[gmx-users] scalability of gromacs-3.3

[David van der Spoel]

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