<DIV> <div><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: 'Times New Roman'">Dear all,<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><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 <?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><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?<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><p> 
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