SLURM header templates#

BATTER renders SLURM scripts by combining a user-editable header with a packaged body. On first use of the CLI, headers are copied into ~/.batter (or run.slurm_header_dir if set). You can also seed them explicitly:

batter seed-headers           # seeds into ~/.batter
batter seed-headers --dest /path/to/dir
batter seed-headers --force   # overwrite existing headers

Once seeded, edit the headers to match your cluster defaults (queue/partition, env exports, executable paths). Do not edit the body files; they are managed by the package. The packaged Rondror defaults source Amber with source /home/groups/rondror/software/amber26/setup_amber.sh > /dev/null 2>&1.

Header files#

  • SLURMM-Am.header: equilibration/FE runs

  • SLURMM-BATCH-remd.header: REMD runs

  • job_manager.header: manager script used by batter run --slurm-submit

Common environment overrides#

Headers include commented examples for overriding executables:

  • PMEMD_EXEC (default: pmemd.cuda)

  • PMEMD_MPI_EXEC (default: pmemd.cuda.MPI; used by REMD templates)

  • PMEMD_DPFP_EXEC (default: pmemd.cuda_DPFP)

  • PMEMD_CPU_EXEC (default: pmemd)

  • PMEMD_CPU_MPI_EXEC (default: pmemd.MPI)

  • SANDER_EXEC (default: sander)

  • MPI_EXEC (default: mpirun)

Edit exports in the header files to point to site-specific binaries/modules. The packaged bodies will be appended during rendering; only the headers are meant for customization.