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<p class=MsoNormal>Hi,<o:p></o:p></p>
<p class=MsoNormal>I had the chance to run the GROMACS 4.0.4 on another
cluster. Same problem still persists. But what I found is that it can be run on
a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, …
it will crash. Following are the last lines reported in different files:<o:p></o:p></p>
<p class=MsoNormal>“In the log file of the code”:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>There are: 1611 Atoms<o:p></o:p></p>
<p class=MsoNormal>There are: 1611 VSites<o:p></o:p></p>
<p class=MsoNormal>Charge group distribution at step 0: 101 147 137 152<o:p></o:p></p>
<p class=MsoNormal>Grid: 5 x 3 x 3 cells<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>“in the output file reported by cluster”:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>pwd= /home/ppirzade/GROMACS/mytests/small-box-of-water<o:p></o:p></p>
<p class=MsoNormal>Got 4 slots.<o:p></o:p></p>
<p class=MsoNormal>compute-1-34<o:p></o:p></p>
<p class=MsoNormal>compute-1-34<o:p></o:p></p>
<p class=MsoNormal>compute-2-20<o:p></o:p></p>
<p class=MsoNormal>compute-2-20<o:p></o:p></p>
<p class=MsoNormal>Starting run at: Mon Jun 8 10:27:52 MDT 2009<o:p></o:p></p>
<p class=MsoNormal>p2_22627: p4_error: Timeout in establishing connection
to remote process: 0<o:p></o:p></p>
<p class=MsoNormal>rm_l_2_22748: (301.332031) net_send: could not write to
fd=5, errno = 32<o:p></o:p></p>
<p class=MsoNormal>p2_22627: (301.332031) net_send: could not write to fd=5,
errno = 32<o:p></o:p></p>
<p class=MsoNormal>p0_21851: (302.351562) net_recv failed for fd = 6<o:p></o:p></p>
<p class=MsoNormal>p0_21851: p4_error: net_recv read, errno = : 104<o:p></o:p></p>
<p class=MsoNormal>p0_21851: (306.359375) net_send: could not write to fd=4,
errno = 32<o:p></o:p></p>
<p class=MsoNormal> Ending run at: Mon Jun 8 10:32:59 MDT 2009<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>“in the error file reported by cluster”:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Reading file npttest.tpr, VERSION 4.0.4 (single precision)<o:p></o:p></p>
<p class=MsoNormal>Making 1D domain decomposition 4 x 1 x 1<o:p></o:p></p>
<p class=MsoNormal>Killed by signal 2.^M<o:p></o:p></p>
<p class=MsoNormal>Killed by signal 2.^M<o:p></o:p></p>
<p class=MsoNormal>Killed by signal 2.^M<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>To me, it seems that code can not communicate through more
than one node. I am suspicious of doing sth wrong during installation! I tried
wiki, but I can not find the documents as before, and I eally do not know in
which step I might have gone wrong.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Payman<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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