[gmx-users] A SGI Altix 3700 system with 512 Itanium 2 processors and 1Terabyte of memory

[Naser, Md Abu]

Hi All,

A double precision version of gromacs (3.2.1) was installed on A SGI Altix 3700 . Everything else is fine but when I run mdrun_d it gives me following error. Can any one advise me where might be the problems?

With regards,

Abu
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MPI: --------stack traceback-------
Source file not found or not readable, tried...
    ./../sysdeps/unix/sysv/linux/waitpid.c
    /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/../sysdeps/unix/sysv/linux/waitpid.c
    ./waitpid.c
    /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/waitpid.c
(Cannot find source file ../sysdeps/unix/sysv/linux/waitpid.c)
MPI: Linux Application Debugger for Itanium(R)-based applications, Version 8.1-7, Build 20050128
MPI: Reading symbolic information from /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/mdrun_d...No debugging symbols found
MPI: Attached to process id 8012  ....
MPI: stopped at [__pid_t __libc_waitpid(__pid_t, int*, int):32 0x2000000000cf5551]    
MPI: >0  0x2000000000cf5551 in __libc_waitpid(pid=8682, stat_loc=0x60000fffffff7960, options=0) "../sysdeps/unix/sysv/linux/waitpid.c":32
MPI: #1  0x200000000011e440 in mpi_sgi_system(...) in /usr/lib/libmpi.so
MPI: #2  0x200000000011e930 in first_arriver_handler(...) in /usr/lib/libmpi.so
MPI: #3  0x200000000011e280 in slave_sig_handler(...) in /usr/lib/libmpi.so
MPI: #4  0xa0000000000040c0
MPI: #5  0x4000000000231f40 in inl3330(...) in /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/mdrun_d
MPI: #6  0x400000000012c3a0 in do_fnbf(...) in /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/mdrun_d
MPI: #7  0x4000000000060eb0 in force(...) in /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/mdrun_d
MPI: #8  0x40000000000cca80 in do_force(...) in /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/mdrun_d
MPI: #9  0x400000000002a7d0 in do_md(...) in /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/mdrun_d
MPI: #10 0x4000000000027d50 in mdrunner(...) in /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/mdrun_d
MPI: #11 0x400000000002ef30 in main(...) in /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/mdrun_d
MPI: #12 0x200000000101a990 in __libc_start_main(main=0x4000000000379020, argc=8, ubp_av=0x60000fffffffa628, init=0x20000000011f0200, fini=0x2000000000d09a18, rtld_fini=0x200000000011e440, stack_end=0xc000000000000288) "../sysdeps/generic/libc-start.c":205
MPI: #13 0x4000000000004940 in _start(...) in /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/mdrun_d

MPI: -----stack traceback ends-----
MPI: On host newtd, Program /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/mdrun_d, Rank 30, Process 8012: Dumping core on signal SIGSEGV(11) into directory /home/shabna/cramwater
MPI: MPI_COMM_WORLD rank 30 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 11

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