Dear GRMxers: We need some help in running our Gromacs 3.2.1 parallel environment in 5 nodes of SunFires V20v (dual-core Opteron 2.2, 4 GB DDR2 RAM), gigabit eth, mpich-1.2.7, using Sun Grid Engine 6.0. In a 2 processors job (single node), the results are O.K. but in a 4, 6 or 8 processors (2, 3 or 4 nodes) in the machine log files we have:
In “ -np 4” the error was : p4_5991: p4_error: Timeout in establishing connection to remote process: 0 p0_8456: p4_error: net_recv read: probable EOF on socket: 1 p5_5996: p4_error: Timeout in establishing connection to remote process: 0 p0_8456: (333.761719) net_send: could not write to fd=4, errno = 32 In “ –np 8” the error was: p0_16398: p4_error: interrupt SIGSEGV: 11 In all the cases, we obtain a “Killed by signal 2” at the end of the gromacs log, and process stopped. Grompp was executed with the -np option, and our final script was: #$ -v MPIRUN #$ -v MPICH_PROCESS_GROUP MPIRUN -np $NSLOTS -machinefile $TMPDIR/machinefile /nfs/gromacs-3.2. 1_paralelo/x86_64-unknown-linux-gnu/bin/mdrun -np 6 -s ABint/ABint_md.tpr -o ABint/ABint_md.trr -c ABint/ABint_md.gro -e ABint/ABintener.edr -g ABint/ ABintmd.log -nice 0 Any help will be extremely appreciated: Jorge H.F. -- == Dr. JORGE HERNANDEZ FERNANDEZ == ====== Center of Applied Toxinology ====== ===== CAT-CEPID - Instituto Butantan ===== ====== Ave Vital Brasil, 1500 S.P. ====== Tel: 055 11 3726 7222 r.2042 Fax: 055 11 3721 6605 ==== S.B.I.- EMBRAPA - BioInformatica ==== C.p. 6041 Cidade Universitária "Zeferino Vaz" ===== Barão Geraldo Campinas S.P. ======== =========== 13080-970 ==================== Tel: 055 19-37895828 Cell: 055 11-97126104 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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