[phenixbb] mr_rosetta on a supercomputer
Patricia Amara
patricia.amara at ibs.fr
Wed May 18 06:40:27 PDT 2011
Hello,
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
MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1
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
MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1
directories
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
#!/bin/bash
#MSUB -e ros1_%I.e
#MSUB -o ros1_%I.o
#MSUB -n 6
#MSUB -T 86400
cd /scratch/cont003/amara/Rosetta-NadA
./rosetta.run
and the script itself:
phenix.mr_rosetta \
seq_file=/scratch/cont003/amara/Rosetta-NadA/NADA.seq \
data=/scratch/cont003/amara/Rosetta-NadA/NadA-7-BM16-remote-no_ano-P21212-Rfree_shell.mtz
\
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 \
group_run_command=
"/usr/share/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/bsub -n 1 -q mono -W
03:00"
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