Abaqus

Abaqus FEA is a software suite for finite element analysis and computer-aided engineering.

Using your own license

Abaqus is available on Compute Canada clusters, but you must provide your own license. To configure your cluster account, create a file named $HOME/.licenses/abaqus.lic corresponding to the module version you want to use (otherwise abaqus jobs will fail). This must be done on each cluster where you plan to run abaqus as follows:

Module Version 2020

File : abaqus.lic

prepend_path("ABAQUSLM_LICENSE_FILE","port@server")

Module Version 6.14.1

File : abaqus.lic

prepend_path("LM_LICENSE_FILE","port@server")

Replace port@server with the port number and name of your Abaqus license server. Your license server must be reachable by our compute nodes, so your firewall will need to be configured appropriately. This usually requires our technical team to get in touch with the technical people managing your license software. Please contact our technical support and we will provide a list of IP addresses used by our clusters and obtain the information we need on the port and IP address of your server.

Cluster batch job submission

Below is a sample slurm script to submit a parallel job to a compute node using 4 cores:

File : "abaqus_job.sh"

#!/bin/bash
#SBATCH --time=00-06:00        # days-hours:minutes
#SBATCH --mem=4000M            # memory on node
#SBATCH --cpus-per-task=4      # number of cores
 
module load abaqus/6.14.1      # (or abaqus/2020)
unset SLURM_GTIDS
export MPI_IC_ORDER='tcp'

abaqus job=Test input=Sample.inp scratch=$SCRATCH cpus=$SLURM_CPUS_ON_NODE interactive mp_mode=threads

For a list of available Abaqus' command line options, load an abaqus module and run command: abaqus -help | less

Site specific usage

Sharcnet license

Sharcnet provides a small but free license consisting of 2cae and 21 execute tokens where usage limits are imposed 10 tokens/user and 15 tokens/group. For groups that have purchased tokens, the free token usage limits are added to their reservation. The free tokens are available on a first come first serve basis and mainly intended for testing and light usage before deciding whether or not to purchase dedicated tokens. The license can be used by any Compute Canada member but only on SHARCNET hardware. Groups that purchase dedicated tokens to run on the SHARCNET license server may likewise only use them on SHARCNET hardware. Such hardware includes gra-vdi for running abaqus in full graphical mode and graham cluster for submitting compute batch jobs to the queue. Before you can use the license you must open ticket at <support@computecanada.ca> and request access. In your email 1) mention that it is for use on Sharcnet systems and 2) include a copy/paste of the following License Agreement statement with your full name and Compute Canada username entered in the indicated locations. Please note that every user must do this ie) cannot be done one time only for a group (including PIs who have purchased their own dedicated tokens).

License agreement

----------------------------------------------------------------------------------
Subject: Abaqus Sharcnet Academic License User Agreement

This email is to confirm that i "_____________" with username "___________" will
only use “SIMULIA Academic Software” with tokens from the SHARCNET license server
for the following purposes:

1) on SHARCNET hardware where the software is already installed
2) in affiliation with a canadian degree-granting academic institution
3) for education, institutional or instruction purposes and not for any commercial
   or contract related purposes where results are not publishable
4) for experimental, theoretical and/or digital research work, undertaken primarily
   to acquire new knowledge of the underlying foundations of phenomena and observable
   facts, up to the point of proof-of-concept in a laboratory    
-----------------------------------------------------------------------------------

Configure license file

The configuration of your abaqus license on each cluster depends on the module version being used:

Module Version 2020

[gra-login1:~] cat ~/.licenses/abaqus.lic
prepend_path("ABAQUSLM_LICENSE_FILE","27050@license3.sharcnet.ca")

Module Version 6.14.1

[gra-login1:~] cat ~/.licenses/abaqus.lic
prepend_path("LM_LICENSE_FILE","27050@license3.sharcnet.ca")

If your abaqus jobs fail with error message [*** ABAQUS/eliT_CheckLicense rank 0 terminated by signal 11 (Segmentation fault)] in the slurm output file verify your abaqus.lic file contains ABAQUSLM_LICENSE_FILE to use abaqus/2020. If your abaqus jobs fail with error message starting [License server machine is down or not responding etc] in the output file verify your abaqus.lic file contains LM_LICENSE_FILE to use abaqus/6.14.1 as shown.

Check license status

To query the sharcnet license server for started jobs, queued jobs, and reservations by purchasing groups run:

ssh graham.computecanada.ca
module load abaqus
abaqus licensing lmstat -c $LM_LICENSE_FILE -a | grep "Users\|start\|queued\|RESERVATIONs"

When abaqus licensing lmstat shows your job is "queued" this means it has entered the "R"unning state from the perspective of either the squeue -j jobid or sacct -j jobid commands but is waiting for a license (not started) and therefore idle. This will have the same impact on your account priority as if the job were consuming cputime and thus should be avoided. When abaqus licensing lmstat indicates the job is in the "start" state then it has acquired the required abaqus tokens from the license and consuming cputime ...

Specify job resources

To ensure optimal usage of both your Abaqus tokens and the Compute Canada resources its important to carefully specify the required memory and ncpus in your slurm script. The values can be determined by submitting a few short test jobs to the queue then checking their utilization. For completed jobs use seff JobNumber to show the total "Memory Utilized" and "Memory Efficiency"; If the "Memory Efficiency" is less than ~90% decrease the value of "#SBATCH --mem=" setting in your slurm script accordingly. Notice that the seff JobNumber command also shows the total "CPU (time) Utilized" and "CPU Efficiency"; If the "CPU Efficiency" is less than ~90% perform scaling tests to determine the optimal number of cpu's for optimal performance and then update the value of then update the value of "#SBATCH --cpus-per-task=" in your slurm script. For running jobs use the srun --jobid=29821580 --pty top -d 5 -u $USER command to watch the %CPU, %MEM and RES for each abaqus parent process on the compute node; The %CPU and %MEM columns display the percent usage relative to the total available on the node while the RES column shows the per process resident memory size (in human readable format for values over 1gb). Further information regarding howto Monitor Jobs is available in the Compute Canada wiki.

Core token mapping

TOKENS 5  6  7  8  10  12  14  16  19  21  25  28  34  38
CORES  1  2  3  4   6   8  12  16  24  32  48  64  96 128

where TOKENS = floor[5 X CORES^0.422]

Remote visualization

A) First install the TigerVNC client on your desktop as described in VNC. Once logged in, start abaqus as follows:

1. Connect to gra-vdi.computecanada.ca with TigerVNC
2. module load SnEnv
3. module load abaqus
4. abaqus cae

B) If you want to use your own license server (not the SHARCNET license server) do the following:

1. Connect to gra-vdi.computecanada.ca with TigerVNC
2. module load SnEnv
3. module load abaqus
4. export ABAQUSLM_LICENSE_FILE="port@server"
5. abaqus cae

You must first request your "port@server" be setup by submitting a ticket before jobs can be run on graham.

Western license

The Western site license may only be used by Western researchers with hardware located on Western's campus such as the Dusky legacy cluster. Graham and gra-vdi are excluded since they are located at Waterloo (use the Sharcnet License for these systems as described above). Contact the Western abaqus license server administrator (located in Robarts) to make arrangements before attempting to use the Western abaqus license. Submit a ticket to Compute Canada support to request the admins contact information if necessary. You will need to provide your Compute Canada username and likely make arrangements to purchase tokens. If you are granted access request the port and server values and enter them into your abaqus.lic file as shown in 1) near the top of this wiki which will in turn be used by the Compute Canada module on dusky when it loads.

Message Passing Interface