How to use cp2k¶
|
Software
|
Version
|
Cluster
|
|---|---|---|
|
cp2k
|
2022.2
|
Dardel
|
The CP2K installation contained in this module was built with support for the programs and libraries ELPA, Libint-CP2K, libvori, libxc, libxsmm, PLUMED, and spglib.
To display info on which environment variables are set when loading the module, use
ml PDC/22.06
ml show cp2k/2022.2-cpeGNU-22.06
To load the CP2K module
ml PDC/22.06
ml cp2k/2022.2-cpeGNU-22.06
Below follows an example job script for CP2K, for running on a single Dardel node using 16 MPI ranks and 8 threads. You need to replace pdc.staff with an active project that you belong to.
#!/bin/bash -l
#SBATCH -J cp2k-test
#SBATCH -A pdc.staff
#SBATCH -p main
#SBATCH -t 1-00:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#SBATCH --cpus-per-task=16
ml PDC/22.06
ml cp2k/2022.2-cpeGNU-22.06
export OMP_NUM_THREADS=8
export OMP_PLACES=cores
srun cp2k.psmp -i inputfile.inp -o logfile.log
Assuming the script is named jobscriptCP2K.sh, it can be submitted using:
sbatch jobscriptCP2K.sh
It can happen that the threads exceed their stack space which results in segmentation fault. If this happens, try increasing the stack space by adding the lines
export OMP_STACKSIZE=256M
ulimit -Ss unlimited
to the job script.
For the CP2K benchmark case H2O-dft-ls.NREP4.inp the optimal setting for running on 8 nodes on Dardel is
#!/bin/bash -l
#SBATCH -J cp2k-test
#SBATCH -A pdc.staff
#SBATCH -p main
#SBATCH -t 01:00:00
#SBATCH --nodes=8
#SBATCH --ntasks-per-node=16
#SBATCH --cpus-per-task=16
ml PDC/22.06
ml cp2k/2022.2-cpeGNU-22.06
export OMP_NUM_THREADS=8
export OMP_PLACES=cores
srun cp2k.psmp -i inputfile.inp -o logfile.log
For using CP2K together with PLUMED, we suggest to use 128 MPI ranks and 1 thread per node
#!/bin/bash -l
#SBATCH -J cp2k-test
#SBATCH -A pdc.staff
#SBATCH -p main
#SBATCH -t 1-00:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=128
#SBATCH --cpus-per-task=1
ml PDC/22.06
ml cp2k/2022.2-cpeGNU-22.06
export OMP_NUM_THREADS=1
export OMP_PLACES=cores
srun cp2k.psmp -i inputfile.inp -o logfile.log
Please consult the official CP2K documentation for more details https://www.cp2k.org/
Known issue¶
If geometry optimization got stuck in first optimization step, consider adding
PREFERRED_DIAG_LIBRARY SL
in the &GLOBAL section.
See https://github.com/cp2k/cp2k/issues/1696 for details.
Disclaimer¶
PDC takes no responsibility for the correctness of results produced with the binaries. Always evaluate the binaries against known results for the systems and properties you are investigating before using the binaries for production jobs.