sf-mx/crystfel_tools
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change output file locations

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Beale John Henry
2023-07-19 14:57:31 +02:00
parent fad0f3b518
commit ee0178864e
1 changed files with 4 additions and 6 deletions
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10
clen_tools/crystfel_chunk.py
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@@ -60,8 +60,7 @@ def write_crystfel_run( proc_dir, name, chunk, chunk_lst_file, geom_file, cell_f
run_sh.write( " --pdb={0} \\\n".format( cell_file ) ) run_sh.write( " --pdb={0} \\\n".format( cell_file ) )
run_sh.write( " --indexing=xgandalf-latt-cell --peaks=peakfinder8 \\\n" ) run_sh.write( " --indexing=xgandalf-latt-cell --peaks=peakfinder8 \\\n" )
run_sh.write( " --threshold=15 --min-snr=10 --int-radius=3,5,9 \\\n" ) run_sh.write( " --threshold=15 --min-snr=10 --int-radius=3,5,9 \\\n" )
run_sh.write( " -j 36 --no-multi --no-retry --max-res=3000 --min-pix-count=2 --min-res=85\\\n" ) run_sh.write( " -j 32 --no-multi --no-retry --max-res=3000 --min-pix-count=2 --min-res=85\\\n" )
run_sh.write( " --temp-dir={0}".format( proc_dir ) )
run_sh.close() run_sh.close()
# make file executable # make file executable
@@ -78,10 +77,10 @@ def make_process_dir( proc_dir ):
if e.errno != errno.EEXIST: if e.errno != errno.EEXIST:
raise raise
def submit_job( job_file, slurm_output_dir ): def submit_job( job_file ):
# submit the job # submit the job
submit_cmd = ["sbatch", job_file] submit_cmd = ["sbatch", "--cpus-per-task=32", "--" ,job_file]
job_output = subprocess.check_output(submit_cmd) job_output = subprocess.check_output(submit_cmd)
# scrub job id from - example Submitted batch job 742403 # scrub job id from - example Submitted batch job 742403
@@ -143,10 +142,9 @@ def run_splits( cwd, name, lst, chunk_size, geom_file, cell_file, progress ):
# submitted job set # submitted job set
submitted_job_ids = set() submitted_job_ids = set()
slurm_output_dir = "{0}/{1}".format( cwd, name, chunk )
# submit jobs # submit jobs
for job_file in job_list: for job_file in job_list:
job_id = submit_job( job_file, slurm_output_dir ) job_id = submit_job( job_file )
submitted_job_ids.add( job_id ) submitted_job_ids.add( job_id )
print(f"Job submitted: { job_id }") print(f"Job submitted: { job_id }")