Merge pull request #1447 from jedwards4b/pio2_external_update

Update to version 2.2.1 of the pio external

Test suite: scripts_regression_tests.py with PIO_VERSION set to 2 in driver config_components.xml
Test baseline:
Test namelist changes:
Test status: bit for bit

Fixes

User interface changes?:

Code review: jayesh

src/externals/pio2/CMakeLists.txt

@@ -46,29 +46,6 @@ else()
   set(USE_MPI_SERIAL 0)
 endif()
 
-#===== Library Variables =====
-set (PIO_FILESYSTEM_HINTS IGNORE CACHE STRING "Filesystem hints (lustre or gpfs)")
-
-#===== Testing Options =====
-option (PIO_ENABLE_TESTS  "Enable the testing builds"                           ON)
-option (PIO_VALGRIND_CHECK  "Enable memory leak check using valgrind"           OFF)
-
-#==============================================================================
-#  BACKWARDS COMPATIBILITY
-#==============================================================================
-
-# Old NETCDF_DIR variable --> NetCDF_PATH
-if (DEFINED NETCDF_DIR)
-  set (NetCDF_PATH ${NETCDF_DIR}
-    CACHE STRING "Location of the NetCDF library installation")
-endif ()
-
-# Old PNETCDF_DIR variable --> PnetCDF_PATH
-if (DEFINED PNETCDF_DIR)
-  set (PnetCDF_PATH ${PNETCDF_DIR}
-    CACHE STRING "Location of the PnetCDF library installation")
-endif ()
-
 #==============================================================================
 #  PREPEND TO CMAKE MODULE PATH
 #==============================================================================
@@ -97,6 +74,46 @@ set (USER_CMAKE_MODULE_PATH ${USER_CMAKE_MODULE_PATH}
   CACHE STRING "Location of the CMake_Fortran_utils")
 list (APPEND CMAKE_MODULE_PATH ${USER_CMAKE_MODULE_PATH})
 
+INCLUDE (CheckTypeSize)
+
+#===== MPI =====
+if (PIO_USE_MPISERIAL)
+  find_package (MPISERIAL COMPONENTS C REQUIRED)
+  if (MPISERIAL_C_FOUND)
+    set (CMAKE_REQUIRED_INCLUDES ${MPISERIAL_C_INCLUDE_DIRS})
+  endif ()
+else ()
+  find_package (MPI REQUIRED)
+  set (CMAKE_REQUIRED_INCLUDES ${MPI_INCLUDE_PATH})
+endif ()
+
+SET(CMAKE_EXTRA_INCLUDE_FILES "mpi.h")
+check_type_size("MPI_Offset" SIZEOF_MPI_OFFSET)
+SET(CMAKE_EXTRA_INCLUDE_FILES)
+
+#===== Library Variables =====
+set (PIO_FILESYSTEM_HINTS IGNORE CACHE STRING "Filesystem hints (lustre or gpfs)")
+
+#===== Testing Options =====
+option (PIO_ENABLE_TESTS  "Enable the testing builds"                           ON)
+option (PIO_VALGRIND_CHECK  "Enable memory leak check using valgrind"           OFF)
+
+#==============================================================================
+#  BACKWARDS COMPATIBILITY
+#==============================================================================
+
+# Old NETCDF_DIR variable --> NetCDF_PATH
+if (DEFINED NETCDF_DIR)
+  set (NetCDF_PATH ${NETCDF_DIR}
+    CACHE STRING "Location of the NetCDF library installation")
+endif ()
+
+# Old PNETCDF_DIR variable --> PnetCDF_PATH
+if (DEFINED PNETCDF_DIR)
+  set (PnetCDF_PATH ${PNETCDF_DIR}
+    CACHE STRING "Location of the PnetCDF library installation")
+endif ()
+
 #==============================================================================
 #  HELPFUL GLOBAL VARIABLES
 #==============================================================================

src/externals/pio2/CTestScript.cmake

@@ -18,7 +18,7 @@ else ()
     set (CTEST_DASHBOARD_ROOT "$ENV{HOME}/pio-dashboard")
 endif ()
 
-## -- Compiler ID 
+## -- Compiler ID
 if (DEFINED ENV{PIO_COMPILER_ID})
     set (compid "$ENV{PIO_COMPILER_ID}")
 else ()
@@ -49,7 +49,8 @@ if (HOSTNAME MATCHES "^yslogin" OR
     HOSTNAME MATCHES "^pronghorn")
     set (HOSTNAME_ID "nwsc")
 # New UCAR/NWSC SGI Machines
-elseif (HOSTNAME MATCHES "^laramie")
+elseif (HOSTNAME MATCHES "^laramie" OR
+        HOSTNAME MATCHES "^chadmin")
    set (HOSTNAME_ID "nwscla")
 # ALCF/Argonne Machines
 elseif (HOSTNAME MATCHES "^mira" OR
@@ -109,9 +110,9 @@ find_program (CTEST_GIT_COMMAND NAMES git)
 ## -- make command
 find_program (MAKE NAMES make)
 
-#-----------------------------------------------------------  
+#-----------------------------------------------------------
 #-- Generate build-specific information
-#-----------------------------------------------------------  
+#-----------------------------------------------------------
 
 ## -- CTest Site Name
 
@@ -124,25 +125,25 @@ set (CTEST_BUILD_NAME "${osname}-${osrel}-${cpu}-${compid}")
 ## -- SRC Dir (where this script exists)
 set (CTEST_SOURCE_DIRECTORY   "${CTEST_SCRIPT_DIRECTORY}")
 
-## -- BIN Dir 
+## -- BIN Dir
 set (CTEST_BINARY_DIRECTORY   "${CTEST_DASHBOARD_ROOT}/build-${CTEST_BUILD_NAME}-${CTEST_BUILD_GROUP}")
 
 ## -- Add the CTest script directory to the module path
 set (CTEST_EXTRA_SCRIPT_PATH "${CTEST_SOURCE_DIRECTORY}/ctest")
 list (APPEND CMAKE_MODULE_PATH ${CTEST_EXTRA_SCRIPT_PATH})
 
-# -----------------------------------------------------------  
+# -----------------------------------------------------------
 # -- Store Build-Specific Info (environment variables)
-# -----------------------------------------------------------  
+# -----------------------------------------------------------
 
 set (ENV{PIO_DASHBOARD_SITE}        ${CTEST_SITE})
 set (ENV{PIO_DASHBOARD_BUILD_NAME}  ${CTEST_BUILD_NAME})
 set (ENV{PIO_DASHBOARD_SOURCE_DIR}  ${CTEST_SOURCE_DIRECTORY})
 set (ENV{PIO_DASHBOARD_BINARY_DIR}  ${CTEST_BINARY_DIRECTORY})
 
-# -----------------------------------------------------------  
+# -----------------------------------------------------------
 # -- Run CTest
-# -----------------------------------------------------------  
+# -----------------------------------------------------------
 
 ## -- Empty the binary directory
 ctest_empty_binary_directory(${CTEST_BINARY_DIRECTORY})
@@ -157,7 +158,7 @@ message (" -- Update source - ${CTEST_BUILD_NAME} --")
 set (CTEST_UPDATE_COMMAND "${CTEST_GIT_COMMAND}")
 ctest_update ()
 
-## -- Configure 
+## -- Configure
 message (" -- Configure build - ${CTEST_BUILD_NAME} --")
 include (CTestEnvironment-${HOSTNAME_ID})
 set (CTEST_CONFIGURE_COMMAND "${CMAKE_COMMAND} ${CTEST_CONFIGURE_OPTIONS} ${CTEST_SOURCE_DIRECTORY}")
@@ -179,9 +180,9 @@ message (" -- Submit to dashboard - ${CTEST_BUILD_NAME} --")
 message ("** -- PIO_DASHBOARD_SITE=$ENV{PIO_DASHBOARD_SITE}")
 ctest_submit ()
 
-# -----------------------------------------------------------  
+# -----------------------------------------------------------
 # -- Clear environment
-# -----------------------------------------------------------  
+# -----------------------------------------------------------
 
 unset (ENV{PIO_DASHBOARD_SITE})
 unset (ENV{PIO_DASHBOARD_BUILD_NAME})

src/externals/pio2/ctest/CTestEnvironment-anlworkstation.cmake

@@ -23,3 +23,8 @@ endif ()
 if (DEFINED ENV{VALGRIND_CHECK})
     set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DPIO_VALGRIND_CHECK=ON")
 endif ()
+
+# If USE_MALLOC environment variable is set, then use native malloc (instead of bget package)
+if (DEFINED ENV{USE_MALLOC})
+    set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DPIO_USE_MALLOC=ON")
+endif ()

src/externals/pio2/ctest/CTestEnvironment-nwsc.cmake

@@ -14,5 +14,5 @@ set (CTEST_CONFIGURE_OPTIONS "-DCMAKE_VERBOSE_MAKEFILE=TRUE -DPIO_ENABLE_DOC=OFF
 
 # If MPISERIAL environment variable is set, then enable MPISERIAL
 if (DEFINED ENV{MPISERIAL})
-    set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DPIO_USE_MPISERIAL=ON")
+    set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DPIO_USE_MPISERIAL=ON -DPIO_ENABLE_EXAMPLES=OFF ")
 endif ()

src/externals/pio2/ctest/runcdash-cgd-gnu-openmpi.sh

@@ -0,0 +1,38 @@
+#!/bin/sh
+
+# Get/Generate the Dashboard Model
+if [ $# -eq 0 ]; then
+	model=Experimental
+else
+	model=$1
+fi
+
+module purge
+module load compiler/gnu/5.4.0
+module load tool/parallel-netcdf/1.8.1/gnu-5.4.0/openmpi
+
+export CC=mpicc
+export FC=mpif90
+export PIO_DASHBOARD_SITE="cgd"
+export PIO_DASHBOARD_ROOT=/scratch/cluster/jedwards/dashboard
+export CTEST_SCRIPT_DIRECTORY=${PIO_DASHBOARD_ROOT}/src
+export PIO_DASHBOARD_SOURCE_DIR=${CTEST_SCRIPT_DIRECTORY}
+export PIO_COMPILER_ID=gcc-`gcc --version | head -n 1 | cut -d' ' -f3`
+
+if [ ! -d "$PIO_DASHBOARD_ROOT" ]; then
+  mkdir "$PIO_DASHBOARD_ROOT"
+fi
+cd "$PIO_DASHBOARD_ROOT"
+
+echo "CTEST_SCRIPT_DIRECTORY="${CTEST_SCRIPT_DIRECTORY}
+echo "PIO_DASHBOARD_SOURCE_DIR="${PIO_DASHBOARD_SOURCE_DIR}
+
+if [ ! -d src ]; then
+  git clone --branch develop https://github.com/PARALLELIO/ParallelIO src
+fi
+cd src
+git checkout develop
+git pull origin develop
+
+
+ctest -S CTestScript.cmake,${model} -VV

src/externals/pio2/ctest/runcdash-cgd-nag.sh

@@ -14,7 +14,7 @@ module load tool/parallel-netcdf/1.7.0/nag/mvapich2
 export CC=mpicc
 export FC=mpif90
 export PIO_DASHBOARD_SITE="cgd"
-export PIO_DASHBOARD_ROOT=/scratch/cluster/katec/dashboard
+export PIO_DASHBOARD_ROOT=/scratch/cluster/jedwards/dashboard
 export CTEST_SCRIPT_DIRECTORY=${PIO_DASHBOARD_ROOT}/src
 export PIO_DASHBOARD_SOURCE_DIR=${CTEST_SCRIPT_DIRECTORY}
 export PIO_COMPILER_ID=Nag-6.1-gcc-`gcc --version | head -n 1 | cut -d' ' -f3`

src/externals/pio2/ctest/runcdash-nwsc-intel-mpiserial.sh

@@ -14,7 +14,7 @@ module load git/2.3.0
 module load cmake/3.0.2
 module load netcdf/4.3.3.1
 
-export MPISERIAL=/glade/p/work/katec/installs/intel_15.0.3
+export MPISERIAL=/glade/u/home/jedwards/mpi-serial/intel15.0.3/
 
 export CC=icc
 export FC=ifort

src/externals/pio2/ctest/runcdash-nwscla-intel.sh

@@ -11,18 +11,18 @@ source /etc/profile.d/modules.sh
 
 module reset
 module unload netcdf
-module swap intel intel/16.0.3
-module load git/2.10.0
-module load cmake/3.6.2
-module load netcdf-mpi/4.4.1
+module swap intel intel/17.0.1
+module load cmake/3.7.2
+module load netcdf-mpi/4.4.1.1
 module load pnetcdf/1.8.0
+module switch mpt mpt/2.15
 echo "MODULE LIST..."
 module list
 
 export CC=mpicc
 export FC=mpif90
 
-export PIO_DASHBOARD_ROOT=`pwd`/dashboard
+export PIO_DASHBOARD_ROOT=/glade/scratch/jedwards/dashboard
 export PIO_COMPILER_ID=Intel-`$CC --version | head -n 1 | cut -d' ' -f3`
 
 if [ ! -d "$PIO_DASHBOARD_ROOT" ]; then

src/externals/pio2/ctest/runctest-cgd.sh

@@ -29,7 +29,7 @@ echo "\$CTESTCMD -S ${scrdir}/CTestScript-Test.cmake,${model} -V" >> runctest.sh
 chmod +x runctest.sh
 
 # Submit the job to the queue
-jobid=`/usr/local/bin/qsub -l nodes=1:ppn=4 runctest.sh -q short`
+jobid=`/usr/local/bin/qsub -l nodes=1:ppn=8 runctest.sh -q short`
 
 # Wait for the job to complete before exiting
 while true; do

src/externals/pio2/ctest/runctest-nwscla.sh

@@ -1,8 +1,8 @@
 #!/bin/sh
 #==============================================================================
 #
-#  This script defines how to run CTest on the NCAR Wyoming Supercomputing 
-#  Center systems (yellowstone/caldera/geyser).
+#  This script defines how to run CTest on the NCAR Wyoming Supercomputing
+#  Center systems (cheyenne/laramie).
 #
 #  This assumes the CTest model name (e.g., "Nightly") is passed to it when
 #  run.
@@ -19,7 +19,8 @@ model=$2
 echo "#!/bin/sh" > runctest.sh
 echo "#PBS -l walltime=01:00:00" >> runctest.sh
 echo "#PBS -l select=1:ncpus=8:mpiprocs=8" >> runctest.sh
-echo "#PBS -A SCSG0002" >> runctest.sh
+echo "#PBS -A P93300606" >> runctest.sh
+echo "#PBS -q regular" >> runctest.sh
 echo "export PIO_DASHBOARD_SITE=nwscla-${HOSTNAME}" >> runctest.sh
 echo "CTESTCMD=`which ctest`" >> runctest.sh
 echo "\$CTESTCMD -S ${scrdir}/CTestScript-Test.cmake,${model} -V" >> runctest.sh
@@ -28,18 +29,16 @@ echo "\$CTESTCMD -S ${scrdir}/CTestScript-Test.cmake,${model} -V" >> runctest.sh
 chmod +x runctest.sh
 
 # Submit the job to the queue
-jobid=`qsub runctest.sh`
+jobid=`qsub -l walltime=01:00:00 runctest.sh`
 
 # Wait for the job to complete before exiting
 while true; do
-	status=`qstat $jobid`
-	echo $status
-	if [ "$status" == "" ]; then
-		break
+	qstat $jobid
+	if [ $? -eq 0 ]; then
+		sleep 30
 	else
-		sleep 10
+		break;
 	fi
 done
 
 exit 0
-

src/externals/pio2/doc/source/contributing_code.txt

@@ -13,7 +13,7 @@
  * Documents produced by Doxygen are derivative works derived from the
  * input used in their production; they are not affected by this license.
  *
- */ /*! \page code_style Code Style for Contributors
+ */ /*! \page contributing_code Guide for Contributors
 
 # Introduction #
 

src/externals/pio2/examples/c/CMakeLists.txt

@@ -33,12 +33,22 @@ ADD_EXECUTABLE(example1 example1.c)
 TARGET_LINK_LIBRARIES(example1 pioc)
 add_dependencies(tests example1)
 
+ADD_EXECUTABLE(darray_no_async darray_no_async.c)
+TARGET_LINK_LIBRARIES(darray_no_async pioc)
+add_dependencies(tests darray_no_async)
+
+ADD_EXECUTABLE(darray_async darray_async.c)
+TARGET_LINK_LIBRARIES(darray_async pioc)
+add_dependencies(tests darray_async)
+
 if (PIO_USE_MPISERIAL)
   add_test(NAME examplePio COMMAND examplePio)
   add_test(NAME example1 COMMAND example1)
 else ()
   add_mpi_test(examplePio EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/examplePio NUMPROCS 4 TIMEOUT 60)
   add_mpi_test(example1 EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/example1 NUMPROCS 4 TIMEOUT 60)
+  #add_mpi_test(darray_async EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/darray_async NUMPROCS 5 TIMEOUT 60)
+  add_mpi_test(darray_no_async EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/darray_no_async NUMPROCS 4 TIMEOUT 60)
 endif ()