Hi, This is a technical question for cluster experts. I tried to run phenix.composite-omit-map which can divide the calculations into separate jobs, on a very large cluster controlled by the PBS system. I used this command of which the first 2 lines specify to divide the work up into 16 processes, and each process will use 1 of the CPU's in the cluster. phenix.composite_omit_map nproc=16 background=False technology=pbs \ qsub_command="qsub -V -l procs=1,walltime=00:30:00,mem=2000mb,qos=flux -j oe -M [email protected] -q flux -m abe " \ omit_type=anneal map_type=2mFo-Dfc output.file_name=composite_omit_map9.mtz \ reflections3_5percent.mtz Refine_122.pdb This is the end of the log file before it aborted: ----------Calculating individual omit maps---------- |-----------------------------------------------------------------------------| | target_work(ml) = 4.65539 r_work = 0.1750 r_free = 0.2066 | |-----------------------------------------------------------------------------| And this is the error log: Traceback (most recent call last): File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 238, in <module> run(sys.argv[1:]) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 166, in run out=out) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/phenix/phenix/automation/composite_omit_map.py", line 395, in __init__ preserve_exception_message=True) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/easy_mp.py", line 502, in parallel_map display_stderr = not preserve_exception_message, File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/queuing_system_utils/processing/__init__.py", line 405, in PBS raise RuntimeError, "PBS does not support synchronous submission" RuntimeError: PBS does not support synchronous submission I know that PBS doesn't support synchronous submission. Perhaps each job (or map region) requires more than one processor? Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan c/o Biophysics, Chem 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. [email protected] phone (734) 764-3353 fax (734) 764-3323