Open vsoch opened 11 months ago
@johanneskoester I am very close to getting this working! The step runs successfully:
rule calc_pi: input: "pi_MPI", output: "pi.calc", log: "logs/calc_pi.log", resources: mem_mb=0, tasks=1, mpi="mpiexec", shell: "chmod +x {input};" "{resources.mpi} -hostfile $BATCH_HOSTS_FILE -n {resources.tasks} {input} 10 > {output} 2> {log};"
And I'm copying the logic from https://github.com/snakemake/snakemake/blob/6aabb5db16634c077ba808dbd000a3ed67d6a3c0/tests/test_slurm_mpi/Snakefile#L48-L49 but adding the hostfile. However when I download pi.calc, the output is empty. Are we sure this is the correct usage? When this last step is running I can open a PR to add this full example for intel mpi on Google batch!
@johanneskoester I am very close to getting this working! The step runs successfully:
And I'm copying the logic from https://github.com/snakemake/snakemake/blob/6aabb5db16634c077ba808dbd000a3ed67d6a3c0/tests/test_slurm_mpi/Snakefile#L48-L49 but adding the hostfile. However when I download pi.calc, the output is empty. Are we sure this is the correct usage? When this last step is running I can open a PR to add this full example for intel mpi on Google batch!