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Computational Fluid Dynamics

ANSYS-Fluent (CFD)

Module

Check available versions of Ansys:

module avail 2>&1 | grep -i Ansys

Load the correct version of Ansys, e.g.,

module load *your preferred module*

available modules on VSC-4:

  • ANSYS/2019R3
  • ANSYS/2020R2
  • ANSYS/2021R1

General Workflow

The subsequent figure shows an overview of the general workflow if you use Fluent on your local machine for Pre- and Postprocessing and the cluster for solving your case, respectively.
For this workflow a graphical connection isn't necessary.

All files needed for this testcase are provided here: fluent_testcase.zip

Input file

Create a journal file (fluent.jou) which is written in a dialect of Lisp called Scheme and contains all the instructions that are to be executed during the run. A basic form of this file, is as follows:

# -----------------------------------------------------------
# SAMPLE JOURNAL FILE
#
# read case file (*.cas.gz) that had previously been prepared
file/read-case "tubench1p4b.cas.gz"
file/autosave/data-frequency 10
solve/init/initialize-flow
solve/iterate 500
file/write-data "tubench1p4b.dat.gz"
exit yes

The autosave/data-frequency setting will save a *.dat file every 10 iterations.
But preferably do this settings in the GUI as shown in subsequent graphic.

Keep in mind to set the appropriate path for the cluster. Here the files will be saved in the same directory as the journal file is located. It could be better for the sake of clarity to create a additional directory for this backupfiles, i.e.

./Autosave/*your_filename*.gz

Job script

A script for running Ansys/Fluent called fluent_run.sh is shown below.

#!/bin/sh
#SBATCH -J fluent
#SBATCH -N 2
#SBATCH -o job.%j.out
#SBATCH --ntasks-per-node=24
#SBATCH --threads-per-core=1
#SBATCH --time=04:00:00

module purge
module load *your preferred module*

JOURNALFILE=fluent.jou

if [ $SLURM_NNODES -eq 1 ]; then
    # Single node with shared memory
    fluent 3ddp -g -t $SLURM_NTASKS -i $JOURNALFILE > fluent.log 
else
    # Multi-node
    fluent 3ddp  \                # call fluent with 3D double precision solver
    -g \                          # run without GUI
    -slurm -t $SLURM_NTASKS \     # run via SLURM with NTASKS
    -pinfiniband \                # use Infiniband interconnect
    -mpi=openmpi \                # use IntelMPI
    -i $JOURNALFILE > fluent.log  # input file
fi

This job script allows a variable definition of desired configuration. You can manipulate the number of compute nodes very easily and the job script generates the appropriate command to start the calculation with Fluent.


License server settings

These variables are defined when loading the fluent module file:

setenv       ANSYSLI_SERVERS 2325@LICENSE.SERVER
setenv       ANSYSLMD_LICENSE_FILE 1055@LICENSE.SERVER

Submit job

sbatch fluent_run.sh

Restarting a calculation

To restart a fluent job, you can read in the latest data file:

# read case file (*.cas.gz) that had previously been prepared
file/read-case "MyCaseFile.cas.gz"
file/read-data "MyCase_-1-00050.dat.gz"   # read latest data file and continue calculation
solve/init/initialize-flow
solve/iterate 500
file/write-data "MyCase.dat.gz"
exit yes

ABAQUS

ABAQUS 2016

Sample job script

/opt/ohpc/pub/examples/slurm/mul/abaqus

#!/bin/bash
#
#SBATCH -J abaqus
#SBATCH -N 2
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=8
#SBATCH --mem=16G

module purge
module load Abaqus/2016

export LM_LICENSE_FILE=<license_port>@license_server>:$LM_LICENSE_FILE

# specify some variables:
JOBNAME=My_job_name
INPUT=My_Abaqus_input.inp
SCRATCHDIR="/scratch"

# MODE can be 'mpi' or 'threads':
#MODE="threads"
MODE="mpi"

scontrol show hostname $SLURM_NODELIST | paste -d -s > hostlist
cpu=`expr $SLURM_NTASKS / $SLURM_JOB_NUM_NODES`
echo $cpu

mp_host_list="("
for i in $(cat hostlist)
do
  mp_host_list="${mp_host_list}('$i',$cpu),"
done

mp_host_list=`echo ${mp_host_list} | sed -e "s/,$/,)/"`

echo "mp_host_list=${mp_host_list}" >> abaqus_v6.env

abaqus interactive job=$JOBNAME cpus=$SLURM_NTASKS mp_mode=$MODE scratch=$SCRATCHDIR input=$INPUT

ABAQUS 2016

Checkpointing and restart

Users sometimes find that their jobs take longer than the maximaum runtime permitted by the scheduler to complete. Providing that your model does not automatically re-mesh (for example, after a fracture), you may be able to make use of Abaqus’ built-in checkpointing function.

This will create a restart file (.res file extension) from which a job that is killed can be restarted.

  1. Activate the restart feature by adding the line:
*restart, write

at the top of your input file and run your job as normal. It should produce a restart file with a .res file extension.

  1. Run the restart analysis with

abaqus job=jobName oldjob=oldjobName ...

where oldJobName is the initial input file and newJobName is a file which contains only the line:

*restart, read

ABAQUS 2016

Checkpointing and restart

Example:

INPUT: dynam.inp

JOB SCRIPT: job.sh

INPUT FOR RESTART: dynamr.inp


COMSOL

Module

Available version of Comsol can be found by executing the following line:

module avail 2>&1 | grep -i comsol

Currently these versions can be loaded:

  • Comsol/5.5
  • Comsol/5.6
module load *your preferred module*

Workflow

In general you define your complete case on your local machine and save it as *.mph file.
This file contains all necessary information to run a successfull calculation on the cluster.


Job script

An example of a Job script is shown below.

#!/bin/bash
# slurmsubmit.sh

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=24
#SBATCH --job-name="karman"
#SBATCH --partition=mem_0384
#SBATCH --qos=mem_0384

module purge
module load Comsol/5.6

MODELTOCOMPUTE="karman"
path=$(pwd)

INPUTFILE="${path}/${MODELTOCOMPUTE}.mph"
OUTPUTFILE="${path}/${MODELTOCOMPUTE}_result.mph"
BATCHLOG="${path}/${MODELTOCOMPUTE}.log"

echo "reading the inputfile"
echo $INPUTFILE
echo "writing the resultfile to"
echo $OUTPUTFILE
echo "COMSOL logs written to"
echo $BATCHLOG
echo "and the usual slurm...out"

# COMSOL's internal command for number of nodes -nn and so on (-np, -nnhost, ...) are deduced from SLURM
comsol batch -mpibootstrap slurm -inputfile ${INPUTFILE} -outputfile ${OUTPUTFILE} -batchlog ${BATCHLOG} -alivetime 15 -recover -mpidebug 10

doku/cfd.txt · Last modified: 2021/07/23 08:40 by sfrank