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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Well, bad luck then. So you have most likely a miscompiled CP2K binary.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">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
<a href="https://github.com/cp2k/cp2k/blob/master/arch/Linux-x86-64-intel-minimal.psmp">
Linux-x86-64-intel-minimal.psmp</a>?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">make –j 16 ARCH=Linux-x86-64-intel-minimal VERSION=psmp<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Moreover, I suggest the Intel 18.4 compiler version.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Matthias<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> cp...@googlegroups.com <...@googlegroups.com>
<b>On Behalf Of </b>Rainer Rutka<br>
<b>Sent:</b> Dienstag, 15. September 2020 12:24<br>
<b>To:</b> cp2k <...@googlegroups.com><br>
<b>Subject:</b> Re: [CP2K:13888] Re: cp2k invalid memory reference in SCF wavefunction optimization<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I did.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Same crash.... .-(<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
Am Dienstag, 15. September 2020 09:59:40 UTC+2 schrieb Matthias Krack:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Rainer</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Can you run the test input interactively?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Matthias</span><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D">
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
<a href="javascript:" target="_blank">c...@googlegroups.com</a> <<a href="javascript:" target="_blank">c...@googlegroups.com</a>>
<b>On Behalf Of </b>Rainer Rutka<br>
<b>Sent:</b> Dienstag, 15. September 2020 09:56<br>
<b>To:</b> cp2k <<a href="javascript:" target="_blank">c...@googlegroups.com</a>><br>
<b>Subject:</b> Re: [CP2K:13883] Re: cp2k invalid memory reference in SCF wavefunction optimization</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi Matthias.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I changed the value from 200000 to unlimited.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Unfortunately no change. I still get the same error.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">:-(<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Matthias Krack schrieb am Dienstag, 15. September 2020 um 09:27:35 UTC+2:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Rainer</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Your stack size is 200000 which is most likely not large enough. Try unlimited or millions.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">HTH</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Matthias</span><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D">
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
<a href="mailto:c...@googlegroups.com">c...@googlegroups.com</a> <<a href="mailto:c...@googlegroups.com">c...@googlegroups.com</a>>
<b>On Behalf Of </b>Rainer Rutka</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><br>
<b>Sent:</b> Dienstag, 15. September 2020 09:20<br>
<b>To:</b> cp2k <<a href="mailto:c...@googlegroups.com">c...@googlegroups.com</a>></span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Subject:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> [CP2K:13879] Re: cp2k invalid
memory reference in SCF wavefunction optimization</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi Matthias.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thank you for your fast answer.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">See the attached file with my ulimit-setups (and more). It's unlimited (IMO).<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><br>
Am Dienstag, 15. September 2020 08:49:38 UTC+2 schrieb Rainer Rutka:<o:p></o:p></p>
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<pre>Hi.<o:p></o:p></pre>
<pre>My name is Rainer. I am a cluster admin at the<o:p></o:p></pre>
<pre>University of Konstanz/Germany.<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Last week i got the order to build cp2k for our<o:p></o:p></pre>
<pre>Chemical Cluster Justus. Compillation was fine,<o:p></o:p></pre>
<pre>I got no errors in the build process.<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Unfortunately the tests are not running. I get<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>These are the modules i load:<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre># Load required modules for build process<o:p></o:p></pre>
<pre>module load compiler/intel/19.1<o:p></o:p></pre>
<pre>module load compiler/gnu/system<o:p></o:p></pre>
<pre>module load mpi/openmpi<o:p></o:p></pre>
<pre>module load numlib/mkl<o:p></o:p></pre>
<pre>module load devel/cmake<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Toolchain options i used:<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre># ./install_cp2k_toolchain.sh \<o:p></o:p></pre>
<pre> --math-mode=openblas \<o:p></o:p></pre>
<pre> --with-sirius=no \<o:p></o:p></pre>
<pre> --mpi-mode=openmpi \<o:p></o:p></pre>
<pre> --with-cmake=system \<o:p></o:p></pre>
<pre> --with-mpich=no \<o:p></o:p></pre>
<pre> --with-libxc=install \<o:p></o:p></pre>
<pre> --libint-lmax=6 \<o:p></o:p></pre>
<pre> --with-fftw=install \<o:p></o:p></pre>
<pre> --with-openblas=install \<o:p></o:p></pre>
<pre> --with-scalapack=install \<o:p></o:p></pre>
<pre> --with-reflapack=no \<o:p></o:p></pre>
<pre> --with-mkl=no \<o:p></o:p></pre>
<pre> --with-libxsmm=install \<o:p></o:p></pre>
<pre> --with-elpa=no \<o:p></o:p></pre>
<pre> --with-superlu=install \<o:p></o:p></pre>
<pre> --with-quip=install \<o:p></o:p></pre>
<pre> --with-plumed=install \<o:p></o:p></pre>
<pre> --with-gsl=install \<o:p></o:p></pre>
<pre> --with-libvdwxc=install \<o:p></o:p></pre>
<pre> --with-spglib=install \<o:p></o:p></pre>
<pre> --with-hdf5=install<o:p></o:p></pre>
<pre>#<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>cp2k.out with error (excerpt):<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Total Electron Density at R=0:<o:p></o:p></pre>
<pre>0.000068<o:p></o:p></pre>
<pre> Re-scaling the density matrix to get the right number of electrons<o:p></o:p></pre>
<pre> # Electrons Trace(P)<o:p></o:p></pre>
<pre>Scaling factor<o:p></o:p></pre>
<pre> 32 31.944<o:p></o:p></pre>
<pre> 1.002<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre> SCF WAVEFUNCTION OPTIMIZATION<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre> Step Update method Time Convergence Total energy<o:p></o:p></pre>
<pre> Change<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>------------------------------------------------------------------------------<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Program received signal SIGSEGV: Segmentation fault - invalid memory<o:p></o:p></pre>
<pre>reference.<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Backtrace for this error:<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Program received signal SIGSEGV: Segmentation fault - invalid memory<o:p></o:p></pre>
<pre>reference.<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>[...]<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Slurm parameter in submit-script:<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>#SBATCH --nodes=8<o:p></o:p></pre>
<pre>#SBATCH --tasks-per-node=32<o:p></o:p></pre>
<pre>#SBATCH --mem-per-cpu=2000M<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>echo "### Set some cp2k envs ..."<o:p></o:p></pre>
<pre>export HWLOC_HIDE_ERRORS=1 #<o:p></o:p></pre>
<pre><a href="https://www.open-mpi.org/projects/hwloc/doc/v2.0.2/a00326.php" target="_blank">https://www.open-mpi.org/projects/hwloc/doc/v2.0.2/a00326.php</a><o:p></o:p></pre>
<pre>export COSMA_CPU_MAX_MEMORY=64000<o:p></o:p></pre>
<pre># HWLOC_COMPONENTS=x86<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>echo "### Running application ..."<o:p></o:p></pre>
<pre>srun cp2k.psmp -i ${TMP_WORK_DIR}/${INPUT} > cp2k7_1.out 2>&1<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>[...]<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Attachments:<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>cp2k7_1.out : CP2K Output with error<o:p></o:p></pre>
<pre>bwforcluster-cp2k-example.sbatch : Slurm submit script<o:p></o:p></pre>
<pre>argon-vdW-DF-optPBE.inp<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>I would appreciate help very much!<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Thanx in advance.<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Rainer<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<div>
<pre>-- <o:p></o:p></pre>
<pre>Rainer Rutka<o:p></o:p></pre>
<pre>Universität Konstanz<o:p></o:p></pre>
<pre>Kommunikations-, Informations-, Medienzentrum (KIM)<o:p></o:p></pre>
<pre> * Abteilung IT-Dienste Forschung und Lehre<o:p></o:p></pre>
<pre> * Wissenschaftliches Rechnen/bwHPC-S5<o:p></o:p></pre>
<pre> * KIM Ausbildung<o:p></o:p></pre>
<pre>78457 Konstanz<o:p></o:p></pre>
<pre>+49 7531 88 54 13, Raum: B 803<o:p></o:p></pre>
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