Merge pull request #4 from PARALLELIO/master

Merge up to the head of the master

CTestScript.cmake

@@ -59,8 +59,18 @@ elseif (HOSTNAME MATCHES "^edison" OR
         HOSTNAME MATCHES "^hopper" OR
         HOSTNAME MATCHES "^nid")
     set (HOSTNAME_ID "nersc")
+# Blue Waters at NCSA
+elseif (HOSTNAME MATCHES "^h2ologin" )
+    set (HOSTNAME_ID "ncsa")
+# CGD local linux cluster
+elseif (HOSTNAME MATCHES "^hobart")
+    set (HOSTNAME_ID "cgd")
 else ()
-    set (HOSTNAME_ID "unknown")
+     if (CMAKE_SYSTEM_NAME MATCHES "Catamount")
+        set (HOSTNAME_ID "ncsa")
+     else ()
+     	set (HOSTNAME_ID "unknown")
+     endif ()
 endif ()
 
 ## -- Get system info
@@ -122,6 +132,7 @@ set (ENV{PIO_DASHBOARD_BINARY_DIR}  ${CTEST_BINARY_DIRECTORY})
 ctest_empty_binary_directory(${CTEST_BINARY_DIRECTORY})
 
 ## -- Start
+message (" -- Hostname_id = ${HOSTNAME_ID}")
 message (" -- Start dashboard - ${CTEST_BUILD_NAME} --")
 ctest_start("${CTEST_SCRIPT_ARG}")
 

README.md

@@ -2,6 +2,15 @@
 
 A high-level Parallel I/O Library for structured grid applications
 
+## Website
+
+For complete documentation, see our website at [http://parallelio.github.io/ParallelIO/](http://parallelio.github.io/ParallelIO/).
+
+## Nightly Tests
+
+The results of our nightly tests on multiple platforms can be found on our
+cdash site at [http://my.cdash.org/index.php?project=PIO](http://my.cdash.org/index.php?project=PIO).
+
 ## Dependencies
 
 PIO can use NetCDF (version 4.3.3+) and/or PnetCDF (version 1.6.0+) for I/O.

cmake/FindGPTL.cmake

@@ -46,29 +46,26 @@ foreach (GPTL_comp IN LISTS GPTL_FIND_VALID_COMPONENTS)
     if (NOT GPTL_${GPTL_comp}_FOUND)
 
         # Manually add the MPI include and library dirs to search paths
-        if (GPTL_comp STREQUAL C)
-            if (MPI_C_FOUND)
-                set (GPTL_${GPTL_comp}_PATHS ${MPI_C_INCLUDE_PATH})
-                foreach (lib IN LISTS MPI_C_LIBRARIES)
-                    get_filename_component (libdir ${lib} PATH)
-                    list (APPEND GPTL_${GPTL_comp}_PATHS ${libdir})
-                    unset (libdir)
-                endforeach ()
-            endif ()
-        else ()
-            if (MPI_Fortran_FOUND)
-                set (GPTL_${GPTL_comp}_PATHS ${MPI_Fortran_INCLUDE_PATH})
-                foreach (lib IN LISTS MPI_Fortran_LIBRARIES)
-                    get_filename_component (libdir ${lib} PATH)
-                    list (APPEND GPTL_${GPTL_comp}_PATHS ${libdir})
-                    unset (libdir)
-                endforeach ()
-            endif ()
+        if (GPTL_comp STREQUAL C AND MPI_C_FOUND)
+            set (mpiincs ${MPI_C_INCLUDE_PATH})
+            set (mpilibs ${MPI_C_LIBRARIES})
+            set (mpifound ${MPI_C_FOUND})
+        elseif (MPI_Fortran_FOUND)
+            set (mpiincs ${MPI_Fortran_INCLUDE_PATH})
+            set (mpilibs ${MPI_Fortran_LIBRARIES})
+            set (mpifound ${MPI_Fortran_FOUND})
         endif ()
-
+        
         # Search for the package component
-        find_package_component(GPTL COMPONENT ${GPTL_comp}
-                               PATHS ${GPTL_${GPTL_comp}_PATHS})
+        if (mpifound)
+            initialize_paths (GPTL_${GPTL_comp}_PATHS
+                              INCLUDE_DIRECTORIES ${mpiincs}
+                              LIBRARIES ${mpilibs})
+            find_package_component(GPTL COMPONENT ${GPTL_comp}
+                                   PATHS ${GPTL_${GPTL_comp}_PATHS})
+        else ()
+            find_package_component(GPTL COMPONENT ${GPTL_comp})
+        endif ()
 
     endif ()
 

cmake/FindHDF5.cmake

@@ -52,29 +52,26 @@ foreach (HDF5_comp IN LISTS HDF5_FIND_VALID_COMPONENTS)
     if (NOT HDF5_${HDF5_comp}_FOUND)
 
         # Manually add the MPI include and library dirs to search paths
-        if (HDF5_comp STREQUAL C OR HDF5_comp STREQUAL HL)
-            if (MPI_C_FOUND)
-                set (HDF5_${HDF5_comp}_PATHS ${MPI_C_INCLUDE_PATH})
-                foreach (lib IN LISTS MPI_C_LIBRARIES)
-                    get_filename_component (libdir ${lib} PATH)
-                    list (APPEND HDF5_${HDF5_comp}_PATHS ${libdir})
-                    unset (libdir)
-                endforeach ()
-            endif ()
-        else ()
-            if (MPI_Fortran_FOUND)
-                set (HDF5_${HDF5_comp}_PATHS ${MPI_Fortran_INCLUDE_PATH})
-                foreach (lib IN LISTS MPI_Fortran_LIBRARIES)
-                    get_filename_component (libdir ${lib} PATH)
-                    list (APPEND HDF5_${HDF5_comp}_PATHS ${libdir})
-                    unset (libdir)
-                endforeach ()
-            endif ()
+        if ( (HDF5_comp STREQUAL C OR HDF5_comp STREQUAL HL) AND MPI_C_FOUND)
+            set (mpiincs ${MPI_C_INCLUDE_PATH})
+            set (mpilibs ${MPI_C_LIBRARIES})
+            set (mpifound ${MPI_C_FOUND})
+        elseif (MPI_Fortran_FOUND)
+            set (mpiincs ${MPI_Fortran_INCLUDE_PATH})
+            set (mpilibs ${MPI_Fortran_LIBRARIES})
+            set (mpifound ${MPI_Fortran_FOUND})
         endif ()
 
         # Search for the package component
-        find_package_component(HDF5 COMPONENT ${HDF5_comp}
-                               PATHS ${HDF5_${HDF5_comp}_PATHS})
+        if (mpifound)
+            initialize_paths (HDF5_${HDF5_comp}_PATHS
+                              INCLUDE_DIRECTORIES ${mpiincs}
+                              LIBRARIES ${mpilibs})
+            find_package_component(HDF5 COMPONENT ${HDF5_comp}
+                                   PATHS ${HDF5_${HDF5_comp}_PATHS})
+        else ()
+            find_package_component(HDF5 COMPONENT ${HDF5_comp})
+        endif ()
 
         # Continue only if found
         if (HDF5_${HDF5_comp}_FOUND)

cmake/FindLIBZ.cmake

@@ -22,18 +22,16 @@ define_package_component (LIBZ
 # SEARCH FOR PACKAGE
 if (NOT LIBZ_FOUND)
 
-    # Manually add the MPI include and library dirs to search paths
+    # Manually add the MPI include and library dirs to search paths 
+    # and search for the package component
     if (MPI_C_FOUND)
-        set (LIBZ_PATHS ${MPI_C_INCLUDE_PATH})
-        foreach (lib IN LISTS MPI_C_LIBRARIES)
-            get_filename_component (libdir ${lib} PATH)
-            list (APPEND LIBZ_PATHS ${libdir})
-            unset (libdir)
-        endforeach ()
+        initialize_paths (LIBZ_PATHS
+                          INCLUDE_DIRECTORIES ${MPI_C_INCLUDE_PATH}
+                          LIBRARIES ${MPI_C_LIBRARIES})
+        find_package_component(LIBZ
+                               PATHS ${LIBZ_PATHS})
+    else ()
+        find_package_component(LIBZ)
     endif ()
-
-    # Search for the package
-    find_package_component(LIBZ
-                           PATHS ${LIBZ_PATHS})
 
 endif ()

cmake/FindNetCDF.cmake

@@ -41,18 +41,16 @@ foreach (NCDFcomp IN LISTS NetCDF_FIND_VALID_COMPONENTS)
     if (NOT NetCDF_${NCDFcomp}_FOUND)
 
         # Manually add the MPI include and library dirs to search paths
+        # and search for the package component
         if (MPI_${NCDFcomp}_FOUND)
-            set (NetCDF_${NCDFcomp}_PATHS ${MPI_${NCDFcomp}_INCLUDE_PATH})
-            foreach (lib IN LISTS MPI_${NCDFcomp}_LIBRARIES)
-                get_filename_component (libdir ${lib} PATH)
-                list (APPEND NetCDF_${NCDFcomp}_PATHS ${libdir})
-                unset (libdir)
-            endforeach ()
+            initialize_paths (NetCDF_${NCDFcomp}_PATHS
+                              INCLUDE_DIRECTORIES ${MPI_${NCDFcomp}_INCLUDE_PATH}
+                              LIBRARIES ${MPI_${NCDFcomp}_LIBRARIES})
+            find_package_component(NetCDF COMPONENT ${NCDFcomp}
+                                   PATHS ${NetCDF_${NCDFcomp}_PATHS})
+        else ()
+            find_package_component(NetCDF COMPONENT ${NCDFcomp})
         endif ()
-
-        # Search for the package component    
-        find_package_component(NetCDF COMPONENT ${NCDFcomp}
-                               PATHS ${NetCDF_${NCDFcomp}_PATHS})
 
         # Continue only if component found
         if (NetCDF_${NCDFcomp}_FOUND)

cmake/FindPnetCDF.cmake

@@ -41,18 +41,16 @@ foreach (PNCDFcomp IN LISTS PnetCDF_FIND_VALID_COMPONENTS)
     if (NOT PnetCDF_${PNCDFcomp}_FOUND)
 
         # Manually add the MPI include and library dirs to search paths
+        # and search for the package component
         if (MPI_${PNCDFcomp}_FOUND)
-            set (PnetCDF_${PNCDFcomp}_PATHS ${MPI_${PNCDFcomp}_INCLUDE_PATH})
-            foreach (lib IN LISTS MPI_${PNCDFcomp}_LIBRARIES)
-                get_filename_component (libdir ${lib} PATH)
-                list (APPEND PnetCDF_${PNCDFcomp}_PATHS ${libdir})
-                unset (libdir)
-            endforeach ()
+            initialize_paths (PnetCDF_${PNCDFcomp}_PATHS
+                              INCLUDE_DIRECTORIES ${MPI_${PNCDFcomp}_INCLUDE_PATH}
+                              LIBRARIES ${MPI_${PNCDFcomp}_LIBRARIES})
+            find_package_component(PnetCDF COMPONENT ${PNCDFcomp}
+                                   PATHS ${PnetCDF_${PNCDFcomp}_PATHS})
+        else ()
+            find_package_component(PnetCDF COMPONENT ${PNCDFcomp})
         endif ()
-
-        # Search for the package component
-        find_package_component(PnetCDF COMPONENT ${PNCDFcomp}
-                               PATHS ${PnetCDF_${PNCDFcomp}_PATHS})
 
         # Continue only if component found
         if (PnetCDF_${PNCDFcomp}_FOUND)

cmake/FindSZIP.cmake

@@ -22,18 +22,16 @@ define_package_component (SZIP
 # SEARCH FOR PACKAGE
 if (NOT SZIP_FOUND)
 
-    # Manually add the MPI include and library dirs to search paths
+    # Manually add the MPI include and library dirs to search paths 
+    # and search for the package component
     if (MPI_C_FOUND)
-        set (SZIP_PATHS ${MPI_C_INCLUDE_PATH})
-        foreach (lib IN LISTS MPI_C_LIBRARIES)
-            get_filename_component (libdir ${lib} PATH)
-            list (APPEND SZIP_PATHS ${libdir})
-            unset (libdir)
-        endforeach ()
+        initialize_paths (SZIP_PATHS
+                          INCLUDE_DIRECTORIES ${MPI_C_INCLUDE_PATH}
+                          LIBRARIES ${MPI_C_LIBRARIES})
+        find_package_component(SZIP
+                               PATHS ${SZIP_PATHS})
+    else ()
+        find_package_component(SZIP)
     endif ()
-
-    # Search for the package
-    find_package_component(SZIP
-                           PATHS ${SZIP_PATHS})
 
 endif ()

cmake/LibFind.cmake

@@ -122,6 +122,46 @@ function (find_valid_components PKG)
 endfunction ()
 
 
+#______________________________________________________________________________
+# - Initialize a list of paths from a list of includes and libraries
+#
+# Input:
+#   INCLUDE_DIRECTORIES
+#   LIBRARIES
+#
+# Ouput:
+#   ${PATHLIST}
+#
+function (initialize_paths PATHLIST)
+
+    # Parse the input arguments
+    set (multiValueArgs INCLUDE_DIRECTORIES LIBRARIES)
+    cmake_parse_arguments (INIT "" "" "${multiValueArgs}" ${ARGN})
+
+    set (paths)
+    foreach (inc IN LISTS INIT_INCLUDE_DIRECTORIES)
+        list (APPEND paths ${inc})
+        get_filename_component (dname ${inc} NAME)
+        if (dname MATCHES "include")
+            get_filename_component (prefx ${inc} PATH)
+            list (APPEND paths ${prefx})
+        endif ()
+    endforeach ()
+    foreach (lib IN LISTS INIT_LIBRARIES)
+        get_filename_component (libdir ${lib} PATH)
+        list (APPEND paths ${libdir})
+        get_filename_component (dname ${libdir} PATH)
+        if (dname MATCHES "lib")
+            get_filename_component (prefx ${libdir} PATH)
+            list (APPEND paths ${prefx})
+        endif ()
+    endforeach ()
+
+    set (${PATHLIST} ${paths} PARENT_SCOPE)
+
+endfunction ()
+
+
 #______________________________________________________________________________
 # - Basic find package macro for a specific component
 #
@@ -272,20 +312,14 @@ function (find_package_component PKG)
             set (${PKGCOMP}_INCLUDE_DIRS ${${PKGCOMP}_INCLUDE_DIR})
             set (${PKGCOMP}_LIBRARIES ${${PKGCOMP}_LIBRARY})
         endif ()
-
-        # Set cache variables
-        set (${PKGCOMP}_FOUND        ${${PKGCOMP}_FOUND}
-             CACHE BOOL "Whether the ${PKGCOMP} package was found" FORCE)
-        set (${PKGCOMP}_INCLUDE_DIR  ${${PKGCOMP}_INCLUDE_DIR}
-             CACHE PATH "Directory containing the ${PKGCOMP} include file" FORCE)
-        set (${PKGCOMP}_INCLUDE_DIRS ${${PKGCOMP}_INCLUDE_DIRS}
-             CACHE STRING "Include path for the ${PKGCOMP} package" FORCE)
-        set (${PKGCOMP}_LIBRARY      ${${PKGCOMP}_LIBRARY}
-             CACHE FILEPATH "Location of the ${PKGCOMP} library file" FORCE)
-        set (${PKGCOMP}_LIBRARIES    ${${PKGCOMP}_LIBRARIES}
-             CACHE STRING "Libraries for the ${PKGCOMP} package" FORCE)
-        set (${PKGCOMP}_IS_SHARED    ${${PKGCOMP}_IS_SHARED}
-             CACHE BOOL "Whether the ${PKGCOMP} library is dynamic" FORCE)
+
+        # Set variables in parent scope
+        set (${PKGCOMP}_FOUND        ${${PKGCOMP}_FOUND}         PARENT_SCOPE)
+        set (${PKGCOMP}_INCLUDE_DIR  ${${PKGCOMP}_INCLUDE_DIR}   PARENT_SCOPE)
+        set (${PKGCOMP}_INCLUDE_DIRS ${${PKGCOMP}_INCLUDE_DIRS}  PARENT_SCOPE)
+        set (${PKGCOMP}_LIBRARY      ${${PKGCOMP}_LIBRARY}       PARENT_SCOPE)
+        set (${PKGCOMP}_LIBRARIES    ${${PKGCOMP}_LIBRARIES}     PARENT_SCOPE)
+        set (${PKGCOMP}_IS_SHARED    ${${PKGCOMP}_IS_SHARED}     PARENT_SCOPE)
 
     endif ()
 

cmake/LibMPI.cmake

@@ -35,6 +35,11 @@ function (platform_name RETURN_VARIABLE)
         SITENAME MATCHES "^hopper")
 
         set (${RETURN_VARIABLE} "nersc" PARENT_SCOPE)
+
+    # NCSA Machine (Blue Waters)
+    elseif (SITENAME MATCHES "^h2ologin")
+
+        set (${RETURN_VARIABLE} "ncsa" PARENT_SCOPE)
 
     else ()
 

cmake/mpiexec.ncsa

@@ -0,0 +1,12 @@
+#!/bin/bash
+#
+# Arguments:
+#
+#   $1  - Number of MPI Tasks
+#   $2+ - Executable and its arguments
+#
+
+NP=$1
+shift
+
+aprun -n $NP $@

ctest/CTestEnvironment-cgd.cmake

@@ -0,0 +1,17 @@
+#==============================================================================
+#
+#  This file sets the environment variables needed to configure and build
+#  on the NCAR CGD cluster Hobart
+#
+#==============================================================================
+
+# Assume all package locations (NetCDF, PnetCDF, HDF5, etc) are already
+# set with existing environment variables: NETCDF, PNETCDF, HDF5, etc.
+
+# Define the extra CMake configure options
+set (CTEST_CONFIGURE_OPTIONS "-DCMAKE_VERBOSE_MAKEFILE=TRUE -DPNETCDF_DIR=$ENV{PNETCDF_PATH} -DNETCDF_DIR=$ENV{NETCDF_PATH}")
+
+# If MPISERIAL environment variable is set, then enable MPISERIAL
+if (DEFINED ENV{MPISERIAL})
+    set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DPIO_USE_MPISERIAL=ON")
+endif ()

ctest/CTestEnvironment-ncsa.cmake

@@ -0,0 +1,22 @@
+#==============================================================================
+#
+#  This file sets the environment variables needed to configure and build
+#  on the NCSA systems 
+#  (Blue Waters).
+#
+#==============================================================================
+
+# Assume all package locations (NetCDF, PnetCDF, HDF5, etc) are already
+# set with existing environment variables: NETCDF, PNETCDF, HDF5, etc.
+
+# Define the extra CMake configure options
+set (CTEST_CONFIGURE_OPTIONS "-DCMAKE_VERBOSE_MAKEFILE=TRUE")
+set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DPREFER_STATIC=TRUE")
+set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DNetCDF_PATH=$ENV{NETCDF_DIR}")
+set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DPnetCDF_PATH=$ENV{PARALLEL_NETCDF_DIR}")
+set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DHDF5_PATH=$ENV{HDF5_DIR}")
+set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DMPI_C_INCLUDE_PATH=$ENV{MPICH_DIR}/include")
+set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DMPI_Fortran_INCLUDE_PATH=$ENV{MPICH_DIR}/include")
+set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DMPI_C_LIBRARIES=$ENV{MPICH_DIR}/lib/libmpich.a")
+set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DMPI_Fortran_LIBRARIES=$ENV{MPICH_DIR}/lib/libmpichf90.a")
+set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DCMAKE_SYSTEM_NAME=Catamount")