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+ | \\ | ||
+ | **[[cluster: | ||
+ | |||
+ | |||
+ | |||
+ | ===== NAMD ===== | ||
+ | |||
+ | Most of your question can be answered on the web site [[http:// | ||
+ | |||
+ | 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 '' | ||
+ | |||
+ | Here is a sample job. | ||
+ | |||
+ | < | ||
+ | |||
+ | #!/bin/bash | ||
+ | |||
+ | #BSUB -q imw | ||
+ | #BSUB -R " | ||
+ | #BSUB -J namd | ||
+ | #BSUB -o out | ||
+ | #BSUB -e err | ||
+ | |||
+ | #BSUB -n 4 | ||
+ | |||
+ | MPIRUN="/ | ||
+ | |||
+ | PATH=/ | ||
+ | export PATH | ||
+ | |||
+ | # scratch dirs | ||
+ | MYSANSCRATCH=/ | ||
+ | MYLOCALSCRATCH=/ | ||
+ | #cd $MYSANSCRATCH | ||
+ | |||
+ | rm -rf err out | ||
+ | |||
+ | export LD_LIBRARY_PATH=/ | ||
+ | $MPIRUN / | ||
+ | |||
+ | </ | ||
+ | |||
+ | 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/ | ||
+ | |||
+ | < | ||
+ | |||
+ | ./configure --prefix=/ | ||
+ | --enable-orterun-prefix-by-default \ | ||
+ | --with-gm=/ | ||
+ | --with-openib=/ | ||
+ | --with-tm=/ | ||
+ | |||
+ | make -j8 | ||
+ | make install | ||
+ | |||
+ | </ | ||
+ | |||
+ | now i can select what communication to use by default through / | ||
+ | |||
+ | 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: | ||