[CP2K-user] cp2k invalid memory reference in SCF wavefunction optimization

Rainer Rutka raine... at uni-konstanz.de
Tue Sep 15 07:20:22 UTC 2020


Hi Matthias.
Thank you for your fast answer.
See the attached file with my ulimit-setups (and more). It's unlimited 
(IMO).



Am Dienstag, 15. September 2020 08:49:38 UTC+2 schrieb Rainer Rutka:
>
> 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 #https://www.open-mpi.org/projects/hwloc/doc/v2.0.2/a00326.php
> 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
>
> -- 
> 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
>
>
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