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

[Shirts, Michael (mrs5pt)]

And the issue was that I was just changing GMX_OPENMP=NO in the
CMakeCache.txt, rather than setting it at the beginning of CMakeCache.txt --
works for some variables, like double precision and debug/release, not for
others.  

So, I'm getting consistent results now.  Though autodetecting this issue is
probably something worth putting in.

Sorry for causing problems that could have been found looking over the
Redmine site!

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Sun, 1 Apr 2012 15:27:10 +0200
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] Problems building for OS X with threads
> 
> 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
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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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>> 
> 
> 
> -- 
> 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
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