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cluster:69 [2008/10/22 10:54] (current)
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 +\\
 +**[[cluster:​0|Back]]**
 +
 +
 +
 +===== NAMD =====
 +
 +Most of your question can be answered on the web site [[http://​www.ks.uiuc.edu/​Research/​namd/​| NAMD]] or subscribe to their community supported list ''​namd-l''​.
 +
 +The rest of this page are simple instruction to get you going.
 +
 +===== Jobs =====
 +
 +The NAMD binary was compiled against the Topspin libraries, hence can only run on the ''​imw''​ queue (Infiniband switch). ​ You need to be a member of the "​inf_nodes"​ unix group to successfully run the bianry.
 +
 +Here is a sample job.
 +
 +<​code>​
 +
 +#!/bin/bash
 +
 +#BSUB -q imw
 +#BSUB -R "​span[ptile=1]"​
 +#BSUB -J namd
 +#BSUB -o out
 +#BSUB -e err
 +
 +#BSUB -n 4
 +
 +MPIRUN="/​share/​apps/​bin/​lsf.topspin.wrapper"​
 +
 +PATH=/​usr/​local/​topspin/​mpi/​mpich/​bin:​$PATH
 +export PATH
 +
 +# scratch dirs
 +MYSANSCRATCH=/​sanscratch/​$LSB_JOBID
 +MYLOCALSCRATCH=/​localscratch/​$LSB_JOBID
 +#cd $MYSANSCRATCH
 +
 +rm -rf err out 
 +
 +export LD_LIBRARY_PATH=/​usr/​local/​topspin/​mpi/​mpich/​lib64
 +$MPIRUN /​share/​apps/​NAMD/​NAMD_2.6_Source/​Linux-amd64-MPI/​namd2 /​home/​hmeij/​1g6r/​named-pgm/​alanin
 +
 +</​code>​
 +
 +You may browse that directory to view the type of output it generates.
 +
 +===== OpenMPI =====
 +
 +Axel's commentary on how to get NAMD to run with OpenMPI.
 +
 +the way i'm compiling openmpi is the following (with support for infiniband, myrinet, and job launch directly through OpenPBS without host/​nodefiles):​
 +
 +<​code>​
 +
 +./configure --prefix=/​cmm/​pkg/​openmpi-1.2.7 \ 
 +            --enable-orterun-prefix-by-default \
 +            --with-gm=/​opt/​gm-2.1.29 \
 +            --with-openib=/​opt/​ofed-1.3.1 \
 +            --with-tm=/​opt
 +
 +make -j8
 +make install
 +
 +</​code>​
 +
 +now i can select what communication to use by default through /​cmm/​pkg/​openmpi/​etc/​openmpi-mca-params.conf , which has either **btl = openib,​self** ​ or **btl = gm,​self** ​
 +
 +if i run on the frontend, i override that with **-mca btl tcp,self**
 +
 +the very same charm++ megatest binary works fine on all four clusters and the front end without any other modifications.
 +
 +one of the nicest things about a (normal) openmpi installation is that the resulting executables only depend on the openmpi libraries and _not_ on any other lowlevel communication libs, so one can actually use the same binary on a different installation of openmpi with different lowlevel protocols, provided it is of the same openmpi version and uses the same gcc/libc and so on.
 +
 +\\
 +**[[cluster:​0|Back]]**
  
cluster/69.txt ยท Last modified: 2008/10/22 10:54 (external edit)