Merge pull request #1388 from UV-CDAT/issue_1324_netcdf_parallel

Issue 1324 netcdf parallel

CMake/cdat_modules/cffi_deps.cmake

@@ -1 +1 @@
-set(cffi_deps ${pip_pkg} ${six_pkg} ${ffi_pkg})
+set(CFFI_deps ${pip_pkg} ${six_pkg} ${ffi_pkg} ${pycparser_pkg} )

CMake/cdat_modules/cython_pkg.cmake

@@ -1,10 +1,10 @@
 set(CYTHON_MAJOR 0)
-set(CYTHON_MINOR 21)
-set(CYTHON_PATCH 2)
-set(CYTHON_VERSION ${CYTHON_MAJOR}.${CYTHON_MINOR}.${CYTHON_PATCH})
+set(CYTHON_MINOR 22)
+set(CYTHON_PATCH )
+set(CYTHON_VERSION ${CYTHON_MAJOR}.${CYTHON_MINOR})
 set(CYTHON_URL ${LLNL_URL} )
 set(CYTHON_GZ Cython-${CYTHON_VERSION}.tar.gz)
-set(CYTHON_MD5 d21adb870c75680dc857cd05d41046a4)
+set(CYTHON_MD5 e67b03e8b3667c8e4e7c774ef2e2b638)
 set(CYTHON_SOURCE ${CYTHON_URL}/${CYTHON_GZ})
 
 add_cdat_package_dependent(Cython "" "" OFF "CDAT_BUILD_LEAN" OFF)

CMake/cdat_modules/hdf5_deps.cmake

@@ -1 +1,4 @@
 set(HDF5_deps ${pkgconfig_pkg} ${libxml2_pkg} ${libxslt_pkg} ${zlib_pkg})
+if (CDAT_BUILD_PARALLEL)
+  list(APPEND HDF5_deps ${mpi_pkg})
+endif()

CMake/cdat_modules/hdf5_external.cmake

@@ -5,7 +5,15 @@ set(HDF5_install "${cdat_EXTERNALS}")
 configure_file(${cdat_CMAKE_SOURCE_DIR}/cdat_modules_extra/hdf5_patch_step.cmake.in
   ${cdat_CMAKE_BINARY_DIR}/hdf5_patch_step.cmake
   @ONLY)
-
+if (CDAT_BUILD_PARALLEL)
+  set(hdf5_configure_args "--enable-parallel")
+  set(hdf5_additional_cflags "-w -fPIC")
+  set(configure_file "cdatmpi_configure_step.cmake")
+else()
+  set(hdf5_configure_args "")
+  set(hdf5_additional_cflags "-w")
+  set(configure_file "cdat_configure_step.cmake")
+endif()
 # we disable HDF5 warnings because it has way too many of them.
 ExternalProject_Add(HDF5
   DOWNLOAD_DIR ${CDAT_PACKAGE_CACHE_DIR}
@@ -15,7 +23,9 @@ ExternalProject_Add(HDF5
   URL_MD5 ${HDF5_MD5}
   BUILD_IN_SOURCE 1
   #PATCH_COMMAND ${CMAKE_COMMAND} -DWORKING_DIR=<SOURCE_DIR> -P ${cdat_CMAKE_BINARY_DIR}/hdf5_patch_step.cmake
-  CONFIGURE_COMMAND ${CMAKE_COMMAND} -DADDITIONAL_CFLAGS=-w -DADDITIONAL_CPPFPAGS=-w -DINSTALL_DIR=<INSTALL_DIR> -DWORKING_DIR=<SOURCE_DIR> -P ${cdat_CMAKE_BINARY_DIR}/cdat_configure_step.cmake
+  CONFIGURE_COMMAND ${CMAKE_COMMAND} -DCONFIGURE_ARGS=${hdf5_configure_args} -DADDITIONAL_CFLAGS=${hdf5_additional_cflags} -DADDITIONAL_CPPFPAGS=-w -DINSTALL_DIR=<INSTALL_DIR> -DWORKING_DIR=<SOURCE_DIR> -P ${cdat_CMAKE_BINARY_DIR}/${configure_file}
+  BUILD_COMMAND ${CMAKE_COMMAND} -Dmake=$(MAKE) -DWORKING_DIR=<SOURCE_DIR> -P ${cdat_CMAKE_BINARY_DIR}/cdat_make_step.cmake
+  INSTALL_COMMAND ${CMAKE_COMMAND} -DWORKING_DIR=<SOURCE_DIR> -P ${cdat_CMAKE_BINARY_DIR}/cdat_install_step.cmake
   LOG_BUILD 1
   DEPENDS ${HDF5_deps}
   ${ep_log_options}

CMake/cdat_modules/hdf5_pkg.cmake

@@ -1,9 +1,9 @@
 set(HDF5_MAJOR_SRC 1)
 set(HDF5_MINOR_SRC 8)
-set(HDF5_PATCH_SRC 13)
+set(HDF5_PATCH_SRC 15)
 set(HDF5_URL ${LLNL_URL})
 set(HDF5_GZ hdf5-${HDF5_MAJOR_SRC}.${HDF5_MINOR_SRC}.${HDF5_PATCH_SRC}.tar.gz)
-set(HDF5_MD5 c03426e9e77d7766944654280b467289)
+set(HDF5_MD5 03cccb5b33dbe975fdcd8ae9dc021f24 )
 
 set (nm HDF5)
 string(TOUPPER ${nm} uc_nm)

CMake/cdat_modules/netcdf_deps.cmake

@@ -1 +1,4 @@
 set(NetCDF_deps ${pkgconfig_pkg} ${hdf5_pkg} ${curl_pkg} ${zlib_pkg} ${jpeg_pkg} )
+if (CDAT_BUILD_PARALLEL)
+  list(APPEND NetCDF_deps ${mpi_pkg} )
+endif()

CMake/cdat_modules/netcdf_external.cmake

@@ -1,6 +1,11 @@
 set(netcdf_source "${CMAKE_CURRENT_BINARY_DIR}/build/netcdf")
 set(netcdf_install "${cdat_EXTERNALS}")
 set(netcdf_configure_args "--enable-netcdf-4")
+if (CDAT_BUILD_PARALLEL)
+  set(configure_file "cdatmpi_configure_step.cmake")
+else()
+  set(configure_file "cdat_configure_step.cmake")
+endif()
 
 configure_file(${cdat_CMAKE_SOURCE_DIR}/cdat_modules_extra/netcdf_patch_step.cmake.in
   ${cdat_CMAKE_BINARY_DIR}/netcdf_patch_step.cmake
@@ -17,7 +22,9 @@ ExternalProject_Add(NetCDF
   URL_MD5 ${NC4_MD5}
   BUILD_IN_SOURCE 1
   PATCH_COMMAND ${netcdf_PATCH_COMMAND}
-  CONFIGURE_COMMAND ${CMAKE_COMMAND} -DINSTALL_DIR=<INSTALL_DIR> -DWORKING_DIR=<SOURCE_DIR> -D CONFIGURE_ARGS=${netcdf_configure_args} -P ${cdat_CMAKE_BINARY_DIR}/cdat_configure_step.cmake
+  CONFIGURE_COMMAND ${CMAKE_COMMAND} -DINSTALL_DIR=<INSTALL_DIR> -DWORKING_DIR=<SOURCE_DIR> -DCONFIGURE_ARGS=${netcdf_configure_args} -P ${cdat_CMAKE_BINARY_DIR}/${configure_file}
+  BUILD_COMMAND ${CMAKE_COMMAND} -Dmake=$(MAKE) -DWORKING_DIR=<SOURCE_DIR> -P ${cdat_CMAKE_BINARY_DIR}/cdat_make_step.cmake
+  INSTALL_COMMAND ${CMAKE_COMMAND} -DWORKING_DIR=<SOURCE_DIR> -P ${cdat_CMAKE_BINARY_DIR}/cdat_install_step.cmake
   DEPENDS ${NetCDF_deps}
   ${ep_log_options}
 )

CMake/cdat_modules/netcdf_pkg.cmake

@@ -1,9 +1,9 @@
 set(NC4_MAJOR_SRC 4)
 set(NC4_MINOR_SRC 3)
-set(NC4_PATCH_SRC 2)
+set(NC4_PATCH_SRC 3.1)
 set(NC4_URL ${LLNL_URL})
 set(NC4_GZ netcdf-${NC4_MAJOR_SRC}.${NC4_MINOR_SRC}.${NC4_PATCH_SRC}.tar.gz)
-set(NC4_MD5 2fd2365e1fe9685368cd6ab0ada532a0)
+set(NC4_MD5 5c9dad3705a3408d27f696e5b31fb88c )
 
 set (nm NC4)
 string(TOUPPER ${nm} uc_nm)

CMake/cdat_modules/pnetcdf_deps.cmake

@@ -0,0 +1 @@
+set(PNETCDF_deps ${pkgconfig_pkg} ${mpi_pkg})

CMake/cdat_modules/pnetcdf_external.cmake

@@ -0,0 +1,17 @@
+set(pnetcdf_source "${CMAKE_CURRENT_BINARY_DIR}/build/pnetcdf")
+set(pnetcdf_install "${cdat_EXTERNALS}")
+set(pnetcdf_configure_args "--with-mpi=${cdat_EXTERNALS}")
+set(pnetcdf_additional_cflags "-fPIC")
+
+ExternalProject_Add(PNETCDF
+  LIST_SEPARATOR ^^
+  DOWNLOAD_DIR ${CDAT_PACKAGE_CACHE_DIR}
+  SOURCE_DIR ${pnetcdf_source}
+  INSTALL_DIR ${pnetcdf_install}
+  URL ${PNETCDF_URL}/${PNETCDF_GZ}
+  URL_MD5 ${PNETCDF_MD5}
+  BUILD_IN_SOURCE 1
+  CONFIGURE_COMMAND ${CMAKE_COMMAND} -DADDITIONAL_CFLAGS=${pnetcdf_additional_cflags} -DINSTALL_DIR=<INSTALL_DIR> -DWORKING_DIR=<SOURCE_DIR> -D CONFIGURE_ARGS=${pnetcdf_configure_args} -P ${cdat_CMAKE_BINARY_DIR}/cdat_configure_step.cmake
+  DEPENDS ${PNETCDF_deps}
+  ${ep_log_options}
+)

CMake/cdat_modules/pnetcdf_pkg.cmake

@@ -0,0 +1,13 @@
+set(PNETCDF_MAJOR_SRC 1)
+set(PNETCDF_MINOR_SRC 6)
+set(PNETCDF_PATCH_SRC 0)
+set(PNETCDF_URL ${LLNL_URL})
+set(PNETCDF_GZ parallel-netcdf-${PNETCDF_MAJOR_SRC}.${PNETCDF_MINOR_SRC}.${PNETCDF_PATCH_SRC}.tar.gz)
+set(PNETCDF_MD5 4893a50ddcd487a312c64383bdeb2631)
+
+set (nm PNETCDF)
+string(TOUPPER ${nm} uc_nm)
+set(${uc_nm}_VERSION ${${nm}_MAJOR_SRC}.${${nm}_MINOR_SRC}.${${nm}_PATCH_SRC})
+set(PNETCDF_SOURCE ${PNETCDF_URL}/${PNETCDF_GZ})
+
+add_cdat_package(PNETCDF "" "" OFF)

CMake/cdat_modules/pycparser_deps.cmake

@@ -0,0 +1 @@
+set(PYCPARSER_deps ${python_pkg} ${pip_pkg})

CMake/cdat_modules/pycparser_external.cmake

@@ -0,0 +1,6 @@
+
+# create an external project to install MyProxyClient,
+# and configure and build it
+set(nm PYCPARSER)
+
+include(pipinstaller)

CMake/cdat_modules/pycparser_pkg.cmake

@@ -0,0 +1,10 @@
+set(PYCPARSER_MAJOR_SRC 2)
+set(PYCPARSER_MINOR_SRC 13)
+set(PYCPARSER_PATCH_SRC )
+
+set(PYCPARSER_VERSION ${PYCPARSER_MAJOR_SRC}.${PYCPARSER_MINOR_SRC})
+set(PYCPARSER_GZ pycparser-${PYCPARSER_VERSION}.tar.gz)
+set(PYCPARSER_SOURCE ${LLNL_URL}/${PYCPARSER_GZ})
+set(PYCPARSER_MD5 e4fe1a2d341b22e25da0d22f034ef32f )
+
+add_cdat_package_dependent(PYCPARSER "" "" ON "CDAT_BUILD_LEAN" OFF)

CMake/cdat_modules/pyopenssl_deps.cmake

@@ -1 +1 @@
-set(PYOPENSSL_deps ${python_pkg} ${pip_pkg})
+set(PYOPENSSL_deps ${python_pkg} ${pip_pkg} ${six_pkg} ${cryptography_pkg} ${cffi_pkg} ${ffi_pkg} ${pycparser_pkg} )

CMake/cdat_modules/scipy_pkg.cmake

@@ -1,12 +1,12 @@
 set(SCIPY_MAJOR 0)
-set(SCIPY_MINOR 10)
+set(SCIPY_MINOR 16)
 set(SCIPY_PATCH 0)
-set(SCIPY_MAJOR_SRC dde07a64407ffaa9442b3d8298c6c26ff91fb384)
-set(SCIPY_MINOR_SRC)
-set(SCIPY_PATCH_SRC)
+set(SCIPY_MAJOR_SRC 0)
+set(SCIPY_MINOR_SRC 16)
+set(SCIPY_PATCH_SRC 0b2)
 set(SCIPY_URL ${LLNL_URL})
-set(SCIPY_GZ scipy-dde07a64407ffaa9442b3d8298c6c26ff91fb384.zip)
-set(SCIPY_MD5 03fed4942984c0220615fac2d8d675c7)
+set(SCIPY_GZ scipy-${SCIPY_MAJOR_SRC}.${SCIPY_MINOR_SRC}.${SCIPY_PATCH_SRC}.tar.gz)
+set(SCIPY_MD5 cf2ca99b54a3951ecafb5c95730aa17f )
 set(SCIPY_SOURCE ${SCIPY_URL}/${SCIPY_GZ})
 
 set (nm SCIPY)

CMake/cdat_modules_extra/cdat_common_environment.cmake.in

@@ -1,12 +1,12 @@
 message("[INFO] ADDITIONAL CFLAGS ${ADDITIONAL_CFLAGS}")
 set(ENV{PATH} "@cdat_EXTERNALS@/bin:$ENV{PATH}")
-set(ENV{@LIBRARY_PATH@} "@CMAKE_INSTALL_PREFIX@/lib:@cdat_EXTERNALS@/lib:@cdat_EXTERNALS@/lib/paraview-@PARAVIEW_MAJOR@.@PARAVIEW_MINOR@:$ENV{@LIBRARY_PATH@}")
+set(ENV{@LIBRARY_PATH@} "@CMAKE_INSTALL_PREFIX@/lib:@cdat_EXTERNALS@/lib:@cdat_EXTERNALS@/lib64:@cdat_EXTERNALS@/lib/paraview-@PARAVIEW_MAJOR@.@PARAVIEW_MINOR@:$ENV{@LIBRARY_PATH@}")
 if (NOT DEFINED SKIP_LDFLAGS)
- set(ENV{LDFLAGS} "-L@cdat_EXTERNALS@/lib @cdat_external_link_directories@ @cdat_rpath_flag@@CMAKE_INSTALL_PREFIX@/lib @cdat_rpath_flag@@cdat_EXTERNALS@/lib")
+ set(ENV{LDFLAGS} "-L@cdat_EXTERNALS@/lib -L@cdat_EXTERNALS@/lib64 @cdat_external_link_directories@ -Wl,-rpath,@cdat_EXTERNALS@/lib64 @cdat_rpath_flag@@CMAKE_INSTALL_PREFIX@/lib @cdat_rpath_flag@@cdat_EXTERNALS@/lib")
 endif()
-set(ENV{CFLAGS} "-I@cdat_EXTERNALS@/include @cdat_osx_flags@ @cdat_external_include_directories@ ${ADDITIONAL_CFLAGS}")
-set(ENV{CPPFLAGS} "-I@cdat_EXTERNALS@/include @cdat_osx_cppflags@ @cdat_external_include_directories@ ${ADDITIONAL_CPPFLAGS}")
-set(ENV{CXXFLAGS} "-I@cdat_EXTERNALS@/include @cdat_osx_cxxflags@ ${ADDITIONAL_CXXFLAGS}")
+set(ENV{CFLAGS} "-I@cdat_EXTERNALS@/include -I@cdat_EXTERNALS@/lib/libffi-3.1/include @cdat_osx_flags@ @cdat_external_include_directories@ ${ADDITIONAL_CFLAGS}")
+set(ENV{CPPFLAGS} "-I@cdat_EXTERNALS@/include -I@cdat_EXTERNALS@/lib/libffi-3.1/include @cdat_osx_cppflags@ @cdat_external_include_directories@ ${ADDITIONAL_CPPFLAGS}")
+set(ENV{CXXFLAGS} "-I@cdat_EXTERNALS@/include -I@cdat_EXTERNALS@/lib/libffi-3.1/include @cdat_osx_cxxflags@ ${ADDITIONAL_CXXFLAGS}")
 set(ENV{PKG_CONFIG_PATH} "@cdat_EXTERNALS@/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/share/pkgconfig:$ENV{PKG_CONFIG_PATH}")
 set(ENV{PKG_CONFIG} "@cdat_PKG_CONFIG_EXECUTABLE@")
 set(ENV{FC} "")

CMake/cdat_modules_extra/cdatmpi_configure_step.cmake.in

@@ -0,0 +1,21 @@
+set(ENV{PKG_CONFIG_PATH} "@cdat_EXTERNALS@/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/share/pkgconfig:$ENV{PKG_CONFIG_PATH}")
+set(ENV{PKG_CONFIG} "@cdat_PKG_CONFIG_EXECUTABLE@")
+
+include(@cdat_CMAKE_BINARY_DIR@/cdat_common_environment.cmake)
+
+set(ENV{CC} mpicc)
+
+message("CONFIGURE_ARGS IS ${CONFIGURE_ARGS}")
+message("LD_ARGS IS $ENV{@LIBRARY_PATH@}")
+message("CFLAGS : $ENV{CFLAGS}")
+
+execute_process(
+  COMMAND env CC=$ENV{CC} CFLAGS=$ENV{CFLAGS} LD_LIBRARY_PATH=$ENV{@LIBRARY_PATH@} DYLD_FALLBACK_LIBRARY_PATH=$ENV{@LIBRARY_PATH@} @LIBRARY_PATH@=$ENV{@LIBRARY_PATH@} PKG_CONFIG=$ENV{PKG_CONFIG} PKG_CONFIG_PATH=$ENV{PKG_CONFIG_PATH} sh configure --prefix=${INSTALL_DIR} ${CONFIGURE_ARGS}
+  WORKING_DIRECTORY "${WORKING_DIR}"
+  RESULT_VARIABLE res)
+
+if(NOT ${res} EQUAL 0)
+  message("Config Errors detected: \n${CDAT_OUT}\n${CDAT_ERR}")
+  message(FATAL_ERROR "Error in config")
+endif()
+message("Config succeeded.")

CMake/cmake_modules/pipinstaller.cmake

@@ -1,7 +1,7 @@
 # create an external project to install MyProxyClient,
 # and configure and build it
 
-include(@cdat_CMAKE_BINARY_DIR@/cdat_common_environment.cmake)
+include(${cdat_CMAKE_BINARY_DIR}/cdat_common_environment.cmake)
 string(TOUPPER ${nm} uc_nm)
 
 if(NOPREFIXOPT )
@@ -33,7 +33,7 @@ ExternalProject_Add(${nm}
   BUILD_IN_SOURCE 1
   CONFIGURE_COMMAND ""
   BUILD_COMMAND ""
-  INSTALL_COMMAND env PYTHONPATH=${PYTHONPATH} ${USR_ENVS} ${PYTHON_EXECUTABLE} setup.py install ${PRFX}
+  INSTALL_COMMAND env LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH} CFLAGS=$ENV{CFLAGS} LDFLAGS=$ENV{LDFLAGS} PKG_CONFIG_PATH=$ENV{PKG_CONFIG_PATH} PYTHONPATH=${PYTHONPATH} ${USR_ENVS} ${PYTHON_EXECUTABLE} setup.py install ${PRFX}
   DEPENDS ${${nm}_deps}
   ${ep_log_options}
 )

CMakeLists.txt

@@ -296,6 +296,7 @@ if (CDAT_BUILD_ESGF)
 endif()
 set(CDAT_BUILD_MODE "DEFAULT" CACHE STRING "Build mode for CDAT <ALL, LEAN, DEFAULT>")
 set_property(CACHE CDAT_BUILD_MODE PROPERTY STRINGS "DEFAULT" "ALL" "LEAN")
+message([INFO] BUILD MODE} ${CDAT_BUILD_MODE})
 
 # Set the state of LEAN all based on the MODE
 if (CDAT_BUILD_MODE STREQUAL "LEAN")
@@ -304,9 +305,11 @@ if (CDAT_BUILD_MODE STREQUAL "LEAN")
 elseif (CDAT_BUILD_MODE STREQUAL "ALL")
   set(CDAT_BUILD_LEAN OFF)
   set(CDAT_BUILD_ALL ON)
-else()
+elseif (CDAT_BUILD_MODE STREQUAL "DEFAULT")
   set(CDAT_BUILD_LEAN OFF)
   set(CDAT_BUILD_ALL OFF)
+else()
+  message(FATAL_ERROR "[ERROR] Unknown CDAT_BUILD_MODE \"${CDAT_BUILD_MODE}\" VALID MODES ARE \"DEFAULT\" \"ALL\" \"LEAN\"")
 endif()
 
 # First of all if LEAN then turn OFF GRAPHICS and PARALLEL
@@ -486,8 +489,12 @@ include(libcf_pkg)
 include(libdrs_pkg)
 include(matplotlib_pkg)
 include(six_pkg)
+include(cryptography_pkg)
+include(cffi_pkg)
+include(ffi_pkg)
 include(dateutils_pkg)
 include(pyparsing_pkg)
+include(pycparser_pkg)
 include(md5_pkg)
 include(mpi4py_pkg)
 include(pyopenssl_pkg)
@@ -601,8 +608,8 @@ configure_file(${cdat_CMAKE_SOURCE_DIR}/cdat_modules_extra/cleanenv_configure_st
     @ONLY
 )
 
-configure_file(${cdat_CMAKE_SOURCE_DIR}/cdat_modules_extra/cdat_configure_step.cmake.in
-    ${cdat_CMAKE_BINARY_DIR}/cdat_configure_step.cmake
+configure_file(${cdat_CMAKE_SOURCE_DIR}/cdat_modules_extra/cdatmpi_configure_step.cmake.in
+    ${cdat_CMAKE_BINARY_DIR}/cdatmpi_configure_step.cmake
     @ONLY
 )
 
@@ -675,6 +682,7 @@ set(SETUP_LIBRARY_PATHS
   "Externals/lib/paraview-${PARAVIEW_MAJOR}.${PARAVIEW_MINOR} "
   "Externals/lib/R/lib "
   "Externals/lib "
+  "Externals/lib64 "
   "lib "
 )
 string(REPLACE ";" " " SETUP_LIBRARY_PATHS ${SETUP_LIBRARY_PATHS})

Packages/cdms2/Lib/__init__.py

@@ -27,7 +27,14 @@
 from grid import createGenericGrid, createGlobalMeanGrid, createRectGrid, createUniformGrid, createZonalGrid, setClassifyGrids, createGaussianGrid, writeScripGrid, isGrid
 
 # Dataset functions
-from dataset import createDataset, openDataset, useNetcdf3, getNetcdfClassicFlag, getNetcdfShuffleFlag, getNetcdfDeflateFlag, getNetcdfDeflateLevelFlag, setNetcdfClassicFlag, setNetcdfShuffleFlag, setNetcdfDeflateFlag, setNetcdfDeflateLevelFlag, setCompressionWarnings
+from dataset import createDataset, openDataset, useNetcdf3, \
+        getNetcdfClassicFlag, getNetcdfShuffleFlag, getNetcdfDeflateFlag, getNetcdfDeflateLevelFlag,\
+        setNetcdfClassicFlag, setNetcdfShuffleFlag, setNetcdfDeflateFlag, setNetcdfDeflateLevelFlag,\
+        setNetcdfUseNCSwitchModeFlag,getNetcdfUseNCSwitchModeFlag,\
+        setCompressionWarnings,\
+        setNetcdf4Flag, getNetcdf4Flag,\
+        setNetcdfUseParallelFlag, getNetcdfUseParallelFlag
+
 open = openDataset
 
 # Database functions

Packages/cdms2/Lib/cdmsobj.py

@@ -463,7 +463,11 @@ def _setatts(self,value):
 
     def __init__(self, node = None):
         if not hasattr(self,'___cdms_internals__'):
-            self.__dict__['___cdms_internals__']=['__cdms_internals__','___cdms_internals__','_node_','parent','attributes','shape','autoApiInfo']
+            self.__dict__['___cdms_internals__']=[
+                '__cdms_internals__','___cdms_internals__',
+                '_node_','_obj_',
+                '_numericType_','_grid_','_bounds_',
+                'parent','attributes','shape','autoApiInfo']
         self.attributes={}
         self._node_ = node
         if node is not None: