[gmx-users] Paralell problems...

[Jorge Hernandez Fernandez]

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



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