On Sun, Apr 10, 2011 at 6:34 PM, Wei Huang <whuang.cct.lsu.edu> wrote:
> Yes, I just ran another test to confirm. I didn't see any problem with the
> serial run.
>
> The MPI version for MMPBSA.py is just simple divide and conquer. Right? So
> I can just write a script to have several serial runs with different start
> frames and end frames.
>
You can, but then you'll have to combine the results at the end. Have you
tried the default PBSA solver? Also, if you try to run too many threads on
the same node, it may be running out of memory.
All the best,
Jason
> Wei
> On Apr 10, 2011, at 7:25 PM, Bill Miller III wrote:
>
> > Have you tried running MMPBSA.py in serial using sander.APBS as the PB
> solver? Did that work even just on a few frames?
> >
> > -Bill
> >
> >
> > On Apr 10, 2011, at 6:52 PM, Wei Huang <whuang.cct.lsu.edu> wrote:
> >
> >> Dear Amber users,
> >>
> >> I am using the MPI version to MMPBSA.py to carry out some calculations.
> The PB solver that I used here is APBS, built with iAPBS to generate
> sander.APBS. No error is found during the independent test runs for both
> MMPBSA.py.MPI and sander.APBS. However, when I used it in MMPBSA.py.MPI. I
> got the following error messages. Could you help me figure our what the
> problem is? Thank you very much!
> >>
> >> Regards,
> >> Wei
> >>
> >> Starting to paste error message:
> >> #############
> >> MMPBSA.py.MPI being run on 8 processors
> >> ptraj found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
> >> sander found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
> >> sander.APBS found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander.APBS for PB
> calculations
> >>
> >> Preparing trajectories with ptraj...
> >> 149 frames were read in and processed by ptraj for use in calculation.
> >>
> >> Starting calculations
> >>
> >> Starting pb calculation...
> >>
> >> calculating ligand contribution...
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> calculating receptor contribution...
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> calculating complex contribution...
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >>
> >> Calculations complete. Writing output file(s)...
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> forrtl: severe (168): Program Exception - illegal instruction
> >> Image PC Routine Line
> Source
> >> sander.APBS 00000000004EFFDA Unknown Unknown
> Unknown
> >> sander.APBS 0000000000657933 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004BAAC4 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004AC3E8 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A9E37 Unknown Unknown
> Unknown
> >> sander.APBS 00000000004A54DC Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DBCC Unknown Unknown
> Unknown
> >> libc.so.6 0000003EA6D1C4CB Unknown Unknown
> Unknown
> >> sander.APBS 000000000040DAFA Unknown Unknown
> Unknown
> >> [21685 refs]
> >> [21685 refs]
> >> [21685 refs]
> >> [21685 refs]
> >> [21685 refs]
> >> [21685 refs]
> >> [21685 refs]
> >> Error: No potential terms in sander output! Check output files.
> >> NOTE: All files have been retained for debugging purposes. Type
> MMPBSA.py --clean to erase these files.
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
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Received on Sun Apr 10 2011 - 21:30:02 PDT
