[gmx-users] scalability of gromacs-3.3
David van der Spoel
spoel at xray.bmc.uu.se
Wed Dec 26 08:54:14 CET 2007
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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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