<div dir="ltr"><div><div><div>Hello Michael,<br><br></div>You are welcome to register and file the bug at the <a href="https://redmine.gromacs.org/" target="_blank">https://redmine.gromacs.org/</a> issue tracker. <br>There you can attach the input file and the logs as well (so that we know the exact Gromacs version, etc).<br><br></div>Best regards,<br></div>Aleksei<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, May 5, 2017 at 10:23 AM, Michael Brunsteiner <span dir="ltr"><<a href="mailto:mbx0009@yahoo.com" target="_blank">mbx0009@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="color:#000;background-color:#fff;font-family:Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif;font-size:13px"><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3415"> </div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3472" class="m_-7619593779675071499signature"><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3601">hi,</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_4132"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3688">I post this here as it might be developers rather than a user issue ...</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3689">I ran an NPT sim with simulated annealing of an amorphous solid sample with</div><div dir="ltr" id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3690">some organic molecules,as in:</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3892" dir="ltr"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3953" dir="ltr">gmx grompp -f md-1bar-353-253.mdp -p sis3-7-simp.top -c up-nr2-3.gro -o do-nr2-3.tpr<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3951">nohup gmx mdrun -v -deffnm do-nr2-3 > er 2>&1 &<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3952"></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3975" dir="ltr"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3974" dir="ltr"> after around 30 nano secs the simulation stops without further notice.</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_4030" dir="ltr">neither in the log-file nor in stdout or stderr there are any indicators of what happened</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3981" dir="ltr">but when i look into the relevant syslog file i find:<br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3976" dir="ltr"><br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3886">May 5 03:24:38 rcpe-sbd-node03 kernel: [82541302.295784] gmx[2218]: <br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3887">segfault at ffffffff9d3ebea0 ip 00007f5b708be3a1 sp 00007f5b657f9dc0 error 7 in libgromacs.so.2.3.0[<wbr>7f5b706d9000+1d1e000]<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3888"><br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3889">when i restart the sim on the same computer and from the last cpt file, as in: <br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_4198" dir="ltr"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_4200" dir="ltr">nohup gmx mdrun -v -deffnm do-nr2-3 -cpi do-nr2-3.cpt -noappend > er 2>&1 &<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3891"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3816" dir="ltr">the sim happily continues beyond the point where it previously seg-faulted without any further issues ... <br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_4201" dir="ltr"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_4202" dir="ltr">tpr file is too large to attach (if anybody's interested i can upload it somewhere)</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5280" dir="ltr">below i put the last 30 or so lines of both stderr+stdout and the log-file</div>I believe the warning at the end of stderr is harmless, but even if it actually is the reason<div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5035" dir="ltr">for the segfault this still does not explain why nothing is written to stderr when it happens</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_4524" dir="ltr">and why the sim works when restarted from the cpt file ... can it be that this is a hardware issue??</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5034" dir="ltr"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_4525" dir="ltr">regards,</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5385" dir="ltr">Michael</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_4526" dir="ltr"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5412" dir="ltr"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5036" dir="ltr"> stderr+stdout:</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5037" dir="ltr">[..]</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5055" dir="ltr"> Brand: Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5229"> SIMD instructions most likely to fit this hardware: AVX_256<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5230"> SIMD instructions selected at GROMACS compile time: AVX_256<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5231"><br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5232"> Hardware topology: Full, with devices<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5233"> GPU info:<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5234"> Number of GPUs detected: 1<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5235"> #0: NVIDIA GeForce GTX 780, compute cap.: 3.5, ECC: no, stat: compatible<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5236"><br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5237">Reading file do-nr2-3.tpr, VERSION 2016.3 (single precision)<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5238">Changing nstlist from 20 to 40, rlist from 1.2 to 1.2<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5239"><br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5240">Using 1 MPI thread<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5241">Using 12 OpenMP threads <br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5242"><br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5243">1 compatible GPU is present, with ID 0<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5244">1 GPU auto-selected for this run.<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5245">Mapping of GPU ID to the 1 PP rank in this node: 0<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5246"><br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5247">starting mdrun 'system'<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5248">110000000 steps, 110000.0 ps.<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5249">step 80: timed with pme grid 40 40 24, coulomb cutoff 1.200: 81.2 M-cycles<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5250">step 80: the box size limits the PME load balancing to a coulomb cut-off of 1.368<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5251">step 160: timed with pme grid 32 36 24, coulomb cutoff 1.368: 72.9 M-cycles<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5252">step 240: timed with pme grid 36 36 24, coulomb cutoff 1.264: 75.7 M-cycles<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5253">step 320: timed with pme grid 36 40 24, coulomb cutoff 1.216: 78.6 M-cycles<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5254">step 400: timed with pme grid 40 40 24, coulomb cutoff 1.200: 81.2 M-cycles<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5255"> optimal pme grid 32 36 24, coulomb cutoff 1.368<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5256">step 31031000, will finish Fri May 5 14:27:08 2017<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5257">Step 31031061 Warning: pressure scaling more than 1%, mu: 0.999153 0.982333 0.997814<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5258"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5075" dir="ltr"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5065" dir="ltr"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5064" dir="ltr">log-file:</div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5062" dir="ltr">[..]<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5131"></div></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3473" class="m_-7619593779675071499qtdSeparateBR"> Step Time<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5132"> 31030000 31030.00000<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5133"><br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5134">Current ref_t for group System: 327.9<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5135"> Energies (kJ/mol)<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5136"> Bond Angle Proper Dih. Improper Dih. LJ-14<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5137"> 8.65826e+03 1.38650e+04 1.08781e+04 4.26101e+02 6.01339e+03<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5138"> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5139"> -2.98635e+04 -1.12638e+04 1.63267e+04 2.11350e+02 1.52514e+04<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5140"> Kinetic En. Total Energy Temperature Pressure (bar)<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5141"> 2.22541e+04 3.75055e+04 3.28069e+02 6.14802e+02<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5142"><br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5143"> Step Time<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5144"> 31031000 31031.00000<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5145"><br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5146">Current ref_t for group System: 327.8<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5147"> Energies (kJ/mol)<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5148"> Bond Angle Proper Dih. Improper Dih. LJ-14<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5149"> 8.41290e+03 1.38660e+04 1.08950e+04 3.51583e+02 5.79937e+03<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5150"> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5151"> -2.99386e+04 -1.15255e+04 1.64549e+04 2.30994e+02 1.45468e+04<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5152"> Kinetic En. Total Energy Temperature Pressure (bar)<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5153"> 2.27307e+04 3.72775e+04 3.35095e+02 -1.54620e+00<br id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5154"><div><br></div><div><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5321"><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5322"><br></div><div><br></div><div><br></div><div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_5320" dir="ltr"><br></div><br></div><div style="display:block" id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3373" class="m_-7619593779675071499yahoo_quoted"> <div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3372" style="font-family:Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif;font-size:13px"> <div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3371" style="font-family:HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif;font-size:16px"> <div id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3474" class="m_-7619593779675071499y_msg_container"> <font id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3369" size="2" face="Arial"> <hr id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3600" size="1"><span class="HOEnZb"><font color="#888888"><b id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3533"><span id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3532" style="font-weight:bold"></span></b></font></span></font><span class="HOEnZb"><font color="#888888">-- <br>Gromacs Developers mailing list<br><br>* Please search the archive at <a id="m_-7619593779675071499yui_3_16_0_ym19_1_1493970610003_3599" href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/<wbr>Support/Mailing_Lists/GMX-<wbr>developers_List </a>before posting!<br><br>* Can't post? 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