Merge pull request #1 from NCAR/master

Merging in changes from the root

.gitignore

@@ -1,2 +1,4 @@
 .project
 html/
+*~
+

cmake/FindMPE.cmake

@@ -0,0 +1,50 @@
+# - Try to find MPE
+#
+# This can be controlled by setting the MPE_PATH (or, equivalently,
+# the MPE environment variable), or MPE_<lang>_PATH CMake variables,
+# where <lang> is the COMPONENT language one needs.
+#
+# Once done, this will define:
+#
+#   MPE_<lang>_FOUND        (BOOL) - system has MPE
+#   MPE_<lang>_IS_SHARED    (BOOL) - whether library is shared/dynamic
+#   MPE_<lang>_INCLUDE_DIR  (PATH) - Location of the C header file
+#   MPE_<lang>_INCLUDE_DIRS (LIST) - the MPE include directories
+#   MPE_<lang>_LIBRARY      (FILE) - Path to the C library file
+#   MPE_<lang>_LIBRARIES    (LIST) - link these to use MPE
+#
+# The available COMPONENTS are: C 
+include (LibFind)
+include (LibCheck)
+
+# Define MPE C Component
+define_package_component (MPE DEFAULT
+  COMPONENT C
+  INCLUDE_NAMES mpe.h
+  LIBRARY_NAMES mpe)
+
+# Search for list of valid components requested
+find_valid_components (MPE)
+
+#==============================================================================
+# SEARCH FOR VALIDATED COMPONENTS
+foreach (NCDFcomp IN LISTS MPE_FIND_VALID_COMPONENTS)
+
+  # If not found already, search...
+  if (NOT MPE_${NCDFcomp}_FOUND)
+
+    # Manually add the MPI include and library dirs to search paths
+    # and search for the package component
+    if (MPI_${NCDFcomp}_FOUND)
+      initialize_paths (MPE_${NCDFcomp}_PATHS
+        INCLUDE_DIRECTORIES ${MPI_${NCDFcomp}_INCLUDE_PATH}
+        LIBRARIES ${MPI_${NCDFcomp}_LIBRARIES})
+      find_package_component(MPE COMPONENT ${NCDFcomp}
+        PATHS ${MPE_${NCDFcomp}_PATHS})
+    else ()
+      find_package_component(MPE COMPONENT ${NCDFcomp})
+    endif ()
+
+  endif ()
+
+endforeach ()

doc/Doxyfile.in

@@ -187,7 +187,7 @@ SHORT_NAMES            = NO
 # description.)
 # The default value is: NO.
 
-JAVADOC_AUTOBRIEF      = NO
+JAVADOC_AUTOBRIEF      = YES
 
 # If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
 # line (until the first dot) of a Qt-style comment as the brief description. If

doc/source/Examples.txt

@@ -28,7 +28,12 @@ The C examples are in the examples/c subdirectory.
 - examplePio.c A simple example showing a write, then read, of a 1D variable.
 
 - example1.c Another simple example showing a write, then read, of a
-  1D variable.
+  1D variable. This produces the same output as examplePio.c.
+
+- example2.c This example writes a 3D floating point variable, with an
+  unlimited dimension. The data are written in slices along the
+  unlimited dimension. This example also incorporates (if installed)
+  the MPE profiling system to generate graphical output.
 
 ### Fortran Examples
 

doc/source/api.txt

@@ -41,6 +41,7 @@
     - \ref PIO_inq_attname
     - \ref PIO_inq_att
     - \ref PIO_inq_attlen
+    - \ref PIO_inq_var
     - \ref PIO_inq_varid
     - \ref PIO_inq_varname
     - \ref PIO_inq_vartype
@@ -55,5 +56,6 @@
     - \ref PIO_inq_natts
     - \ref PIO_inquire_variable
     - \ref PIO_inquire_dimension
+    - \ref PIO_inquire_dimension
 
 */

examples/c/CMakeLists.txt

@@ -12,8 +12,25 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -O0")
 
 SET(SRC examplePio.c)
 ADD_EXECUTABLE(examplePio_c ${SRC})
-TARGET_LINK_LIBRARIES(examplePio_c piof pioc)
+TARGET_LINK_LIBRARIES(examplePio_c pioc)
 
 SET(SRC example1.c)
 ADD_EXECUTABLE(example1 ${SRC})
-TARGET_LINK_LIBRARIES(example1 piof pioc)
+TARGET_LINK_LIBRARIES(example1 pioc)
+
+SET(SRC example2.c)
+ADD_EXECUTABLE(example2 ${SRC})
+TARGET_LINK_LIBRARIES(example2 pioc)
+
+#===== MPE =====
+find_package (MPE "2.4.8" COMPONENTS C)
+if (MPE_C_FOUND)
+    target_include_directories (example2
+        PUBLIC ${MPE_C_INCLUDE_DIRS})
+    target_compile_definitions (example2
+        PUBLIC HAVE_MPE)
+    target_link_libraries (example2 pioc lmpe mpe pthread m)
+else ()
+    target_compile_definitions (example2
+        PUBLIC _NOMPE)
+endif ()