Merge pull request #7109 from hajgato/psi4

{chem}[intel/2018b] PSI4 1.2.1 (REVIEW)
easybuilders · Nov 14, 2018 · 7c7d051 · 7c7d051
2 parents 63339b9 + ae38b01
commit 7c7d051
Show file tree

Hide file tree

Showing 6 changed files with 286 additions and 0 deletions.
diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.8-intel-2018b.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.8-intel-2018b.eb
@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'CheMPS2'
+version = '1.8.8'
+
+homepage = 'https://github.com/SebWouters/CheMPS2'
+description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the
+density matrix renormalization group (DMRG) for ab initio quantum chemistry."""
+
+toolchain = {'name': 'intel', 'version': '2018b'}
+
+source_urls = ['https://github.com/SebWouters/CheMPS2/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['c64a0572d333c7c071c3ef59cd95eeb39abe766496cb28df184ce44bdb38f75c']
+
+builddependencies = [('CMake', '3.12.1')]
+
+dependencies = [
+    ('HDF5', '1.10.2')
+]
+
+runtest = 'test'
+
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'],
+    'dirs': ['include/chemps2']
+}
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-2.7.15.eb
@@ -0,0 +1,32 @@
+easyblock = 'PythonBundle'
+
+name = 'deepdiff'
+version = '3.3.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://deepdiff.readthedocs.io/en/latest/'
+description = """DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively."""
+
+toolchain = {'name': 'intel', 'version': '2018b'}
+
+dependencies = [('Python', '2.7.15')]
+
+use_pip = True
+
+exts_list = [
+    ('jsonpickle', '1.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/j/jsonpickle/'],
+        'checksums': ['d43ede55b3d9b5524a8e11566ea0b11c9c8109116ef6a509a1b619d2041e7397'],
+    }),
+    (name, version, {
+        'source_urls': ['https://pypi.python.org/packages/source/d/deepdiff/'],
+        'checksums': ['ecad8e16a96ffd27e8f40c9801a6ab16ec6a7e7e6e6859a7710ba4695f22702c'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-2.7.15.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'networkx'
+version = '2.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://pypi.python.org/pypi/networkx'
+description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics,
+ and functions of complex networks."""
+
+toolchain = {'name': 'intel', 'version': '2018b'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_ZIP]
+checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b']
+
+dependencies = [('Python', '2.7.15')]
+
+use_pip = True
+download_dep_fail = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.2.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.2.1-intel-2018b-Python-2.7.15.eb
@@ -0,0 +1,57 @@
+easyblock = 'EB_PSI'
+
+name = 'PSI4'
+version = '1.2.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://www.psicode.org/'
+description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for
+ efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform
+ computations with more than 2500 basis functions running serially or in parallel."""
+
+toolchain = {'name': 'intel', 'version': '2018b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://github.com/psi4/psi4/archive']
+sources = ['v%(version)s.tar.gz']
+patches = ['PSI4-%(version)s_fix_cmake_release.patch']
+checksums = [
+    'fbde7ee67174f7ba7b7f6f4e8117ce8b80f5fd10414577f5b0fcdbaa6c8ba020',  # v1.2.1.tar.gz
+    '38e964973d2f0797f28a9a09165ae67fc1dba454e44e5e40e9d3f06a22092efb',  # PSI4-1.2.1_fix_cmake_release.patch
+]
+
+dependencies = [
+    ('Python', '2.7.15'),
+    #  PCMSolver recent versions fail with recent intel compilers.
+    #  Tried with intel/201{7,8}b, and versions 1.1.12, and 1.2.1
+    #  See in more details: https://github.com/PCMSolver/pcmsolver/issues/159
+    #  ('PCMSolver', '1.2.1'),
+    ('CheMPS2', '1.8.8'),
+    #  Tests are failing with pytest 3.9.2
+    ('pytest', '3.8.2', versionsuffix),
+    ('networkx', '2.2', versionsuffix),
+    ('deepdiff', '3.3.0', versionsuffix),
+]
+
+builddependencies = [
+    ('CMake', '3.12.1'),
+    # Perl needed for the ctest test suite during the installation, not for the pytest test suite after the installation
+    # ('Perl', '5.28.0'),
+]
+
+configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF '
+#  Install python mudule to the standard location instead of lib
+configopts += '-DPYMOD_INSTALL_LIBDIR=/python%(pyshortver)s/site-packages '
+#  Add bundled (downloaded) packages
+# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore
+configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON '
+
+# runtest uses ctest, and some of the thests have to be manually compared
+# to the reference output (those tests are marked failed)
+# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework)
+# runtest = '-L smoke'
+runtest = False
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.2.1_fix_cmake_release.patch b/easybuild/easyconfigs/p/PSI4/PSI4-1.2.1_fix_cmake_release.patch
@@ -0,0 +1,81 @@
+# remove CMAKE_BUILD_TYPE check (beacuse it is set to EasyBuildRelease to avoid -O3 optimization flag)
+# November 02nd 2018 by B. Hajgato - (Free University Brussels - VUB)
+diff --new-file -ru psi4-1.2.1.orig/cmake/autocmake_safeguards.cmake psi4-1.2.1/cmake/autocmake_safeguards.cmake
+--- psi4-1.2.1.orig/cmake/autocmake_safeguards.cmake	2018-07-25 04:11:25.000000000 +0200
++++ psi4-1.2.1/cmake/autocmake_safeguards.cmake	2018-10-30 16:18:26.650251435 +0100
+@@ -19,8 +19,8 @@
+ string(TOLOWER "${CMAKE_BUILD_TYPE}" cmake_build_type_tolower)
+ string(TOUPPER "${CMAKE_BUILD_TYPE}" cmake_build_type_toupper)
+
+-if(NOT cmake_build_type_tolower STREQUAL "debug" AND
+-   NOT cmake_build_type_tolower STREQUAL "release" AND
+-   NOT cmake_build_type_tolower STREQUAL "relwithdebinfo")
+-    message(FATAL_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo (case-insensitive).")
+-endif()
++#if(NOT cmake_build_type_tolower STREQUAL "debug" AND
++#   NOT cmake_build_type_tolower STREQUAL "release" AND
++#   NOT cmake_build_type_tolower STREQUAL "relwithdebinfo")
++#    message(FATAL_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo (case-insensitive).")
++#endif()
+diff --new-file -ru psi4-1.2.1.orig/external/upstream/gau2grid/CMakeLists.txt psi4-1.2.1/external/upstream/gau2grid/CMakeLists.txt
+--- psi4-1.2.1.orig/external/upstream/gau2grid/CMakeLists.txt	2018-07-25 04:11:25.000000000 +0200
++++ psi4-1.2.1/external/upstream/gau2grid/CMakeLists.txt	2018-10-30 16:36:23.558755892 +0100
+@@ -16,6 +16,7 @@
+         GIT_REPOSITORY https://github.com/dgasmith/gau2grid
+         GIT_TAG v1.1.0
+         UPDATE_COMMAND ""
++        PATCH_COMMAND  sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake
+         CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX}
+                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                    -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+diff --new-file -ru psi4-1.2.1.orig/external/upstream/libint/CMakeLists.txt psi4-1.2.1/external/upstream/libint/CMakeLists.txt
+--- psi4-1.2.1.orig/external/upstream/libint/CMakeLists.txt	2018-07-25 04:11:25.000000000 +0200
++++ psi4-1.2.1/external/upstream/libint/CMakeLists.txt	2018-10-30 16:40:02.623920471 +0100
+@@ -15,6 +15,7 @@
+         GIT_REPOSITORY https://github.com/evaleev/libint
+         GIT_TAG 024738c  # v1.2.1+2 release-1-2-1
+         UPDATE_COMMAND ""
++        PATCH_COMMAND  sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake
+         CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX}
+                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                    -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+--- psi4-1.2.1/external/upstream/dkh/CMakeLists.txt.orig	2018-07-25 04:11:25.000000000 +0200
++++ psi4-1.2.1/external/upstream/dkh/CMakeLists.txt	2018-10-31 12:48:38.125438986 +0100
+@@ -16,6 +16,7 @@
+             GIT_REPOSITORY https://github.com/psi4/dkh
+             GIT_TAG v1.2
+             UPDATE_COMMAND ""
++            PATCH_COMMAND  sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake
+             CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX}
+                        -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                        -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+--- psi4-1.2.1/external/upstream/libefp/CMakeLists.txt.orig	2018-07-25 04:11:25.000000000 +0200
++++ psi4-1.2.1/external/upstream/libefp/CMakeLists.txt	2018-10-31 12:59:04.215388286 +0100
+@@ -17,6 +17,7 @@
+             GIT_REPOSITORY https://github.com/ilyak/libefp
+             GIT_TAG 15cd7ce  # v1.5.0 + 10 (docs and a cmake lapack patch)
+             UPDATE_COMMAND ""
++            PATCH_COMMAND  sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake
+             CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX}
+                        -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                        -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+--- psi4-1.2.1/external/upstream/gdma/CMakeLists.txt.orig	2018-07-25 04:11:25.000000000 +0200
++++ psi4-1.2.1/external/upstream/gdma/CMakeLists.txt	2018-10-31 12:49:20.773048665 +0100
+@@ -16,6 +16,7 @@
+             GIT_REPOSITORY https://github.com/psi4/gdma
+             GIT_TAG 9d607d7  # v2.2.6-2-g9d607d7
+             UPDATE_COMMAND ""
++            PATCH_COMMAND  sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake
+             CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX}
+                        -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                        -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+--- psi4-1.2.1/external/upstream/libxc/CMakeLists.txt.orig	2018-11-05 10:15:58.840945366 +0100
++++ psi4-1.2.1/external/upstream/libxc/CMakeLists.txt	2018-11-05 10:14:59.248068042 +0100
+@@ -15,6 +15,7 @@
+         GIT_REPOSITORY https://github.com/psi4/libxc
+         GIT_TAG libxc4retweaked  # v4.0 (0387b1d1) + !62 + MVS corr + 4.0.2 bump + 2 build commits = c754e28
+         UPDATE_COMMAND ""
++        PATCH_COMMAND  sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake
+         CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX}
+                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                    -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-2.7.15.eb
@@ -0,0 +1,58 @@
+easyblock = 'PythonBundle'
+
+name = 'pytest'
+version = '3.8.2'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://pytest.org'
+description = """pytest: simple powerful testing with Python"""
+
+toolchain = {'name': 'intel', 'version': '2018b'}
+
+dependencies = [('Python', '2.7.15')]
+
+use_pip = True
+
+exts_list = [
+    ('py', '1.7.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/p/py/'],
+        'checksums': ['bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694'],
+    }),
+    ('attrs', '18.2.0', {
+        'modulename': 'attr',
+        'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'],
+        'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'],
+    }),
+    ('pluggy', '0.8.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'],
+        'checksums': ['447ba94990e8014ee25ec853339faf7b0fc8050cdc3289d4d71f7f410fb90095'],
+    }),
+    ('atomicwrites', '1.2.1', {
+        'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'],
+        'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'],
+    }),
+    ('more-itertools', '4.3.0', {
+        'modulename': 'more_itertools',
+        'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'],
+        'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'],
+    }),
+    ('scandir', '1.9.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'],
+        'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'],
+    }),
+    ('pathlib2', '2.3.2', {
+        'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'],
+        'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'],
+    }),
+    (name, version, {
+        'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'],
+        'checksums': ['9332147e9af2dcf46cd7ceb14d5acadb6564744ddff1fe8c17f0ce60ece7d9a2'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/pytest'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'tools'