<div dir="ltr">Hi,<div><br></div><div>there are some statically compiled cp2k executable available on the sourceforge page</div><div><br></div><div>http://sourceforge.net/projects/cp2k/files/precompiled/</div><div><br></div><div>if you are running on a standard machine linux machine the should "just work" - not very quickly and only in serial/ssmp modes. But you could test smaller jobs to see whether problems are with your input or your executable.</div><div><br></div><div>Matt<br><br>On Thursday, July 31, 2014 8:09:30 PM UTC+1, Huan Wang wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi Matt,<div><br></div><div>Thanks for your reply and suggestion. But I am not sure about what you said "one of the precompiled ones to test". Should I try to install and compile the new version 2.6? </div> <div><br></div><div>Regards,</div><div>Huan</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div><br><br><div class="gmail_quote">On Thu, Jul 31, 2014 at 7:24 PM, Matt W <span dir="ltr"><<a href="javascript:" target="_blank" gdf-obfuscated-mailto="kFef8PuXEqoJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">Matt...@gmail.com</a>></span> wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi,</div><div><br></div>your first input runs fine for me on my laptop (in a virtual box with 2GB of RAM). Your executable must be incorrectly built. Try one of the precompiled ones to test, maybe.<div> <br></div><div>Matt<div><div><br><br>On Thursday, July 31, 2014 3:33:18 PM UTC+1, <a>hua...@mail.huji.ac.il</a> wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"> <div dir="ltr"><p style="text-align:left;clear:both">Dear All,</p><div>I tried to submit the H2O-128.inp which is the MD simulation of 128 water molecules in the cp2k/test/QS/benchmark directory. Unfortunately, I got the same error.</div> <div><br></div><div>Another test is for the 64 water molecules with one proton as I asked yesterday. This time, I used # to comment one of the coordinates of water molecule in the &COORD section. After this modification, the program run without any error!</div> <div><br></div><div>I was wondering if it because of the limitation of my computer that could not deal with more than 64 atoms? But for DZVP basis sets the 64-H2O with one excess proton system is 1477 orbital functions, only 5 more functions compared with 64-H2O neutral system. Furthermore, in the literature of <b>Computer Physics Communications 167 (2005) 103–128</b>，as shown in the Fig. 13 below, that even 256 water molecules could be run in 4, 8, 16 or 32 CPUs. The difference between them just the cost of time.<br> </div><div><p style="text-align:center;clear:both"><a href="https://lh5.googleusercontent.com/-q_V5FcV5kAU/U9pSkxxjHII/AAAAAAAAAGQ/coqej90xWkE/s1600/Fig-13.png" style="margin-left:1em;margin-right:1em" target="_blank" onmousedown="this.href='https://lh5.googleusercontent.com/-q_V5FcV5kAU/U9pSkxxjHII/AAAAAAAAAGQ/coqej90xWkE/s1600/Fig-13.png';return true;" onclick="this.href='https://lh5.googleusercontent.com/-q_V5FcV5kAU/U9pSkxxjHII/AAAAAAAAAGQ/coqej90xWkE/s1600/Fig-13.png';return true;"><img border="0" width="205" height="320"></a></p> <div><span></span><span></span>I totally have no ideal about what happened in my test. Could someone give me some suggestion? Thanks a lot.</div><div><br></div><div>Regards,</div><div>Huan</div><div><br></div><div><br></div> <div><br></div><div><br></div><div><br></div><div><br>On Tuesday, July 29, 2014 3:23:10 PM UTC+3, <a>hua...@mail.huji.ac.il</a> wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"> Dear All,<div><br></div><div>I am running MD simulation test on 64 water molecules and 64 water with one proton systems with CP2K/Quickstep. For 64 water molecules, the program went well, however for 64 water molecules with on proton, it returned error. Please find the attached input file "p-H2O_64_BLYP_300K.inp". This file was based on the test file of H2O-64.inp at the ..cp2k/test/QS/benchmark directory of CP2K program. I changed the CHARGE to 1 to adapt the excess proton, the rest of settings were the same as the input file of neutral 64-H2O molecules. </div> <div><br></div><div>The version of CP2K I used is 2.3. The CPU information is Intel(R) Xeon(R) CPU E5-2665 0 @ 2.40GHz, and the total memory is 32 GB available. I use 24 cores in one node for this test. The reported error are shown below,</div> <div><br></div><div><br></div><div><div>[proton17:42359] *** Process received signal ***</div><div>[proton17:42359] Signal: Segmentation fault (11)</div><div>[proton17:42359] Signal code: (128)</div><div>[proton17:42359] Failing at address: (nil)</div> <div>[proton17:42357] *** Process received signal ***</div><div>[proton17:42357] Signal: Segmentation fault (11)</div><div>[proton17:42357] Signal code: (128)</div><div>[proton17:42357] Failing at address: (nil)</div><div> [proton17:42364] *** Process received signal ***</div><div>[proton17:42364] Signal: Segmentation fault (11)</div><div>[proton17:42364] Signal code: (128)</div><div>[proton17:42364] Failing at address: (nil)</div><div>[proton17:42366] *** Process received signal ***</div> <div>[proton17:42366] Signal: Segmentation fault (11)</div><div>[proton17:42366] Signal code: (128)</div><div>[proton17:42366] Failing at address: (nil)</div><div>[proton17:42371] *** Process received signal ***</div><div> [proton17:42371] Signal: Segmentation fault (11)</div><div>[proton17:42371] Signal code: (128)</div><div>[proton17:42371] Failing at address: (nil)</div><div>[proton17:42376] *** Process received signal ***</div><div>[proton17:42376] Signal: Segmentation fault (11)</div> <div>[proton17:42376] Signal code: (128)</div><div>[proton17:42376] Failing at address: (nil)</div><div>[proton17:42377] *** Process received signal ***</div><div>[proton17:42377] Signal: Segmentation fault (11)</div><div> [proton17:42377] Signal code: (128)</div><div>[proton17:42377] Failing at address: (nil)</div><div>[proton17:42355] *** Process received signal ***</div><div>[proton17:42355] Signal: Segmentation fault (11)</div><div>[proton17:42355] Signal code: (128)</div> <div>[proton17:42355] Failing at address: (nil)</div><div>[proton17:42356] *** Process received signal ***</div><div>[proton17:42356] Signal: Segmentation fault (11)</div><div>[proton17:42356] Signal code: (128)</div><div> [proton17:42356] Failing at address: (nil)</div><div>[proton17:42358] *** Process received signal ***</div><div>[proton17:42358] Signal: Segmentation fault (11)</div><div>[proton17:42358] Signal code: (128)</div><div>[proton17:42358] Failing at address: (nil)</div> <div>[proton17:42362] *** Process received signal ***</div><div>[proton17:42362] Signal: Segmentation fault (11)</div><div>[proton17:42362] Signal code: (128)</div><div>[proton17:42362] Failing at address: (nil)</div><div> [proton17:42365] *** Process received signal ***</div><div>[proton17:42365] Signal: Segmentation fault (11)</div><div>[proton17:42365] Signal code: (128)</div><div>[proton17:42365] Failing at address: (nil)</div><div>[proton17:42367] *** Process received signal ***</div> <div>[proton17:42367] Signal: Segmentation fault (11)</div><div>[proton17:42367] Signal code: (128)</div><div>[proton17:42367] Failing at address: (nil)</div><div>[proton17:42369] *** Process received signal ***</div><div> [proton17:42369] Signal: Segmentation fault (11)</div><div>[proton17:42369] Signal code: (128)</div><div>[proton17:42369] Failing at address: (nil)</div><div>[proton17:42370] *** Process received signal ***</div><div>[proton17:42370] Signal: Segmentation fault (11)</div> <div>[proton17:42370] Signal code: (128)</div><div>[proton17:42370] Failing at address: (nil)</div><div>[proton17:42372] *** Process received signal ***</div><div>[proton17:42372] Signal: Segmentation fault (11)</div><div> [proton17:42372] Signal code: (128)</div><div>[proton17:42372] Failing at address: (nil)</div><div>[proton17:42373] *** Process received signal ***</div><div>[proton17:42373] Signal: Segmentation fault (11)</div><div>[proton17:42373] Signal code: (128)</div> <div>[proton17:42373] Failing at address: (nil)</div><div>[proton17:42363] *** Process received signal ***</div><div>[proton17:42363] Signal: Segmentation fault (11)</div><div>[proton17:42363] Signal code: (128)</div><div> [proton17:42363] Failing at address: (nil)</div><div>[proton17:42361] *** Process received signal ***</div><div>[proton17:42361] Signal: Segmentation fault (11)</div><div>[proton17:42361] Signal code: (128)</div><div>[proton17:42361] Failing at address: (nil)</div> <div>[proton17:42368] *** Process received signal ***</div><div>[proton17:42368] Signal: Segmentation fault (11)</div><div>[proton17:42368] Signal code: (128)</div><div>[proton17:42368] Failing at address: (nil)</div><div> [proton17:42374] *** Process received signal ***</div><div>[proton17:42374] Signal: Segmentation fault (11)</div><div>[proton17:42374] Signal code: (128)</div><div>[proton17:42374] Failing at address: (nil)</div><div>[proton17:42375] *** Process received signal ***</div> <div>[proton17:42375] Signal: Segmentation fault (11)</div><div>[proton17:42375] Signal code: (128)</div><div>[proton17:42375] Failing at address: (nil)</div><div>[proton17:42354] *** Process received signal ***</div><div> [proton17:42360] *** Process received signal ***</div><div>[proton17:42360] Signal: Segmentation fault (11)</div><div>[proton17:42360] Signal code: (128)</div><div>[proton17:42360] Failing at address: (nil)</div><div>[proton17:42354] Signal: Segmentation fault (11)</div> <div>[proton17:42354] Signal code: (128)</div><div>[proton17:42354] Failing at address: (nil)</div><div>[proton17:42377] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b46ae872d00]</div><div>[proton17:42377] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42377] *** End of error message ***</div><div>[proton17:42357] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b4fb84c9d00]</div><div>[proton17:42357] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42357] *** End of error message ***</div><div>[proton17:42376] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b35e5f2cd00]</div><div>[proton17:42376] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42376] *** End of error message ***</div><div>[proton17:42359] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b1c774d5d00]</div><div>[proton17:42359] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42359] *** End of error message ***</div><div>[proton17:42356] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2add3a4fed00]</div><div>[proton17:42356] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42356] *** End of error message ***</div><div>[proton17:42364] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b51161f1d00]</div><div>[proton17:42364] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42364] *** End of error message ***</div><div>[proton17:42367] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b1aef997d00]</div><div>[proton17:42367] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42367] *** End of error message ***</div><div>[proton17:42366] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b1724dffd00]</div><div>[proton17:42366] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42366] *** End of error message ***</div><div>[proton17:42371] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b4b366efd00]</div><div>[proton17:42371] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42371] *** End of error message ***</div><div>[proton17:42358] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2acbc8278d00]</div><div>[proton17:42358] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42358] *** End of error message ***</div><div>[proton17:42365] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2ba8a6352d00]</div><div>[proton17:42365] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42365] *** End of error message ***</div><div>[proton17:42373] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b7c8c157d00]</div><div>[proton17:42373] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42373] *** End of error message ***</div><div>[proton17:42369] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b951c33ed00]</div><div>[proton17:42369] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42369] *** End of error message ***</div><div>[proton17:42355] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b84d27d1d00]</div><div>[proton17:42355] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42355] *** End of error message ***</div><div>[proton17:42370] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b7e4a2fad00]</div><div>[proton17:42370] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42370] *** End of error message ***</div><div>[proton17:42363] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b1e83351d00]</div><div>[proton17:42363] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42363] *** End of error message ***</div><div>[proton17:42362] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b75186a5d00]</div><div>[proton17:42362] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42362] *** End of error message ***</div><div>[proton17:42372] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b162a405d00]</div><div>[proton17:42372] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42372] *** End of error message ***</div><div>[proton17:42374] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2abdbacb1d00]</div><div>[proton17:42374] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42374] *** End of error message ***</div><div>[proton17:42375] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b2c29737d00]</div><div>[proton17:42375] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42375] *** End of error message ***</div><div>[proton17:42361] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b50610a8d00]</div><div>[proton17:42361] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42361] *** End of error message ***</div><div>[proton17:42368] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b392e382d00]</div><div>[proton17:42368] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42368] *** End of error message ***</div><div>[proton17:42360] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2ba37b3d0d00]</div><div>[proton17:42360] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42360] *** End of error message ***</div><div>[proton17:42354] [ 0] /lib64/libpthread.so.0(+<u></u>0xfd00<wbr>) [0x2b86855ebd00]</div><div>[proton17:42354] [ 1] /opt/cp2k_new_libint/cp2k/<u></u>trun<wbr>k/cp2k/exe/Linux-x86-64-<u></u>gfortr<wbr>an/cp2k.popt() [0x20ec04d]</div> <div>[proton17:42354] *** End of error message ***</div><div>------------------------------<u></u><wbr>------------------------------<u></u><wbr>--------------</div><div>mpirun noticed that process rank 3 with PID 42357 on node proton17 exited on signal 11 (Segmentation fault).</div> <div>------------------------------<u></u><wbr>------------------------------<u></u><wbr>--------------</div><div><br></div><div>[1] Exit 139 /usr/lib64/mpi/gcc/openmpi/<u></u>bi<wbr>n/mpirun -np 24 ...</div></div> <div><br></div><div>The error seems related to the mpi. I am not sure is there any other mistake about my inputs. </div><div>Any suggestion would be greatly appreciated. Thanks a lot.</div><div><br></div><div>Regards,</div> <div>Huan </div><div><br></div><div><br></div><div><br></div></blockquote></div></div></div></blockquote></div></div></div></div><span><font color="#888888"> <p></p> -- <br> You received this message because you are subscribed to a topic in the Google Groups "cp2k" group.<br> To unsubscribe from this topic, visit <a href="https://groups.google.com/d/topic/cp2k/JQf9hvnks-Y/unsubscribe" target="_blank" onmousedown="this.href='https://groups.google.com/d/topic/cp2k/JQf9hvnks-Y/unsubscribe';return true;" onclick="this.href='https://groups.google.com/d/topic/cp2k/JQf9hvnks-Y/unsubscribe';return true;">https://groups.google.com/d/<wbr>topic/cp2k/JQf9hvnks-Y/<wbr>unsubscribe</a>.<br> To unsubscribe from this group and all its topics, send an email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="kFef8PuXEqoJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp2k+uns...@googlegroups.<wbr>com</a>.<br> To post to this group, send email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="kFef8PuXEqoJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a>.<br> Visit this group at <a href="http://groups.google.com/group/cp2k" target="_blank" onmousedown="this.href='http://groups.google.com/group/cp2k';return true;" onclick="this.href='http://groups.google.com/group/cp2k';return true;">http://groups.google.com/<wbr>group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" onmousedown="this.href='https://groups.google.com/d/optout';return true;" onclick="this.href='https://groups.google.com/d/optout';return true;">https://groups.google.com/d/<wbr>optout</a>.<br> </font></span></blockquote></div><br></div> </blockquote></div></div>