AMBER Archive (2004)

Subject: Re: AMBER: parallel Sander (amber8): run-time error under Irix

From: Karol Miaskiewicz (miaskiew_at_ncifcrf.gov)
Date: Thu Jun 03 2004 - 14:15:05 CDT

> We have compiled and run (all sander tests passing) amber8 on our SGI
> without a problem: Irix 6.5.23m, MIPSpro 7.3.1.3m, SGI MPI 4.3 (MPT 1.8).
> We don't have MIPSpro 7.4.x compilers (due to licensing issues) so I
> cannot confirm that sander runs with those.
> Did you try compiling serial (non-MPI) sander? Does it work? This would
> at least isolate possible MPI problems from other problems (I am not
> sure if stack trace points unambiguously at MPI problem and it's easy
> enough to try serial sander)...

Serial sander runs fine, at least, in simple tests that we have tried so
far.

        Karol

>
> Cheers,
> -Viktor
>
> Karol Miaskiewicz wrote:
>
> >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.
> >
>
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