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Hi,<br><br>Older tpr versions are compatible with 4.0.<br>For large systems making a new tpr file with the 4.0 grompp<br>will inprove the performance.<br><br>Berk<br><br><br><hr id="stopSpelling">From: larsson@xray.bmc.uu.se<br>To: gmx-users@gromacs.org<br>Subject: Re: [gmx-users] problem with openmpi and gromacs4.0 <br>Date: Thu, 6 Nov 2008 17:56:28 +0100<br><br><br><div><div>On Nov 6, 2008, at 15:04 , hui sun wrote:</div><br class="EC_Apple-interchange-newline"><blockquote><div> <div><span style="font-size: 10pt; font-family: 'Times New Roman';" lang="EN-US">Dear all,</span></div> <div><span style="font-size: 10pt; font-family: 'Times New Roman';" lang="EN-US"> </span></div> <div><span style="font-size: 10pt; font-family: 'Times New Roman';" lang="EN-US">Recently, we installed the gromacs4.0 with openmpi parallel program. When we started a simulation with np=1, the simulation was finished normally. But when the same tpr file was run with np=n (n>1), I obtained the following error message:</span></div> <div><span style="font-size: 10pt; font-family: 'Times New Roman';" lang="EN-US"> </span></div> <div><span style="font-size: 10pt; font-family: 'Times New Roman';" lang="EN-US">MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1</span></div> <div class="EC_MsoNormal" style=""><span lang="EN-US"><font face="Times New Roman" size="3"> </font></span></div> <div class="EC_MsoNormal" style=""><span style="font-size: 10pt;" lang="EN-US"><font face="Times New Roman">My used command is & mpirun -np 32 -hostfile mpd.hosts mdrun_mpi -s large.tpr -o large.trr -c large.gro -g large.log</font></span></div> <div class="EC_MsoNormal" style=""><span style="font-size: 10pt;" lang="EN-US"><font face="Times New Roman"> </font></span></div> <div class="EC_MsoNormal" style=""><span style="font-size: 10pt;" lang="EN-US"><font face="Times New Roman">The content of the mpd.hosts file is following,</font></span></div> <div class="EC_MsoNormal" style=""><span style="font-size: 10pt;" lang="EN-US"><font face="Times New Roman"><span style=""> </span><span style=""> </span><span style=""> </span>node1<span style=""> </span>slots=8</font></span></div> <div class="EC_MsoNormal" style="text-indent: 65pt;"><span style="font-size: 10pt;" lang="EN-US"><font face="Times New Roman">. </font></span></div> <div class="EC_MsoNormal" style="text-indent: 65pt;"><span style="font-size: 10pt;" lang="EN-US"><font face="Times New Roman">.</font></span></div> <div class="EC_MsoNormal" style="text-indent: 65pt;"><span style="font-size: 10pt;" lang="EN-US"><font face="Times New Roman">.</font></span></div> <div class="EC_MsoNormal" style="text-indent: 65pt;"><span style="font-size: 10pt;" lang="EN-US"></span><span style="font-size: 10pt;" lang="EN-US"><font face="Times New Roman">nodex<span style=""> </span>slots=8 </font></span></div> <div class="EC_MsoNormal" style=""><span style="font-size: 10pt;" lang="EN-US"><font face="Times New Roman">It must be noted that my tpr file is produced via the gromacs 3.3.3. Is this related to the error?</font></span></div></div></blockquote><div><br></div><div>Most probably you need to run the same version of grompp as mdrun.</div><div><br></div><div>(Another tip is to use the option "-deffnm large" instead of -s -o -c -g with large names.)</div><br><blockquote><div><div class="EC_MsoNormal" style=""><span style="font-size: 10pt;" lang="EN-US"><font face="Times New Roman"></font></span></div> <div class="EC_MsoNormal" style="text-align: left;" align="left"><font face="Times New Roman"><span style="font-size: 10pt; color: rgb(51, 51, 51);" lang="EN-US">I don't know what to do now and how can I overcome this. Could you help me?</span><span style="font-size: 10pt; color: rgb(51, 51, 51); font-family: Arial;" lang="EN-US"></span></font></div> <div class="EC_MsoNormal" style="text-align: left;" align="left"><font face="Times New Roman"><span style="font-size: 10pt; color: rgb(51, 51, 51);" lang="EN-US"> </span><span style="font-size: 10pt; color: rgb(51, 51, 51); font-family: Arial;" lang="EN-US"></span></font></div> <div class="EC_MsoNormal" style="text-align: left;" align="left"><span style="font-size: 10pt; color: rgb(51, 51, 51);" lang="EN-US"><font face="Times New Roman">Thanks in advance!</font></span></div> <div class="EC_MsoNormal" style="text-align: left;" align="left"><span style="font-size: 10pt; color: rgb(51, 51, 51);" lang="EN-US"><font face="Times New Roman"> </font></span></div> <div class="EC_MsoNormal" style="text-align: left;" align="left"><span style="font-size: 10pt; color: rgb(51, 51, 51);" lang="EN-US"><font face="Times New Roman">Hui Sun</font></span><span style="font-size: 10pt; color: rgb(51, 51, 51); font-family: Arial;" lang="EN-US"></span></div></div><div> <br class="EC_webkit-block-placeholder"></div><hr size="1"><a href="http://cn.mail.yahoo.com/"> ÑÅ»¢ÓÊÏ䣬ÄúµÄÖÕÉúÓÊÏ䣡</a>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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