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

[Roland Schulz]

On Wed, Feb 1, 2012 at 3:44 PM, David van der Spoel <spoel at xray.bmc.uu.se>wrote:

> 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.
>

It seems to be fixed by https://gerrit.gromacs.org/#/c/412/ . But because
the merge isn't submitted yet, 4.6 and master still have the issue.

Roland


> >
> > 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
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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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