Use PnetCDF instead of parallel-netcdf to avoid confusion with

parallel netcdf4. Also, update PnetCDF web page.

CMakeLists.txt

@@ -1012,11 +1012,11 @@ ENDIF()
 
 # Options to enable parallel IO for classic formats with parallel-netcdf library.
 SET(STATUS_PNETCDF "OFF")
-OPTION(ENABLE_PNETCDF "Build with parallel I/O for classic and 64-bit offset files using parallel-netcdf." OFF)
+OPTION(ENABLE_PNETCDF "Build with parallel I/O for CDF-1, 2, and 5 files using PnetCDF." OFF)
 
 IF(ENABLE_PNETCDF)
   # Check for ncmpi_create in libpnetcdf, define USE_PNETCDF
-  # Does the user want to turn on PNETCDF read ability?
+  # Does the user want to turn on PnetCDF read ability?
   SET(USE_PNETCDF ON CACHE BOOL "")
   FIND_LIBRARY(PNETCDF NAMES pnetcdf)
   FIND_PATH(PNETCDF_INCLUDE_DIR pnetcdf.h)
@@ -1042,7 +1042,7 @@ IF(ENABLE_PNETCDF)
       SET(STATUS_PNETCDF "ON")
       INCLUDE_DIRECTORIES(${PNETCDF_INCLUDE_DIR})
       SET(HAVE_LIBPNETCDF ON)
-      # pnetcdf => parallel
+      # PnetCDF => parallel
       SET(STATUS_PARALLEL ON)
       SET(USE_PARALLEL ON)
       MESSAGE(STATUS "Using PnetCDF Library: ${PNETCDF}")
@@ -1594,7 +1594,7 @@ MACRO(print_conf_summary)
 
   IF(${STATUS_PNETCDF} OR ${STATUS_PARALLEL})
     MESSAGE("Building Parallel NetCDF")
-    MESSAGE(STATUS "Using pnetcdf:       ${STATUS_PNETCDF}")
+    MESSAGE(STATUS "Using PnetCDF:       ${STATUS_PNETCDF}")
     MESSAGE(STATUS "Using Parallel IO:   ${STATUS_PARALLEL}")
     MESSAGE("")
   ENDIF()

Makefile.am

@@ -58,7 +58,7 @@ DAP4 = libdap4
 NCDAP4TESTDIR = dap4_test
 endif #DAP4
 
-# Build pnetcdf
+# Build PnetCDF
 if USE_PNETCDF
 LIBSRCP = libsrcp
 endif

RELEASE_NOTES.md

@@ -163,7 +163,7 @@ disbled until the testserver situation is resolved.
 
     This cascaded into a number of other changes.
 
-    1. Renamed libsrcp5 -> libsrcp because pnetcdf can do parallel io for CDF-1, CDF-2 and CDF-5, not just CDF-5.
+    1. Renamed libsrcp5 -> libsrcp because PnetCDF can do parallel io for CDF-1, CDF-2 and CDF-5, not just CDF-5.
     2. Given #1, then the NC_PNETCDF mode flag becomes a subset of NC_MPIIO, so made NC_PNETCDF an alias for NC_MPII.
     3. NC_FORMAT_64BIT is now deprecated.  Use NC_FORMAT_64BIT_OFFSET.
 
@@ -279,7 +279,7 @@ Example Work Flow from netcdf-c source directory:
 
 * Added an explicit check in the build systems (autotools, cmake) for the CURL-related option `CURLOPT_CHUNK_BGN_FUNCTION`.  This option was introduced in libcurl version `7.21.0`.  On installations which require libcurl and have this version, `CURLOPT_CHUNK_BGN_FUNCTION` will be available. Otherwise, it will not.
 
-* The pnetcdf support was not properly being used to provide mpi parallel io for netcdf-3 classic files. The wrong dispatch table was being used. [NCF-319](https://bugtracking.unidata.ucar.edu/browse/NCF-319)
+* The PnetCDF support was not properly being used to provide mpi parallel io for netcdf-3 classic files. The wrong dispatch table was being used. [NCF-319](https://bugtracking.unidata.ucar.edu/browse/NCF-319)
 
 * In nccopy utility, provided proper default for unlimited dimension in chunk-size specification instead of requiring explicit chunk size. Added associated test. [NCF-321](https://bugtracking.unidata.ucar.edu/browse/NCF-321)
 
@@ -1188,7 +1188,7 @@ definitions in the DAS, but they will be ignored.
 
 * Many documentation fixes.
 
-* Added capability to use the parallel-netcdf (a.k.a. pnetcdf) library to
+* Added capability to use the PnetCDF library to
 perform parallel I/O on classic and 32-bit offset files. Use the
 NC\_PNETCDF mode flag to get parallel I/O for non-netcdf-4 files.
 

configure.ac

@@ -1095,7 +1095,7 @@ if test "x$enable_netcdf_4" = xyes; then
 fi
 
 # There are several cases for parallelism:
-# 1. pnetcdf enabled => we want to parallelism for CDF-1,CDF-2,and CDF-5
+# 1. PnetCDF enabled => we want to parallelism for CDF-1,CDF-2,and CDF-5
 # 2. hdf5 has mpio enabled
 #    a. do not want to use it for netcdf4
 #    b. do want to use it for netcdf4
@@ -1127,22 +1127,21 @@ else
 fi
 
 # We have already tested for parallel io in netcdf4
-# Now do it for netcdf-3
-# Does the user want parallel I/O for classic and 64-bit offset files using parallel-netcdf (pnetcdf)?
+# parallel I/O for CDF-1, 2, and 5 files can also be done through PnetCDF
 AC_MSG_CHECKING([whether parallel I/O for classic files is to be enabled])
 AC_ARG_ENABLE([pnetcdf], [AS_HELP_STRING([--enable-pnetcdf],
               [build with parallel I/O for classic files])])
 test "x$enable_pnetcdf" = xyes || enable_pnetcdf=no
 AC_MSG_RESULT($enable_pnetcdf)
 
-# See if the pnetcdf lib is available and of the
+# See if the PnetCDF lib is available and of the
 # right version (1.6.0 or later)
 if test "x$enable_pnetcdf" = xyes; then
   pnetcdf_conflict=no
   AC_CHECK_LIB([pnetcdf], [ncmpi_create], [],[pnetcdf_conflict=yes])
 
   if test "x$pnetcdf_conflict" = xyes ; then
-     AC_MSG_ERROR([Cannot link to pnetcdf library.])
+     AC_MSG_ERROR([Cannot link to PnetCDF library.])
   fi
 
   # Pnetcdf did not support utf-8 until 1.6.0
@@ -1160,13 +1159,12 @@ if test "x$enable_pnetcdf" = xyes; then
   fi
 fi
 
-# Now, set enable_parallel if either pnetcdf or parallel4 is set
+# Now, set enable_parallel if either enable_pnetcdf or enable_parallel4 is set
 if test "x$enable_pnetcdf" = xyes -o "x$enable_parallel4" = xyes; then
-enable_parallel=yes
+  enable_parallel=yes
 else
-enable_parallel=no
+  enable_parallel=no
 fi
-
 AM_CONDITIONAL(ENABLE_PARALLEL, [test x$enable_parallel = xyes ])
 
 if test "x$hdf5_parallel" = xyes; then
@@ -1181,12 +1179,12 @@ if test "x$enable_parallel4" = xyes; then
 fi
 
 if test "x$enable_pnetcdf" = xyes; then
-  AC_DEFINE([USE_PNETCDF], [1], [if true, parallel netCDF is used])
+  AC_DEFINE([USE_PNETCDF], [1], [if true, PnetCDF is used])
 fi
 
 # If enable_parallel is in use, enable it in the C code. Also add some stuff to netcdf.h.
 if test "x$enable_parallel" = xyes; then
-  AC_DEFINE([USE_PARALLEL], [1], [if true, pnetcdf or parallel netcdf-4 is in use])
+  AC_DEFINE([USE_PARALLEL], [1], [if true, PnetCDF or parallel netcdf-4 is in use])
 fi
 
 AC_ARG_ENABLE([erange_fill],

docs/architecture.dox

@@ -10,7 +10,7 @@ The netCDF C-based libraries depend on a core C library and some externally deve
 - NetCDF-Java is an independent implementation, not shown here
 - C-based 3rd-party netCDF APIs for other languages include Python, Ruby, Perl, Fortran-2003, MATLAB, IDL, and R
 - Libraries that don't support netCDF-4 include Perl and old C++
-- 3rd party libraries are optional (HDF5, HDF4, zlib, szlib, pnetcdf, libcurl), depending on what features are needed and how netCDF is configured
+- 3rd party libraries are optional (HDF5, HDF4, zlib, szlib, PnetCDF, libcurl), depending on what features are needed and how netCDF is configured
 - "Apps" in the above means applications, not mobile apps!
 
 */

docs/guide.dox

@@ -261,7 +261,7 @@ The netCDF C-based libraries depend on a core C library and some externally deve
 - NetCDF-Java is an independent implementation, not shown here
 - C-based 3rd-party netCDF APIs for other languages include Python, Ruby, Perl, Fortran-2003, MATLAB, IDL, and R
 - Libraries that don't support netCDF-4 include Perl and old C++
-- 3rd party libraries are optional (HDF5, HDF4, zlib, szlib, pnetcdf, libcurl), depending on what features are needed and how netCDF is configured
+- 3rd party libraries are optional (HDF5, HDF4, zlib, szlib, PnetCDF, libcurl), depending on what features are needed and how netCDF is configured
 - "Apps" in the above means applications, not mobile apps!
 
 \section performance What about Performance?

docs/install.md

@@ -296,7 +296,7 @@ directory, configure netCDF with the "--enable-pnetcdf" option. If PnetCDF
 is built with static library only, add "--disable-shared" option.
 
 ~~~~{.py}
-    $ # Build, test, and install netCDF-4 with pnetcdf support
+    $ # Build, test, and install netCDF-4 with PnetCDF support
     $ CC=mpicc CPPFLAGS="-I${H5DIR}/include -I${PNDIR}/include" \
       LDFLAGS="-L${H5DIR}/lib -L${PNDIR}/lib" ./configure \
 	  --enable-pnetcdf  --enable-parallel-tests \
@@ -309,7 +309,7 @@ Linking to netCDF-C {#linking}
 -------------------
 
 For static builds of applications that use netCDF-4 you must link to all the
-libraries, netCDF, HDF5, zlib, szip (if used with HDF5 build), pnetcdf (if used
+libraries, netCDF, HDF5, zlib, szip (if used with HDF5 build), PnetCDF (if used
 with PnetCDF build), and curl (if the remote access client has not been
 disabled). This will require -L options to your build for the locations of the
 libraries, and -l (lower-case L) for the names of the libraries.

docs/internal.dox

@@ -27,7 +27,7 @@ To date, at least the following dispatch tables are supported.
 - netcdf enhanced files (netcdf-4)
 - DAP2 to netcdf-3
 - DAP4 to netcdf-4
-- pnetcdf (parallel cdf5)
+- PnetCDF (parallel I/O for classic files)
 - HDF4 SD files
 
 The dispatch table represents a distillation of the netcdf API down to
@@ -338,7 +338,7 @@ these don't have to be re-implemented in each read-only dispatch layer:
 \subsubsection classic_functions Classic NetCDF Only Functions
 
 There are two functions that are only used in the classic code. All
-other dispatch layers (except pnetcdf) return error ::NC_ENOTNC3 for
+other dispatch layers (except PnetCDF) return error ::NC_ENOTNC3 for
 these functions. The following functions are provided for this
 purpose:
 

docs/old/netcdf-f90.texi

@@ -6098,7 +6098,7 @@ The variable can be changed from collective to independent, and back,
 as often as desired.
 
 Classic and 64-bit offset files, when opened for parallel access, use
-the parallel-netcdf (a.k.a. pnetcdf) library, which does not allow
+the PnetCDF (Parallel-netCDF) library, which does not allow
 per-variable changes of access mode - the entire file must be access
 independently or collectively. For classic and 64-bit offset files,
 the nf90_var_par_access function changes the access for all variables

docs/old/netcdf-install.texi

@@ -665,7 +665,7 @@ users.
 
 @item --enable-pnetcdf
 Allows parallel I/O with classic and 64-bit offset format files, using
-the parallel-netcdf (formerly pnetcdf) library from
+the PnetCDF (Parallel-netCDF) library from
 Argonne/Northwestern. The parallel-netcdf library must be installed,
 and a specially modified pnetcdf.h must be used. (Get it at
 ftp://ftp.unidata.ucar.edu/pub/netcdf/user/contrib/pnetcdf.h)

docs/old/netcdf.texi

@@ -872,8 +872,8 @@ servers, full support for the enhanced netCDF-4 data model in the
 ncgen utility, a new nccopy utility for copying and conversion among
 netCDF format variants, ability to read some HDF4/HDF5 data archives
 through the netCDF C or Fortran interfaces, support for parallel I/O
-on netCDF classic and 64-bit offset files using the parallel-netcdf
-(formerly pnetcdf) library from Argonne/Northwestern, a new nc-config
+on netCDF classic and 64-bit offset files using the PnetCDF
+(Parallel-netCDF) library from Argonne/Northwestern, a new nc-config
 utility to help compile and link programs that use netCDF, inclusion
 of the UDUNITS library for hadling ``units'' attributes, and inclusion
 of libcf to assist in creating data compliant with the Climate and
@@ -3064,8 +3064,8 @@ NetCDF uses the HDF5 parallel programming model for parallel I/O
 with netCDF-4/HDF5 files. The HDF5 tutorial
 (@uref{@value{hdf5-tutorial-url}}) is a good reference.
 
-For classic and 64-bit offset files, netCDF uses the parallel-netcdf
-(formerly pnetcdf) library from Argonne National Labs/Nortwestern
+For classic and 64-bit offset files, netCDF uses the PnetCDF
+(Parallel-netCDF) library from Argonne National Labs/Nortwestern
 University. For parallel access of classic and 64-bit offset files,
 netCDF must be configured with the --with-pnetcdf option at build
 time. See the parallel-netcdf site for more information

docs/static-pages/software.html

@@ -234,7 +234,7 @@ <h2><a href="#freely">Freely Available Software</a></h2>
         <a href="#Panoply" >Panoply</a>
       </li>
       <li>
-        <a href="#Parallel-NetCDF" >Parallel-NetCDF</a>
+        <a href="#PnetCDF" >PnetCDF</a>
       </li>
       <li>
         <a href="#Paraview" >Paraview and vtkCSCSNetCDF</a>
@@ -2344,26 +2344,26 @@ <h2><a id="Panoply" name="Panoply">Panoply</a></h2>
       B. Schmunk</a>.
     </p>
     <p></p>
-    <h2><a id="Parallel-NetCDF" name="Parallel-NetCDF">Parallel-NetCDF</a></h2>
+    <h2><a id="PnetCDF" name="PnetCDF">PnetCDF</a></h2>
     <p>
       A group of researchers at Northwestern University and Argonne National
       Laboratory (Jianwei Li, Wei-keng Liao, Alok Choudhary, Robert Ross, Rajeev
       Thakur, William Gropp, and Rob Latham) have designed and implemented a new
-      <a href="http://www.mcs.anl.gov/parallel-netcdf/" > parallel interface for writing and reading netCDF data</a>, tailored for use on
+      <a href="https://parallel-netcdf.github.io">parallel interface for writing and reading netCDF data</a>, tailored for use on
       high performance platforms with parallel I/O.  The implementation builds on
       the MPI-IO interface, providing portability to most platforms in use and
       allowing users to leverage the many optimizations built into MPI-IO
       implementations.  Testing so far has been on Linux platforms with ROMIO and
       IBM SP machines using IBM's MPI.
     </p>
     <p>
-      Documentation and code for Parallel-NetCDF is now available for
+      Documentation and code for PnetCDF is now available for
       testing.
       Although a few interfaces are not implemented yet, the current implementation
       is complete enough to provide significant I/O performance improvements on
       parallel platforms, as described in a <a
       href="ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1048.pdf"
-      >technical report</a>.   Users are invited to test Parallel-NetCDF
+      >technical report</a>.   Users are invited to test PnetCDF
       in their applications.
     </p>
     <p></p>
@@ -2604,7 +2604,7 @@ <h2><a id="Python" name="Python">Python interfaces</a></h2>
     <p>
       Vicente Galiano of Miguel Hernandez University has developed a Python interface to
       PnetCDF. This Python's package called "PyPnetCDF" allows access to NetCDF files using MPI and
-      the library pnetCDF developed by http://www.mcs.anl.gov/parallel-netcdf/.
+      the library PnetCDF developed by https://parallel-netcdf.github.io.
       The tools are very similar to Konrad Hinsen's NetCDF package to Python
       but can read and write in a parallel way. For more information, see:
       <a

examples/C/parallel_vara.c

@@ -149,7 +149,7 @@ int main(int argc, char** argv)
     /* do not forget to exit define mode */
     err = nc_enddef(ncid); ERR
 
-    /* set to use MPI/PnetCDF collective I/O */
+    /* set to use MPI collective I/O */
     err = nc_var_par_access(ncid, NC_GLOBAL, NC_COLLECTIVE); ERR
 
     /* now we are in data mode */
@@ -175,7 +175,7 @@ int main(int argc, char** argv)
     /* obtain variable ID */
     err = nc_inq_varid(ncid, "var", &varid); ERR
 
-    /* set to use MPI/PnetCDF collective I/O */
+    /* set to use MPI collective I/O */
     err = nc_var_par_access(ncid, NC_GLOBAL, NC_COLLECTIVE); ERR
 
     /* each process reads its subarray from the file */

include/netcdf.h

@@ -156,7 +156,7 @@ Use this in mode flags for both nc_create() and nc_open(). */
 
 #define NC_INMEMORY      0x8000  /**< Read from memory. Mode flag for nc_open() or nc_create() => NC_DISKLESS */
 
-#define NC_PNETCDF       (NC_MPIIO) /**< Use parallel-netcdf library; alias for NC_MPIIO. */
+#define NC_PNETCDF       (NC_MPIIO) /**< Use PnetCDF library; alias for NC_MPIIO. */
 
 #define NC_UDF0          0x0080  /**< User-defined format 0. */
 #define NC_UDF1          0x0002  /**< User-defined format 1. */

include/netcdf_meta.h.in

@@ -39,17 +39,17 @@
 
 #define NC_HAS_NC2       @NC_HAS_NC2@ /*!< API version 2 support. */
 #define NC_HAS_NC4       @NC_HAS_NC4@ /*!< API version 4 support. */
-#define NC_HAS_HDF4      @NC_HAS_HDF4@ /*!< hdf4 support. */
-#define NC_HAS_HDF5      @NC_HAS_HDF5@ /*!< hdf5 support. */
-#define NC_HAS_SZIP      @NC_HAS_SZIP@ /*!< szip support (hdf5 only) */
+#define NC_HAS_HDF4      @NC_HAS_HDF4@ /*!< HDF4 support. */
+#define NC_HAS_HDF5      @NC_HAS_HDF5@ /*!< HDF5 support. */
+#define NC_HAS_SZIP      @NC_HAS_SZIP@ /*!< szip support (HDF5 only) */
 #define NC_HAS_DAP2      @NC_HAS_DAP2@ /*!< DAP2 support. */
 #define NC_HAS_DAP4      @NC_HAS_DAP4@ /*!< DAP4 support. */
 #define NC_HAS_DISKLESS  @NC_HAS_DISKLESS@ /*!< diskless support. */
 #define NC_HAS_MMAP      @NC_HAS_MMAP@ /*!< mmap support. */
 #define NC_HAS_JNA       @NC_HAS_JNA@ /*!< jna support. */
-#define NC_HAS_PNETCDF   @NC_HAS_PNETCDF@ /*!< pnetcdf support. */
-#define NC_HAS_PARALLEL4 @NC_HAS_PARALLEL4@ /*!< parallel IO support via hdf5 */
-#define NC_HAS_PARALLEL  @NC_HAS_PARALLEL@ /*!< parallel IO support via hdf5 and/or pnetcdf. */
+#define NC_HAS_PNETCDF   @NC_HAS_PNETCDF@ /*!< PnetCDF support. */
+#define NC_HAS_PARALLEL4 @NC_HAS_PARALLEL4@ /*!< parallel IO support via HDF5 */
+#define NC_HAS_PARALLEL  @NC_HAS_PARALLEL@ /*!< parallel IO support via HDF5 and/or PnetCDF. */
 
 #define NC_HAS_CDF5      @NC_HAS_CDF5@  /*!< CDF5 support. */
 #define NC_HAS_ERANGE_FILL @NC_HAS_ERANGE_FILL@ /*!< ERANGE_FILL Support */

libdispatch/dfile.c

@@ -2093,7 +2093,7 @@ NC_create(const char *path0, int cmode, size_t initialsz,
 #endif
 #ifdef USE_PNETCDF
     if (model == NC_FORMATX_UNDEFINED && (cmode & NC_MPIIO))
-        /* pnetcdf is used for parallel io on CDF-1, CDF-2, and CDF-5 */
+        /* PnetCDF is used for parallel io on CDF-1, CDF-2, and CDF-5 */
         model = NC_FORMATX_PNETCDF;
 #else
     if (model == NC_FORMATX_UNDEFINED && (cmode & NC_MPIIO))

liblib/Makefile.am

@@ -34,7 +34,7 @@ endif # BUILD_V2
 libnetcdf_la_LIBADD += ${top_builddir}/libdispatch/libdispatch.la	\
 			${top_builddir}/libsrc/libnetcdf3.la
 
-# + pnetcdf
+# + PnetCDF
 if USE_PNETCDF
 AM_CPPFLAGS += -I${top_srcdir}/libsrcp
 libnetcdf_la_LIBADD += ${top_builddir}/libsrcp/libnetcdfp.la

libnetcdf.settings.in

@@ -28,7 +28,7 @@ NetCDF-2 API:		@HAS_NC2@
 HDF4 Support:		@HAS_HDF4@
 NetCDF-4 API:		@HAS_NC4@
 NC-4 Parallel Support:	@HAS_PARALLEL4@
-PNetCDF Support:	@HAS_PNETCDF@
+PnetCDF Support:	@HAS_PNETCDF@
 DAP2 Support:		@HAS_DAP@
 DAP4 Support:		@HAS_DAP4@
 Diskless Support:	@HAS_DISKLESS@

libsrcp/Makefile.am

@@ -8,10 +8,10 @@ include $(top_srcdir)/lib_flags.am
 
 libnetcdfp_la_CPPFLAGS = ${AM_CPPFLAGS}
 
-# This is the code for a dispatch table for pnetcdf
+# This is the code for a dispatch table for PnetCDF
 # (which has CDF5 as its magic number)
 
-# These files comprise the pnetcdf dispatch library code.
+# These files comprise the PnetCDF dispatch library code.
 libnetcdfp_la_SOURCES = ncpdispatch.c
 
 noinst_LTLIBRARIES = libnetcdfp.la

nc-config.cmake.in

@@ -150,9 +150,9 @@ Available values for OPTION include:
   --has-hdf5     whether HDF5 is used in build (always the same as --has-nc4)
   --has-hdf4     whether HDF4 was used in build
   --has-logging  whether logging is enabled with --enable-logging.
-  --has-pnetcdf  whether parallel-netcdf (a.k.a. pnetcdf) was used in build
+  --has-pnetcdf  whether PnetCDF was used in build
   --has-szlib    whether szlib is included in build
-  --has-parallel whether has parallel IO support via hdf5 and/or pnetcdf
+  --has-parallel whether has parallel IO support via HDF5 and/or PnetCDF
   --libs         library linking information for netcdf
   --prefix       Install prefix
   --includedir   Include directory

nc-config.in

@@ -82,9 +82,9 @@ Available values for OPTION include:
   --has-hdf5    whether HDF5 is used in build (always the same as --has-nc4)
   --has-hdf4    whether HDF4 was used in build
   --has-logging whether logging is enabled with --enable-logging.
-  --has-pnetcdf whether parallel-netcdf (a.k.a. pnetcdf) was used in build
+  --has-pnetcdf whether PnetCDF was used in build
   --has-szlib   whether szlib is included in build
-  --has-parallel whether has parallel IO support via hdf5 and/or pnetcdf
+  --has-parallel whether has parallel IO support via HDF5 and/or PnetCDF
   --has-cdf5    whether cdf5 support is included in build
   --libs        library linking information for netcdf
   --prefix      Install prefixx