[phenixbb] mr_rosetta on a supercomputer

Patricia Amara patricia.amara at ibs.fr
Wed May 18 06:40:27 PDT 2011


I have been trying to run phenix.mr_rosetta on a supercomputer
where we are limited to 24h for parallel jobs and we have different 
queues for job mono.
Thus to run we have two files.
We do not really understand how the code proceeds with nproc so we just 
put 6 for now.
When we sent it, it created 1000 jobs on 
it sent 10 jobs mono, but ran only 5 first than the other five. Then the 
job running the script hangs.
when we looked at the log files in the 
it filled up only 4 if we re-run only 3 and never the same.
do you have any idea what we're doing wrong?
thanks in advance for your input

Patricia Amara

ps; Thus to run we have two files.
One to send the script
#MSUB -e ros1_%I.e
#MSUB -o ros1_%I.o
#MSUB -n 6
#MSUB -T 86400
cd /scratch/cont003/amara/Rosetta-NadA

and the script itself:

phenix.mr_rosetta \
  seq_file=/scratch/cont003/amara/Rosetta-NadA/NADA.seq \
  search_models=/scratch/cont003/amara/Rosetta-NadA/model_2.pdb \
  run_prerefine=True \
  number_of_prerefine_models=1000 \
  fragment_files = 
/scratch/cont003/amara/Rosetta-NadA/aat000_03_05.200_v1_3.gz  \
  fragment_files = 
/scratch/cont003/amara/Rosetta-NadA/aat000_09_05.200_v1_3.gz \
  rescore_mr.relax=False \
  rosetta_models=20 \
  ncs_copies=3 \
  space_group=p21212  \
  use_all_plausible_sg=False \
  max_wait_time=100 \
  nproc=6 \
"/usr/share/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/bsub -n 1  -q mono -W 

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