hi, On Thursday 01 June 2006 21:43, Jorge Hernandez Fernandez wrote: > 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.
Update to gromacs 3.3.1, with normal system sizes gromacs run well up to 4 cpus here (dual boards). Else update your interconnection type. > 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 Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list [email protected] 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
