[gmx-developers] Problems building for OS X with threads

[David van der Spoel]

On 2012-04-01 15:23, Shirts, Michael (mrs5pt) wrote:
>> Michael's issue is a different because it is gcc 4.1.2
>
> And on double checking, I read it wrong -- it's gcc 4.2.1!  So it might be
> the same thing.
>
>> and because it is
>> not a segfault but the linker errorr.
>
> I do get a segfault when I run on multiple threads when it compiles.
> However, when shared libraries is on, it link fails instead.
>
> Setting -DGMX_OPENMP:BOOL=OFF does not appear to fix the problem; it still
> crashes on multiple threads.  I'll keep poking to make sure I've run through
> all the options.
>
Is this with a fresh compile?
If I run a simple system on two threads it crashes in the first call to 
anything gomp related, from fft5d.c.



> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>
>
>> From: Roland Schulz<roland at utk.edu>
>> Reply-To: Discussion list for GROMACS development<gmx-developers at gromacs.org>
>> Date: Sun, 1 Apr 2012 09:05:03 -0400
>> To: Discussion list for GROMACS development<gmx-developers at gromacs.org>
>> Subject: Re: [gmx-developers] Problems building for OS X with threads
>>
>> On Sun, Apr 1, 2012 at 6:20 AM, David van der Spoel
>> <spoel at xray.bmc.uu.se>wrote:
>>
>>> On 2012-04-01 05:50, Shirts, Michael (mrs5pt) wrote:
>>>> Hi, all-
>>>>
>>>> I'm very recently (with 4.6 updates in the last couple of weeks) having
>>>> issues with building gromacs with threads on OS X.  When I try to compile
>>>> with shared libraries, I get:
>>>>
>>>> ld: warning: in /usr/local/lib/libgomp.dylib, file was built for i386
>>> which
>>>> is not the architecture being linked (x86_64)
>>>>
>>>> When I build without shared libraries, it compiles, but crashes when run
>>>> with -nt more than 1.
>>>>
>>>> Currently using OS X 10.6.8, gcc 4.1.2 to compile.
>>>>
>>>> Everything works fine with 4.5.5, and with earlier versions of 4.6.
>>>>
>>>> Anyone else having similar problems, or know what changes could have
>>> caused
>>>> this?
>>>
>>> There is a redmine for this (900).
>>>
>>
>> Michael's issue is a different because it is gcc 4.1.2 and because it is
>> not a segfault but the linker errorr.
>> I'm surprised that you get a linker error. gcc 4.1 doesn't support OpenMP
>> and if run cmake with gcc 4.1 on Linux I get:
>> Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
>>
>> If you rerun cmake (without a cache), do you still not get any error during
>> cmake?
>>
>> BTW: We probably should automatic disable OpenMP if the flags can't be
>> found (e.g. for clang and gcc<4.2)
>>
>> Roland
>>
>>>
>>> Your simplest solution is cmake -DGMX_OPENMP:BOOL=OFF
>>>
>>>>
>>>> Thanks!
>>>> ~~~~~~~~~~~~
>>>> Michael Shirts
>>>> Assistant Professor
>>>> Department of Chemical Engineering
>>>> University of Virginia
>>>> michael.shirts at virginia.edu
>>>> (434)-243-1821
>>>>
>>>
>>>
>>> --
>>> 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
>>> --
>>> 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
>> --
>> 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.
>


-- 
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