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.
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Received on Sun Apr 10 2011 - 17:30:04 PDT
