I newly built a paralleled Rosetta2.3.0 with OpenMPI 1.4.3. I used "make mpilam" to build it.
After building, I tested it with the following command:
mpirun -np 16 /home/knight/softwares/Rosetta-2.3.0/rosetta++/bin/rosetta.mpilam -mpi_task_distribution -s 1ubq.pdb -design -fixbb -resfile resfile -ex1 -pdbout test -ndruns 2000 > 1ubq_fixbb_mine.log
-np = 16 since I have 16 cores.
All cpus were running with 100%, however, I found this didn't speed up the calculations. Instead, it seems that Rosetta just put the VERY same job every core. In other words, every cores does the same thing. So I am wondering if Rosetta works correctly here? Why it didn't distribute the jobs correctly? Any suggestions? Thanks in advance!!!
P.S. My OS is RHEL5.4-32bit-server.
Ming Liu, Ph.D