[gmx-developers] gmx master: compiling on mac and segfault

[Roland Schulz]

On Thu, Jul 26, 2012 at 10:26 PM, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
> On Fri, Jul 27, 2012 at 4:06 AM, Szilárd Páll <szilard.pall at cbr.su.se>
> wrote:
>>
>> On Thu, Jul 26, 2012 at 2:09 PM, Jochen Hub <jhub at gwdg.de> wrote:

>>> Program received signal EXC_BAD_ACCESS, Could not access memory.
>>> Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000048
>>> [Switching to process 44300 thread 0x1b03]
>>> 0x0000000100050ebd in gomp_resolve_num_threads ()
>>> (gdb) bt
>>> #0  0x0000000100050ebd in gomp_resolve_num_threads ()
>>> #1  0x0000000100050fc3 in GOMP_parallel_start ()
>>> #2  0x00000001004c0bc2 in fft5d_plan_3d ()
>>> #3  0x0000000100434a52 in gmx_parallel_3dfft_init ()
>>> #4  0x000000010046b6fc in gmx_pme_init ()
>>> #5  0x0000000100026ab3 in mdrunner (nthreads_requested=4, fplog=0x0,
>>> cr=0x102100b40, nfile=36, fnm=0x103808200, oenv=0x101000c10, bVerbose=0,
>>> bCompact=1, nstglobalcomm=-1, ddxyz=0x1013c0e04, dd_node_order=1, rdd=0,
>>> rconstr=0, dddlb_opt=0x10002e26a "auto", dlb_scale=0.800000012, ddcsx=0x0,
>>> ddcsy=0x0, ddcsz=0x0, nstepout=100, resetstep=-1, nmultisim=0,
>>> repl_ex_nst=0, repl_ex_nex=0, repl_ex_seed=-1, pforce=-1, cpt_period=15,
>>> max_hours=-1, deviceOptions=0x10002e276 "", Flags=7168) at
>>> /Users/jhub/src/gmx/gromacs/src/programs/mdrun/runner.c:844
>>> #6  0x0000000100024f2d in mdrunner_start_fn (arg=0x101005d60) at
>>> /Users/jhub/src/gmx/gromacs/src/programs/mdrun/runner.c:173
>>> #7  0x0000000100242bfb in tMPI_Thread_starter ()
>>> #8  0x00007fff9785f8bf in _pthread_start ()
>>> #9  0x00007fff97862b75 in thread_start ()
>>
>>
>> Can't confirm this one right now as there's no gcc 4.4 on the Mac OS build
>> server. Will check it later. However, it sounds like it's a similar issue to
>> the ones we've had with an ordered clause in a #pragma omp statment.
>
>
> Unfortunately, I can confirm this crash. It seems to occur with
> OMP_NUM_THREADS=m and -nt n, where m>1 and n >1.

The bug also occurs for release-4.6 but only on Mac.
It is fixed with gcc 4.5 (tested on jenkins-mac). I guess the gcc4.4
OpenMP implementation on Mac is broken too. The only reference to this
(potential)
bug I found is:
http://lists.apple.com/archives/coreaudio-api/2009/May/msg00035.html
It is confirmed for gcc4.2 (we already knew that) and reported (but
not confirmed) there also for 4.4.
Should we blacklist OpenMP on Mac for GCC <4.5?

Roland

>>
>>
>>>
>>>
>>> Can anyone give me a hint how to fix this? Or is the master so
>>> experimental that it is not interned to be used at all right now?
>>
>>
>> Unfortunately, this affects the release-4-6 branch as well. Could you
>> please file a bug on Redmine on the first issue and have a look at the
>> related issue on the second.
>>
>> Cheers,
>> --
>> Sz.
>>
>>>
>>> Many thanks,
>>> Jochen
>>>
>>>
>>> --
>>> ---------------------------------------------------
>>> Dr. Jochen Hub
>>> Computational Molecular Biophysics Group
>>> Institute for Microbiology and Genetics
>>> Georg-August-University of Göttingen
>>> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
>>> Phone: +49-551-39-14189
>>> http://cmb.bio.uni-goettingen.de/
>>> ---------------------------------------------------
>>> --
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-developers-request at gromacs.org.
>>
>>
>



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