Merge pull request #372 from sourceryinstitute/issue-355-upgrade-mpich

Issue 355 upgrade mpich

Author: Damian Rouson

INSTALL.md

@@ -199,7 +199,7 @@ acceptable prerequisite or reaching the end of a branch.
 ```text
 opencoarrays
 ├── cmake-3.4.0
-└── mpich-3.1.4
+└── mpich-3.2
     └── gcc-6.1.0
         ├── flex-2.6.0
         │   └── bison-3.0.4

doc/dependency_tree/opencoarrays-tree.txt

@@ -1,6 +1,6 @@
 opencoarrays
 ├── cmake-3.4.0
-└── mpich-3.1.4
+└── mpich-3.2
     └── gcc-6.1.0
         ├── flex-2.6.0
         │   └── bison-3.0.4

doc/dependency_tree/opencoarrays/mpich-3.1.4/gcc-6.1.0/flex-2.6.0/bison-3.0.4/m4-1.4.17/.gitkeep renamed to doc/dependency_tree/opencoarrays/mpich-3.2/gcc-6.1.0/flex-2.6.0/bison-3.0.4/m4-1.4.17/.gitkeep

@@ -1,7 +1,8 @@
 # Make the build directory, configure, and build
 # shellcheck disable=SC2154
 
-source ${OPENCOARRAYS_SRC_DIR}/prerequisites/build-functions/edit_GCC_download_prereqs_file_if_necessary.sh
+# shellcheck source=prerequisites/build-functions/edit_GCC_download_prereqs_file_if_necessary.sh
+source "${OPENCOARRAYS_SRC_DIR}/prerequisites/build-functions/edit_GCC_download_prereqs_file_if_necessary.sh"
 
 build_and_install()
 {
@@ -20,6 +21,12 @@ build_and_install()
 
   if [[ "${package_to_build}" != "gcc" ]]; then
 
+    if [[ "${package_to_build}" == "mpich" && "${version_to_build}" == "3.2" ]]; then
+      info "Patching MPICH 3.2 on Mac OS due to segfault bug (see http://lists.mpich.org/pipermail/discuss/2016-May/004764.html)."
+      sed 's/} MPID_Request ATTRIBUTE((__aligned__(32)));/} ATTRIBUTE((__aligned__(32))) MPID_Request;/g' \
+        "${download_path}/${package_source_directory}/src/include/mpiimpl.h"
+    fi
+
     info "Configuring ${package_to_build} ${version_to_build} with the following command:"
     info "FC=\"${FC:-'gfortran'}\" CC=\"${CC:-'gcc'}\" CXX=\"${CXX:-'g++'}\" \"${download_path}/${package_source_directory}\"/configure --prefix=\"${install_path}\""
     FC="${FC:-'gfortran'}" CC="${CC:-'gcc'}" CXX="${CXX:-'g++'}" "${download_path}/${package_source_directory}"/configure --prefix="${install_path}"

doc/dependency_tree/opencoarrays/mpich-3.1.4/gcc-6.1.0/gmp/.gitkeep renamed to doc/dependency_tree/opencoarrays/mpich-3.2/gcc-6.1.0/gmp/.gitkeep

@@ -14,7 +14,7 @@ replace_wget()
     sed -i${backup_extension} -e '2 a\'$'\n'". ${OPENCOARRAYS_SRC_DIR}/prerequisites/build-functions/ftp_url.sh"$'\n' "${download_prereqs_file}"
   fi
 
-  arg_string="${gcc_prereqs_fetch_args[@]:-}"
+  arg_string="${gcc_prereqs_fetch_args[*]:-}"
 
   info "Using the following command to replace wget in the GCC download_prerequisites file:"
   info "sed -i${backup_extension} s/\"${wget_command}\"/\"${gcc_prereqs_fetch} ${arg_string} \"/ \"${download_prereqs_file}\""
@@ -31,7 +31,7 @@ edit_GCC_download_prereqs_file_if_necessary()
   download_prereqs_file="${PWD}/contrib/download_prerequisites"
 
   # Grab the line with the first occurence of 'wget'
-  wget_line=`grep wget "${download_prereqs_file}" | head -1` || true
+  wget_line=$(grep wget "${download_prereqs_file}" | head -1) || true
   wget_command="${wget_line%%ftp*}" # grab everything before ftp
 
   # Check for wget format used before GCC 7

doc/dependency_tree/opencoarrays/mpich-3.1.4/gcc-6.1.0/mpc/.gitkeep renamed to doc/dependency_tree/opencoarrays/mpich-3.2/gcc-6.1.0/mpc/.gitkeep

@@ -28,7 +28,7 @@ set_or_print_default_version()
   package_version=(
     "cmake:3.4.0"
     "gcc:6.1.0"
-    "mpich:3.1.4"
+    "mpich:3.2"
     "wget:1.16.3"
     "flex:2.6.0"
     "bison:3.0.4"

doc/dependency_tree/opencoarrays/mpich-3.1.4/gcc-6.1.0/mpfr/.gitkeep renamed to doc/dependency_tree/opencoarrays/mpich-3.2/gcc-6.1.0/mpfr/.gitkeep

@@ -4,7 +4,7 @@ print_header()
   clear
   echo ""
   echo "*** By default, building OpenCoarrays requires CMake 3.4.0 or later,      ***"
-  echo "*** MPICH 3.1.4, and GCC Fortran (gfortran) 6.1.0 or later.  To see       ***"
+  echo "*** MPICH 3.2, and GCC Fortran (gfortran) 6.1.0 or later.  To see         ***"
   echo "*** options for forcing the use of older or alternative packages, execute ***"
   echo "*** this script with the -h flag.  This script will recursively traverse  ***"
   echo "*** the following dependency tree, asking permission to download, build,  ***"