[gmx-users] Building using FFTW3 for FFT and MKL for BLAS/LAPACK
mark.j.abraham at gmail.com
Thu Dec 8 17:00:43 CET 2016
On Fri, Dec 9, 2016 at 12:20 AM Will Furnass <w.furnass at sheffield.ac.uk>
> Hi all,
> I understand that FFTW3 is considered preferable to MKL for FFTs in Gromacs
> but am having difficulty getting Gromacs to compile so that it uses a
> self-built single-precision FFTW but uses the MKL for BLAS/LAPACK linear
> algebra routines.
> Is there a recommended way of doing this?
Not really. There's only a tiny fraction of GROMACS runs that use both FFT
and linear algebra, and I'd want to see some evidence that such a hybrid
ought to run faster before going to the trouble (e.g. compare relevant
component timings for all-MKL vs FFTW+whatever builds)
> FYI I'm wanting to build Gromacs 2016.1 using
> - FFTW 3.3.5 (built by Gromacs)
> - MKL 2017
> - GCC 4.9.2
> - No CUDA/MPI support (for now)
> I tried passing the following to cmake:
> to cmake but got the following errors:
are some further options, but your main friend is the Intel documentation
for finding out what you need for your setup - it's generally more complex
than a single static library.
> -- Checking that user BLAS library
> -- Looking for dgemm_
> -- Looking for dgemm_ - not found
Looking at the CMakeError.log and CMakeOutput.log may prove instructive,
after you've checked the Intel docs.
> CMake Warning at cmake/gmxManageLinearAlgebraLibraries.cmake:78 (message):
> GMX_BLAS_USER library
> was specified, but it may not provide BLAS. We are proceeding by
> you know what you are doing and that linking F77-style to this library
> Call Stack (most recent call first):
> CMakeLists.txt:693 (include)
> -- MKL and GMX_BLAS_USER were both specified. Using the latter for BLAS.
> [100%] Linking CXX executable ../../bin/gmx
> ../../lib/libgromacs.so.2.1.0: undefined reference to `mkl_lapack_dlacpy'
> ../../lib/libgromacs.so.2.1.0: undefined reference to `mkl_blas_dcopy'
> Dr Will Furnass | Research Computing Support Officer
> CiCS | University of Sheffield | +44 (0)114 22 23130
> http://www.sheffield.ac.uk/cics/research | http://docs.hpc.sheffield.ac.uk
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