snakemake / snakemake-executor-plugin-googlebatch

Snakemake executor plugin for Google Batch
MIT License
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pi.calc output example is empty #18

Open vsoch opened 11 months ago

vsoch commented 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!