Merge branch 'master' into vehre/failed-images

Author: vehre

.VERSION

@@ -2,4 +2,4 @@
 # version, i.e., code is from SCM/git. This project uses semantic
 # versioning. For details see http://semver.org
 
-1.8.5
+1.8.7

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,6 +8,16 @@
 | --------------------------------- | ---------------------------|
 | ![Issue Stats][PR response img]   | ![Codecov branch][coverage]|
 
+## Summary of changes ##
+
+Summarize what you changed
+
+## Rationale for changes ##
+
+Why did you make these changes?
+
+## Additional info and certifications ##
+
 This pull request (PR) is a:
  - [ ] Bug fix
  - [ ] Feature addition
@@ -46,13 +56,6 @@ I certify that:
        check and following the directions on the CLA assistant webpage
  - [ ] I have ensured that the test coverage hasn't gone down and added new [unit tests] to cover an new code added to the library
 
-## Summary of changes ##
-
-Summarize what you changed
-
-## Rationale for changes ##
-
-Why did you make these changes?
 
 ## For contributors and SI team members with code review priviledges ##
 

.travis.yml

@@ -86,9 +86,9 @@ before_install:
       git tag -v ${TRAVIS_TAG}
     fi
     set +o errexit
-  - 
-  - 
-  - 
+  -
+  -
+  -
   - |
     set -o errexit
     if [[ $TRAVIS ]] && [[ "X$TRAVIS_OS_NAME" = "Xosx" ]]; then
@@ -191,49 +191,49 @@ after_success:
   - gcov-6 --version
   - bash <(curl -s https://codecov.io/bash) -x $(which gcov-6)
 
-before_deploy:
-  - git archive -v --prefix "OpenCoarrays-${TRAVIS_TAG}/" -o "OpenCoarrays-${TRAVIS_TAG}.tar.gz" ${TRAVIS_TAG}
-  - |
-    echo '# To verify cryptographic checksums `shasum -c opencoarrays-'"${TRAVIS_TAG}"'-SHA256.txt` on Mac OS X,' > "opencoarrays-${TRAVIS_TAG}-SHA256.txt
-    echo '# `sha256sum -c  opencoarrays-'"${TRAVIS_TAG}"'-SHA256.txt` on Linux.' >> "opencoarrays-${TRAVIS_TAG}-SHA256.txt
-    if [[ "X$(uname -s)" == "XDarwin" ]]; then
-      shasum -a 256 "OpenCoarrays-${TRAVIS_TAG}.tar.gz" >> "opencoarrays-${TRAVIS_TAG}-SHA256.txt
-    else
-      sha256sum  "OpenCoarrays-${TRAVIS_TAG}.tar.gz" >> "opencoarrays-${TRAVIS_TAG}-SHA256.txt
-    fi
-  - |
-    set -o errexit
-    openssl aes-256-cbc -K $encrypted_ef4535c39461_key -iv $encrypted_ef4535c39461_iv -in subkey-328B3A0E-secret.asc.enc -out ./subkey-328B3A0E-secret.asc -d
-    gpg --allow-secret-key-import --import ./subkey-328B3A0E-secret.asc && rm subkey-328B3A0E-secret.asc
-    rm subkey-328B3A0E-secret.* || true
-    unset encrypted_ef4535c39461_key || true
-    unset encrypted_ef4535c39461_iv || true
-    gpg --armor --detach-sign -u 328B3A0E --comment 'Mac users can use GPGTools - https://gpgtools.org' \
-      --comment "Download Izaak Beekman's GPG public key from your" \
-      --comment 'trusted key server or from' \
-      --comment 'https://izaakbeekman.com/izaak.pubkey.txt' \
-      --comment 'Next add it to your GPG keyring, e.g.,' \
-      --comment '`curl https://izaakbeekman.com/izaak.pubkey.txt | gpg --import`' \
-      --comment "Make sure you have verified that the release archive's" \
-      --comment 'SHA256 checksum matches the provided' \
-      --comment "opencoarrays-${TRAVIS_TAG}-SHA256.txt and ensure that this file" \
-      --comment "and it's signature are in the same directory. Then" \
-      --comment 'verify with:' \
-      --comment '`gpg --verify opencoarrays-'"${TRAVIS_TAG}"'-SHA256.txt.asc`' \
-      "opencoarrays-${TRAVIS_TAG}-SHA256.txt"
-    set +o errexit
+# before_deploy:
+#   - git archive -v --prefix "OpenCoarrays-${TRAVIS_TAG}/" -o "OpenCoarrays-${TRAVIS_TAG}.tar.gz" ${TRAVIS_TAG}
+#   - |
+#     echo '# To verify cryptographic checksums `shasum -c opencoarrays-'"${TRAVIS_TAG}"'-SHA256.txt` on Mac OS X,' > "opencoarrays-${TRAVIS_TAG}-SHA256.txt
+#     echo '# `sha256sum -c  opencoarrays-'"${TRAVIS_TAG}"'-SHA256.txt` on Linux.' >> "opencoarrays-${TRAVIS_TAG}-SHA256.txt
+#     if [[ "X$(uname -s)" == "XDarwin" ]]; then
+#       shasum -a 256 "OpenCoarrays-${TRAVIS_TAG}.tar.gz" >> "opencoarrays-${TRAVIS_TAG}-SHA256.txt
+#     else
+#       sha256sum  "OpenCoarrays-${TRAVIS_TAG}.tar.gz" >> "opencoarrays-${TRAVIS_TAG}-SHA256.txt
+#     fi
+#   - |
+#     set -o errexit
+#     openssl aes-256-cbc -K $encrypted_ef4535c39461_key -iv $encrypted_ef4535c39461_iv -in subkey-328B3A0E-secret.asc.enc -out ./subkey-328B3A0E-secret.asc -d
+#     gpg --allow-secret-key-import --import ./subkey-328B3A0E-secret.asc && rm subkey-328B3A0E-secret.asc
+#     rm subkey-328B3A0E-secret.* || true
+#     unset encrypted_ef4535c39461_key || true
+#     unset encrypted_ef4535c39461_iv || true
+#     gpg --armor --detach-sign -u 328B3A0E --comment 'Mac users can use GPGTools - https://gpgtools.org' \
+#       --comment "Download Izaak Beekman's GPG public key from your" \
+#       --comment 'trusted key server or from' \
+#       --comment 'https://izaakbeekman.com/izaak.pubkey.txt' \
+#       --comment 'Next add it to your GPG keyring, e.g.,' \
+#       --comment '`curl https://izaakbeekman.com/izaak.pubkey.txt | gpg --import`' \
+#       --comment "Make sure you have verified that the release archive's" \
+#       --comment 'SHA256 checksum matches the provided' \
+#       --comment "opencoarrays-${TRAVIS_TAG}-SHA256.txt and ensure that this file" \
+#       --comment "and it's signature are in the same directory. Then" \
+#       --comment 'verify with:' \
+#       --comment '`gpg --verify opencoarrays-'"${TRAVIS_TAG}"'-SHA256.txt.asc`' \
+#       "opencoarrays-${TRAVIS_TAG}-SHA256.txt"
+#     set +o errexit
 
-deploy:
-  provider: releases
-  api_key:
-    secure: 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
-  file: 
-    - "OpenCoarrays-${TRAVIS_TAG}.tar.gz"
-    - "opencoarrays-${TRAVIS_TAG}-SHA256.txt"
-    - "opencoarrays-${TRAVIS_TAG}-SHA256.txt.asc"
-  skip_cleanup: true
-  on:
-    tags: true
+# deploy:
+#   provider: releases
+#   api_key:
+#     secure: 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
+#   file:
+#     - "OpenCoarrays-${TRAVIS_TAG}.tar.gz"
+#     - "opencoarrays-${TRAVIS_TAG}-SHA256.txt"
+#     - "opencoarrays-${TRAVIS_TAG}-SHA256.txt.asc"
+#   skip_cleanup: true
+#   on:
+#     tags: true
 #    repo: sourceryinstitute/opencoarrays
 
 notifications:

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.2)
 
 # Set the type/configuration of build to perform
 set ( CMAKE_CONFIGURATION_TYPES "Debug" "Release" "MinSizeRel" "RelWithDebInfo" "CodeCoverage" )
@@ -90,7 +90,7 @@ the C compiler if it matches the Fortran compiler ID." )
   endif()
   set( CMAKE_Fortran_COMPILER_VERSION "${DETECTED_VER}" )
 endif()
-  
+
   # We have populated CMAKE_Fortran_COMPILER_VERSION if it was missing
   if(gfortran_compiler AND (CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER 5.0.0))
     set(opencoarrays_aware_compiler true)
@@ -155,7 +155,7 @@ endif()
 
 find_package( MPI )
 
-if ( (NOT MPI_C_FOUND) OR (NOT MPI_Fortran_FOUND) )
+if ( (NOT MPI_C_FOUND) OR (NOT MPI_Fortran_FOUND) OR (NOT MPIEXEC))
   find_program (MY_MPI_EXEC NAMES mpirun mpiexec lamexec srun
     PATHS "${CMAKE_SOURCE_DIR/prerequisites/installations/mpich/3.1.4}" "${CMAKE_SOURCE_DIR}/prerequisites/installations/mpich/*" ENV PATH
     HINTS "${FTN_COMPILER_DIR}" "${C_COMPILER_DIR}"
@@ -164,6 +164,68 @@ if ( (NOT MPI_C_FOUND) OR (NOT MPI_Fortran_FOUND) )
   find_package( MPI REQUIRED )
 endif()
 
+# Test for consistent MPI environment
+if (NOT MPIEXEC)
+  message ( ERROR "CMake failed to find `mpiexec` or similar. If building with `./install.sh` please
+report this bug to the OpenCoarrays developers at
+https://github.com/sourceryinstitute/opencoarrays/issues, otherwise use point CMake
+to the desired MPI runtime.")
+endif()
+
+get_filename_component(MPIEXEC_RELATIVE_LOC "${MPIEXEC}"
+  PROGRAM)
+get_filename_component(MPIEXEC_ABS_LOC "${MPIEXEC_RELATIVE_LOC}"
+  REALPATH)
+get_filename_component(MPIEXEC_DIR "${MPIEXEC_ABS_LOC}"
+  DIRECTORY)
+
+get_filename_component(MPICC_RELATIVE_LOC "${MPI_C_COMPILER}"
+  PROGRAM)
+get_filename_component(MPICC_ABS_LOC "${MPICC_RELATIVE_LOC}"
+  REALPATH)
+get_filename_component(MPICC_DIR "${MPICC_ABS_LOC}"
+  DIRECTORY)
+
+get_filename_component(MPIFC_RELATIVE_LOC "${MPI_Fortran_COMPILER}"
+  PROGRAM)
+get_filename_component(MPIFC_ABS_LOC "${MPIFC_RELATIVE_LOC}"
+  REALPATH)
+get_filename_component(MPIFC_DIR "${MPIFC_ABS_LOC}"
+  DIRECTORY)
+
+if ((MPIEXEC_DIR STREQUAL MPICC_DIR) AND (MPIEXEC_DIR STREQUAL MPIFC_DIR))
+  message ( STATUS "MPI runtime and compile time environments appear to be consistent")
+else()
+  message ( WARNING "MPIEXEC is in \"${MPIEXEC_DIR},\"
+which differs from the location of MPICC and/or MPIFC which are in
+\"${MPICC_DIR}\" and \"${MPIFC_DIR},\" respectively.
+This is likely indicative of a problem. If building with `./install.sh` please report
+this to the OpenCoarrays developers by filing a new issue at:
+https://github.com/sourceryinstitute/OpenCoarrays/issues/new")
+endif()
+
+#-----------------------------------------------
+# Work around bug #317 present on fedora systems
+#-----------------------------------------------
+if( (MPI_C_LINK_FLAGS MATCHES "noexecstack") OR (MPI_Fortran_LINK_FLAGS MATCHES "noexecstack") )
+  message ( WARNING
+"The `noexecstack` linker flag was found in the MPI_<lang>_LINK_FLAGS variable. This is
+known to cause segmentation faults for some Fortran codes. See, e.g.,
+https://gcc.gnu.org/bugzilla/show_bug.cgi?id=71729 or
+https://github.com/sourceryinstitute/OpenCoarrays/issues/317.
+
+`noexecstack` is being replaced with `execstack`"
+    )
+  string(REPLACE "noexecstack"
+    "execstack" MPI_C_LINK_FLAGS_FIXED ${MPI_C_LINK_FLAGS})
+  string(REPLACE "noexecstack"
+    "execstack" MPI_Fortran_LINK_FLAGS_FIXED ${MPI_Fortran_LINK_FLAGS})
+  set(MPI_C_LINK_FLAGS "${MPI_C_LINK_FLAGS_FIXED}" CACHE STRING
+    "MPI C linking flags" FORCE)
+  set(MPI_Fortran_LINK_FLAGS "${MPI_Fortran_LINK_FLAGS_FIXED}" CACHE STRING
+    "MPI Fortran linking flags" FORCE)
+endif()
+
 #--------------------------------------------------------
 # Make sure a simple "hello world" C mpi program compiles
 #--------------------------------------------------------

GETTING_STARTED.md

@@ -107,7 +107,7 @@ If the `caf` compiler wrapper cannot process the source code in question, invoke
 the underlying communication library directly:
 
 ```bash
-mpif90 -fcoarray=lib -L/opt/opencoarrays/ tally.f90 \ -lcaf_mpi -o htally-I<OpenCoarrays-install-path>/mod
+mpif90 -fcoarray=lib -L/opt/opencoarrays/ tally.f90 \ -lcaf_mpi -o htally -I<OpenCoarrays-install-path>/mod
 ```
 
 and also run the program with the lower-level communication library: