diff --git a/em_workflows/config.py b/em_workflows/config.py index cca6bbd7..73d0814b 100644 --- a/em_workflows/config.py +++ b/em_workflows/config.py @@ -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") @@ -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, diff --git a/em_workflows/sem_tomo/config.py b/em_workflows/sem_tomo/config.py index 0bb44e9b..8319f442 100644 --- a/em_workflows/sem_tomo/config.py +++ b/em_workflows/sem_tomo/config.py @@ -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") diff --git a/em_workflows/utils/utils.py b/em_workflows/utils/utils.py index 4df1cb6b..cf98bff8 100644 --- a/em_workflows/utils/utils.py +++ b/em_workflows/utils/utils.py @@ -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( diff --git a/setup.py b/setup.py index 154eb16e..ea891913 100644 --- a/setup.py +++ b/setup.py @@ -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="bioinformatics@niaid.nih.gov", description="Workflows for Microscopy related file processing.",