Abaqus/en: Difference between revisions

Abaqus software modules are available on Compute Canada clusters however you must provide your own license.  To configure your home account on a given cluster, login and create a file named <tt>$HOME/.licenses/abaqus.lic</tt> containing the following two lines which support versions 202X and 6.14.1 respectively. Next replace <code>port@server</code> with the flex port number and server IP address (or fully qualified hostname) of your Abaqus license server.

If your license has not been setup for a cluster then some additional configuration changes by the system administrators will need to be done.  Such changes are necessary to ensure the flex and vendor tcp ports of your abaqus server are reachable from all cluster compute nodes when jobs are run in the queue.  So we may help you get this done open a ticket with [[Technical support|technical support]].  Please be sure to include the following three items: flexlm port number, static vendor port number, IP address of your abaqus license server.  You will then be sent a list of cluster IP addresses so your administrator can open the local server firewall to allow connections from the cluster on both ports.  Please note that a special license agreement must generally be negotiated and signed with SIMULIA before a local institutional license maybe used on remote Compute Canada hardware.  Your local abaqus license server server administrator can confirm if such an agreement is in place otherwise additional costs maybe required.

Below are proto-type slurm scripts for submitting thread and mpi based parallel simulations to single or multiple compute nodes.  Most users will find it sufficient to use one of the <i>project directory script's</i> provided in the Single Node Computing section. The optional "memory=" argument found in the last line of the scripts is intended for larger memory or problematic jobs where 3072MB offset value may require tuning.  A listing of all abaqus command line arguments can be obtained by loading an abaqus module and running: <code>abaqus -help | less</code>.  Single Node jobs that run less than one day should find the <i>project directory script</i> located in the first tab sufficient. Single node jobs that run for more than a day however should use one of the restart scripts.  Jobs that create large restart files will benefit by writing to local disc through the use of the SLURM_TMPDIR environment variable utilized in the <i>temporary directory scripts</i> provided in the two rightmost tabs of the Single Node standard and explicit analysis sections.  The restart scripts shown here will continue jobs that have been terminated early for some reason.  Such job failures can occur if a job reaches its maximum requested runtime before completing and is killed by the queue or if the compute node the job was running on crashed due to an unexpected hardware failure.  Other restart types are possible by further tailoring of the input file (not shown here) to continue a job with additional steps or change the analysis (see the documentation for version specific details).  Jobs that require large memory or larger compute resources (beyond that which a single compute node can provide) should use the mpi scripts in the Multiple Node sections below to distribute computing over arbitrary node ranges determined automatically by the schedular.  Short scaling test jobs should be run to determine wall clock times (and memory requirements) as a function of the number of cores (2, 4, 8, etc) to determine the optimal number before running any long jobs.  

Users with large memory or compute needs (and correspondingly large licenses) can use the following script to perform mpi-based computing over a arbitrary range of nodes ideally left to the schedular to  automatically determine.  A companion template script to perform restart multi-node jobs is not currently provided due to additional limitations when they can be used.

An estimate for the total slurm node memory (--mem=) required for a simulation to run fully in ram (without being virtualized to scratch disk) can be obtained by examining the abaqus output <code>test.dat</code> file.  For example a simulation that requires a fairly large amount of memory might show:

To run your simulation interactively and monitor the memory consumption do the following:

  1) ssh into a compute canada cluster, obtain an allocation on a compute node (such as gra100), run abaqus ie)

  2) ssh into the compute canada cluster again, ssh into the compute node with the allocation, run top ie)

To completely satisfy the recommended "MEMORY TO OPERATIONS REQUIRED MINIMIZE I/O" (MRMIO) value at least the same amount of non-swapped physical memory (RES) must be available to abaqus.  Since the RES will in general be less than the virtual memory (VIRT) by some relatively constant amount for a given simulation, it is necessary to slightly over allocate the requested slurm node memory <code>-mem=</code>.  In the above sample slurm script this over-allocation has been hardcoded to a conservative value of 3072MB based on initial testing of the standard abaqus solver.  To avoid long queue wait times associated with large values of MRMIO, it maybe worth investigating the simulation performance impact associated with reducing the RES memory that is made available to abaqus significantly below the MRMIO.  This can be done by lowering the <code>-mem=</code> value which in turn will set an artificially low value of <code>memory=</code> in the abaqus command (found in the last line of the slurm script).  In doing this one should be careful the RES does not dip below the "MINIMUM MEMORY REQUIRED" (MMR) otherwise abaqus will exit due to "Out Of Memory" (OOM).  As an example, if your MRMIO is 96GB try running a series of short test jobs with <code>#SBATCH --mem=8G, 16G, 32G, 64G</code> until an acceptable minimal performance impact is found, noting that smaller values will result in increasingly larger scratch space used by temporary files.

There must be be at least 1 license free (not in use) for <code>abaqus cae</code> to start according to:

= Site specific use =

== 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 dedicated 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 costs for dedicated tokens in cdn are approximately 110 per compute token and 400 per gui token, submit a ticket to request an official quote.  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 including gra-vdi (for running abaqus in full graphical mode) and graham or dusky clusters (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 <tt>License Agreement</tt> 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).

Subject: Abaqus Sharcnet Academic License User Agreement

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 <code>abaqus.lic</code> 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 <code>abaqus.lic</code> file contains LM_LICENSE_FILE to use abaqus/6.14.1 as shown.  The <code>abaqus.lic</code> file shown contains both so you should not see this problem.

I) To check the Sharcnet license server for started and queued jobs by username run:

II) To check the Sharcnet license server for reservations of products by purchasing groups run:

III) To check the Sharcnet license server for license usage of the cae, standard and explicit products run:

When the output of query I) above indicatesa that a job for a particular username is "queued" this means the job has entered the "R"unning state from the perspective of <code>squeue -j jobid</code> or <code>sacct -j jobid</code> and is therefore idle on a compute node waiting for a license.  This will have the same impact on your account priority as if the job were performing computations and consuming cputime.  Eventually when sufficient licenses come available the "queued" job will "start".  To demonstrate, the following shows the license server and queue output for the situation where a user submits two jobs, but only the first job acquires enough licenses to start:

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 <b>completed</b> jobs use <code>seff JobNumber</code> 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 <code>seff JobNumber</code> 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 <b>running</b> jobs use the <code>srun --jobid=29821580 --pty top -d 5 -u $USER</code> 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 [https://docs.computecanada.ca/wiki/Running_jobs#Monitoring_jobs Monitor Jobs] is available in the Compute Canada wiki.

The Western site license may only be used by Western researchers on hardware located at Western's campus.  Currently Dusky cluster is the only system that satisfies these conditions. Graham and gra-vdi are excluded since they are located on Waterloo's campus.  Contact the Western abaqus license server administrator <jmilner@robarts.ca> to inquire about using the Western abaqus license.  You will need to provide your Compute Canada username and possibly make arrangements to purchase tokens.  If you are granted access then you may proceed to configure your <code>abaqus.lic</code> file to point to the Western license server as follows:

Once configured, submit your jobd as described above in the Cluster job submission section.  If there are any problems submit a problem ticket to [[Technical support|technical support]].  Specify that you are using the abaqus Western license on dusky as well as the failed job number along with a paste of any error message if applicable.