[gmx-users] Improving Scaling w/ mpi

[Anton Feenstra]

Hi All,


I've asked similar questions before, but the issues are not yet
solved over here.

My problem is I get absolutely *no* scaling on single CPU nodes in 
our Linux/Athlon/eth100 cluster (17 ps/h on 2 nodes vs 16 on 1). 
We have mpich and lammpi installed, but I am currently using mpich 
configured with --with-comm=shared --with-pkt_size=524288 (which 
presumably is similar to the lammpi magic message size option).
My first benchmarks were without these options, and it doesn't
make a difference.

I want to try lam, but failed to get the Gromacs configure to work
either with lam's mpicc, or with explicitly set CFLAGS and LDFLAGS.

# ../../configure --prefix=/home/sgifar/feenstra/progs --enable-mpi --program-suffix=_lam MPICC=/usr/local/lam-6.5.6/bin/mpicc
[...snip...]
checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with
/usr/local/lam-6.5.6/bin/mpicc

# ../../configure --prefix=/home/sgifar/feenstra/progs --enable-mpi --program-suffix=_ch
CPPFLAGS=-I/usr/local/lam-6.5.6/include LDFLAGS=-L/usr/local/lam-6.5.6/lib
[...snip...]
checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with cc


Any suggestions, anyone? Should I keep on trying to improve on the
mpich performance, or forget about it and use lam in stead?


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "Three Little Fonzies" (Pulp Fiction)                     |
|________|___________________________________________________________|