<div dir="ltr"><pre class="moz-quote-pre" wrap="">Hi.
My name is Rainer. I am a cluster admin at the
University of Konstanz/Germany.
Last week i got the order to build cp2k for our
Chemical Cluster Justus. Compillation was fine,
I got no errors in the build process.
Unfortunately the tests are not running. I get
These are the modules i load:
# Load required modules for build process
module load compiler/intel/19.1
module load compiler/gnu/system
module load mpi/openmpi
module load numlib/mkl
module load devel/cmake
Toolchain options i used:
# ./install_cp2k_toolchain.sh \
--math-mode=openblas \
--with-sirius=no \
--mpi-mode=openmpi \
--with-cmake=system \
--with-mpich=no \
--with-libxc=install \
--libint-lmax=6 \
--with-fftw=install \
--with-openblas=install \
--with-scalapack=install \
--with-reflapack=no \
--with-mkl=no \
--with-libxsmm=install \
--with-elpa=no \
--with-superlu=install \
--with-quip=install \
--with-plumed=install \
--with-gsl=install \
--with-libvdwxc=install \
--with-spglib=install \
--with-hdf5=install
#
cp2k.out with error (excerpt):
Total Electron Density at R=0:
0.000068
Re-scaling the density matrix to get the right number of electrons
# Electrons Trace(P)
Scaling factor
32 31.944
1.002
SCF WAVEFUNCTION OPTIMIZATION
Step Update method Time Convergence Total energy
Change
------------------------------------------------------------------------------
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
[...]
Slurm parameter in submit-script:
#SBATCH --nodes=8
#SBATCH --tasks-per-node=32
#SBATCH --mem-per-cpu=2000M
echo "### Set some cp2k envs ..."
export HWLOC_HIDE_ERRORS=1 #
<a class="moz-txt-link-freetext" href="https://www.open-mpi.org/projects/hwloc/doc/v2.0.2/a00326.php">https://www.open-mpi.org/projects/hwloc/doc/v2.0.2/a00326.php</a>
export COSMA_CPU_MAX_MEMORY=64000
# HWLOC_COMPONENTS=x86
echo "### Running application ..."
srun cp2k.psmp -i ${TMP_WORK_DIR}/${INPUT} > cp2k7_1.out 2>&1
[...]
Attachments:
cp2k7_1.out : CP2K Output with error
bwforcluster-cp2k-example.sbatch : Slurm submit script
argon-vdW-DF-optPBE.inp
I would appreciate help very much!
Thanx in advance.
Rainer
<div class="moz-txt-sig">--
Rainer Rutka
Universität Konstanz
Kommunikations-, Informations-, Medienzentrum (KIM)
* Abteilung IT-Dienste Forschung und Lehre
* Wissenschaftliches Rechnen/bwHPC-S5
* KIM Ausbildung
78457 Konstanz
+49 7531 88 54 13, Raum: B 803
</div></pre></div>