<div dir="ltr">Thanks a lot, Manav. I'm compiling it myself. Could you please point me to tests files that you mentioned revealed the problem?<div><br></div><div>Thanks<br><br>On Monday, February 20, 2017 at 12:36:14 PM UTC-8, Manav Kumar wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi Luiz,<div><br></div><div>James's recommendation of using a downgraded version of openmpi worked. If there is a CP2K module that you are using, you might want to ask your HPC system administrators to re-compile it for you. There are some tests that come with CP2K that weren't run and they revealed the problem with our version of CP2K.</div><div><br></div><div>Best,</div><div>Manav</div><div><br><br>On Monday, February 20, 2017 at 1:26:14 PM UTC-5, Luiz Fernando Lopes Oliveira wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Manav.<div><br></div><div>We are having similar problems and were wondering if you had a solution for that.</div><div><br></div><div>Do you think the problem was finally with the intel compilers?</div><div><br></div><div>Thanks!</div><div><div><br>On Saturday, April 25, 2015 at 2:26:16 AM UTC-7, Manav Kumar wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi James,<div><br></div><div>No, I haven't tried that yet. I will pass on the information to the system administrators at our HPC and see what they say. Did that fix the issue with you?</div><div><br></div><div>Best,</div><div>Manav Kumar</div><div><br></div><div><br>On Saturday, April 25, 2015 at 5:05:16 AM UTC-4, JamesChen wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Manav,<div>I have a similar issue with mvapich2 and some buggy version of Intel compilers. It seems that you are using rather standard software stack. Have you ever downgraded your openmpi to 1.6.5 (prior stable version)? </div><div>James<br><div><br><div class="gmail_quote">On Sat, Apr 25, 2015 at 6:08 AM, Manav Kumar <span dir="ltr"><<a rel="nofollow">mk3...@nyu.edu</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">Hi James,<div><br></div><div>I'm assuming when you say the software environment, you mean the dependencies for CP2K. Here are the dependencies that are added to my environment when I use the CP2K module:</div><div><br></div><div><p style="margin-bottom:0px;font-size:11px;line-height:normal;font-family:Menlo">'gcc/4.9.1'</p> <p style="margin-bottom:0px;font-size:11px;line-height:normal;font-family:Menlo">'openmpi/gcc_4.9.1/1.8.3'</p> <p style="margin-bottom:0px;font-size:11px;line-height:normal;font-family:Menlo">'mpiblacs/gcc_4.9.1/openmpi_1.<wbr>8.3/2.0.2'</p> <p style="margin-bottom:0px;font-size:11px;line-height:normal;font-family:Menlo">'lapack/gcc_4.9.1/3.5.0'</p> <p style="margin-bottom:0px;font-size:11px;line-height:normal;font-family:Menlo">'scalapack/gcc_4.9.1/openmpi_<wbr>1.8.3/2.0.2'</p> <p style="margin-bottom:0px;font-size:11px;line-height:normal;font-family:Menlo">'fftw3/gcc_4.9.1/3.3.4'</p> <p style="margin-bottom:0px;font-size:11px;line-height:normal;font-family:Menlo"><br></p><p style="margin-bottom:0px;line-height:normal"><font face="arial, sans-serif" size="2">Let me know if there is any other information that might help!</font></p><p style="margin-bottom:0px;line-height:normal"><font face="arial, sans-serif" size="2"><br></font></p><p style="margin-bottom:0px;line-height:normal"><font face="arial, sans-serif" size="2">Best,</font></p><p style="margin-bottom:0px;line-height:normal"><font face="arial, sans-serif" size="2">MK</font></p><span><br>On Friday, April 24, 2015 at 5:56:32 PM UTC-4, JamesChen wrote:</span><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><span>Hi,<div>Could you provide us your software environment? Are you using mvapich2 as MPI? I will suggest you follow the CP2K manual and choose Gfortran/Gnu compiler, Netlib Math library and Openmpi as the reference software stack.</div><div><a href="http://www.cp2k.org/howto:compile" rel="nofollow" target="_blank" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.cp2k.org%2Fhowto%3Acompile\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFoSXliL0Xt5CCLMJC1CQvAOIs_oA';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.cp2k.org%2Fhowto%3Acompile\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFoSXliL0Xt5CCLMJC1CQvAOIs_oA';return true;">http://www.cp2k.org/howto:<wbr>compile</a> </div></span><div><div><br></div><div>Cheers,</div><div>James</div><div><br><div class="gmail_quote"><div><div>On Sat, Apr 25, 2015 at 5:08 AM, Manav Kumar <span dir="ltr"><<a rel="nofollow">mk3...@nyu.edu</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><div><div dir="ltr">Hi Matt,<div><br></div><div>Thank you for your response!</div><div><br></div><div>I'm sorry I mis-spoke earlier, I meant to say that NVT not NVE that's my mistake. When I ran NVT with CP2K module it worked fine.</div><div><br></div><div>I ran a cell optimization using the CP2K module, and it went through fine.</div><div><br></div><div>I have talked to some of the other members in my group, and they mentioned that it is possible that when I am running the simulation on multiple nodes that one of them is faulty and therefore causing the calculations to hang. However, it seems like the probability of me hitting the same faulty node every time I submit a job seems highly unlikely. Also, if this was the case then wouldn't the jobs that I submit using my own compiled version of CP2K also hang?<br><br>When you said that the it was a problem with the cell size, what did you mean exactly?</div><div><br></div><div>Best,</div><div>Manav Kumar<div><div><br><br>On Friday, April 24, 2015 at 11:51:29 AM UTC-4, Matt W wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>nothing is obviously wrong with your input that I can see. Maybe (i) problem with the executable (ii) problem with cell size.</div><div><br></div><div><br></div><div>To start debugging -</div><div>You say you can run NVE - can you run NVT as you've got it set up?</div><div>Can you run a cell optimization, maybe just a few steps, to check that the stress tensor/cell volume change is working OK.</div><div><br></div><div>Matt<br><br>On Friday, April 24, 2015 at 12:52:48 PM UTC+1, Manav Kumar wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div dir="ltr">Hi users and developers,<div><br></div><div>This is my first project using CP2K, so I'm sorry in advance if some of the things I say might be wrong.</div><div><br></div><div>I am currently trying to generate a trajectory for a simulation of diacetone diperoxide (DADP) using a NPT ensemble. I am attaching the input file, and the submit script below.</div><div><br></div><div>The HPC that I am using has a CP2K module. I performed a wave-function optimization, geometry optimization, cell optimization, and a NVE ensemble calculation all using the module. However, now that I am running the NPT calculation using the module it seems to hang. It reads in all the parameters from a previous restart file, it starts to initiate the process but gets stuck in the SCF optimization routine. It doesn't print an error message, it just stays at that position until the wall time comes along and kills the process. Sometimes it completes a lot of SCF optimization steps, sometimes it gets through none.</div><div><br></div><div>What I've done so far to try to remedy the problem is that I've tried compiling CP2K myself and running the calculation using that executable instead of the module. I've had a bit more success with my own compiled executable, but even with that it sometimes hangs. The system administrators responsible for the HPC checked the binaries and said that everything was fine.</div><div><br></div><div>Has anyone else had an issue similar to this?</div><div><br></div><div>Best,</div><div>Manav Kumar</div><div><br></div><div>I will attach my input file, output file, and submit script below so that you can see what I have been doing.<br></div></div></div></blockquote></div></div></blockquote></div></div></div></div></div></div><div><div><div><div> <p></p> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br></div></div> To unsubscribe from this group and stop receiving emails from it, send an email to <a rel="nofollow">cp2k+...@googlegroups.com</a>.<br> To post to this group, send email to <a rel="nofollow">cp...@googlegroups.com</a>.<span><br> Visit this group at <a href="http://groups.google.com/group/cp2k" rel="nofollow" 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" rel="nofollow" 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> </span></div></div></blockquote></div><br></div></div></div> </blockquote></div></div><div><div> <p></p> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a rel="nofollow">cp2k+...@googlegroups.com</a>.<br> To post to this group, send email to <a rel="nofollow">cp...@googlegroups.com</a>.<br> Visit this group at <a href="http://groups.google.com/group/cp2k" rel="nofollow" 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" rel="nofollow" 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> </div></div></blockquote></div><br></div></div></div> </blockquote></div></div></blockquote></div></div></div></blockquote></div></div></blockquote></div></div>