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.
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
>
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Received on Sun Apr 10 2011 - 19:00:02 PDT
