AMBER Archive (2004)

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

From: Karol Miaskiewicz (miaskiew_at_ncifcrf.gov)
Date: Tue Jun 08 2004 - 15:04:14 CDT

The problem has been fixed. The problem was with the "-big" flag passed to
the configure program. Initially, we configured Amber8 with the following:

 ./configure -big -mpi sgi_mips

This actually produces erroneous config.h with lines containing both -n32
and -64 compilers flags (and also the -i8 flag). We fixed the config.h by
either switching everything (i.e. compiler and loader directives) to -n32
or to -64. However, the -i8 flag always remained there. And, it looks that
SGI MPI libraries have some problems handling double precision integers.
After removing "-i8" and building Sander as N32 object, we see no runtime
errors.

The simple solution is not to use the "-big" configure flag for parallel
Sander on SGI MIPS. 

--
Karol Miaskiewicz

On Thu, 3 Jun 2004, 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.
>
>
> --
> Karol Miaskiewicz
> Advanced Biomedical Computing Center
> NCI-Frederick, PO Box B, Frederick, MD 21702
> miaskiew_at_ncifcrf.gov, phone 301-8465664, fax 301-8465762
>
>
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