[gmx-users] gmx 4.5 and openmm on Mac, still not compiling

[Szilárd Páll]

Hi,

FYI, now building the GPU accelerated version in a non-clean build
tree (used to build the CPU version) should work as well as the other
way around.

_However_, be warned that in the latter case the CPU build-related
parameters do _not_ get reset to their default values (e.g.
GMX_ACCELERATION != auto, GMX_THREADS != on)!

The safest way (and what I strongly recommend) is to have different
build trees for different builds or, as Rossen suggested, just remove
the cache before building something different.

Regards,
--
Szilárd



On Tue, Aug 24, 2010 at 2:39 PM, Rossen Apostolov
<rossen.apostolov at cbr.su.se> wrote:
>  Hi Alan,
>
> With OpenMM you don't need SSE kernels. If you look at CMakeCache.txt you'll
> see that
>
>
>> Hi there,
>>
>> I've tried before and the error still basically the same (line error in
>> 'nb_kernel400_x86_64_sse.c' was 630, now's 629) .
>>
>> I am using gmx 4.5 release-4-5-patches branch.
>>
>> git pull
>> rm -fr build
>> mkdir -p build
>> cd build
>> cmake -D BUILD_SHARED_LIBS=ON -DGMX_OPENMM=OFF ..
>
> Since GMX_OPENMM=OFF, GMX_ACCELERATION is automatically set to SSE.
>>
>> make clean
>
> This command doesn't remove CMaceCache.txt!
>>
>> make -j 2
>> sudo make install # all fine till here
>> make clean
>> export OPENMM_ROOT_DIR=/usr/local/openmm
>> cmake -D BUILD_SHARED_LIBS=OFF -DGMX_OPENMM=ON ..
>
> Now GMX_OPENMM is ON, *but* GMX_ACCELERATION is still SSE (the value is read
> from the cache). This is an issue with the cmake system. You should either
> remove CMakeCache.txt or add an explicit -DGMX_ACCELERATION=OFF to the cmake
> command.
>
> This is a workaround at the moment but the issue should be fixed.
>
> Rossen
>>
>> make mdrun
>>
>> [snip]
>> [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/version.c.o
>> [ 56%] Building C object
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o
>>
>> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:
>> In function ‘nb_kernel400nf_x86_64_sse’:
>>
>> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
>> error: ‘gmx_invsqrt_exptab’ undeclared (first use in this function)
>>
>> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
>> error: (Each undeclared identifier is reported only once
>>
>> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
>> error: for each function it appears in.)
>>
>> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
>> error: ‘gmx_invsqrt_fracttab’ undeclared (first use in this function)
>> make[3]: ***
>> [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o]
>> Error 1
>> make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
>> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
>> make: *** [mdrun] Error 2
>>
>> Any help would be appreciated.
>>
>> Thanks,
>>
>> Alan
>> --
>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>> Department of Biochemistry, University of Cambridge.
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
>
> --
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