*** Wartungsfenster jeden ersten Mittwoch vormittag im Monat ***

Skip to content
Snippets Groups Projects
Commit cd88a2d1 authored by Zabloudil, Jan's avatar Zabloudil, Jan
Browse files

deleted applications.md-safe

parent 257b7b3f
Branches
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
applications/applications.md-safe deleted 100644 → 0
+ 0
− 534
View file @ 257b7b3f
---
author: Jan Zabloudil
title: Applications
revealOptions:
transition: 'fade'
---
====== VASP ======
==== Modules ====
<code>
module purge
module load autotools
module load gnu7/7.2.0
module load openmpi3/3.0.0
module load openblas/0.2.20
module load scalapack/2.0.2
module load fftw/3.3.6
module load prun
</code>
----
===== VASP =====
==== vasp.5.lib ====
<code>
ln -s makefile.linux_gfortran makefile
export CC=gcc
make
</code>
----
===== VASP 5.4.1/5.4.4 =====
==== makefile.include ====
<code>
OFLAG = -O2 -march=broadwell
LIBDIR = /opt/ohpc/pub/libs/gnu7/openblas/0.2.20/lib
BLAS = -L$(LIBDIR) -lopenblas
LAPACK =
BLACS =
SCALAPACK = -L$(LIBDIR) -lscalapack $(BLACS)
FFTW ?= /opt/ohpc/pub/libs/gnu7/openmpi3/fftw/3.3.6
</code>
----
===== VASP 5.4.1/5.4.4 =====
==== Compile ====
<code>
make all
</code>
==== If you have to recompile ====
<code>
make veryclean
make all
</code>
==== To build only specific version ====
<code>
make std
</code>
----
===== VASP 5.4.1/5.4.4 =====
==== Job script ====
''%%/opt/ohpc/pub/examples/slurm/mul/vasp%%''
<code>
#!/bin/bash
#
#SBATCH -J vasp
#SBATCH -N 2
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=28
#SBATCH --threads-per-core=1
#SBATCH --mem=16G
export OMP_NUM_THREADS=1
exe=/path/to/my/vasp/vasp.5.4.4/bin/vasp_std
time mpirun -np $SLURM_NPROCS $exe
</code>
----
====== LAMMPS ======
===== LAMMPS =====
''%%/opt/ohpc/pub/examples/slurm/mul/lammps%%''
<code>
#!/bin/bash
#
#SBATCH -J lammps
#SBATCH -N 2
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=28
#SBATCH --threads-per-core=1
#SBATCH --mem=16G
module purge
module load lammps
mpirun -np $SLURM_NTASKS lmp_mul -in ./in.put
</code>
----
====== Wien2k ======
----
===== Wien2k =====
Example job script in:
<code>
/opt/ohpc/pub/examples/slurm/mul/wien2k
</code>
----
====== COMSOL ======
----
===== COMSOL 5.2a =====
==== Module ====
<code>
load module COMSOL/5.2a
</code>
----
===== COMSOL 5.2a =====
==== Job script threaded version (no MPI) ====
You can use only one node in this case. Create a job file called ''%%job_smp.sh%%'':
''%%/opt/ohpc/pub/examples/slurm/mul/comsol%%''
<code>
#!/bin/bash
#
#SBATCH -J comsol
#SBATCH -N 1
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=28
#SBATCH --threads-per-core=1
#SBATCH --time=04:00:00
#SBATCH --mem=16G
# Details of your input and output files
INPUTFILE=micromixer_cluster.mph
OUTPUTFILE=micromixer.out
# Load our comsol module
module purge
module load COMSOL/5.2a
# create tmpdir
TMPDIR="/tmp1/comsol"
mkdir -p $TMPDIR
## Now, run COMSOL in batch mode with the input and output detailed above.
comsol batch -np $SLURM_NTASKS -inputfile $INPUTFILE -outputfile $OUTPUTFILE -tmpdir $TMPDIR
</code>
----
===== COMSOL 5.2a =====
==== Job script with MPI ====
You can use more than one node in this case. Create a job file called ''%%job_mpi.sh%%'':
''%%/opt/ohpc/pub/examples/slurm/mul/comsol%%''
<code>
#!/bin/bash
#
#SBATCH -J comsol
#SBATCH -N 2
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=28
#SBATCH --threads-per-core=1
#SBATCH --time=04:00:00
#SBATCH --mem=16G
# Details of your input and output files
INPUTFILE=micromixer_cluster.mph
OUTPUTFILE=micromixer.out
# Load our comsol module
module purge
module load COMSOL/5.2a
module load intel-mpi/2018
# create tmpdir
TMPDIR="/tmp1/comsol"
mkdir -p $TMPDIR
## Now, run COMSOL in batch mode with the input and output detailed above.
comsol -clustersimple batch \
-inputfile $INPUTFILE \
-outputfile $OUTPUTFILE \
-tmpdir $TMPDIR \
-mpiroot $MPIROOT -mpi intel -mpifabrics shm:dapl
</code>
----
===== COMSOL 5.2a =====
==== Submit job ====
<code>
sbatch job_xyz.sh
</code>
----
===== COMSOL 5.2a =====
==== Restarting jobs ====
To continue your calculation from the last saved state on use the options:
<code>
-recover -continue
</code>
====== ANSYS Fluent ======
===== ANSYS Fluent =====
==== Module ====
Check available Fluent versions:
<code>
module avail 2>&1 |grep Fluent
</code>
Load the correct version of fluent:
<code>
module load ANSYS-Fluent/17.1
</code>
----
===== ANSYS Fluent =====
==== 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:
''%%/opt/ohpc/pub/examples/slurm/mul/ansys%%''
<code>
# -----------------------------------------------------------
# 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
</code>
The ''%%autosave/data-frequency%%'' setting will save a data file every 10 iterations.
----
===== ANSYS Fluent =====
==== ANSYS 17: Job script ====
A script for running Ansys/Fluent called fluent_run.sh is shown below.
<code>
#!/bin/sh
#SBATCH -J fluent
#SBATCH -N 2
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=28
#SBATCH --threads-per-core=1
#SBATCH --time=04:00:00
#SBATCH --mem=16G
module purge
module load ANSYS-Fluent/17.1
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
</code>
----
===== ANSYS Fluent =====
==== ANSYS 18: Job script ====
There are slightly different command line switch in version 18:
<code>
#!/bin/sh
#SBATCH -J fluent
#SBATCH -N 2
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=28
#SBATCH --threads-per-core=1
#SBATCH --time=04:00:00
#SBATCH --mem=16G
module purge
module load ANSYS-Fluent/18.1
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
-pib \ # use Infiniband interconnect
-platform=intel \ # run on Intel processors
-mpi=openmpi \ # use OpenMPI
-i $JOURNALFILE > fluent.log #input file
fi
</code>
----
===== ANSYS Fluent =====
==== License server settings ====
These variables are defined when loading the fluent module file:
<code>
setenv ANSYSLI_SERVERS 2325@LICENSE.SERVER
setenv ANSYSLMD_LICENSE_FILE 1055@LICENSE.SERVER
</code>
----
===== ANSYS Fluent =====
==== Submit job ====
<code>
sbatch fluent_run.sh
</code>
----
===== ANSYS Fluent =====
==== Restarting a calculation ====
To restart a fluent job, you can read in the latest data file:
<code>
# read case file (*.cas.gz) that had previously been prepared
file/read-case "MyCaseFile.cas.gz"
file/read-data "MyCase_-1-00050.dat.gz" # read latest data file and continue calculation
file/autosave/data-frequency 10
solve/init/initialize-flow
solve/iterate 500
file/write-data "MyCase.dat.gz"
exit yes
</code>
----
====== ABAQUS ======
===== ABAQUS 2016 =====
==== Sample job script ====
''%%/opt/ohpc/pub/examples/slurm/mul/abaqus%%''
<code>
#!/bin/bash
#
#SBATCH -J abaqus
#SBATCH -N 2
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=8
#SBATCH --mem=16G
module purge
module load Abaqus/2016
export LM_LICENSE_FILE=<license_port>@license_server>:$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
</code>
----
===== 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.
- Activate the restart feature by adding the line:
<code>
*restart, write
</code>
at the top of your input file and run your job as normal. It should produce a restart file with a .res file extension.
<HTML><ol start="2" style="list-style-type: decimal;"></HTML>
<HTML><li></HTML>Run the restart analysis with<HTML></li></HTML><HTML></ol></HTML>
<code>
abaqus job=jobName oldjob=oldjobName ...
</code>
where oldJobName is the initial input file and newJobName is a file which contains only the line:
<code>
*restart, read
</code>
----
===== ABAQUS 2016 =====
==== Checkpointing and restart ====
Example:
INPUT: [[examples/ABAQUS/dynam.inp|dynam.inp]]
JOB SCRIPT: [[examples/ABAQUS/job.sh|job.sh]]
INPUT FOR RESTART: [[examples/ABAQUS/dynamr.inp|dynamr.inp]]
----
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment

[ 22.Nov 12h : 4,509 users | 1,084 groups | 6,413 projects ]