<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Nov 6, 2008, at 15:04 , hui sun wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div> <div><span lang="EN-US" style="FONT-SIZE: 10pt; FONT-FAMILY: 'Times New Roman'">Dear all,<o:p></o:p></span></div> <div><span lang="EN-US" style="FONT-SIZE: 10pt; FONT-FAMILY: 'Times New Roman'"> <o:p></o:p></span></div> <div><span lang="EN-US" style="FONT-SIZE: 10pt; FONT-FAMILY: 'Times New Roman'">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:<o:p></o:p></span></div> <div><span lang="EN-US" style="FONT-SIZE: 10pt; FONT-FAMILY: 'Times New Roman'"><o:p> </o:p></span></div> <div><span lang="EN-US" style="FONT-SIZE: 10pt; FONT-FAMILY: 'Times New Roman'">MPI_ABORT invoked on rank <st1:chmetcnv w:st="on" tcsc="0" numbertype="1" negative="False" hasspace="True" sourcevalue="0" unitname="in">0 in</st1:chmetcnv> communicator MPI_COMM_WORLD with errorcode -1<o:p></o:p></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><o:p><font face="Times New Roman" size="3"> </font></o:p></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 10pt"><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<o:p></o:p></font></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 10pt"><o:p><font face="Times New Roman"> </font></o:p></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 10pt"><font face="Times New Roman">The content of the mpd.hosts file is following,<o:p></o:p></font></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 10pt"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span>node1<span style="mso-spacerun: yes"> </span>slots=8<o:p></o:p></font></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 65pt; mso-char-indent-count: 6.5"><span lang="EN-US" style="FONT-SIZE: 10pt"><font face="Times New Roman">. <o:p></o:p></font></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 65pt; mso-char-indent-count: 6.5"><span lang="EN-US" style="FONT-SIZE: 10pt"><font face="Times New Roman">.<o:p></o:p></font></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 65pt; mso-char-indent-count: 6.5"><span lang="EN-US" style="FONT-SIZE: 10pt"><font face="Times New Roman">.</font></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 65pt; mso-char-indent-count: 6.5"><span lang="EN-US" style="FONT-SIZE: 10pt"></span><span lang="EN-US" style="FONT-SIZE: 10pt"><font face="Times New Roman">nodex<span style="mso-spacerun: yes"> </span>slots=8 <o:p></o:p></font></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 10pt"><font face="Times New Roman">It must be noted that my tpr file is produced via the gromacs <st1:chsdate w:st="on" isrocdate="False" islunardate="False" day="30" month="12" year="1899">3.3.3</st1:chsdate>. 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 type="cite"><div><div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 10pt"><font face="Times New Roman"><o:p></o:p></font></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan" align="left"><font face="Times New Roman"><span lang="EN-US" style="FONT-SIZE: 10pt; COLOR: #333333; mso-font-kerning: 0pt">I don't know what to do now and how can I overcome this. Could you help me?</span><span lang="EN-US" style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: Arial; mso-font-kerning: 0pt"><o:p></o:p></span></font></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan" align="left"><font face="Times New Roman"><span lang="EN-US" style="FONT-SIZE: 10pt; COLOR: #333333; mso-font-kerning: 0pt"> </span><span lang="EN-US" style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: Arial; mso-font-kerning: 0pt"><o:p></o:p></span></font></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan" align="left"><span lang="EN-US" style="FONT-SIZE: 10pt; COLOR: #333333; mso-font-kerning: 0pt"><font face="Times New Roman">Thanks in advance!<o:p></o:p></font></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan" align="left"><span lang="EN-US" style="FONT-SIZE: 10pt; COLOR: #333333; mso-font-kerning: 0pt"><o:p><font face="Times New Roman"> </font></o:p></span></div> <div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan" align="left"><span lang="EN-US" style="FONT-SIZE: 10pt; COLOR: #333333; mso-font-kerning: 0pt"><font face="Times New Roman">Hui Sun</font></span><span lang="EN-US" style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: Arial; mso-font-kerning: 0pt"><o:p></o:p></span></div></div><div> <br class="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. 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