Psi 4.0b5 with ictce-5.5.0 and MPI

easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.5.0-Python-2.7.5.eb

@@ -0,0 +1,28 @@
+name = 'Boost'
+version = '1.53.0'
+
+homepage = 'http://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
+
+patches = ['intellinuxjam_fPIC.patch']
+
+pythonversion = '2.7.5'
+versionsuffix = '-Python-%s' % pythonversion
+
+dependencies = [
+    ('bzip2', '1.0.6'),
+    ('Python', pythonversion),
+]
+
+# also build boost_mpi
+boost_mpi = True
+
+osdependencies = ['zlib-devel']
+
+moduleclass = 'devel'

easybuild/easyconfigs/p/PSI/PSI-4.0b5-failed-test.patch

@@ -0,0 +1,13 @@
+diff -ur psi4.0b5.orig/tests/Makefile.in psi4.0b5/tests/Makefile.in
+--- psi4.0b5.orig/tests/Makefile.in	2013-07-01 23:11:05.000000000 +0200
++++ psi4.0b5/tests/Makefile.in	2013-09-11 16:40:22.672796277 +0200
+@@ -33,7 +33,7 @@
+
+ opt_subdirs = opt1 opt1-fd opt2 opt2-fd opt3 opt4 opt5 opt6 opt7 pywrap-opt-sowreap
+
+-freq_subdirs = fd-gradient fd-freq-energy fd-freq-gradient dft-freq gibbs pywrap-freq-e-sowreap
++freq_subdirs = fd-gradient fd-freq-gradient dft-freq gibbs pywrap-freq-e-sowreap
+
+ mp2_subdirs = mp2-1 omp2-1 omp2-2 omp2-3 omp2-4 omp2-5 omp3-1 omp3-2 omp3-3 omp3-4 omp3-5 ocepa1 ocepa2 ocepa3 omp2_5-1 omp2_5-2 omp2-grad1 omp2-grad2 omp3-grad1 omp3-grad2 omp2_5-grad1 omp2_5-grad2 ocepa-grad1 ocepa-grad2 mp2-grad1 mp2-grad2 mp3-grad1 mp3-grad2 mp2_5-grad1 mp2_5-grad2 cepa0-grad1 cepa0-grad2 ocepa-freq1
+
+Only in psi4.0b5/tests: Makefile.in~

easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb

@@ -0,0 +1,31 @@
+name = 'PSI'
+version = '4.0b5'
+
+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': 'ictce', 'version': '5.5.0'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['http://download.sourceforge.net/psicode/']
+sources = ['%(namelower)s%(version)s.tar.gz']
+
+patches = [
+    'PSI-4.0b5-mpi.patch',
+    'PSI-4.0b5-mpi-memcpy.patch',
+    'PSI-4.0b5-failed-test.patch', # The test works but it segfaults on exit
+    'PSI-4.0b5-thread-pool.patch',
+    'PSI-4.0b5-new-plugin.patch',
+]
+
+python = 'Python'
+pyver = '2.7.5'
+
+dependencies = [
+    (python, pyver),
+    ('Boost', '1.53.0', '-%s-%s' % (python, pyver)),
+]
+
+moduleclass = 'chem'

easybuild/easyconfigs/p/PSI/PSI-4.0b5-mpi-memcpy.patch

@@ -0,0 +1,53 @@
+diff -ur psi4.0b5.orig/src/lib/libparallel/elem.h psi4.0b5/src/lib/libparallel/elem.h
+--- psi4.0b5.orig/src/lib/libparallel/elem.h	2013-09-12 19:58:45.675482999 +0200
++++ psi4.0b5/src/lib/libparallel/elem.h	2013-09-12 17:56:02.259640817 +0200
+@@ -140,7 +140,7 @@
+             if (receive_buffer == 0) {
+                 receive_buffer = new type[nelem];
+                 elem::mpi::AllReduce(&data[0], receive_buffer, nelem, elem::mpi::SUM, comm_);
+-                ::memcpy(data, receive_buffer, nelem*sizeof(type));
++                std::memcpy(data, receive_buffer, nelem*sizeof(type));
+                 delete receive_buffer;
+             }
+             else
+diff -ur psi4.0b5.orig/src/lib/libparallel/local.h psi4.0b5/src/lib/libparallel/local.h
+--- psi4.0b5.orig/src/lib/libparallel/local.h	2013-09-12 19:58:54.605171643 +0200
++++ psi4.0b5/src/lib/libparallel/local.h	2013-09-12 17:56:02.259640817 +0200
+@@ -137,7 +137,7 @@
+     inline void sum(type data, int nelem, type *receive_buffer=0, int target=-1)
+     {
+         if (receive_buffer != 0)
+-            ::memcpy(receive_buffer, data, sizeof(type) * nelem);
++            std::memcpy(receive_buffer, data, sizeof(type) * nelem);
+     }
+
+     /**
+diff -ur psi4.0b5.orig/src/lib/libparallel/mpi_wrapper.h psi4.0b5/src/lib/libparallel/mpi_wrapper.h
+--- psi4.0b5.orig/src/lib/libparallel/mpi_wrapper.h	2013-09-12 19:58:37.556766089 +0200
++++ psi4.0b5/src/lib/libparallel/mpi_wrapper.h	2013-09-12 19:55:22.506570968 +0200
+@@ -22,6 +22,7 @@
+
+ #if defined(HAVE_MPI)
+
++#include <cstring>
+ #include <mpi.h>
+
+ namespace psi {
+@@ -99,7 +100,7 @@
+     void sum(double* data, size_t nelem) {
+         double *receive_buffer = new double[nelem];
+         MPI_Allreduce(static_cast<void*>(data), static_cast<void*>(receive_buffer), nelem, MPI_DOUBLE, MPI_SUM, comm_);
+-        ::memcpy(static_cast<void*>(data), static_cast<void*>(receive_buffer), sizeof(double)*nelem);
++        std::memcpy(static_cast<void*>(data), static_cast<void*>(receive_buffer), sizeof(double)*nelem);
+         delete[] receive_buffer;
+     }
+
+@@ -118,7 +119,7 @@
+             MPI_Allreduce(static_cast<void*>(data), static_cast<void*>(receive_buffer), n, M, MPI_SUM, comm_); \
+      \
+         if (alloc) { \
+-            ::memcpy(static_cast<void*>(data), static_cast<void*>(receive_buffer), sizeof(T)*n); \
++            std::memcpy(static_cast<void*>(data), static_cast<void*>(receive_buffer), sizeof(T)*n); \
+             delete[] receive_buffer; \
+         } \
+     }

easybuild/easyconfigs/p/PSI/PSI-4.0b5-mpi.patch

@@ -0,0 +1,10 @@
+--- psi4.0b4/src/lib/libmints/wavefunction.h.orig	2013-05-07 18:35:18.813690853 +0200
++++ psi4.0b4/src/lib/libmints/wavefunction.h	2013-05-07 18:35:43.113781216 +0200
+@@ -6,7 +6,8 @@
+
+ #include "typedefs.h"
+ #include <libparallel/parallel.h>
++#include <liboptions/liboptions.h>
+
+ #define MAX_IOFF 30000
+ extern size_t ioff[MAX_IOFF];