[CP2K-user] [CP2K:13888] Re: cp2k invalid memory reference in SCF wavefunction optimization

Krack Matthias (PSI) matthi... at psi.ch
Tue Sep 15 11:07:49 UTC 2020


Well, bad luck then. So you have most likely a miscompiled CP2K binary.

You are using the Intel compiler with MKL available, but you request a toolchain installation of ScaLAPACK and openmpi instead of using the mpich based Intel MPI and the ScaLAPACK/LAPACK/BLAS and FFTW libraries coming with MKL. Did you try to compile first using the minimal Intel arch file Linux-x86-64-intel-minimal.psmp<https://github.com/cp2k/cp2k/blob/master/arch/Linux-x86-64-intel-minimal.psmp>?

make –j 16 ARCH=Linux-x86-64-intel-minimal VERSION=psmp

Moreover, I suggest the Intel 18.4 compiler version.

Matthias

From: cp... at googlegroups.com <cp... at googlegroups.com> On Behalf Of Rainer Rutka
Sent: Dienstag, 15. September 2020 12:24
To: cp2k <cp... at googlegroups.com>
Subject: Re: [CP2K:13888] Re: cp2k invalid memory reference in SCF wavefunction optimization

Hi.

I did.

Same crash.... .-(



Am Dienstag, 15. September 2020 09:59:40 UTC+2 schrieb Matthias Krack:
Hi Rainer

Can you run the test input interactively?

Matthias

From: c... at googlegroups.com<javascript:> <c... at googlegroups.com<javascript:>> On Behalf Of Rainer Rutka
Sent: Dienstag, 15. September 2020 09:56
To: cp2k <c... at googlegroups.com<javascript:>>
Subject: Re: [CP2K:13883] Re: cp2k invalid memory reference in SCF wavefunction optimization

Hi Matthias.
I changed the value from 200000 to unlimited.
Unfortunately no change. I still get the same error.
:-(

Matthias Krack schrieb am Dienstag, 15. September 2020 um 09:27:35 UTC+2:
Hi Rainer

Your stack size is 200000 which is most likely not large enough. Try unlimited or millions.

HTH

Matthias

From: c... at googlegroups.com<mailto:c... at googlegroups.com> <c... at googlegroups.com<mailto:c... at googlegroups.com>> On Behalf Of Rainer Rutka

Sent: Dienstag, 15. September 2020 09:20
To: cp2k <c... at googlegroups.com<mailto:c... at googlegroups.com>>
Subject: [CP2K:13879] Re: cp2k invalid memory reference in SCF wavefunction optimization

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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