site/abaqus_v6.env .
/apps/commercial/abaqus/Commands/abq6146 job=c2 cpus=${TOTAL_CPUS} int

  • The sections highlighted in blue above must be appropriately modified by the user.

  • As of March 2019, jobs will not be submitted without the “#PBS -A abaqus” option.

  • Job submission is only allowed in the scratch directory.

  • Each user's scratch directory is located at /scratch/$USER.

  • Since the scratch disk is subject to automatic deletion after a certain period (policy as of August 2023: 15 days), it is recommended to back up your data as soon as possible after the job is completed.

  • For other PBS commands and usage instructions, please refer to the Nurion user guide.

※ The following example is for ABAQUS version 6.14-6 on the Nurion system. (Performing in threads mode on a single node)

#!/bin/sh
#PBS -V
#PBS -N abaqus_test # Specify the job name
#PBS -q commercial # Specify the PBS queue
#PBS -l select=1:ncpus=40:mpiprocs=1:ompthreads=40 # Specify the resources to be used
#PBS -l walltime=04:00:00 # Specify the estimated job duration (hh:mm)
#PBS –A abaqus

cd $PBS_O_WORKDIR
cp /apps/commercial/abaqus/6146/6.14-6/SMA/site/abaqus_v6.env .
/apps/commercial/abaqus/Commands/abq6146 job=c2 cpus=${NCPUS} mp_mode=threads int

  • The sections highlighted in blue above must be appropriately modified by the user.

  • As of March 2019, job submissions will not be accepted without the #PBS -A abaqus option.

  • Job submission is only allowed in the scratch directory.

  • Each user's scratch directory is located at /scratch/$USER.

  • Since the scratch disk is subject to automatic deletion after a certain period (policy as of August 2023: 15 days), it is recommended to back up your data as soon as possible after the job is completed.

  • For other PBS commands and usage instructions, please refer to the Nurion user guide.

※ The following example is for ABAQUS version 6.14-6 on the Nurion system.(Performed on multiple nodes)

#!/bin/sh
#PBS -V
#PBS -N abaqus_test # Specify the job name
#PBS -q commercial # Specify the PBS queue
#PBS -l select=2:ncpus=40:mpiprocs=20:ompthreads=1 # Specify the resources to be used
#PBS -l walltime=04:00:00 # Specify the estimated job duration (hh:mm)
#PBS -A abaqus
cd $PBS_O_WORKDIR
###### Do not edit #####
export MPI_IC_ORDER=TCP
TOTAL_CPUS=$(wc -l $PBS_NODEFILE

  • Do not modify the sections highlighted in red above.

  • As of March 2019, job submissions will not be accepted without the #PBS -A abaqus option.

  • The sections highlighted in blue above must be appropriately modified by the user.

  • Job submission is only allowed in the scratch directory.

  • Each user's scratch directory is located at /scratch/$USER.

  • Since the scratch disk is subject to automatic deletion after a certain period (policy as of August 2023: 15 days), it is recommended to back up your data as soon as possible after the job is completed.

  • For other PBS commands and usage instructions, please refer to the Nurion user guide.

3. How to submit a job

  • Example: If the script file name is abaqus.sh

$ qsub abaqus.sh

4. Check job status

$ qstat (or qstat –u $USER)

5. Forcefully terminate a submitted job

  • Usage : qdel

  • The job ID is the information displayed on the far left when the qstat command is executed. (ex. 1771476.pbs)

  • Example : If the job ID is 1771476.pbs

$ qdel  1771476.pbs

6. Check available resources on PBS

$ pbs_status

D. Regarding errors during Abaqus execution

  • During the June maintenance, a feature to improve the I/O performance of the Lustre file system was applied to the /scratch file system.

  • As a result, the following **[related error message]** may appear during Abaqus execution, indicating an error accessing files. (In some cases, specific jobs may not produce an error message and may not progress from the R state.)

  • If a file access error similar to the one below occurs, please follow these steps before submitting your job.

[Stripe count setting method]

$ mkdir
$ lfs setstripe -c 4
$ cp *.inp # The .inp file refers to the input file for Abaqus.
$ cp *.sh # The .sh file refers to the Abaqus job submission script.
$ cd
$ qsub

  • The directory where the input data is located and where the output data will be recorded.

  • If you create subdirectories, you must perform the same steps.

※ If you need to use existing files for a restart job, \ please copy the existing files to the directory with the stripe count setting using the cp command before proceeding with the job.\ (Using the mv command may cause errors because it retains the original attributes.)

[Related error message]

(1) ***ERROR: *** Error: Extend failed (utl_File: read)

(2) NOTE: DUE TO AN INPUT ERROR THE ANALYSIS PRE-PROCESSOR HAS BEEN UNABLE TO INTERPRET SOME DATA. SUBSEQUENT ERRORS MAY BE CAUSED BY THIS OMISSION

(3) terminate called after throwing an instance of 'utl_FileExceptionExtend'

ABAQUS/pre rank 0 received signal 6 (Aborted)

Last updated on November 06, 2024.

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