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1.1 Run NAMD

MPI version was compiled with TCL or FFTW, since Charm++ MPI network layer performs better than the verbs layer, and Intel Omni-Path networks are incompatible with the pre-built ibverbs NAMD binaries.

NAMD MPI binaries may be launched with mpiexec:

  • setenv MPI_DSM_VERBOSE 1
  • setenv MPI_MEMMAP_OFF true
  • mpiexec_mpt -np $npr namd2 conf

1.2 Compile NAMD

The following is the building process.

1 Install NAMD2.13 at HPE SGI 8600 using intel Omni-Path networks