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Merge pull request #481 from niaid/fix/update_brt_version
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tag brt runs, update imod version
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philipmac authored Aug 9, 2024
2 parents a1d8e7a + 4d41135 commit abbc3f6
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Showing 4 changed files with 13 additions and 9 deletions.
11 changes: 6 additions & 5 deletions em_workflows/config.py
Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@ def SLURM_exec(asynchronous: bool = False, **cluster_kwargs):
asynchronous=asynchronous,
**cluster_kwargs,
)
cluster.scale(1)
cluster.scale(5)
# cluster.adapt(minimum=1, maximum=6)
# to get logger, we must be within an active flow/task run
print("Dask cluster started")
Expand All @@ -73,14 +73,15 @@ def SLURM_exec(asynchronous: bool = False, **cluster_kwargs):

class Config:
# location in RML HPC
imod_root = "/gs1/apps/user/spack-0.16.0/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.1/imod-4.12.47-2fcggru32s3f4jl3ar5m2rztuqz5h2or"
bioformats2raw = os.environ.get(
"BIOFORMATS2RAW_LOC",
"/gs1/apps/user/spack-0.16.0/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.1/bioformats2raw-0.7.0-7kt7dff7f7fxmdjdk57u6xjuzmsxqodn/bin/bioformats2raw",
)
brt_binary = os.environ.get("BRT_LOC", "/opt/rml/imod/bin/batchruntomo")
header_loc = os.environ.get("HEADER_LOC", "/opt/rml/imod/bin/header")
mrc2tif_loc = os.environ.get("MRC2TIF_LOC", "/opt/rml/imod/bin/mrc2tif")
newstack_loc = os.environ.get("NEWSTACK_LOC", "/opt/rml/imod/bin/newstack")
brt_binary = os.environ.get("BRT_LOC", f"{imod_root}/bin/batchruntomo")
header_loc = os.environ.get("HEADER_LOC", f"{imod_root}/bin/header")
mrc2tif_loc = os.environ.get("MRC2TIF_LOC", f"{imod_root}/bin/mrc2tif")
newstack_loc = os.environ.get("NEWSTACK_LOC", f"{imod_root}/bin/newstack")

HIGH_SLURM_EXECUTOR = DaskTaskRunner(
cluster_class=SLURM_exec,
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7 changes: 4 additions & 3 deletions em_workflows/sem_tomo/config.py
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ class SEMConfig(Config):
convert_loc = os.environ.get(
"CONVERT_LOC", "/usr/bin/convert"
) # requires imagemagick
tif2mrc_loc = os.environ.get("TIF2MRC_LOC", "/opt/rml/imod/bin/tif2mrc")
xfalign_loc = os.environ.get("XFALIGN_LOC", "/opt/rml/imod/bin/xfalign")
xftoxg_loc = os.environ.get("XFTOXG_LOC", "/opt/rml/imod/bin/xftoxg")
imod_root = "/gs1/apps/user/spack-0.16.0/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.1/imod-4.12.47-2fcggru32s3f4jl3ar5m2rztuqz5h2or"
tif2mrc_loc = os.environ.get("TIF2MRC_LOC", f"{imod_root}/bin/tif2mrc")
xfalign_loc = os.environ.get("XFALIGN_LOC", f"{imod_root}/bin/xfalign")
xftoxg_loc = os.environ.get("XFTOXG_LOC", f"{imod_root}/bin/xftoxg")
2 changes: 2 additions & 0 deletions em_workflows/utils/utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -322,6 +322,8 @@ def copy_template(working_dir: Path, template_name: str) -> Path:

@task(
name="Batchruntomo conversion",
tags=["brt"],
# timeout_seconds=600,
on_failure=[collect_exception_task_hook],
)
def run_brt(
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2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@

setup(
name="em_workflows",
version="2.1.1",
version="2.1.2",
author="Philip MacMenamin, Bradley Lowekamp, Anish Shrestha",
author_email="[email protected]",
description="Workflows for Microscopy related file processing.",
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