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FEM Software

Its all in the modules

All packages described in this section, are organized in so-called modules. To list the available versions of a package and load a particular, e.g., ANSYS, version, invoke the commands

marie@login$ module avail ANSYS
[...]
marie@login$ module load ANSYS/<version>

The section runtime environment provides a comprehensive overview on the module system and relevant commands.

Abaqus

Abaqus is a general-purpose finite element method program designed for advanced linear and nonlinear engineering analysis applications with facilities for linking-in user developed material models, elements, friction laws, etc.

Guide by User

Eike Dohmen (from Inst. f. Leichtbau und Kunststofftechnik) sent us the description of his Abaqus calculations. Please try to adapt your calculations in that way. Eike is normally a Windows user and his description contains also some hints for basic Unix commands: Abaqus-Slurm.pdf (only in German).

General

Abaqus calculations should be started using a job file (aka. batch script). Please refer to the page covering the batch system Slurm if you are not familiar with Slurm or writing job files.

Usage of Abaqus

(Thanks to Benjamin Groeger, Inst. f. Leichtbau und Kunststofftechnik)).

  1. Prepare an Abaqus input-file. You can start with the input example from Benjamin: Rot-modell-BenjaminGroeger.inp
  2. Prepare a job file on ZIH systems like this
    #!/bin/bash
    ### needs ca 20 sec with 4cpu
    ### generates files:
    ###  yyyy.com
    ###  yyyy.dat
    ###  yyyy.msg
    ###  yyyy.odb
    ###  yyyy.prt
    ###  yyyy.sim
    ###  yyyy.sta
    #SBATCH --nodes=1               # with >1 node Abaqus needs a nodeliste
    #SBATCH --ntasks-per-node=4
    #SBATCH --mem=500               # total memory
    #SBATCH --time=00:04:00
    #SBATCH --job-name=yyyy         # give a name, what ever you want
    #SBATCH --mail-type=END,FAIL    # send email when the job finished or failed
    #SBATCH --mail-user=<name>@mailbox.tu-dresden.de  # set your email
    #SBATCH -A p_xxxxxxx            # charge compute time to your project
    
    
    # Abaqus has its own MPI
    unset SLURM_GTIDS
    
    # load module and start Abaqus
    module load ABAQUS/2019
    abaqus interactive input=Rot-modell-BenjaminGroeger.inp job=yyyy cpus=4 mp_mode=mpi
    
  3. Start the job file (e.g., name batch-Rot-modell-BenjaminGroeger.sh)
    marie@login$ sbatch batch-Rot-modell-BenjaminGroeger.sh      # Slurm will provide the Job Id (e.g., 3130522)
    
  4. Control the status of the job
    marie@login squeue -u your_login     # in column "ST" (Status) you will find a R=Running or P=Pending (waiting for resources)
    

Ansys

Ansys is a general-purpose finite element method program for engineering analysis, and includes preprocessing, solution, and post-processing functions. It is used in a wide range of disciplines for solutions to mechanical, thermal, and electronic problems. Ansys and Ansys CFX used to be separate packages in the past and are now combined.

In general, HPC systems are not designed for interactive working with GUIs. Even so, it is possible to start a Ansys workbench on the login nodes interactively for short tasks. The second and recommended way is to use job files. Both modes are documented in the following.

Since the MPI library that Ansys uses internally (Platform MPI) has some problems integrating seamlessly with Slurm, you have to unset the enviroment variable SLURM_GTIDS in your environment bevor running Ansysy workbench in interactive andbatch mode.

Using Workbench Interactively

Ansys workbench (runwb2) an be invoked interactively on the login nodes of ZIH systems for short tasks. X11 forwarding needs to enabled when establishing the SSH connection. For OpenSSH the corresponding option is -X and it is valuable to use compression of all data via -C.

# SSH connection established using -CX
marie@login$ module load ANSYS/<version>
marie@login$ runwb2

If more time is needed, a CPU has to be allocated like this (see batch systems Slurm for further information):

marie@login$ module load ANSYS/<version>
marie@login$ srun -t 00:30:00 --x11=first [SLURM_OPTIONS] --pty bash
[...]
marie@login$ runwb2

Better use DCV

The software NICE Desktop Cloud Visualization (DCV) enables to remotly access OpenGL-3D-applications running on ZIH systems using its GPUs (cf. virtual desktops).

Ansys can be used under DCV to make use of GPU acceleration. Follow the instructions within virtual desktops to set up a DCV session. Then, load a Ansys module, unset the environment variable SLURM_GTIDS, and finally start the workbench:

marie@gpu$ module load ANSYS
marie@gpu$ unset SLURM_GTIDS
marie@gpu$ runwb2

Using Workbench in Batch Mode

The Ansys workbench (runwb2) can also be used in a job file to start calculations (the solver, not GUI) from a workbench project into the background. To do so, you have to specify the -B parameter (for batch mode), -F for your project file, and can then either add different commands via -E parameters directly, or specify a workbench script file containing commands via -R.

Ansys Job File
#!/bin/bash
#SBATCH --time=0:30:00
#SBATCH --nodes=1
#SBATCH --ntasks=2
#SBATCH --mem-per-cpu=1000M

unset SLURM_GTIDS              # Odd, but necessary!

module load ANSYS/<version>

runwb2 -B -F Workbench_Taurus.wbpj -E 'Project.Update' -E 'Save(Overwrite=True)'
#or, if you wish to use a workbench replay file, replace the -E parameters with: -R mysteps.wbjn

Running Workbench in Parallel

Unfortunately, the number of CPU cores you wish to use cannot simply be given as a command line parameter to your runwb2 call. Instead, you have to enter it into an XML file in your home directory. This setting will then be used for all your runwb2 jobs. While it is also possible to edit this setting via the Mechanical GUI, experience shows that this can be problematic via X11-forwarding and we only managed to use the GUI properly via DCV, so we recommend you simply edit the XML file directly with a text editor of your choice. It is located under:

$HOME/.mw/Application Data/Ansys/v181/SolveHandlers.xml

(mind the space in there.) You might have to adjust the Ansys version (here v181) in the path to your preferred version. In this file, you can find the parameter

<MaxNumberProcessors>2</MaxNumberProcessors>

that you can simply change to something like 16 oder 24. For now, you should stay within single-node boundaries, because multi-node calculations require additional parameters. The number you choose should match your used --cpus-per-task parameter in your job file.

COMSOL Multiphysics

COMSOL Multiphysics (formerly FEMLAB) is a finite element analysis, solver and Simulation software package for various physics and engineering applications, especially coupled phenomena, or multiphysics.

COMSOL may be used remotely on ZIH systems or locally on the desktop, using ZIH license server.

For using COMSOL on ZIH systems, we recommend the interactive client-server mode (see COMSOL manual).

Client-Server Mode

In this mode, COMSOL runs as server process on the ZIH system and as client process on your local workstation. The client process needs a dummy license for installation, but no license for normal work. Using this mode is almost undistinguishable from working with a local installation. It also works well with Windows clients. For this operation mode to work, you must build an SSH tunnel through the firewall of ZIH. For further information, please refer to the COMSOL manual.

Usage

Server Process

Start the server process with 4 cores, 10 GB RAM and max. 8 hours running time using an interactive Slurm job like this:

marie@login$ module load COMSOL
marie@login$ srun -n 1 -c 4 --mem-per-cpu=2500 -t 8:00 comsol -np 4 server
Interactive Job

If you'd like to work interactively using COMSOL, you can request for an interactive job with, e.g., 4 cores and 2500 MB RAM for 8 hours and X11 forwarding to open the COMSOL GUI:

marie@login$ module load COMSOL
marie@login$ srun -n 1 -c 4 --mem-per-cpu=2500 -t 8:00 --pty --x11=first comsol -np 4

Please make sure, that the option Preferences --> Graphics --> Renedering is set to software rendering. Than, you can work from within the campus network.

Background Job

Interactive working is great for debugging and setting experiments up. But, if you have a huge workload, you should definitively rely on job files. I.e., you put the necessary steps to get the work done into scripts and submit these scripts to the batch system. These two steps are outlined:

  1. Create a job file, e.g.
    #!/bin/bash
    #SBATCH --time=24:00:00
    #SBATCH --nodes=2
    #SBATCH --ntasks-per-node=2
    #SBATCH --cpus-per-task=12
    #SBATCH --mem-per-cpu=2500
    
    module load COMSOL
    srun comsol -mpi=intel batch -inputfile ./MyInputFile.mph
    

LS-DYNA

LS-DYNA is a general-purpose, implicit and explicit FEM software for nonlinear structural analysis. Both, the shared memory version and the distributed memory version (mpp) are installed on ZIH systems.

You need a job file (aka. batch script) to run the MPI version.

Minimal Job File
#!/bin/bash
#SBATCH --time=01:00:00       # walltime
#SBATCH --ntasks=16           # number of processor cores (i.e. tasks)
#SBATCH --mem-per-cpu=1900M   # memory per CPU core

module load ls-dyna
srun mpp-dyna i=neon_refined01_30ms.k memory=120000000

Submit the job file to the batch system via

marie@login$ sbatch <filename>

Please refer to the section Slurm for further details and options on the batch system as well as monitoring commands.