Hi all. First, excuse my English, it is not too good, but I'm learning.
I have a problem with my gromacs. I have a Dell Precision 470 (2 Xeon processor with 2Gb RAM) and I can't run mdrun_mpi for 2 processor. I describe what is happening. I installed gromacs-3.3.3-1.x86_64.rpm and gromacs-mpi-3.3.3-1.x86_64.rpm. My Linux is Fedora 8 x64. If I run mdrun -v -deffnm run or mpiexec -np 2 mdrun_mpi -np 2 -v -deffnm run or mdrun_mpi -np 2 -v -deffnm run The time to conclude dynamics is the same. I think that the the 2 last command will be more fast. But if I look to system monitor and analyze process I see the in the second case the 2 processor is 100%. If I see in the thirty case the process is alternate in the 2 processor, one is 100% other is near 10%, after one is near 10% and other is 100%. If I run grompp -f run.mdp -p topol.top -c run -o run -np 2 mpiexec -np 2 mdrun_mpi -np 2 -v -deffnm run I have this error ------------------------------------------------------- Program mdrun_mpi, VERSION 3.3.3 Source code file: init.c, line: 69 Fatal error: run input file run.tpr was made for 2 nodes, while mdrun_mpi expected it to be for 1 nodes. ------------------------------------------------------- And I see that the gromacs is run in one node, but I put in command to run in two nodes [EMAIL PROTECTED] smase]$ mpiexec -np 2 mdrun_mpi -np 2 -v -deffnm run NNODES=1, MYRANK=0, HOSTNAME=xxx.unesp.br :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) VERSION 3.3.3 (-: I do a test in other machine pentium 4 basic, with one processor and not hyper threading, and the dynamics have same speed that my Xeon. It is very strange for me!!! I like very much if somebody can help me. Thanks for all, and excuse my English again! Mario Jose IBILCE - UNESP www.crystallography.ibilce.unesp.br Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php