string(TOUPPER ${GMX_FFT_LIBRARY} GMX_FFT_LIBRARY)
set(PKG_FFT "")
set(PKG_FFT_LIBS "")
+set(MKL_LIBRARIES_FORMAT_DESCRIPTION "Use full paths to library files, in the right order, and separated by semicolons.")
+set(MKL_LIBRARIES "" CACHE STRING "List of libraries for linking to MKL. Only used with GMX_FFT_LIBRARY=mkl. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
+set(MKL_INCLUDE_DIR "" CACHE PATH "Path to mkl.h (non-inclusive). Only used with GMX_FFT_LIBRARY=mkl.")
+mark_as_advanced(FORCE MKL_LIBRARIES)
+mark_as_advanced(FORCE MKL_INCLUDE_DIR)
if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
if(GMX_DOUBLE)
set(FFTW fftw)
endif()
elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
-# MESSAGE(STATUS "Using external FFT library - Intel MKL")
- find_package(MKL REQUIRED)
- include_directories(${MKL_INCLUDE_DIR})
- set(FFT_LIBRARIES ${MKL_LIBRARIES})
- set(PKG_FFT_LIBS ${MKL_LIBRARIES})
+ MESSAGE(STATUS "Using external FFT library - Intel MKL")
+
+ # Intel 11 and up makes life somewhat easy if you just want to use
+ # all their stuff. It's not easy if you only want some of their
+ # stuff...
+ if (CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_GREATER "11")
+ # The next line takes care of everything for MKL
+ if (WIN32)
+ set(FFT_LINKER_FLAGS "/Qmkl=sequential")
+ else()
+ set(FFT_LINKER_FLAGS "-mkl=sequential")
+ endif()
+ set(MKL_ERROR_MESSAGE "Make sure you have configured your compiler so that ${FFT_LINKER_FLAGS} will work.")
+ else()
+ # The user will have to provide the set of magic libraries in
+ # MKL_LIBRARIES, which we cache (non-advanced), so that they
+ # don't have to keep specifying it, and can easily see that
+ # CMake is still using that information.
+ set(MKL_LIBRARIES "${MKL_LIBRARIES}" CACHE STRING "User-specified libraries for linking to MKL")
+ mark_as_advanced(CLEAR MKL_LIBRARIES)
+ include_directories(${MKL_INCLUDE_DIR})
+ mark_as_advanced(CLEAR MKL_INCLUDE_DIR)
+ set(FFT_LIBRARIES "${MKL_LIBRARIES}")
+ set(MKL_ERROR_MESSAGE "The include path to mkl.h in MKL_INCLUDE_DIR, and the link libraries in MKL_LIBRARIES=${MKL_LIBRARIES} need to match what the MKL documentation says you need for your system. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
+ # Convert the semi-colon separated list to a list of
+ # command-line linker arguments so that code using our
+ # pkgconfig setup can use it.
+ string(REGEX REPLACE ";" " " PKG_FFT_LIBS "${MKL_LIBRARIES}")
+ endif()
+
+ # Check MKL works. If we were in a non-global scope, we wouldn't
+ # have to play nicely.
+ set(old_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
+ set(CMAKE_REQUIRED_FLAGS "${FFT_LINKER_FLAGS}")
+ set(old_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
+ set(CMAKE_REQUIRED_LIBRARIES "${FFT_LIBRARIES}")
+
+ check_function_exists(DftiCreateDescriptor TEST_MKL)
+
+ set(CMAKE_REQUIRED_FLAGS "${old_CMAKE_REQUIRED_FLAGS}")
+ set(CMAKE_REQUIRED_LIBRARIES "${old_CMAKE_REQUIRED_LIBRARIES}")
+
+ if(NOT TEST_MKL)
+ # Hack to help the user vary MKL settings until they work.
+ # TODO Make this logic more useful.
+ unset(TEST_MKL CACHE)
+ message(FATAL_ERROR "Linking with MKL was requested, but was not successful. ${MKL_ERROR_MESSAGE}")
+ endif()
+ # Set variables to signal that we have MKL available and should use it for FFTs.
set(GMX_FFT_MKL 1)
- set(HAVE_MKL 1)
+ set(HAVE_LIBMKL 1)
#elseif(${GMX_FFT_LIBRARY} STREQUAL "ACML")
# MESSAGE(STATUS "Using external FFT library - AMD core math library")
set(GMX_EXTERNAL_BLAS TRUE CACHE BOOL "Use external BLAS instead of built-in")
set(GMX_EXTERNAL_LAPACK TRUE CACHE BOOL "Use external LAPACK instead of built-in")
# MKL has BLAS/LAPACK routines
-if(NOT HAVE_MKL AND NOT ACCELERATE_FRAMEWORK)
+if(NOT HAVE_LIBMKL AND NOT ACCELERATE_FRAMEWORK)
if(GMX_EXTERNAL_BLAS)
if (GMX_BLAS_USER)
list(APPEND GMX_EXTRA_LIBRARIES ${GMX_BLAS_USER})
if (NOT GMX_SKIP_DEFAULT_CFLAGS)
set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${CMAKE_C_FLAGS}")
set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${CMAKE_CXX_FLAGS}")
- set(CMAKE_EXE_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
+ set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
set(CMAKE_SHARED_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
else()
message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
endif()
- message("CMAKE_EXE_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
+ message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
endif()
\subsubsection{\mkl{}}
-Using \mkl{} requires a set of linker flags that \gromacs{} is not
-able to detect for you, so setting up optimal linking is tricky at the
-moment. You will need to consult your compiler documentation and
-use \verb+CMAKE_C_FLAGS+ and \verb+-DCMAKE_EXE_LINKER_FLAGS+
-accordingly.
+Using \mkl{} with \icc{} 11 or higher is very simple. Set up your
+compiler environment correctly, perhaps with a command like
+\verb+source /path/to/compilervars.sh intel64+ (or consult your local
+documentation). Then set \verb+-DGMX_FFT_LIBRARY=mkl+ when you run
+\cmake{}. In this case, \gromacs{} will also use \mkl{} for \blas{}
+and \lapack{} (see \hyperref{linear-algebra}{here}).
+
+Otherwise, you can configure \mkl{} by setting
+\verb+-DGMX_FFT_LIBRARY=mkl
+-DMKL_LIBRARIES="/full/path/to/libone.so;/full/path/to/libtwo.so"
+-DMKL_INCLUDE_DIR="/full/path/to/mkl/include"+,
+where the full list (and order!) of libraries you require are found in
+Intel's \mkl{} documentation for your system.
\subsection{Optional build components}
fine for normal use. If you need to specify a non-standard path to
search, use \verb+-DCMAKE_PREFIX_PATH=/path/to/search+.
+If you are using Intel's \mkl{} for \fft{}, then the \blas{} and
+\lapack{} it provides are used automatically.
+
On Apple platforms where the Accelerate Framework is available, these
will be automatically used for \blas{} and \lapack{}.
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2012,2013, by the GROMACS development team, led by
-# David van der Spoel, Berk Hess, Erik Lindahl, and including many
-# others, as listed in the AUTHORS file in the top-level source
-# directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-#
-# - Find Intel MKL
-# Find the Intel Math Kernel Library, version 6.0 or later
-#
-# MKL_INCLUDE_DIR - where to find mkl_dfti.h
-# MKL_LIBRARIES - List of libraries when using MKL
-# MKL_FOUND - True if MKL was found
-
-if (MKL_INCLUDE_DIR)
- # Already in cache, be silent
- set (MKL_FIND_QUIETLY TRUE)
-endif (MKL_INCLUDE_DIR)
-
-find_path (MKL_INCLUDE_DIR mkl_dfti.h)
-find_library (MKL_LIBRARIES mkl_core)
-
-# handle the QUIETLY and REQUIRED arguments and set MKL_FOUND to TRUE if
-# all listed variables are TRUE
-include (FindPackageHandleStandardArgs)
-find_package_handle_standard_args (MKL DEFAULT_MSG MKL_LIBRARIES MKL_INCLUDE_DIR)
-
-# MKL Libraries change name ALL the time, so the user will have to set these...
-# mark_as_advanced (MKL_LIBRARIES MKL_INCLUDE_DIR)
-
-
+++ /dev/null
-#include <mkl_dfti.h>
-
-int
-main()
-{
- DFTI_DESCRIPTOR *desc;
- MKL_LONG nx = 10;
-
- DftiCreateDescriptor(&desc,DFTI_SINGLE,DFTI_COMPLEX,1,nx);
-}
}
#ifdef HAVE_LIBMKL
/* MKL might be used for LAPACK/BLAS even if FFTs use FFTW, so keep it separate */
- fprintf(fp, "Linked with Intel MKL version %s.%s.%s.\n",
+ fprintf(fp, "Linked with Intel MKL version %d.%d.%d.\n",
__INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__);
#endif
#ifdef GMX_GPU
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff