Jason O'Young wrote:
I have been having similar problems to this. I have posted to the
mailing list with the title "mdrun_mpi stops at random" but no one has
seen my reply :(.
it's been quite hectic on the list lately...
as always if you have a reproducible problem of a crash after a short
time, you are welcome to submit a bugzilla. But be prepared to hand over
lots of information.
Unfortunately there are many factors besides GROMACS that can make
programs crash, e.g. overheating, broken memory chips, broken FFT
libraries, shitty compilers.
It's always a good test to compile with gcc in case you tried something
else first.
It seems to be almost at random which of the processes falls...
Jason
I am running a system of 185K atoms. The structure is energy minimized
and the
dynamics run appears to be going smoothly until it just hangs. The job
still
exists on the first node, but none of the 4 nodes are doing any work
and I don't
get any error messages.
The trajectory looks good and no step.***.pdb files were created.
My only clue is that an energy file was created but was empty -- and
should have
some data based on nstenergy=10000
The last portion of output to my mdrun_mpi -g log file was:
Step Time Lambda
26300 52.60000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. Improper
Dih.
8.77749e+04 1.66791e+05 6.40224e+04 7.13528e+04
6.57086e+03
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul.
recip.
1.01403e+05 1.73522e+05 -3.08556e+03 -2.51895e+06
-1.65998e+06
Position Rest. Potential Kinetic En. Total Energy
Temperature
5.65104e+03 -3.50492e+06 5.44080e+05 -2.96084e+06
2.99289e+02
Pressure (bar)
3.40970e+01
My commands were:
GROMPP:
${ED}/grompp -np 4 -f grompp_md.mdp -n ${MOL}.ndx -c ${MOL}_m.gro -p
${MOL}.top
-o ${MOL}_mm.tpr > output.mm_grompp
MDRUN_MPI:mdrun_mpi stops at random
${ED}/mdrun_mpi -np 4 -nice 4 -s ${MOL}_mm.tpr -o ${MOL}_mm.trr -c
${MOL}_mm.gro
-g output.mm_mdrun -v -deffnm run1g 2> output.mm_mdrun_e
LAM SCRIPT:
#!/bin/sh
PATH=.:/work/lam/bin:$PATH
LAMRSH="ssh -x"
export LAMRSH PATH
cd ${MYDIR}
lamboot -v lamhosts
mpirun N ${MYDIR}/run.sh
lamhalt
And my mdp file was:
title = seriousMD
cpp = /usr/bin/cpp
define = -DPOSRES_LIPID -DPOSRES_PAGP -DPOSRES_LDA
-DPOSRES_XSOL
integrator = md
nsteps = 50000
tinit = 0
dt = 0.002
comm_mode = angular
nstcomm = 1
comm_grps = System
nstxout = 10000
nstvout = 10000
nstfout = 10000
nstlog = 100
nstlist = 10
nstenergy = 10000
nstxtcout = 250
ns_type = grid
pbc = xyz
coulombtype = PME
fourierspacing = 0.15
pme_order = 4
vdwtype = switch
rvdw_switch = 0.9
rvdw = 1.0
rlist = 1.1
DispCorr = no
Pcoupl = Berendsen
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.
tcoupl = nose-hoover
tc_grps = Protein_LDA XSOL_SOL_NA+ POPE
tau_t = 0.05 0.05 0.05
ref_t = 300. 300. 300.
annealing = no no no
gen_vel = yes
gen_temp = 300. 300. 300.
gen_seed = 9896
constraints = hbonds
constraint_algorithm= shake
shake_tol = 0.0001
Thanks.
Chris.
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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