snakemake/profiles/slurm-csd3/submit.py [12:59]:
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cluster_config_file = os.path.join(os.path.dirname(__file__), "config.cluster.yaml")
cluster_config = yaml.load(open(cluster_config_file), Loader=yaml.FullLoader)

jobscript = sys.argv[-1]
job_properties = read_job_properties(jobscript)

options = []

if job_properties["type"] == "single":
    name = job_properties["rule"]
elif job_properties["type"] == "group":
    name = job_properties["groupid"]
else:
    raise NotImplementedError(
        f"Don't know what to do with job_properties['type']=={job_properties['type']}"
    )

options += ["--job-name", name]

partition = cluster_config["cpu-partition"]
account = cluster_config["cpu-account"]

if "resources" in job_properties:
    resources = job_properties["resources"]

    if "gpu" in resources and int(resources["gpu"]) >= 1:
        num_gpu = str(resources["gpu"])
        options += [f"--gres=gpu:{num_gpu}"]

        account = cluster_config["gpu-account"]

        if num_gpu == "1":
            partition = cluster_config["single-gpu-partition"]
        else:
            partition = cluster_config["multi-gpu-partition"]

        cuda_dir = os.getenv("CUDA_DIR")
        if cuda_dir:
            options += ["--export", f'ALL,SINGULARITY_BIND="{cuda_dir}"']

    # we don't need explicit memory limiting for now
    # if 'mem_mb' in resources:
    #     memory = str(resources['mem_mb'])
    #     options += [f'--mem={memory}']

options += ["-p", partition]
options += ["-A", account]
options += ["--nodes=1"]
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snakemake/profiles/slurm-moz/submit.py [12:59]:
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cluster_config_file = os.path.join(os.path.dirname(__file__), "config.cluster.yaml")
cluster_config = yaml.load(open(cluster_config_file), Loader=yaml.FullLoader)

jobscript = sys.argv[-1]
job_properties = read_job_properties(jobscript)

options = []

if job_properties["type"] == "single":
    name = job_properties["rule"]
elif job_properties["type"] == "group":
    name = job_properties["groupid"]
else:
    raise NotImplementedError(
        f"Don't know what to do with job_properties['type']=={job_properties['type']}"
    )

options += ["--job-name", name]

partition = cluster_config["cpu-partition"]
account = cluster_config["cpu-account"]

if "resources" in job_properties:
    resources = job_properties["resources"]

    if "gpu" in resources and int(resources["gpu"]) >= 1:
        num_gpu = str(resources["gpu"])
        options += [f"--gres=gpu:{num_gpu}"]

        account = cluster_config["gpu-account"]

        if num_gpu == "1":
            partition = cluster_config["single-gpu-partition"]
        else:
            partition = cluster_config["multi-gpu-partition"]

    # we don't need explicit memory limiting for now
    # if 'mem_mb' in resources:
    #     memory = str(resources['mem_mb'])
    #     options += [f'--mem={memory}']

cuda_dir = os.getenv("CUDA_DIR")
if cuda_dir:
    options += ["--export", f'ALL,SINGULARITY_BIND="{cuda_dir}"']

options += ["-p", partition]
options += ["-A", account]
options += ["--nodes=1"]
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