<div dir="ltr"><div>Hi Brian,</div><div><br></div><div>Thanks for the information. Just to confirm, if you run<div style="background-color: rgb(250, 250, 250); border-color: rgb(187, 187, 187); border-style: solid; border-width: 1px; overflow-wrap: break-word;" class="prettyprint"><code class="prettyprint"><div class="subprettyprint"><span style="color: #000;" class="styled-by-prettify">ifort </span><span style="color: #660;" class="styled-by-prettify">--</span><span style="color: #000;" class="styled-by-prettify">version</span></div></code></div></div><div><br></div><div>does the command return ifort (IFORT) 17.0.4 ? I need to use a different machine than normally to compile with that version of the Intel compiler, so I need a while to familiarize myself with the proper build process on that machine. Hopefully I'll find the time later this week.<br></div><div><br></div><div>By the way, the error message you posted is quite cryptic and does not point to anything related to writing the cube file. Any chance you could post the full output log file for the crashing simulation? Are you able to reproduce the crash if you decrease the number of MPI tasks to, say 2 or 4, from 14? <br></div><div><br></div><div><br></div><div>BR,</div><div><br></div><div>Nico<br></div><div><br></div><div> <br><br></div><br>maanantai 30. heinäkuuta 2018 23.00.41 UTC+3 Brian Day kirjoitti:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi Nico,<div><br></div><div>I use the following intel compilers: <span style="background-color:rgb(50,50,50);color:rgb(255,255,255);font-family:Menlo;font-size:11px">module load intel/2017.3.196 intel-mpi/2017.3.196 cp2k/6.1</span></div><div><span style="background-color:rgb(50,50,50);color:rgb(255,255,255);font-family:Menlo;font-size:11px"><br></span></div>
<div>Summarized below are the conditions I used and the results I got:</div><div>nodes = 1, tasks = 14, executable = cp2k.popt -i *.inp -o *.out ---> Cube files generated without issue<br></div><div>nodes = 1, tasks = 14, executable = mpirun -np $SLURM_NTASKS cp2k.popt -i *.inp -o *.out ---> </div><div>
<p><span>forrtl: severe (174): SIGSEGV, segmentation fault occurred</span></p>
<p><span>Image<span> </span>PC<span> </span>Routine<span> </span>Line<span> </span>Source</span></p>
<p><span>cp2k.popt<span> </span>000000000D730E14<span> </span>Unknown <span> </span>Unknown<span> </span>Unknown</span></p>
<p><span>libpthread-2.17.s<span> </span>00002ABEB44735E0<span> </span>Unknown <span> </span>Unknown<span> </span>Unknown</span></p>
<p><span><a href="http://libc-2.17.so" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Flibc-2.17.so\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHazZ1VR7HhBzKEq8UMH7E3ErbugA';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Flibc-2.17.so\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHazZ1VR7HhBzKEq8UMH7E3ErbugA';return true;">libc-2.17.so</a><span> </span> <span> </span>00002ABEB61E74DC<span> </span>cfree <span> </span>Unknown<span> </span>Unknown</span></p>
<p><span>cp2k.popt<span> </span>000000000D767FA8<span> </span>Unknown <span> </span>Unknown<span> </span>Unknown</span></p>
<p><span>cp2k.popt<span> </span>000000000109F105<span> </span>qs_dispersion_typ <span> </span>135<span> </span>qs_dispersion_types.F</span></p>
<p><span>cp2k.popt<span> </span>0000000000B88BFF<span> </span>qs_environment_ty<span> </span>1476<span> </span>qs_environment_types.F</span></p>
<p><span>cp2k.popt<span> </span>0000000000B13020<span> </span>force_env_types_m <span> </span>232<span> </span>force_env_types.F</span></p>
<p><span>cp2k.popt<span> </span>0000000000EE66E0<span> </span>f77_interface_mp_ <span> </span>335<span> </span>f77_interface.F</span></p>
<p><span>cp2k.popt<span> </span>000000000043BEF8<span> </span>cp2k_runs_mp_run_ <span> </span>405<span> </span>cp2k_runs.F</span></p>
<p><span>cp2k.popt<span> </span>0000000000432814<span> </span>MAIN__<span> </span>281<span> </span>cp2k.F</span></p>
<p><span>cp2k.popt<span> </span>000000000043151E<span> </span>Unknown <span> </span>Unknown<span> </span>Unknown</span></p>
<p><span><a href="http://libc-2.17.so" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Flibc-2.17.so\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHazZ1VR7HhBzKEq8UMH7E3ErbugA';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Flibc-2.17.so\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHazZ1VR7HhBzKEq8UMH7E3ErbugA';return true;">libc-2.17.so</a><span> </span> <span> </span>00002ABEB6188C05<span> </span>__libc_start_main <span> </span>Unknown<span> </span>Unknown</span></p>
<p><span>cp2k.popt<span> </span>0000000000431429<span> </span>Unknown <span> </span>Unknown<span> </span>Unknown</span></p></div>
<div>Note that I had to run these simulations on a different cluster here, as the one I was using previously requires the submission file to declare a minimum of 2 nodes. I can talk to our computing center and see if they can test this themselves. </div><div><br></div><div>To (hopefully) clarify my earlier message, when I ran with 2 nodes, the last line in the cp2k output file would be:</div><div>
<p><span><span> </span>The sum of alpha and beta density is written in cube file format to the file:</span></p>
<p><span></span><br></p>
<p><span><span> </span>/scratch/slurm-1244788/water-<wbr>dimer-frag-b-pbe-energy-<wbr>ELECTRON_DENSITY-1_0.cube</span></p></div><div>and the electron density file would appear in the submission directory, but it would be empty. If I re-ran the simulation and passed this blank file to the cluster which I was running on, it would run successfully, but when trying to open the file in another program such as Avogadro, or using it in a subsequent simulation, it would not work. Maybe this is because it is only partially writing as you pointed out. </div><div><br></div><div>I will try and update this with the compiling information and a detailed debugging output. (Sorry if any of the above does not make sense, I am still fairly new to computational work). </div><div><br></div><div>Thanks again.</div><div><br></div><div>-Brian</div></div></blockquote></div>