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

[Rossen Apostolov]

  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><<