{chem,data}[intel/2020a] h5py v2.10.0, yaff v1.6.0 w/ Python 3.8.2 + add patch for h5py 2.10.0 to avoid triggering MPI_Init at import

easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-Python-3.7.4.eb

@@ -14,7 +14,11 @@ toolchainopts = {'usempi': True}
 
 source_urls = [PYPI_SOURCE]
 sources = [SOURCE_TAR_GZ]
-checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d']
+patches = ['h5py-%(version)s_avoid-mpi-init.patch']
+checksums = [
+    '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d',  # h5py-2.10.0.tar.gz
+    '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f',  # h5py-2.10.0_avoid-mpi-init.patch
+]
 
 builddependencies = [('pkgconfig', '1.5.1', versionsuffix)]
 

easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb

@@ -14,7 +14,11 @@ toolchainopts = {'usempi': True}
 
 source_urls = [PYPI_SOURCE]
 sources = [SOURCE_TAR_GZ]
-checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d']
+patches = ['h5py-%(version)s_avoid-mpi-init.patch']
+checksums = [
+    '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d',  # h5py-2.10.0.tar.gz
+    '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f',  # h5py-2.10.0_avoid-mpi-init.patch
+]
 
 builddependencies = [('pkgconfig', '1.5.1', versionsuffix)]
 

easybuild/easyconfigs/h/h5py/h5py-2.10.0-fosscuda-2019b-Python-3.7.4.eb

@@ -14,7 +14,11 @@ toolchainopts = {'usempi': True}
 
 source_urls = [PYPI_SOURCE]
 sources = [SOURCE_TAR_GZ]
-checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d']
+patches = ['h5py-%(version)s_avoid-mpi-init.patch']
+checksums = [
+    '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d',  # h5py-2.10.0.tar.gz
+    '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f',  # h5py-2.10.0_avoid-mpi-init.patch
+]
 
 builddependencies = [('pkgconfig', '1.5.1', versionsuffix)]
 

easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2019b-Python-3.7.4.eb

@@ -14,7 +14,11 @@ toolchainopts = {'usempi': True}
 
 source_urls = [PYPI_SOURCE]
 sources = [SOURCE_TAR_GZ]
-checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d']
+patches = ['h5py-%(version)s_avoid-mpi-init.patch']
+checksums = [
+    '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d',  # h5py-2.10.0.tar.gz
+    '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f',  # h5py-2.10.0_avoid-mpi-init.patch
+]
 
 builddependencies = [('pkgconfig', '1.5.1', versionsuffix)]
 

easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb

@@ -0,0 +1,37 @@
+easyblock = 'PythonPackage'
+
+name = 'h5py'
+version = '2.10.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://www.h5py.org/'
+description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
+ version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
+ amounts of data."""
+
+toolchain = {'name': 'intel', 'version': '2020a'}
+toolchainopts = {'usempi': True}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+patches = ['h5py-%(version)s_avoid-mpi-init.patch']
+checksums = [
+    '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d',  # h5py-2.10.0.tar.gz
+    '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f',  # h5py-2.10.0_avoid-mpi-init.patch
+]
+
+builddependencies = [('pkgconfig', '1.5.1', versionsuffix)]
+
+dependencies = [
+    ('Python', '3.8.2'),
+    ('SciPy-bundle', '2020.03', versionsuffix),
+    ('HDF5', '1.10.6'),
+]
+
+use_pip = False
+download_dep_fail = True
+
+# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip
+prebuildopts = 'python setup.py configure --mpi --hdf5=$EBROOTHDF5 && '
+
+moduleclass = 'data'

easybuild/easyconfigs/h/h5py/h5py-2.10.0_avoid-mpi-init.patch

@@ -0,0 +1,85 @@
+avoid that 'import h5py' triggers MPI_Init via mpi4py
+
+backported to h5py 2.10.0 from https://github.com/h5py/h5py/pull/1552 by Kenneth Hoste (HPC-UGent)
+
+diff -ru h5py-2.10.0.orig/h5py/api_types_ext.pxd h5py-2.10.0/h5py/api_types_ext.pxd
+--- h5py-2.10.0.orig/h5py/api_types_ext.pxd	2019-09-06 23:29:33.000000000 +0200
++++ h5py-2.10.0/h5py/api_types_ext.pxd	2020-05-25 19:30:30.000000000 +0200
+@@ -12,7 +12,7 @@
+ include 'config.pxi'
+
+ IF MPI:
+-    from mpi4py.MPI cimport MPI_Comm, MPI_Info, Comm, Info
++    from mpi4py.libmpi cimport MPI_Comm, MPI_Info
+
+ cdef extern from "stdlib.h":
+   ctypedef long size_t
+@@ -52,6 +52,7 @@
+ cdef extern from "Python.h":
+   ctypedef void PyObject
+   ctypedef ssize_t Py_ssize_t
++  ctypedef size_t Py_uintptr_t
+
+   PyObject* PyErr_Occurred()
+   void PyErr_SetString(object type, char *message)
+diff -ru h5py-2.10.0.orig/h5py/h5p.pyx h5py-2.10.0/h5py/h5p.pyx
+--- h5py-2.10.0.orig/h5py/h5p.pyx	2019-09-06 23:29:33.000000000 +0200
++++ h5py-2.10.0/h5py/h5p.pyx	2020-05-25 19:33:24.000000000 +0200
+@@ -17,6 +17,7 @@
+ from cpython.buffer cimport PyObject_CheckBuffer, \
+                             PyObject_GetBuffer, PyBuffer_Release, \
+                             PyBUF_SIMPLE
++from cpython.long cimport PyLong_AsVoidPtr
+
+ from utils cimport  require_tuple, convert_dims, convert_tuple, \
+                     emalloc, efree, \
+@@ -1161,7 +1162,7 @@
+
+     IF MPI:
+         @with_phil
+-        def set_fapl_mpio(self, Comm comm not None, Info info not None):
++        def set_fapl_mpio(self, comm, info):
+             """ (Comm comm, Info info)
+
+             Set MPI-I/O Parallel HDF5 driver.
+@@ -1169,7 +1170,12 @@
+             Comm: An mpi4py.MPI.Comm instance
+             Info: An mpi4py.MPI.Info instance
+             """
+-            H5Pset_fapl_mpio(self.id, comm.ob_mpi, info.ob_mpi)
++            from mpi4py.MPI import Comm, Info, _handleof
++            assert isinstance(comm, Comm)
++            assert isinstance(info, Info)
++            cdef Py_uintptr_t _comm = _handleof(comm)
++            cdef Py_uintptr_t _info = _handleof(info)
++            H5Pset_fapl_mpio(self.id, <MPI_Comm>_comm, <MPI_Info>_info)
+
+
+         @with_phil
+@@ -1183,20 +1189,22 @@
+             """
+             cdef MPI_Comm comm
+             cdef MPI_Info info
++            from mpi4py.MPI import Comm, Info, _addressof
+
+             H5Pget_fapl_mpio(self.id, &comm, &info)
+             pycomm = Comm()
+-            pyinfo = Info()
+-            MPI_Comm_dup(comm, &pycomm.ob_mpi)
+-            MPI_Info_dup(info, &pyinfo.ob_mpi)
++            MPI_Comm_dup(comm, <MPI_Comm *>PyLong_AsVoidPtr(_addressof(pycomm)))
+             MPI_Comm_free(&comm)
++
++            pyinfo = Info()
++            MPI_Info_dup(info, <MPI_Info *>PyLong_AsVoidPtr(_addressof(pyinfo)))
+             MPI_Info_free(&info)
+
+             return (pycomm, pyinfo)
+
+
+         @with_phil
+-        def set_fapl_mpiposix(self, Comm comm not None, bint use_gpfs_hints=0):
++        def set_fapl_mpiposix(self, comm, bint use_gpfs_hints=0):
+             """ Obsolete.
+             """
+             raise RuntimeError("MPI-POSIX driver is broken; removed in h5py 2.3.1")

easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb

@@ -0,0 +1,42 @@
+# Updated from previous config
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+#
+# Building this in interactive Slurm session will result in freeze during either
+# runtest phase or sanity_check_commands phase (python -c 'import yaff')
+#
+# If you submit this as non-interactive Slurm job, it will build just fine.
+# Possibly root cause: https://github.com/h5py/h5py/issues/917
+#
+easyblock = 'PythonPackage'
+
+name = 'yaff'
+version = '1.6.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://molmod.github.io/yaff/'
+description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code."""
+
+toolchain = {'name': 'intel', 'version': '2020a'}
+
+source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s']
+sources = [SOURCE_TAR_GZ]
+checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa']
+
+dependencies = [
+    ('Python', '3.8.2'),
+    ('h5py', '2.10.0', versionsuffix),
+    ('molmod', '1.4.5', versionsuffix),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+# required because we're building a Python package using Intel compilers on top of Python built with GCC
+check_ldshared = True
+
+runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; "
+runtest += "python setup.py build_ext -i; nosetests -v"
+
+moduleclass = 'chem'