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@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!
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