<div dir="ltr"><div>Hi.</div><div><br></div><div>I did.</div><div><br></div><div>Same crash.... .-(</div><div><br></div><div><br></div><br>Am Dienstag, 15. September 2020 09:59:40 UTC+2 schrieb Matthias Krack:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hi Rainer</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Can you run the test input interactively?</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span></p>
<p class="MsoNormal"><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><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </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"> <a href="javascript:" target="_blank" gdf-obfuscated-mailto="H4SlkvO3AgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">c...@googlegroups.com</a> <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="H4SlkvO3AgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">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" gdf-obfuscated-mailto="H4SlkvO3AgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">c...@googlegroups.com</a>><br>
<b>Subject:</b> Re: [CP2K:13883] Re: cp2k invalid memory reference in SCF wavefunction optimization</span></p>
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<p class="MsoNormal">Hi Matthias.</p>
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<p class="MsoNormal">I changed the value from 200000 to unlimited.</p>
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<p class="MsoNormal">Unfortunately no change. I still get the same error.</p>
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<p class="MsoNormal">:-(</p>
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<p class="MsoNormal">Matthias Krack schrieb am Dienstag, 15. September 2020 um 09:27:35 UTC+2:</p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hi Rainer</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span></p>
<p class="MsoNormal"><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></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">HTH</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </span></p>
<p class="MsoNormal"><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></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> </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">
<span><a>c...@googlegroups.com</a></span> <<span><a>c...@googlegroups.com</a></span>>
<b>On Behalf Of </b>Rainer Rutka</span></p>
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<p class="MsoNormal"><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 <<span><a>c...@googlegroups.com</a></span>></span></p>
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<p class="MsoNormal"><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></p>
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<p class="MsoNormal">Hi Matthias.</p>
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<p class="MsoNormal">Thank you for your fast answer.</p>
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<p class="MsoNormal">See the attached file with my ulimit-setups (and more). It's unlimited (IMO).</p>
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Am Dienstag, 15. September 2020 08:49:38 UTC+2 schrieb Rainer Rutka:</p>
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<pre>Hi.</pre>
<pre>My name is Rainer. I am a cluster admin at the</pre>
<pre>University of Konstanz/Germany.</pre>
<pre> </pre>
<pre>Last week i got the order to build cp2k for our</pre>
<pre>Chemical Cluster Justus. Compillation was fine,</pre>
<pre>I got no errors in the build process.</pre>
<pre> </pre>
<pre>Unfortunately the tests are not running. I get</pre>
<pre> </pre>
<pre> </pre>
<pre>These are the modules i load:</pre>
<pre> </pre>
<pre># Load required modules for build process</pre>
<pre>module load compiler/intel/19.1</pre>
<pre>module load compiler/gnu/system</pre>
<pre>module load mpi/openmpi</pre>
<pre>module load numlib/mkl</pre>
<pre>module load devel/cmake</pre>
<pre> </pre>
<pre>Toolchain options i used:</pre>
<pre> </pre>
<pre># ./install_cp2k_toolchain.sh \</pre>
<pre> --math-mode=openblas \</pre>
<pre> --with-sirius=no \</pre>
<pre> --mpi-mode=openmpi \</pre>
<pre> --with-cmake=system \</pre>
<pre> --with-mpich=no \</pre>
<pre> --with-libxc=install \</pre>
<pre> --libint-lmax=6 \</pre>
<pre> --with-fftw=install \</pre>
<pre> --with-openblas=install \</pre>
<pre> --with-scalapack=install \</pre>
<pre> --with-reflapack=no \</pre>
<pre> --with-mkl=no \</pre>
<pre> --with-libxsmm=install \</pre>
<pre> --with-elpa=no \</pre>
<pre> --with-superlu=install \</pre>
<pre> --with-quip=install \</pre>
<pre> --with-plumed=install \</pre>
<pre> --with-gsl=install \</pre>
<pre> --with-libvdwxc=install \</pre>
<pre> --with-spglib=install \</pre>
<pre> --with-hdf5=install</pre>
<pre>#</pre>
<pre> </pre>
<pre>cp2k.out with error (excerpt):</pre>
<pre> </pre>
<pre>Total Electron Density at R=0:</pre>
<pre>0.000068</pre>
<pre> Re-scaling the density matrix to get the right number of electrons</pre>
<pre> # Electrons Trace(P)</pre>
<pre>Scaling factor</pre>
<pre> 32 31.944</pre>
<pre> 1.002</pre>
<pre> </pre>
<pre> </pre>
<pre> SCF WAVEFUNCTION OPTIMIZATION</pre>
<pre> </pre>
<pre> Step Update method Time Convergence Total energy</pre>
<pre> Change</pre>
<pre> </pre>
<pre>------------------------------<wbr>------------------------------<wbr>------------------</pre>
<pre> </pre>
<pre>Program received signal SIGSEGV: Segmentation fault - invalid memory</pre>
<pre>reference.</pre>
<pre> </pre>
<pre>Backtrace for this error:</pre>
<pre> </pre>
<pre>Program received signal SIGSEGV: Segmentation fault - invalid memory</pre>
<pre>reference.</pre>
<pre> </pre>
<pre>[...]</pre>
<pre> </pre>
<pre>Slurm parameter in submit-script:</pre>
<pre> </pre>
<pre>#SBATCH --nodes=8</pre>
<pre>#SBATCH --tasks-per-node=32</pre>
<pre>#SBATCH --mem-per-cpu=2000M</pre>
<pre> </pre>
<pre>echo "### Set some cp2k envs ..."</pre>
<pre>export HWLOC_HIDE_ERRORS=1 #</pre>
<pre><a href="https://www.open-mpi.org/projects/hwloc/doc/v2.0.2/a00326.php" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.open-mpi.org%2Fprojects%2Fhwloc%2Fdoc%2Fv2.0.2%2Fa00326.php\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE07axL5IuuRMsIJBU8JO0eA-zInw';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.open-mpi.org%2Fprojects%2Fhwloc%2Fdoc%2Fv2.0.2%2Fa00326.php\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE07axL5IuuRMsIJBU8JO0eA-zInw';return true;">https://www.open-mpi.org/<wbr>projects/hwloc/doc/v2.0.2/<wbr>a00326.php</a></pre>
<pre>export COSMA_CPU_MAX_MEMORY=64000</pre>
<pre># HWLOC_COMPONENTS=x86</pre>
<pre> </pre>
<pre>echo "### Running application ..."</pre>
<pre>srun cp2k.psmp -i ${TMP_WORK_DIR}/${INPUT} > cp2k7_1.out 2>&1</pre>
<pre> </pre>
<pre>[...]</pre>
<pre> </pre>
<pre>Attachments:</pre>
<pre> </pre>
<pre>cp2k7_1.out : CP2K Output with error</pre>
<pre>bwforcluster-cp2k-example.<wbr>sbatch : Slurm submit script</pre>
<pre>argon-vdW-DF-optPBE.inp</pre>
<pre> </pre>
<pre> </pre>
<pre>I would appreciate help very much!</pre>
<pre> </pre>
<pre>Thanx in advance.</pre>
<pre> </pre>
<pre>Rainer</pre>
<pre> </pre>
<div>
<pre>-- </pre>
<pre>Rainer Rutka</pre>
<pre>Universität Konstanz</pre>
<pre>Kommunikations-, Informations-, Medienzentrum (KIM)</pre>
<pre> * Abteilung IT-Dienste Forschung und Lehre</pre>
<pre> * Wissenschaftliches Rechnen/bwHPC-S5</pre>
<pre> * KIM Ausbildung</pre>
<pre>78457 Konstanz</pre>
<pre><a>+49 7531 88 54 13</a>, Raum: B 803</pre>
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