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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