Hi everybody,
I've attempted to run MMPBSA.py on a parallel amber11 installation.
My machine is a quad core iMac running on Intel Core i7
I did edit the MMPBSA.py file as follows:
1. Changed INPUT.append('3') to INPUT.append('4')
2. Changed the next line from INPUT.append('none') to INPUT.append('mpirun -np 4')
The error messages that I get are as follows:
g:MMPBSA george1$ MMPBSA.py -O -i mmpbsa_1b.in -o FINAL_RESULTS_MMPBSA.dat -sp 2wc6_bom_solv.prmtop -cp 2wc6_bom.prmtop -rp 2wc6.prmtop -lp bom.prmtop -y *.mdcrd
ptraj found! Using /Users/george1/Programs/amber11_parallel/bin/ptraj
sander.MPI found! Using /Users/george1/Programs/amber11_parallel/bin/sander.MPI
Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi radii (mbondi)
Preparing trajectories with ptraj...
200 frames were read in and processed by ptraj for use in calculation.
Starting sander calls
Starting gb calculation...
Error: specified more groups ( 2 ) than the number of processors ( 1 ) !
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Error: specified more groups ( 2 ) than the number of processors ( 1 ) !
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Error: specified more groups ( 2 ) than the number of processors ( 1 ) !
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Error: specified more groups ( 2 ) than the number of processors ( 1 ) !
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Starting pb calculation...
Error: specified more groups ( 2 ) than the number of processors ( 1 ) !
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Error: specified more groups ( 2 ) than the number of processors ( 1 ) !
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Error: specified more groups ( 2 ) than the number of processors ( 1 ) !
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Error: specified more groups ( 2 ) than the number of processors ( 1 ) !
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Error: Sander error! GB mdout file was not created.
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Looking forward to your suggestions how to fix this problems,
Best regards
George
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Received on Mon Jun 14 2010 - 09:30:05 PDT
