Anupam Nath Jha wrote:
Dear all
I am trying to scale gromacs on BG/L and I am able to run mdrun on BG/L for
32processors. but when i try to run for 64 or 96, by making the *.tpr file:
grompp -np 96 -f run.mdp -p topol.top -c pr.gro -o run.tpr
and submitting in BG/L:
using the following submission file---
# @ job_type = bluegene
# @ executable = /usr/bin/mpirun
# @ arguments = -exe /home/phd/04/mbuanjha/soft/gmx332/bin/mdrun_mpi -cwd
/gpfs/bglscratch/mbuanjha/test/ -args "-s rum.tpr -o run.trr -c run.gro -e
run.edr -g test.log -v"
you made a typo.
# @ error = test.$(host).$(cluster).$(process).err
# @ output = test.$(host).$(cluster).$(process).out
# @ environment = COPY_ALL
# @ wall_clock_limit=100:00:00
# @ notification = always
# @ bg_size = 96
# @ class = high
# @ queue
i am getting this error--
Getting Loaded...
Reading file rum.tpr, VERSION 3.3.2 (single precision)
-------------------------------------------------------
Program mdrun_mpi, VERSION 3.3.2
Source code file: init.c, line: 69
Fatal error:
run input file rum.tpr was made for 96 nodes,
while mdrun_mpi expected it to be for 128 nodes.
-------------------------------------------------------
"Carry Me Away" (Motors)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 128
--------------------------------------------------
is it something like that gromacs can't run for 64 or 96nodes or what.
not only this when i try to submit for 128nodes, it's giving some memory
corruption error, like:
*** *** glibc detected *** malloc(): memory corruption***
can you help me out?
with best regards
anupam
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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