AMBER8
Irix 6.5.23
MIPSpro 7.4.2 compilers
SGI MPI 4.3 (MPT 1.8)
Sander compiles fine (although we had problems compiling with 7.4
compilers, but the upgrade to 7.4.2 fixed them). However, program aborts
at runtime when trying to run tests that come with the program.
Below is the traceback for parallel version of Sander:
MPI: Program ../../exe/sander, Rank 0, Process 1177431 received signal
SIGSEGV(11)
MPI: --------stack traceback-------
PC: 0x5ddb100 MPI_SGI_stacktraceback in /usr/lib32/libmpi.so
PC: 0x5ddb544 first_arriver_handler in /usr/lib32/libmpi.so
PC: 0x5ddb7d8 slave_sig_handler in /usr/lib32/libmpi.so
PC: 0xfaee79c _sigtramp in /usr/lib32/libc.so.1
PC: 0x5dfb420 MPI_SGI_comm_coll_opt in /usr/lib32/libmpi.so
PC: 0x5dfab20 MPI_SGI_barrier in /usr/lib32/libmpi.so
PC: 0x5dfae80 PMPI_Barrier in /usr/lib32/libmpi.so
PC: 0x5e32dd4 pmpi_barrier_ in /usr/lib32/libmpi.so
PC: 0x10047e48 multisander in ../../exe/sander
PC: 0xad69d74 main in /usr/lib32/libftn.so
MPI: dbx version 7.3.3 (78517_Dec16 MR) Dec 16 2001 07:45:22
MPI: Process 1177431 (sander_parallel) stopped at [__waitsys:24
+0x8,0xfa53338]
MPI: Source (of
/xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/proc/waitsys.s) not
available for Process 1177431
MPI: > 0 __waitsys(0x0, 0x126497, 0x7ffecda0, 0x3, 0x10e4f4, 0x1, 0x0,
0x0) ["/xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/proc/waitsys.s":24,
0xfa53338]
MPI: 1 _system(0x7ffece70, 0x126497, 0x7ffecda0, 0x3, 0x10e4f4, 0x1,
0x0, 0x0)
["/xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/stdio/system.c":116,
fa5f868]
MPI: 2 MPI_SGI_stacktraceback(0x0, 0x126497, 0x7ffecda0, 0x3, 0x10e4f4,
0x1, 0x0, 0x0)
["/xlv4/mpt/1.8/mpi/work/4.3/lib/libmpi/libmpi_n32_M4/adi/sig.c":242,
0x5ddb268]
MPI: 3 first_arriver_handler(0xb, 0x71756974, 0x7ffecda0, 0x3,
0x10e4f4, 0x1, 0x0, 0x0)
["/xlv4/mpt/1.8/mpi/work/4.3/lib/libmpi/libmpi_n32_M4/adi/sig.c":445,
0x5ddb544]
MPI: 4 slave_sig_handler(0xb, 0x126497, 0x7ffecda0, 0x3, 0x10e4f4, 0x1,
0x0, 0x0)
["/xlv4/mpt/1.8/mpi/work/4.3/lib/libmpi/libmpi_n32_M4/adi/sig.c":542,
0x5ddb7e0]
MPI: 5 _sigtramp(0x0, 0x126497, 0x0, 0x3, 0x0, 0x0, 0x0, 0x0)
["/xlv42/6.5.23m/work/irix/lib/libc/libc_n32_M4/signal/sigtramp.s":71,
0xfaee79c]
MPI: 6 MPI_SGI_comm_coll_opt(0x0, 0x43bd700, 0x0, 0x7ffedb70, 0x0, 0x0,
0x0, 0x5db062c)
["/xlv4/mpt/1.8/mpi/work/4.3/lib/libmpi/libmpi_n32_M4/coll/collutil.c":99,
0x5dfb428]
MPI: 7 MPI_SGI_barrier(0x0, 0x43bd700, 0x0, 0x7ffedb70, 0x0, 0x0, 0x0,
0x5db062c)
["/xlv4/mpt/1.8/mpi/work/4.3/lib/libmpi/libmpi_n32_M4/coll/barrier.c":53,
0x5dfab20]
MPI: 8 PMPI_Barrier(0x0, 0x43bd700, 0x0, 0x7ffedb70, 0x0, 0x0, 0x0,
0x5db062c)
["/xlv4/mpt/1.8/mpi/work/4.3/lib/libmpi/libmpi_n32_M4/coll/barrier.c":231,
0x5dfae80
MPI: More (n if no)?]
MPI: 9 pmpi_barrier_(0x0, 0x43bd700, 0x0, 0x7ffedb70, 0x0, 0x0, 0x0,
0x5db062c)
["/xlv4/mpt/1.8/mpi/work/4.3/lib/libmpi/libmpi_n32_M4/sgi77/barrier77.c":24,
0x5e32dd4]
MPI: 10 multisander(0x0, 0x43bd700, 0x0, 0x7ffedb70, 0x0, 0x0, 0x0,
0x5db062c) ["/usr/local/fbscapp/amber8/src/sander/_sander.f":374,
0x10047e48]
MPI: 11 main(0x0, 0x43bd700, 0x0, 0x7ffedb70, 0x0, 0x0, 0x0, 0x5db062c)
["/j7/mtibuild/v742/workarea/v7.4.2m/libF77/main.c":101, 0xad69d74]
MPI: 12 __start()
["/xlv55/kudzu-apr12/work/irix/lib/libc/libc_n32_M4/csu/crt1text.s":177,
0x10009ce8]
MPI: -----stack traceback ends-----
MPI: Program ../../exe/sander, Rank 0, Process 1177431: Dumping core on
signal SIGSEGV(11) into directory /usr/local/fbscapp/amber8/test/cytosine
MPI: Program ../../exe/sander, Rank 1, Process 1203283: Core dump on
signal SIGSEGV(11) suppressed.
MPI: MPI_COMM_WORLD rank 1 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 9
./Run.cytosine: Program error
This is an n32 executable. We tried 64-bit, but the result is similar,
i.e. run-time abort.
--
Karol Miaskiewicz
Advanced Biomedical Computing Center
NCI-Frederick, PO Box B, Frederick, MD 21702
miaskiew.ncifcrf.gov, phone 301-8465664, fax 301-8465762
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Received on Thu Jun 03 2004 - 15:53:01 PDT
