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
Hi Rainer
a reason for such segmentation faults is often a too small stack size. Check your stack size limit with (e,g. for bash with “ulimit –s”). It should be a large value or “unlimited”. I am using the latter setting.
HTH
Matthias
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Hi Rainer
Your stack size is 200000 which is most likely not large enough. Try unlimited or millions.
HTH
Matthias
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Hi Rainer
Can you run the test input interactively?
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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?
make –j 16 ARCH=Linux-x86-64-intel-minimal VERSION=psmp
Moreover, I suggest the Intel 18.4 compiler version.
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PS: The argon test input, you are using, should run on a single core. So, using 256 cores is certainly an overkill which might also trouble.
Matthias
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