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 - 16:00:03 PDT
