[gmx-developers] release-4-5 and 4-6 crash compiled with -DCMAKE_BUILD_TYPE:STRING=Debug. Thread code to blame?

[David van der Spoel]

On 2012-02-01 21:22, Roland Schulz wrote:
>
>
> On Mon, Jan 2, 2012 at 4:48 AM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
>     I'm trying to debug some redmine issues and find myself stuck due to
>     above error:
>
>     Program received signal EXC_BAD_ACCESS, Could not access memory.
>     Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000001
>     0x00000001006521b1 in tMPI_Spinlock_trylock (x=0x100d00fa0) at
>     gcc_x86.h:244
>     244         __asm__ __volatile__("\tmovl $1, %0\n"     /* set eax to
>     1, the
>     locked
>     (gdb) where
>     #0  0x00000001006521b1 in tMPI_Spinlock_trylock (x=0x100d00fa0) at
>     gcc_x86.h:244
>     #1  0x000000010065225f in tMPI_Lock_lock (lock=0x100d00fa0) at lock.c:69
>     #2  0x00000001003d1635 in gmx_fio_lock (fio=0x100d00f20) at gmxfio.c:252
>     #3  0x00000001003d176c in gmx_fio_insert (fio=0x100d00f20) at
>     gmxfio.c:305
>     #4  0x00000001003d1fb3 in gmx_fio_open (fn=0x100d01a20 "md.log",
>     mode=0x100671a8e "w+") at gmxfio.c:570
>     #5  0x00000001003d2273 in gmx_fio_fopen (fn=0x100d01a20 "md.log",
>     mode=0x100671a8e "w+") at gmxfio.c:643
>     #6  0x00000001003e5bbb in gmx_log_open (lognm=0x100d00c10 "md.log",
>     cr=0x100d00900, bMasterOnly=1, Flags=7168, fplog=0x7fff5fbfe4a0) at
>     main.c:310
>     #7  0x00000001000269fe in main (argc=1, argv=0x7fff5fbff790) at
>     mdrun.c:651
>
>     I'm on Mac OSX Lion (10.7.2)
>     [artemisiabmcuuse:713/spc] % gcc -h
>     i686-apple-darwin11-llvm-gcc-4.2: no input files
>
>     Any clues?
>
>
> Any news on this problem? It seems to occur only with llvm backend. GCC
> with standard backend or ICC on Mac are both OK.

Haven't tested this recently, am compiling with regular mpi instead. 
I'll try to clean up my mac from superfluous compilers.
>
> Roland
>
>
>     Will try it on Linux next.
>
>     --
>     David van der Spoel, Ph.D., Professor of Biology
>     Dept. of Cell & Molec. Biol., Uppsala University.
>     Box 596, 75124 Uppsala, Sweden. Phone: +46184714205
>     <tel:%2B46184714205>.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
>     --
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>
>
>
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov <http://cmb.ornl.gov>
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se