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<TITLE>Re: [gmx-users] parallel run problems--please help</TITLE>
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<FONT FACE="Verdana"><SPAN STYLE='font-size:12.0px'>Hi Jee,<BR>
<BR>
Since you can’t even get just 1 process to run, I suspect there might be something wrong with<BR>
the installation. (if 1 process works, then likely it’s some runtime library problem across nodes)<BR>
<BR>
But for a start, just try putting in the full path to mdrun_mpi in your mpirun calls.<BR>
And I presume you compiled with “--enable-mpi” for both FFTw and Gromacs.<BR>
<BR>
cheers,<BR>
Choon-Peng<BR>
-- <BR>
Mr. Choon-Peng CHNG<BR>
Research Associate<BR>
BioInformatics Institute, BMSI, A*STAR<BR>
30 Biopolis Street<BR>
#07-01 Matrix Building<BR>
Singapore 138671<BR>
Tel (O): +65 64788301 Fax (O): +65 64789047<BR>
www.bii.a-star.edu.sg/~cpchng<BR>
<BR>
<BR>
On 2/10/04 9:39 AM, "Jee Eun Rim" <jrim@stanford.edu> wrote:<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Verdana"><SPAN STYLE='font-size:12.0px'>Hello,<BR>
<BR>
I have installed gromacs on an SGI Origin 3800, and tried running the tutorial gmxdemo. <BR>
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,<BR>
<BR>
</SPAN></FONT><SPAN STYLE='font-size:12.0px'><FONT FACE="Arial">input:<BR>
grompp_d -np 1 -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em >& ! output.grompp_em<BR>
mpirun -np 1 mdrun_mpi -np 1 -nice 4 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.mdrun_em<BR>
</FONT><FONT FACE="Verdana"> <BR>
</FONT><FONT FACE="Arial">output:<BR>
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()<BR>
MPI: aborting job<BR>
</FONT><FONT FACE="Verdana"> <BR>
</FONT><FONT FACE="Arial">Also, if I increase the number of processes to 4, I get the following error<BR>
</FONT><FONT FACE="Verdana"> <BR>
</FONT><FONT FACE="Arial">input:<BR>
grompp_d -np 4 -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.grompp_pr<BR>
mpirun -np 4 mdrun_mpi -np 4 -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.mdrun_pr<BR>
<BR>
output:<BR>
Fatal error: run input file cpeptide_pr.tpr was made for 4 nodes,<BR>
while mdrun_mpi expected it to be for 1 nodes.<BR>
Fatal error: run input file cpeptide_pr.tpr was made for 4 nodes,<BR>
while mdrun_mpi expected it to be for 1 nodes.<BR>
Fatal error: run input file cpeptide_pr.tpr was made for 4 nodes,<BR>
while mdrun_mpi expected it to be for 1 nodes.<BR>
Fatal error: run input file cpeptide_pr.tpr was made for 4 nodes,<BR>
while mdrun_mpi expected it to be for 1 nodes.<BR>
<BR>
Even though grompp_d had the option -np 4. <BR>
<BR>
Does this mean that gromacs was not compiled/installed correctly? Any help would be greatly appreciated.<BR>
By the way, gromacs was compiled with MPICH, with --enable-shared.<BR>
<BR>
Thanks a lot.<BR>
<BR>
Jee.<BR>
<BR>
</FONT><FONT FACE="Verdana"><BR>
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