[gmx-users] Haphazard Results with LAM-MPI
spoel at xray.bmc.uu.se
Sun Apr 20 11:20:01 CEST 2003
On Sun, 2003-04-20 at 07:08, Venkat Ramanan K wrote:
> Hi anton,
> We have tried the benchmark files from the gromacs website and we
> could easily see the scaleup of the cluster but the time is
> still not optimized compared with the benchmark. We run GROMACS
> 3.1 on RedHat linux 8, Kernel 2.4.20. We also have
> MOSIX installed. This kernel was compiled by us to implement MOSIX
> on the cluster. The following are the specifications of
> the system we use...
> System harware was that of default IBM Netvista.
> 1. Intel Pentium III (1GHZ)
> 2. 100Mbits ethernet card (Intel)
> 3. 256 Mb RAM on the server node and 128 Mb RAM on all other
> Linux : Redhat Linux 8
> Kernel : 2.4.20 (downloaded and compiled from kernel.org)
> LAM: lam-usysv-6.5.9 with "rsh" RPI.
> We use the folowing commands....
> 1.grompp -v .........-np 16
> 2.mpirun N -lamd -nger -nsigs mdrun -v -s ........
> I always generate an error if i use -c2c option with mpirun. I am
> not able to figure out the problem. I will send u the .config file
> my next mail when i get back to my dept.
Please recompile LAM with the recommended options for tcpshortblocksize
(512k). Without the -c2c option it will never be fast I'm afraid.
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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