[gmx-users] compiling on different architecture than the compute nodes architecture

[Broadbent, Richard]

Dear Silard,

cmake -DGMX_CPU_ACCELERATION=AVX_256 -DGMX_DEFAULT_SUFFIX=OFF
-DGMX_BINARY_SUFFIX="_avx"  -DGMX_OPENMP=ON  -DGMX_MPI=ON -DGMX_DOUBLE=ON
-DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl
-DMKL_INCLUDE_DIR=$MKLROOT/include
-DMKL_LIBRARIES="$MKLROOT/lib/intel64/libmkl_core.so;$MKLROOT/lib/intel64/l
ibmkl_intel_lp64.so;$MKLROOT/lib/intel64/libmkl_sequential.so"
-DCMAKE_INSTALL_PREFIX=$HOME/libs/gromacs

Compiled, linked and installed without warning using intel-suite/2013,
mpi/intel-3.1, and cmake/2.8.9 I was compiling release-4-6 out of the git
repository ( 06935659a3125d9b44b84c57e67cb6788fda42c1 ). The job using
that executable is still in the queue, however, another one built using
the sse2 kernels ran a minimisation on a single core without problems.

How much faster fftw3 is than mkl for gromacs, is the difference likely to
be on the scale of 1-2% or 10%?

Thanks,

Richard


On 07/02/2013 02:17, "Szilárd Páll" <szilard.pall at cbr.su.se> wrote:

>On Wed, Feb 6, 2013 at 6:03 PM, Richard Broadbent <
>richard.broadbent09 at imperial.ac.uk> wrote:
>
>> Dear All,
>>
>> I would like to compile gromacs 4.6 to run with the correct acceleration
>> on the compute nodes on our local cluster. Some of the nodes have intel
>> sandy-bridge whilst others only have sse4.1 and some (including the
>>login
>> and single core job nodes) are still stuck on ssse3 (gmx would use sse2
>> acceleration here).
>>
>> Installing several versions is not a problem however, I'm not sure how
>>to
>> make cmake build a version of the code that is not using the
>>acceleration
>> for the system on which the code is being compiled. Restrictions on job
>> sizes makes running the compilation on the sandy-bridge nodes almost
>> impossible. Can anyone let me know which flags cmake needs to enable
>> avx-256 acceleration?
>>
>> my standard cmake line is:
>>
>> $ CC=mpiicc CXX=mpiicpc ; cmake -DGMX_OPENMP=ON  -DGMX_MPI=ON
>> -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON
>> -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/**include
>> -DMKL_LIBRARIES="$MKLROOT/lib/**intel64/libmkl_core.so;$**
>> 
>>MKLROOT/lib/intel64/libmkl_**intel_lp64.so;$MKLROOT/lib/**intel64/libmkl_
>>sequential.so"
>> -DCMAKE_INSTALL_PREFIX=$HOME/**libs/gromacs  ../
>>
>
>Note that MKL (without the fftw wrappers) is known to not work out of the
>box. Making it work requires a fairly simple workaround described here:
>http://redmine.gromacs.org/issues/1110#note-3
>
>Additionally, note that FFTW is in most cases faster than MKL (but if you
>find the contrary do let us know).
>
>--
>Szilárd
>
>
>
>>
>>
>>
>> Thanks,
>>
>> Richard
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