[gmx-users] mdrun : fatal error with 8 CPUs
sophie.vilarem@laposte.net
sophie.vilarem at laposte.net
Thu Oct 30 11:35:01 CET 2003
Hi,
I've got a fatal error (Fatal error: ci = -2147483648 should
be in 0 .. 1727 [FILE nsgrid.c, LINE 210]) when I try to run
Gromacs on 8 CPUs, on a xeon cluster (bi-processors,
MPICH-1.2.5). It ran without any problem on 1, 2 and 4 CPUs.
Can anybody help me please?
Thanks a lot!
Sophie Vilarem
Here are the command line and the results :
grompp -np 8 -shuffle
mpirun -np 8 -machinefile hostfile
/works/work6/theogone/Gromacs/usr/local/Gromacs/i686-pc-linux-gnu/bin/mdrun
-g pc2_8
Parts of the results :
etc....
creating statusfile for 8 nodes...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 3 of the 3 non-bonded parameter combinations
Excluding 3 bonded neighbours for PE6000 1
Moltype PE6000 #atoms
CPU 0 1 12000
CPU 1 0 0
CPU 2 0 0
CPU 3 0 0
CPU 4 0 0
CPU 5 0 0
CPU 6 0 0
CPU 7 0 0
Made a shuffling table with 1 entries [molecules]
processing coordinates...
Shuffling coordinates...
Entering shuffle_xv
double-checking input for internal consistency...
Cleaning up constraints and constant bonded interactions with
dummy particles
renumbering atomtypes...
converting bonded parameters...
# BONDS: 17997
# ANGLES: 23992
# RBDIHS: 29985
# DUMMY3FD: 29990
# DUMMY3FAD: 10
Setting particle type to Dummy for dummy atoms
initialising group options...
processing index file...
Analysing residue names:
Opening library file
/works/work6/theogone/Gromacs/usr/local/Gromacs/share/gromacs/top/aminoacids.dat
There are: 1 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
Making dummy/rest group for Acceleration containing 12000 elements
Making dummy/rest group for Freeze containing 12000 elements
Making dummy/rest group for Energy Mon. containing 12000 elements
Making dummy/rest group for VCM containing 12000 elements
Number of degrees of freedom in T-Coupling group System is
17997.00
Making dummy/rest group for User1 containing 12000 elements
Making dummy/rest group for User2 containing 12000 elements
Making dummy/rest group for XTC containing 12000 elements
Making dummy/rest group for Or. Res. Fit containing 12000 elements
T-Coupling has 1 element(s): System
Energy Mon. has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
Checking consistency between energy and charge groups...
Back Off! I just backed up deshuf.ndx to ./#deshuf.ndx.1#
splitting topology...
There are 6000 charge group borders and 12000 shake borders
There are 6000 total borders
Division over nodes in atoms:
1500 1500 1500 1500 1500 1500 1500 1500
writing run input file...
Back Off! I just backed up topol.tpr to ./#topol.tpr.1#
gcq#106: "Step Aside, Butch" (Pulp Fiction)
NNODES=8, MYRANK=1, HOSTNAME=lx05
NODEID=1 argc=3
NNODES=8, MYRANK=0, HOSTNAME=lx05
NODEID=0 argc=3
:-) G R O M A C S (-:
NNODES=8, MYRANK=4, HOSTNAME=lx07
NODEID=4 argc=3
NNODES=8, MYRANK=6, HOSTNAME=lx08
NODEID=6 argc=3
NNODES=8, MYRANK=3, HOSTNAME=lx06
NODEID=3 argc=3
NNODES=8, MYRANK=7, HOSTNAME=lx08
NODEID=7 argc=3
NNODES=8, MYRANK=5, HOSTNAME=lx07
NODEID=5 argc=3
NNODES=8, MYRANK=2, HOSTNAME=lx06
NODEID=2 argc=3
etc...
Back Off! I just backed up pc2_86.log to ./#pc2_86.log.1#
Back Off! I just backed up pc2_81.log to ./#pc2_81.log.1#
Back Off! I just backed up pc2_82.log to ./#pc2_82.log.1#
Back Off! I just backed up pc2_84.log to ./#pc2_84.log.1#
Back Off! I just backed up pc2_85.log to ./#pc2_85.log.1#
Back Off! I just backed up pc2_83.log to ./#pc2_83.log.1#
Back Off! I just backed up pc2_87.log to ./#pc2_87.log.1#
Back Off! I just backed up pc2_80.log to ./#pc2_80.log.1#
Reading file topol.tpr, VERSION 3.1.4 (single precision)
Reading file topol.tpr, VERSION 3.1.4 (single precision)
Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'pe'
5000 steps, 5.0 ps.
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Fatal error: ci = -2147483648 should be in 0 .. 1727 [FILE
nsgrid.c, LINE 210]
Fatal error: ci = -2147483648 should be in 0 .. 1727 [FILE
nsgrid.c, LINE 210]
Fatal error: ci = -2147483648 should be in 0 .. 1727 [FILE
nsgrid.c, LINE 210]
Error on node 0, will try to stop all the nodes
[0] MPI Abort by user Aborting program !
[0] Aborting program!
Fatal error: ci = -2147483648 should be in 0 .. 1727 [FILE
nsgrid.c, LINE 210]
Fatal error: ci = -2147483648 should be in 0 .. 1727 [FILE
nsgrid.c, LINE 210]
Fatal error: ci = -2147483648 should be in 0 .. 1727 [FILE
nsgrid.c, LINE 210]
Error on node 3, will try to stop all the nodes
[3] MPI Abort by user Aborting program !
[3] Aborting program!
Error on node 2, will try to stop all the nodes
[2] MPI Abort by user Aborting program !
[2] Aborting program!
Fatal error: ci = -2147483648 should be in 0 .. 1727 [FILE
nsgrid.c, LINE 210]
Error on node 5, will try to stop all the nodes
[5] MPI Abort by user Aborting program !
[5] Aborting program!
Fatal error: ci = -2147483648 should be in 0 .. 1727 [FILE
nsgrid.c, LINE 210]
Error on node 7, will try to stop all the nodes
[7] MPI Abort by user Aborting program !
[7] Aborting program!
Error on node 6, will try to stop all the nodes
[6] MPI Abort by user Aborting program !
[6] Aborting program!
Error on node 1, will try to stop all the nodes
[1] MPI Abort by user Aborting program !
[1] Aborting program!
Error on node 4, will try to stop all the nodes
[4] MPI Abort by user Aborting program !
[4] Aborting program!
Fin du run
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