QMCPACK package: update blas/lapack detection (#6753)
* Fix detection of blas and lapack: provide libraries/includes as arguments to CMake rather than using CMake's auto-detection. This includes a patch to QMCPACK's CMake files to refer to Spack-built blas/lapack implementations. This also includes special-case logic for the intel-mkl implementation of blas/lapack * Break up unit tests and short tests. Only hard failure if the unit tests fail, if short tests fail issue a warning only. * Add QMCPACK 3.3.0, get rid of 3.0.0
This commit is contained in:
Nichols A. Romero
scheibelp
parent
0c1f4a7997
commit
24743b7e5a
55
var/spack/repos/builtin/packages/qmcpack/cmake.diff
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55
var/spack/repos/builtin/packages/qmcpack/cmake.diff
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@ -0,0 +1,55 @@
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diff --git a/CMake/FindMKL.cmake b/CMake/FindMKL.cmake
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index a457eaba0..66dc43ce6 100644
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--- a/CMake/FindMKL.cmake
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+++ b/CMake/FindMKL.cmake
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@@ -7,21 +7,21 @@ FILE( WRITE "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src_mkl.cxx"
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"#include <iostream>\n #include <mkl.h>\n int main() { return 0; }\n" )
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try_compile(HAVE_MKL ${CMAKE_BINARY_DIR}
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${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src_mkl.cxx
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- CMAKE_FLAGS "${CMAKE_CXX_FLAGS} -mkl" )
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+ CMAKE_FLAGS "${CMAKE_CXX_FLAGS} -mkl" "-DINCLUDE_DIRECTORIES=${LAPACK_INCLUDE_DIRS}")
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# Check for mkl_vml_functions.h
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FILE( WRITE "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src_mkl_vml.cxx"
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"#include <iostream>\n #include <mkl_vml_functions.h>\n int main() { return 0; }\n" )
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try_compile(HAVE_MKL_VML ${CMAKE_BINARY_DIR}
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${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src_mkl_vml.cxx
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- CMAKE_FLAGS "${CMAKE_CXX_FLAGS} -mkl" )
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+ CMAKE_FLAGS "${CMAKE_CXX_FLAGS} -mkl" "-DINCLUDE_DIRECTORIES=${LAPACK_INCLUDE_DIRS}")
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# Check for fftw3
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FILE( WRITE "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src_mkl_fftw3.cxx"
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"#include <iostream>\n #include <fftw/fftw3.h>\n int main() { return 0; }\n" )
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try_compile(HAVE_MKL_FFTW3 ${CMAKE_BINARY_DIR}
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${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src_mkl_fftw3.cxx
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- CMAKE_FLAGS "${CMAKE_CXX_FLAGS} -mkl" )
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+ CMAKE_FLAGS "${CMAKE_CXX_FLAGS} -mkl" "-DINCLUDE_DIRECTORIES=${LAPACK_INCLUDE_DIRS}")
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IF ( HAVE_MKL )
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SET( MKL_FOUND 1 )
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diff --git a/CMake/FindVectorMath.cmake b/CMake/FindVectorMath.cmake
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index c0c919746..f5c511253 100644
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--- a/CMake/FindVectorMath.cmake
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+++ b/CMake/FindVectorMath.cmake
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@@ -19,7 +19,7 @@ IF ( NOT HAVE_VECTOR_MATH )
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"#include <iostream>\n #include <mkl_vml_functions.h>\n int main() { return 0; }\n" )
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try_compile(HAVE_MKL_VML ${CMAKE_BINARY_DIR}
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${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src_mkl_vml.cxx
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- CMAKE_FLAGS "${CMAKE_CXX_FLAGS}" )
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+ CMAKE_FLAGS "${CMAKE_CXX_FLAGS}" "-DINCLUDE_DIRECTORIES=${LAPACK_INCLUDE_DIRS}")
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IF (HAVE_MKL_VML)
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# enable VML only when MKL libraries have been picked up
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IF (MKL_FOUND)
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diff --git a/CMakeLists.txt b/CMakeLists.txt
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index 570d8a01f..56d939786 100644
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--- a/CMakeLists.txt
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+++ b/CMakeLists.txt
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@@ -464,6 +464,8 @@ ELSE(CMAKE_TOOLCHAIN_FILE)
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MESSAGE(STATUS "LAPACK libraries: ${LAPACK_LIBRARIES}")
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MESSAGE(STATUS "LAPACK linker flags: ${LAPACK_LINKER_FLAGS}")
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SET(LAPACK_LIBRARY ${LAPACK_LIBRARIES} ${LAPACK_LINKER_FLAGS})
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+ MESSAGE(STATUS "LAPACK_INCLUDE_DIRS: ${LAPACK_INCLUDE_DIRS}")
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+ INCLUDE_DIRECTORIES(${LAPACK_INCLUDE_DIRS})
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ELSE()
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MESSAGE(FATAL_ERROR "Could not find required libraries LAPACK &/or BLAS")
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ENDIF()
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@ -23,6 +23,7 @@
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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import llnl.util.tty as tty
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class Qmcpack(CMakePackage):
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@ -33,13 +34,14 @@ class Qmcpack(CMakePackage):
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homepage = "http://www.qmcpack.org/"
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url = "https://github.com/QMCPACK/qmcpack.git"
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# This download method is untrusted, and is not recommended
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# by the Spack manual. However, it is easier to maintain
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# because github hashes can occasionally change
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# This download method is untrusted, and is not recommended by the
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# Spack manual. However, it is easier to maintain because github hashes
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# can occasionally change.
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# NOTE: 12/19/2017 QMCPACK 3.0.0 does not build properly with Spack.
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version('3.3.0', git=url, tag='v3.3.0')
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version('3.2.0', git=url, tag='v3.2.0')
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version('3.1.1', git=url, tag='v3.1.1')
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version('3.1.0', git=url, tag='v3.1.0')
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version('3.0.0', git=url, tag='v3.0.0')
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version('develop', git=url)
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# These defaults match those in the QMCPACK manual
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@ -57,7 +59,7 @@ class Qmcpack(CMakePackage):
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'Array-of-Structure code. Only for CPU code'
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'and only in mixed precision')
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variant('timers', default=False,
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description='Build with support for timers')
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description='Build with support for timers')
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variant('da', default=False,
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description='Install with support for basic data analysis tools')
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variant('gui', default=False,
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@ -72,7 +74,9 @@ class Qmcpack(CMakePackage):
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conflicts('^openblas+ilp64')
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conflicts('^intel-mkl+ilp64')
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# Dependencies match those in the QMCPACK manual
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# Dependencies match those in the QMCPACK manual.
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# FIXME: once concretizer can unite unconditional and conditional
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# dependencies the some of the '~mpi' will not be necessary.
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depends_on('cmake@3.4.3:', type='build')
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depends_on('mpi', when='+mpi')
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depends_on('libxml2')
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@ -92,7 +96,7 @@ class Qmcpack(CMakePackage):
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# blas and lapack patching fails often and so are disabled at this time
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depends_on('py-numpy~blas~lapack', type='run', when='+da')
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# GUI is optional fpr data anlysis
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# GUI is optional for data anlysis
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# py-matplotlib leads to a long complex DAG for dependencies
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depends_on('py-matplotlib', type='run', when='+gui')
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@ -108,6 +112,10 @@ class Qmcpack(CMakePackage):
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patches=patch(patch_url, sha256=patch_checksum),
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when='~mpi')
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# This is Spack specific patch, we may need to enhance QMCPACK's CMake
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# in the near future.
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patch('cmake.diff')
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def patch(self):
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# FindLibxml2QMC.cmake doesn't check the environment by default
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# for libxml2, so we fix that.
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@ -116,22 +124,23 @@ def patch(self):
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'CMake/FindLibxml2QMC.cmake')
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def cmake_args(self):
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spec = self.spec
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args = []
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if '+mpi' in self.spec:
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mpi = self.spec['mpi']
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if '+mpi' in spec:
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mpi = spec['mpi']
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args.append('-DCMAKE_C_COMPILER={0}'.format(mpi.mpicc))
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args.append('-DCMAKE_CXX_COMPILER={0}'.format(mpi.mpicxx))
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args.append('-DMPI_BASE_DIR:PATH={0}'.format(mpi.prefix))
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# Currently FFTW_HOME and LIBXML2_HOME are used by CMake.
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# Any CMake warnings about other variables are benign.
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xml2_prefix = self.spec['libxml2'].prefix
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xml2_prefix = spec['libxml2'].prefix
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args.append('-DLIBXML2_HOME={0}'.format(xml2_prefix))
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args.append('-DLibxml2_INCLUDE_DIRS={0}'.format(xml2_prefix.include))
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args.append('-DLibxml2_LIBRARY_DIRS={0}'.format(xml2_prefix.lib))
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fftw_prefix = self.spec['fftw'].prefix
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fftw_prefix = spec['fftw'].prefix
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args.append('-DFFTW_HOME={0}'.format(fftw_prefix))
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args.append('-DFFTW_INCLUDE_DIRS={0}'.format(fftw_prefix.include))
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args.append('-DFFTW_LIBRARY_DIRS={0}'.format(fftw_prefix.lib))
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@ -140,15 +149,15 @@ def cmake_args(self):
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args.append('-DHDF5_ROOT={0}'.format(self.spec['hdf5'].prefix))
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# Default is MPI, serial version is convenient for cases, e.g. laptops
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if '+mpi' in self.spec:
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if '+mpi' in spec:
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args.append('-DQMC_MPI=1')
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elif '~mpi' in self.spec:
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elif '~mpi' in spec:
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args.append('-DQMC_MPI=0')
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# Default is real-valued single particle orbitals
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if '+complex' in self.spec:
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if '+complex' in spec:
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args.append('-DQMC_COMPLEX=1')
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elif '~complex' in self.spec:
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elif '~complex' in spec:
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args.append('-DQMC_COMPLEX=0')
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# When '-DQMC_CUDA=1', CMake automatically sets:
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@ -157,44 +166,56 @@ def cmake_args(self):
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# There is a double-precision CUDA path, but it is not as well
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# tested.
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if '+cuda' in self.spec:
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if '+cuda' in spec:
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args.append('-DQMC_CUDA=1')
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elif '~cuda' in self.spec:
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elif '~cuda' in spec:
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args.append('-DQMC_CUDA=0')
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# Mixed-precision versues double-precision CPU and GPU code
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if '+mixed' in self.spec:
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if '+mixed' in spec:
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args.append('-DQMC_MIXED_PRECISION=1')
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elif '~mixed' in self.spec:
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elif '~mixed' in spec:
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args.append('-DQMC_MIXED_PRECISION=0')
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# New Structure-of-Array (SOA) code, much faster than default
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# Array-of-Structure (AOS) code.
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# No support for local atomic orbital basis.
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if '+soa' in self.spec:
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if '+soa' in spec:
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args.append('-DENABLE_SOA=1')
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elif '~soa' in self.spec:
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elif '~soa' in spec:
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args.append('-DENABLE_SOA=0')
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# Manual Timers
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if '+timers' in self.spec:
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if '+timers' in spec:
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args.append('-DENABLE_TIMERS=1')
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elif '~timers' in self.spec:
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elif '~timers' in spec:
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args.append('-DENABLE_TIMERS=0')
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# # Proper MKL detection not working.
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# # Include MKL flags
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# if 'intel-mkl' in self.spec:
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# args.append('-DBLA_VENDOR=Intel10_64lp_seq')
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# args.append('-DQMC_INCLUDE={0}'.format(join_path(env['MKLROOT'],'include')))
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return args
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# Proper detection of optimized BLAS and LAPACK.
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# Based on the code from the deal II Spack package:
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# https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/dealii/package.py
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#
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# Basically, we override CMake's auto-detection mechanism
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# and use the Spack's interface instead
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lapack_blas = spec['lapack'].libs + spec['blas'].libs
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args.extend([
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'-DLAPACK_FOUND=true',
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'-DLAPACK_LIBRARIES=%s' % lapack_blas.joined(';')
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])
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# def setup_environment(self, spack_env, run_env):
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# # Add MKLROOT/lib to the CMAKE_PREFIX_PATH to enable CMake to find
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# # MKL libraries. MKLROOT environment variable must be defined for
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# # this to work properly.
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# if 'intel-mkl' in self.spec:
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# spack_env.append_path('CMAKE_PREFIX_PATH',format(join_path(env['MKLROOT'],'lib')))
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# Additionally, we need to pass the BLAS+LAPACK include directory for
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# header files. Intel MKL requires special case due to differences in
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# Darwin vs. Linux $MKLROOT naming schemes
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if 'intel-mkl' in self.spec:
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args.append(
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'-DLAPACK_INCLUDE_DIRS=%s' %
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format(join_path(env['MKLROOT'], 'include')))
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else:
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args.append(
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'-DLAPACK_INCLUDE_DIRS=%s;%s' % (
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self.spec['lapack'].prefix.include,
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self.spec['blas'].prefix.include))
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return args
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def install(self, spec, prefix):
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"""Make the install targets"""
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@ -228,7 +249,19 @@ def install(self, spec, prefix):
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def check(self):
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"""Run ctest after building binary.
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It can take over 24 hours to run all the regression tests, here we
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only run the unit tests and short tests."""
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only run the unit tests and short tests. If the unit tests fail,
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the QMCPACK installation aborts. On the other hand, the short tests
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are too strict and often fail, but are still useful to run. In the
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future, the short tests will be more reasonable in terms of quality
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assurance (i.e. they will not be so strict), but will be sufficient to
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validate QMCPACK in production."""
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with working_dir(self.build_directory):
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ctest('-L', 'unit')
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ctest('-R', 'short')
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try:
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ctest('-R', 'short')
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except ProcessError:
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warn = 'Unit tests passed, but short tests have failed.\n'
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warn += 'Please review failed tests before proceeding\n'
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warn += 'with production calculations.\n'
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tty.msg(warn)
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