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Running CYSTAL17 on Racham

Version: 2021.09.15

Prerequisites

Make sure you have the following files in folder on Rackham

Installation

On Rackham, copy/paste the following script install-rackham.sh to the same folder which contains the files above. Edit installDIR=${HOME}/bin/crystal17 to point to a project folder if necessary. Make it executable with chmod +x install-rackham.sh or execute the lines manually.

install-rackham.sh

#!/bin/bash

# Destination folder
# Default  installDIR=${HOME}/bin/crystal17
# To share between members of the same project installDIR=/proj/snic-xxx-xx/bin/crystal17

installDIR=${HOME}/bin/crystal17
mkdir -p ${installDIR}

tar xvf crystal17_v1_0_1_Linux-ifort17_XE_openmpi2.1_emt64.tar.gz -C ${installDIR}
unzip utils17.zip -d ${installDIR}/utils17

# Modifying files
# cry17.bashrc
cp ${installDIR}/utils17/cry17.bashrc ${installDIR}/utils17/cry17.bashrc.bak
sed -i -e "s#export CRY17_ROOT=\"/home/CRYSTAL17\"#export CRY17_ROOT=\"${installDIR}\"#"                   ${installDIR}/utils17/cry17.bashrc
sed -i -e "s#export CRY17_ARCH=\"Linux-ifort\"#export CRY17_ARCH=\"Linux-ifort17_XE_openmpi2.1.0_emt64\"#" ${installDIR}/utils17/cry17.bashrc
sed -i -e "s#export VERSION=\"std\"#export VERSION=\"v1.0.1\"#"                                            ${installDIR}/utils17/cry17.bashrc
sed -i -e "s#export CRY17_SCRDIR=\"\$HOME\/tmp\"#export CRY17_SCRDIR=\"\$SNIC_TMP\"#"                      ${installDIR}/utils17/cry17.bashrc

# runmpi17
cp ${installDIR}/utils17/runmpi17 ${installDIR}/utils17/runmpi17.bak
sed -i -e "s#set MPIDIR   = /opt/openmpi-1.4-icc/bin#set MPIDIR   = /opt/openmpi/2.1.0intel17.2/bin#"      ${installDIR}/utils17/runmpi17
sed -i -e "s#\${MPIDIR}/\${MPIBIN} -machinefile \$CRY17P_MACH/machines.LINUX -np \$NPROCS \$TMPDIR/Pcrystal < \$TMPDIR/INPUT >>\& \$OUTDIR/\$OUTFILE#\#\${MPIDIR}/\${MPIBIN} -machinefile \$CRY17P_MACH/machines.LINUX -np \$NPROCS \$TMPDIR/Pcrystal < \$TMPDIR/INPUT >>\& \$OUTDIR/\$OUTFILE\n \${MPIDIR}/\${MPIBIN} \$TMPDIR/Pcrystal < \$TMPDIR/INPUT >>\& \$OUTDIR/\$OUTFILE#"               ${installDIR}/utils17/runmpi17

Submiting non-interactive job to the SLURM

Here is an example SLURM test submission script to the devel partition. Edit the parameters to match your project, number of CPUs, etc. This example will run on 2 devel nodes (40 CPUs) for up to 15 minutes.

run-Pcrystal17.rackham

#!/bin/bash -l
#SBATCH  -n 40
#SBATCH  -p devel
#SBATCH --exclusive 
##SBATCH --ntasks-per-node 20
#SBATCH -t 00:15:00
#SBATCH -J test
#SBATCH -A snic-xxx-xx

module load intel/17.2 openmpi/2.1.0
export OPAL_PREFIX=/opt/openmpi/2.1.0intel17.2

JOB="MgOH2"
DIR=$SLURM_SUBMIT_DIR
CRYSTAL17_root=${HOME}/bin/crystal17

source ${CRYSTAL17_root}/utils17/cry17.bashrc
export CRY17P_MACH=$(pwd)
env > env.txt
scontrol show hostnames $SLURM_JOB_NODELIST > nodes.par && awk '{print $1":"20}' nodes.par > machines.LINUX

${CRYSTAL17_root}/utils17/runmpi17 $SLURM_NTASKS "$JOB"

Example test input

This input file runs full geometry optimization of MgOH2 crystal.

MgOH2.d12

MgOH2
CRYSTAL
1 0 0
P -3 M 1
3.179459082 4.763086088
3
12 0.0 0.0 0.
8 0.3333333333 0.66666666667 0.2193726043057150
1 0.333333333 0.666666667 0.4236468535645939
OPTGEOM
FULLOPTG
ENDOPT
END
12  4
0  0  8  2.  1.
 68371.875      0.0002226
  9699.34009    0.0018982
  2041.176786   0.0110451
   529.862906   0.0500627
   159.186000   0.169123
    54.6848     0.367031
    21.2357     0.400410
     8.74604    0.14987
0  1  5  8.  1.
   156.795     -0.00624    0.00772
    31.0339    -0.07882    0.06427
     9.6453    -0.07992    0.2104
     3.7109     0.29063    0.34314
     1.61164    0.57164    0.3735
0 1 1 0. 1.
    0.68     1.         1.
0 1 1 0. 1.
    0.28     1.         1.
    8  5
  0  0  8    2.  1.
 8.0200E+3  1.0800E-3
 1.3380E+3  8.0400E-3
 2.5540E+2  5.3240E-2
 6.9220E+1  1.6810E-1
 2.3900E+1  3.5810E-1
 9.2640E+0  3.8550E-1
 3.8510E+0  1.4680E-1
 1.2120E+0  7.2800E-2
  0  1  4    7.  1.
 4.9430E+1 -8.8300E-3  9.5800E-3
 1.0470E+1 -9.1500E-2  6.9600E-2
 3.2350E+0 -4.0200E-2  2.0650E-1
 1.2170E+0  3.7900E-1  3.4700E-1
  0  1  1    0.  1.
 4.7800E-1  1.0000E+0  1.0000E+0
  0  1  1    0.  1.
 1.7400E-1  1.0000E+0  1.0000E+0
  2  3  1    0.  1.
  1  3
  0  0  3    1.  1.
 19.238400  0.032828
  2.898720  0.231204
  0.653472  0.817226
  0  0  1    0.  1.
  0.163064  1.000000
  0  2  1    0.  1.
  1.000000  1.000000
99  0
PRINT
END
SCFDIR
DFT
B3LYP
XLGRID
END
BIPOSIZE
5000000
EXCHSIZE
5000000
TOLINTEG
8 8 8 8 16
TOLDEE
9
SHRINK
6 6
LEVSHIFT
4 1
FMIXING
40
END

To submit the job run : $ sbatch run-Pcrystal17.rackham

Contacts:


tags: UPPMAX, SNIC
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