I am working on Amber 7 and as I try to run an md simulation, i get this:
Rohan 8# mpirun -np 2 ./sander -O -i moldyin -o finout -p yaytop -c redo
-r retry
MPI: Program ./sander, Rank 0, Process 1484 called
MPI_Abort(<communicator>, 1)
MPI: --------stack traceback-------
PC: 0x5ddb100 MPI_SGI_stacktraceback in /usr/lib32/libmpi.so
PC: 0x5e02a70 PMPI_Abort in /usr/lib32/libmpi.so
PC: 0x5e32968 pmpi_abort_ in /usr/lib32/libmpi.so
PC: 0x101064dc mexit in ./sander
PC: 0x1008b874 compute_nfft in ./sander
PC: 0x10091d8c read_ewald in ./sander
PC: 0x1008e178 load_ewald_info in ./sander
PC: 0x10048dc4 mdread1 in ./sander
PC: 0x10008c58 sander in ./sander
PC: 0xad39d74 main in /usr/lib32/libftn.so
MPI: dbx version 7.3.4 (86441_Nov11 MR) Nov 11 2002 11:31:55
MPI: Process 1484 (sander) stopped at [__waitsys:24 +0x8,0xfa60f48]
MPI: Source (of
/xlv41/6.5.21m/work/irix/lib/libc/libc_n32_M4/proc/waitsys.s) not
available for Process 1484
MPI: > 0 __waitsys(0x0, 0x5ce, 0x7ffefdc0, 0x3, 0x2, 0x61, 0x69, 0x6e)
["/xlv41/6.5.21m/work/irix/lib/libc/libc_n32_M4/proc/waitsys.s":24,
0xfa60f48]
MPI: 1 _system(0x7ffefe90, 0x5ce, 0x7ffefdc0, 0x3, 0x2, 0x61, 0x69,
0x6e) ["/xlv41/6.5.21m/work/irix/lib/libc/libc_n32_M4/stdio/system.c":116,
0xfa6d398]
MPI: 2 MPI_SGI_stacktraceback(0x0, 0x5ce, 0x7ffefdc0, 0x3, 0x2, 0x61,
0x69, 0x6e)
["/xlv4/mpt/1.8/mpi/work/4.3/lib/libmpi/libmpi_n32_M4/adi/sig.c":242,
0x5ddb268]
MPI: 3 PMPI_Abort(0x0, 0x1, 0x7ffefdc0, 0x3, 0x2, 0x61, 0x69, 0x6e)
["/xlv4/mpt/1.8/mpi/work/4.3/lib/libmpi/libmpi_n32_M4/misc/abort.c":75,
0x5e02a70]
MPI: 4 pmpi_abort_(0x0, 0x5ce, 0x7ffefdc0, 0x3, 0x2, 0x61, 0x69, 0x6e)
["/xlv4/mpt/1.8/mpi/work/4.3/lib/libmpi/libmpi_n32_M4/sgi77/abort77.c":25,
0x5e32968]
MPI: 5 mexit(0x1018fb8c, 0x1018fb88, 0x7ffefdc0, 0x3, 0x2, 0x61, 0x69,
0x6e) ["/usr/local/amber7/src/sander/_mexit_.f":65, 0x101064dc]
MPI: 6 compute_nfft(0x7fff1040, 0x1036b684, 0x7ffefdc0, 0x3, 0x2, 0x61,
0x69, 0x6e) ["/usr/local/amber7/src/sander/_ew_setup_.f":387, 0x1008b874]
MPI: 7 read_ewald(0x7fff12b0, 0x7fff12b8, 0x7fff12c0, 0x3, 0x20000000,
0x61, 0x69, 0x6e) ["/usr/local/amber7/src/sander/_ew_setup_.f":3660,
0x10091d8c]
MPI: 8 load_ewald_info(0x0, 0x1036d930, 0x1036bf58, 0x3, 0x2, 0x61,
0x69, 0x6e) ["/usr/local/amber7/src/sander/_ew_setup_.f":2276, 0x1008e178]
MPI: 9 mdread1(0x0, 0x5ce, 0x7ffefdc0, 0x3, 0x2, 0x61, 0x69, 0x6e)
["/usr/local/amber7/src/sander/_mdread_.f":799, 0x10048dc4]
MPI: 10 sander(0x1, 0x28000000, 0x20, 0x28000000, 0x20, 0x2002000, 0x1,
0x28000000) ["/usr/local/amber7/src/sander/_sander_.f":1061, 0x10008c58]
MPI: More (n if no)? 11 main(0x0, 0x5ce, 0x7ffefdc0, 0x3, 0x2, 0x61,
0x69, 0x6e) ["/j10/mtibuild/v741m/workarea/v7.4.1m/libF77/main.c":101,
0xad39d74]
MPI: 12 __start()
["/xlv55/kudzu-apr12/work/irix/lib/libc/libc_n32_M4/csu/crt1text.s":177,
0x10008868]
MPI: -----stack traceback ends-----
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job
i ran xleap and saved the files yaytop and yaycrd, then ran sander to
minimize it with the program given in the Amber7 manual. Next i try to
run the md simulation using the restart file from the minimize run as the
coordinate file, then i got what you see above.. any idea where my problem
is?
thanks,
pmartin
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Received on Fri Apr 02 2004 - 00:53:00 PST
