From ee0178864eeef137da63a3c13406516f9dde72a7 Mon Sep 17 00:00:00 2001 From: Beale John Henry Date: Wed, 19 Jul 2023 14:57:31 +0200 Subject: [PATCH] change output file locations --- clen_tools/crystfel_chunk.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/clen_tools/crystfel_chunk.py b/clen_tools/crystfel_chunk.py index cfcac11..58552f9 100644 --- a/clen_tools/crystfel_chunk.py +++ b/clen_tools/crystfel_chunk.py @@ -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( " --indexing=xgandalf-latt-cell --peaks=peakfinder8 \\\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( " --temp-dir={0}".format( proc_dir ) ) + run_sh.write( " -j 32 --no-multi --no-retry --max-res=3000 --min-pix-count=2 --min-res=85\\\n" ) run_sh.close() # make file executable @@ -78,10 +77,10 @@ def make_process_dir( proc_dir ): if e.errno != errno.EEXIST: raise -def submit_job( job_file, slurm_output_dir ): +def submit_job( job_file ): # submit the job - submit_cmd = ["sbatch", job_file] + submit_cmd = ["sbatch", "--cpus-per-task=32", "--" ,job_file] job_output = subprocess.check_output(submit_cmd) # 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_ids = set() - slurm_output_dir = "{0}/{1}".format( cwd, name, chunk ) # submit jobs 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 ) print(f"Job submitted: { job_id }")