<div dir="ltr">Hi,<div><br></div><div>This list is intended for the discussion of GROMACS development, whereas usage questions are better put to the gmx-users mailing list in future, please. :-)</div><div><br></div><div>Martin's suggestion will likely do the same thing.</div><div><br></div><div>The error and code are coming from the MPI runtime, and don't have any diagnostic value except, as you say, of working out that MPI may not be set up correctly. Looking at the GROMACS md.log file and the earlier terminal output will be much more instructive, if there's anything GROMACS specific going on here :-)</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Jun 28, 2018 at 5:25 PM Steve Walk <<a href="mailto:swalk.cavium@gmail.com">swalk.cavium@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div>Hello,</div><div><br></div><div>I'm trying to run this version of gromacs on</div><div>recently announced hardware and I'm getting</div><div>a run-time error. I was hoping someone could</div><div>point to where the error code is defined.</div><div><br></div><div>I suspect that it's not recognizing the topology</div><div>correctly (it's kind of a big machine).</div><div><br></div><div>Any hints would be appreciated.</div><div><br></div><div>Steve Walk</div><div>Cavium</div><div><br></div><div>
<span></span>
<p class="m_-326577022017352636gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:15px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_-326577022017352636gmail-s1" style="font-variant-ligatures:no-common-ligatures">OMP_NUM_THREADS=1 mpirun -np 20 gmx_mpi mdrun <lots of args></span></p><p class="m_-326577022017352636gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:15px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_-326577022017352636gmail-s1" style="font-variant-ligatures:no-common-ligatures"><br></span></p><p class="m_-326577022017352636gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:15px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_-326577022017352636gmail-s1" style="font-variant-ligatures:no-common-ligatures">Adding the -print-exit-codes option shows</span></p><p class="m_-326577022017352636gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:15px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_-326577022017352636gmail-s1" style="font-variant-ligatures:no-common-ligatures"><br></span></p></div><div>
<p class="m_-326577022017352636gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_-326577022017352636gmail-s1" style="font-variant-ligatures:no-common-ligatures">===================================================================================</span></p>
<p class="m_-326577022017352636gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_-326577022017352636gmail-s1" style="font-variant-ligatures:no-common-ligatures">= <span class="m_-326577022017352636gmail-Apple-converted-space"> </span>BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES</span></p>
<p class="m_-326577022017352636gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_-326577022017352636gmail-s1" style="font-variant-ligatures:no-common-ligatures">= <span class="m_-326577022017352636gmail-Apple-converted-space"> </span>EXIT CODE: 6</span></p>
<p class="m_-326577022017352636gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_-326577022017352636gmail-s1" style="font-variant-ligatures:no-common-ligatures">= <span class="m_-326577022017352636gmail-Apple-converted-space"> </span>CLEANING UP REMAINING PROCESSES</span></p>
<p class="m_-326577022017352636gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_-326577022017352636gmail-s1" style="font-variant-ligatures:no-common-ligatures">= <span class="m_-326577022017352636gmail-Apple-converted-space"> </span>YOU CAN IGNORE THE BELOW CLEANUP MESSAGES</span></p>
<p class="m_-326577022017352636gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_-326577022017352636gmail-s1" style="font-variant-ligatures:no-common-ligatures">===================================================================================</span></p>
<p class="m_-326577022017352636gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_-326577022017352636gmail-s1" style="font-variant-ligatures:no-common-ligatures">[mpiexec@localhost.localdomain] Exit codes: [localhost.localdomain] 6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0</span></p>
<br></div></div>
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