Although I have yet to determine why, I re-made the .inpcrd and .prmtop files in xLeap, and attempted to run the job again. This was my error message this time.... any thoughts? set_SCR: using existing PBS job directory /scratch/batch/205048MPI: On host co-compute2, Program /usr/apps/chemistry/amber/amber9/amber9/exe/sander.MPI, Rank 0, Process 7718 called MPI_Abort(<communicator>, 1)MPI: --------stack traceback-------Internal Error: Can't read/write file "/dev/mmtimer", (errno = 22)Internal Error: Can't read/write file "/dev/sgi_fetchop", (errno = 22)MPI: Intel(R) Debugger for Itanium(R) -based Applications, Version 9.0-20 , Build 20060218MPI: Reading symbolic information from /usr/apps/chemistry/amber/amber9/amber9/exe/sander.MPI...doneMPI: Attached to process id 7718 ....MPI: stopped at [0xa000000000010641]MPI: >0 0xa000000000010641MPI: #1 0x2000000005873a80 in __waitpid(...) in /lib/tls/libc.so.6.1MPI: #2 0x20000000000e4170 in MPI_SGI_stacktraceback(...) in /usr/lib/libmpi.soMPI: #3 0x20000000001208d0 in PMPI_Abort(...) in /usr/lib/libmpi.soMPI: #4 0x20000000001bdda0 in mpi_abort__(...) in /usr/lib/libmpi.soMPI: #5 0x40000000003641f0 in mexit_(...) in /usr/apps/chemistry/amber/amber9/amber9/exe/sander.MPIMPI: #6 0x4000000000211510 in getcor_(...) in /usr/apps/chemistry/amber/amber9/amber9/exe/sander.MPIMPI: #7 0x40000000001a5440 in sander_(...) in /usr/apps/chemistry/amber/amber9/amber9/exe/sander.MPIMPI: #8 0x4000000000194bc0 in MAIN__(...) in /usr/apps/chemistry/amber/amber9/amber9/exe/sander.MPIMPI: #9 0x4000000000004840 in main(...) in /usr/apps/chemistry/amber/amber9/amber9/exe/sander.MPIMPI: #10 0x2000000005791c50 in __libc_start_main(...) in /lib/tls/libc.so.6.1MPI: #11 0x4000000000004580 in _start(...) in /usr/apps/chemistry/amber/amber9/amber9/exe/sander.MPIMPI: -----stack traceback ends-----MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()MPI: aborting jobFrom: taryn_hartley.hotmail.comTo: amber.scripps.eduSubject: MPI error messageDate: Mon, 23 Jul 2007 11:39:27 -0600
Regarding using Sander on Amber9 to run an MD simulation, my pbs script included AMBERHOME/exe/sander and was receiving this error message:MPI: co-compute1: 0x34b5000042df8b72: forrtl: severe (64): input conversion error, unit 8, file /u/ac/thartley/test/bundlewat.prmtopMPI: co-compute1: 0x34b5000042df8b72: Image PC Routine Line Source MPI: co-compute1: 0x34b5000042df8b72: sander 4000000000C91390 Unknown Unknown UnknownMPI: co-compute1: 0x34b5000042df8b72: sander 4000000000C8C560 Unknown Unknown UnknownMPI: co-compute1: 0x34b5000042df8b72: sander 4000000000C34250 Unknown Unknown UnknownMPI: co-compute1: 0x34b5000042df8b72: sander 4000000000B882E0 Unknown Unknown UnknownMPI: co-compute1: 0x34b5000042df8b72: sander 4000000000B87810 Unknown Unknown UnknownMPI: co-compute1: 0x34b5000042df8b72: sander 4000000000BCB6B0 Unknown Unknown UnknownMPI: co-compute1: 0x34b5000042df8b72: sander 40000000001B13C0 Unknown Unknown UnknownMPI: co-compute1: 0x34b5000042df8b72: sander 400000000018B850 Unknown Unknown UnknownMPI: co-compute1: 0x34b5000042df8b72: sander 40000000001874F0 Unknown Unknown UnknownMPI: co-compute1: 0x34b5000042df8b72: sander 4000000000003D40 Unknown Unknown UnknownMPI: co-compute1: 0x34b5000042df8b72: libc.so.6.1 2000000001D0DC50 Unknown Unknown UnknownMPI: co-compute1: 0x34b5000042df8b72: sander 4000000000003A80 Unknown Unknown UnknownMPI: could not run executable (case #4)It was suggested to me to add .MPI after sander (AMBERHOME/exe/sander.MPI), which I did, and now my error message reads as follows:set_SCR: using existing PBS job directory /scratch/batch/204612forrtl: severe (64): input conversion error, unit 8, file /u/ac/thartley/test/bundlewat.prmtopImage PC Routine Line Source sander.MPI 40000000007F3CD0 Unknown Unknown Unknownsander.MPI 40000000007EEEA0 Unknown Unknown Unknownsander.MPI 4000000000796B90 Unknown Unknown Unknownsander.MPI 40000000006EEEE0 Unknown Unknown Unknownsander.MPI 40000000006EE410 Unknown Unknown Unknownsander.MPI 4000000000731DF0 Unknown Unknown Unknownsander.MPI 40000000001CAA00 Unknown Unknown Unknownsander.MPI 40000000001A4650 Unknown Unknown Unknownsander.MPI 4000000000194BC0 Unknown Unknown Unknownsander.MPI 4000000000004840 Unknown Unknown Unknownlibc.so.6.1 2000000005791C50 Unknown Unknown Unknownsander.MPI 4000000000004580 Unknown Unknown UnknownMPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()MPI: aborting jobIs it my .prmtop file as the 2nd line indicates? .MPI was not used in the PBS script in the tutorials (which I executed successfully before attempting my own project) and that is what I am using as my guide. Help?-Taryn Explore the seven wonders of the world Learn more!
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Received on Wed Jul 25 2007 - 06:07:39 PDT
