<BR><BR><B><I>Mark Abraham <Mark.Abraham@anu.edu.au></I></B> skrev: <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"> <div>Soren Enemark wrote:<BR>> Dear all,<BR>> we are currently trying to set up Gromacs to run in parallel on a 3 <BR>> dual-core machines with centOS ver. 4 .<BR>> <BR>> But we face the following error message when we try to run mdrun_mpi:<BR>> <BR>> Program mdrun_mpi, VERSION 3.3<BR>> Source code file: init.c, line: 69<BR>> <BR>> Fatal error:<BR>> run input file topol.tpr was made for 2 nodes,<BR>> while mdrun_mpi expected it to be for 1 nodes.<BR>> -------------------------------------------------------<BR>> <BR>> Can anybody help us with this?<BR>> <BR>> The error message came after running:<BR>> grompp -f md.mdp -c b.gro -p topol.top -v -np 2<BR>> followed by:<BR>> mpirun -np 2 mdrun_mpi -s -v -np 2<BR><BR>The second -np 2 is only
needed for old versions of MPI, but I don't <BR>know if this will help your problem.<BR></div> <div> </div> <div> </div> <div>Thanks for taking the time to answer, I really appreciate this!</div> <div>I tried:</div> <div>grompp -f md.mdp -c b.gro -p topol.top -v -np 2</div> <div>followed by:<BR>mpirun -np 2 mdrun_mpi -s -v</div> <div> </div> <div>with the same result as previously. Was this what you meant?</div> <div>If so, are there any other flags that I could try to set?</div> <div> </div> <div>For some reason it seems that mpirun does not send the information </div> <div>(that 2 processors are to be used) to mdrun_mpi, or that mdrun_mpi does not receive the information from mpirun. What could be the reason for that?</div> <div> </div> <div>Thanks,</div> <div>Søren Enemark</div> <div> </div> <div> </div> <div> </div> <div> </div> <div><BR>Mark<BR>_______________________________________________<BR>gmx-users
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