<div dir="ltr">Hi Nico,<div><br></div><div>I use the following intel compilers: <span style="font-variant-ligatures: no-common-ligatures; 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="font-variant-ligatures: no-common-ligatures; background-color: rgb(50, 50, 50); color: rgb(255, 255, 255); font-family: Menlo; font-size: 11px;"><br></span></div>
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<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>
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<p class="p1"><span class="s1">forrtl: severe (174): SIGSEGV, segmentation fault occurred</span></p>
<p class="p1"><span class="s1">Image<span class="Apple-converted-space"> </span>PC<span class="Apple-converted-space"> </span>Routine<span class="Apple-converted-space"> </span>Line<span class="Apple-converted-space"> </span>Source</span></p>
<p class="p1"><span class="s1">cp2k.popt<span class="Apple-converted-space"> </span>000000000D730E14<span class="Apple-converted-space"> </span>Unknown <span class="Apple-converted-space"> </span>Unknown<span class="Apple-converted-space"> </span>Unknown</span></p>
<p class="p1"><span class="s1">libpthread-2.17.s<span class="Apple-converted-space"> </span>00002ABEB44735E0<span class="Apple-converted-space"> </span>Unknown <span class="Apple-converted-space"> </span>Unknown<span class="Apple-converted-space"> </span>Unknown</span></p>
<p class="p1"><span class="s1">libc-2.17.so<span class="Apple-tab-span"> </span> <span class="Apple-converted-space"> </span>00002ABEB61E74DC<span class="Apple-converted-space"> </span>cfree <span class="Apple-converted-space"> </span>Unknown<span class="Apple-converted-space"> </span>Unknown</span></p>
<p class="p1"><span class="s1">cp2k.popt<span class="Apple-converted-space"> </span>000000000D767FA8<span class="Apple-converted-space"> </span>Unknown <span class="Apple-converted-space"> </span>Unknown<span class="Apple-converted-space"> </span>Unknown</span></p>
<p class="p1"><span class="s1">cp2k.popt<span class="Apple-converted-space"> </span>000000000109F105<span class="Apple-converted-space"> </span>qs_dispersion_typ <span class="Apple-converted-space"> </span>135<span class="Apple-converted-space"> </span>qs_dispersion_types.F</span></p>
<p class="p1"><span class="s1">cp2k.popt<span class="Apple-converted-space"> </span>0000000000B88BFF<span class="Apple-converted-space"> </span>qs_environment_ty<span class="Apple-converted-space"> </span>1476<span class="Apple-converted-space"> </span>qs_environment_types.F</span></p>
<p class="p1"><span class="s1">cp2k.popt<span class="Apple-converted-space"> </span>0000000000B13020<span class="Apple-converted-space"> </span>force_env_types_m <span class="Apple-converted-space"> </span>232<span class="Apple-converted-space"> </span>force_env_types.F</span></p>
<p class="p1"><span class="s1">cp2k.popt<span class="Apple-converted-space"> </span>0000000000EE66E0<span class="Apple-converted-space"> </span>f77_interface_mp_ <span class="Apple-converted-space"> </span>335<span class="Apple-converted-space"> </span>f77_interface.F</span></p>
<p class="p1"><span class="s1">cp2k.popt<span class="Apple-converted-space"> </span>000000000043BEF8<span class="Apple-converted-space"> </span>cp2k_runs_mp_run_ <span class="Apple-converted-space"> </span>405<span class="Apple-converted-space"> </span>cp2k_runs.F</span></p>
<p class="p1"><span class="s1">cp2k.popt<span class="Apple-converted-space"> </span>0000000000432814<span class="Apple-converted-space"> </span>MAIN__<span class="Apple-converted-space"> </span>281<span class="Apple-converted-space"> </span>cp2k.F</span></p>
<p class="p1"><span class="s1">cp2k.popt<span class="Apple-converted-space"> </span>000000000043151E<span class="Apple-converted-space"> </span>Unknown <span class="Apple-converted-space"> </span>Unknown<span class="Apple-converted-space"> </span>Unknown</span></p>
<p class="p1"><span class="s1">libc-2.17.so<span class="Apple-tab-span"> </span> <span class="Apple-converted-space"> </span>00002ABEB6188C05<span class="Apple-converted-space"> </span>__libc_start_main <span class="Apple-converted-space"> </span>Unknown<span class="Apple-converted-space"> </span>Unknown</span></p>
<p class="p1"><span class="s1">cp2k.popt<span class="Apple-converted-space"> </span>0000000000431429<span class="Apple-converted-space"> </span>Unknown <span class="Apple-converted-space"> </span>Unknown<span class="Apple-converted-space"> </span>Unknown</span></p></div>
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<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>
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<p class="p1"><span class="s1"><span class="Apple-converted-space"> </span>The sum of alpha and beta density is written in cube file format to the file:</span></p>
<p class="p2"><span class="s1"></span><br></p>
<p class="p1"><span class="s1"><span class="Apple-converted-space"> </span>/scratch/slurm-1244788/water-dimer-frag-b-pbe-energy-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><style type="text/css">
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