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<DIV>Hello,</DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV>I have installed gromacs on an SGI Origin 3800, and tried running the
tutorial gmxdemo. </DIV>
<DIV>I have no problem running the serial version, but when I modify the
script and try to run the parallel version with mpirun, I get the following
errors,</DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>input:</FONT></DIV>
<DIV><FONT face=Arial size=2>grompp_d -np 1 -f em -c ${MOL}_b4em -p ${MOL}
-o ${MOL}_em >& ! output.grompp_em</FONT></DIV>
<DIV><FONT face=Arial size=2>mpirun -np 1 mdrun_mpi -np 1 -nice 4 -s ${MOL}_em
-o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.mdrun_em</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>output:</FONT></DIV>
<DIV><FONT size=2><FONT face=Arial>MPI: MPI_COMM_WORLD rank 0 has terminated
without calling MPI_Finalize()</FONT></FONT></DIV>
<DIV><FONT face=Arial size=2>MPI: aborting job</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Also, if I increase the number of processes to 4, I
get the following error</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>
<DIV><FONT face=Arial size=2>input:</FONT></DIV>
<DIV><FONT face=Arial size=2>grompp_d -np 4 -f pr -c ${MOL}_b4pr -r
${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& !
output.grompp_pr</FONT></DIV>
<DIV><FONT face=Arial size=2>mpirun -np 4 mdrun_mpi -np 4 -nice 4 -s
${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& !
output.mdrun_pr</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>output:</FONT></DIV>
<DIV><FONT size=2><FONT face=Arial>Fatal error: run input file cpeptide_pr.tpr
was made for 4 nodes,</FONT></FONT></DIV>
<DIV>
while mdrun_mpi expected it to
be for 1 nodes.</DIV>
<DIV>
<DIV><FONT size=2><FONT face=Arial>Fatal error: run input file cpeptide_pr.tpr
was made for 4 nodes,</FONT></FONT></DIV>
<DIV>
while mdrun_mpi expected it to
be for 1 nodes.</DIV>
<DIV>
<DIV><FONT size=2><FONT face=Arial>Fatal error: run input file cpeptide_pr.tpr
was made for 4 nodes,</FONT></FONT></DIV>
<DIV>
while mdrun_mpi expected it to
be for 1 nodes.</DIV>
<DIV>
<DIV><FONT size=2><FONT face=Arial>Fatal error: run input file cpeptide_pr.tpr
was made for 4 nodes,</FONT></FONT></DIV>
<DIV>
while mdrun_mpi expected it to
be for 1 nodes.</DIV>
<DIV> </DIV>
<DIV>Even though grompp_d had the option -np 4. </DIV>
<DIV> </DIV>
<DIV>Does this mean that gromacs was not compiled/installed correctly? Any help
would be greatly appreciated.</DIV>
<DIV>By the way, gromacs was compiled with MPICH, with --enable-shared.</DIV>
<DIV> </DIV>
<DIV>Thanks a lot.</DIV>
<DIV> </DIV>
<DIV>Jee.</DIV>
<DIV> </DIV></DIV></DIV></DIV></FONT></DIV></BODY></HTML>