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More replacement of "parallel-netcdf" with "PnetCDF".

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Wei-keng Liao 2018-09-20 11:45:25 -05:00
parent 28512f77f0
commit 5ed6c239e1
10 changed files with 28 additions and 31 deletions
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2
CMakeLists.txt
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@ -1010,7 +1010,7 @@ IF(ENABLE_PARALLEL4 AND ENABLE_NETCDF_4)
ENDIF()
ENDIF()
# Options to enable parallel IO for classic formats with parallel-netcdf library.
# Options to enable parallel IO for classic formats with PnetCDF library.
SET(STATUS_PNETCDF "OFF")
OPTION(ENABLE_PNETCDF "Build with parallel I/O for CDF-1, 2, and 5 files using PnetCDF." OFF)

9
INSTALL.md
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@ -184,7 +184,7 @@ Building netCDF with Classic Library Only {#build_classic}
---------------------------------------
It is possible to build the netCDF C libraries and utilities so that
only the netCDF classic and 64-bit offset formats are supported, or
only the netCDF classic, 64-bit offset, and CDF-5 formats are supported, or
the remote data access client is not built. (See \ref netcdf_format)
for more information about the netCDF format variants. See the <a
href="http://opendap.org/netCDF-DAP">netCDF-DAP site</a>
@ -307,8 +307,8 @@ $ make check install
~~~
If parallel I/O access to netCDF classic and 64-bit offset files is
also needed, the parallel-netcdf library should also be installed.
If parallel I/O access to netCDF classic, 64-bit offset, CDF-5 files is
also needed, the PnetCDF library should also be installed.
(Note: the previously recommended <a
href=ftp://ftp.unidata.ucar.edu/pub/netcdf/contrib/pnetcdf.h>replacement
pnetcdf.h</a> should no longer be used.) Then configure netCDF with the
@ -358,8 +358,7 @@ Note: --disable prefix indicates that the option is normally enabled.
<tr><td>--enable-netcdf4<td>synonym for enable-netcdf-4
<tr><td>--enable-hdf4<td>build netcdf-4 with HDF4 read capability<td>HDF4, HDF5 and zlib
<tr><td>--enable-hdf4-file-tests<td>test ability to read HDF4 files<td>selected HDF4 files from Unidata ftp site
<tr><td>--enable-pnetcdf<td>build netcdf-4 with parallel I/O for classic and
64-bit offset files using parallel-netcdf
<tr><td>--enable-pnetcdf<td>build netcdf-4 with parallel I/O for classic, 64-bit offset, and CDF-5 files using PnetCDF
<tr><td>--enable-extra-example-tests<td>Run extra example tests<td>--enable-netcdf-4,GNU sed
<tr><td>--enable-parallel-tests <td>run extra parallel IO tests<td>--enable-netcdf-4, parallel IO support
<tr><td>--enable-logging<td>enable logging capability<td>--enable-netcdf-4

4
RELEASE_NOTES.md
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@ -607,7 +607,7 @@ subgroup getting the wrong dimension IDs for its dimensions. [NCF-247]
[NCF-247]: https://bugtracking.unidata.ucar.edu/browse/NCF-247
* Fixed bug with incorrect fixed-size variable offsets in header getting
written when schema changed for files created by parallel-netcdf. Thanks
written when schema changed for files created by PnetCDF Thanks
to Wei-keng Liao for developing and contributing the fix. [NCF-234]
[NCF-234]: https://bugtracking.unidata.ucar.edu/browse/NCF-234
@ -645,7 +645,7 @@ options for specifying which groups or variables are to be copied.
[NCF-216]: https://bugtracking.unidata.ucar.edu/browse/NCF-216
* Merged in parallel-netcdf bugs fixes from Greg Sjaardema. [NCF-214]
* Merged in PnetCDF bugs fixes from Greg Sjaardema. [NCF-214]
[NCF-214]: https://bugtracking.unidata.ucar.edu/browse/NCF-214

2
docs/old/defines.texi
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@ -46,7 +46,7 @@
@set curl-url http://curl.haxx.se
@set xml2-url http://xmlsoft.org
@set opendap-url http://opendap.org
@set pnetcdf-url http://www.mcs.anl.gov/parallel-netcdf
@set pnetcdf-url https://parallel-netcdf.github.io
@c urls for netcdf documents
@set docs-url @value{netcdf-url}/docs

4
docs/old/netcdf-c.texi
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@ -1385,7 +1385,7 @@ and placed in define mode, ready for you to add dimensions, variables,
and attributes.
If the NC_NETCDF4 flag is used, the HDF5 library is used for parallel
I/O. If not, the parallel-netcdf library is used.
I/O. If not, the PnetCDF library is used.
When a file is created for parallel access, independent operations are
the default. To use independent access on a variable,
@ -10395,7 +10395,7 @@ The variable can be changed from collective to independent, and back,
as often as desired.
Note that classic and 64-bit offset files are access using the
parallel-netcdf library, which does not allow per-variable setting of
PnetCDF library, which does not allow per-variable setting of
the parallel access mode. For these files, calling nc_var_par_access
sets the access for all of the variables in the file.

2
docs/old/netcdf-f90.texi
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@ -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 PnetCDF (Parallel-netCDF) library, which does not allow
the PnetCDF 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

14
docs/old/netcdf-install.texi
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@ -518,7 +518,7 @@ x86 platforms.
@cindex --enable-parallel-tests
NetCDF makes available the parallel I/O features of HDF5 and the
parallel-netcdf libraries, allowing parallel I/O from netCDF-4 linked
PnetCDF libraries, allowing parallel I/O from netCDF-4 linked
programs.
@subsection Building HDF5 for Parallel I/O
@ -535,9 +535,9 @@ testing system:
CC=mpicc ./configure --enable-parallel --prefix=/shecky/local_par --with-zlib=/shecky/local_par --disable-shared && make check install
@end example
@subsection The parallel-netcdf Library
@subsection The PnetCDF Library
Optionally, the parallel-netcdf library should also be installed, and
Optionally, the PnetCDF library should also be installed, and
the replacement for pnetcdf.h should be copied from
ftp://ftp.unidata.ucar.edu/pub/netcdf/contrib/pnetcdf.h.
@ -560,7 +560,7 @@ option to configure. These tests will be run as mpiexec calls. This
may not be appropriate on all systems, especially those which use some
queue for jobs.
To use parallel-netcdf to perform parallel I/O on classic and 64-bit
To use PnetCDF to perform parallel I/O on classic and 64-bit
offset files, use the --enable-pnetcdf option.
For parallel builds the netCDF examples are not built. This is to
@ -665,8 +665,8 @@ users.
@item --enable-pnetcdf
Allows parallel I/O with classic and 64-bit offset format files, using
the PnetCDF (Parallel-netCDF) library from
Argonne/Northwestern. The parallel-netcdf library must be installed,
the PnetCDF library from
Argonne/Northwestern. The PnetCDF 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)
@ -1329,7 +1329,7 @@ On some systems you must also include -lm for the math library.
If HDF4 was used when building netCDF, you must also use -lmfhdf -ldf
-ljpeg.
Finally, if you use the parallel-netcdf library, you must use
Finally, if you use the PnetCDF library, you must use
-lpnetcdf.
The worst case scenario is, using all of the above libraries:

2
docs/old/netcdf-tutorial.texi
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@ -2293,7 +2293,7 @@ Argonne/Northwestern. Unfortunately the two methods involve different
APIs, and different binary formats.
For parallel read/write access to classic and 64-bit offset data users
must use the parallel-netcdf library from Argonne/Northwestern
must use the PnetCDF library from Argonne/Northwestern
University. This is not a Unidata software package, but was developed
using the Unidata netCDF C library as a starting point. For more
information see the parallel netcdf web site: @value{pnetcdf-url}.

10
docs/old/netcdf.texi
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@ -873,7 +873,7 @@ 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 PnetCDF
(Parallel-netCDF) library from Argonne/Northwestern, a new nc-config
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
@ -1035,12 +1035,12 @@ multiple concurrent writers.
NetCDF-4 supports parallel read/write access to netCDF-4/HDF5 files,
using the underlying HDF5 library and parallel read/write access to
classic and 64-bit offset files using the parallel-netcdf library.
classic and 64-bit offset files using the PnetCDF library.
For more information about HDF5, see the HDF5 web site:
@uref{@value{hdf5-url}}.
For more information about parallel-netcdf, see their web site:
For more information about PnetCDF see their web site:
@uref{@value{pnetcdf-url}}.
@node Future , References, Limitations, Introduction
@ -3065,10 +3065,10 @@ 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 PnetCDF
(Parallel-netCDF) library from Argonne National Labs/Nortwestern
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
time. See the PnetCDF site for more information
(@uref{@value{pnetcdf-url}}).
@node Interoperability with HDF5, DAP Support, Parallel Access, Structure

10
libdispatch/dparallel.c
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@ -16,8 +16,7 @@ This function creates a new netCDF file for parallel I/O access.
Parallel I/O access is only available in library build which support
parallel I/O. To support parallel I/O, netCDF must be built with
netCDF-4 enabled, and with a HDF5 library that supports parallel I/O,
or with support for the parallel-netcdf library via the
enable-pnetcdf option.
or with support for the PnetCDF library via the enable-pnetcdf option.
See nc_create() for a fuller discussion of file creation.
@ -121,8 +120,7 @@ file.
Parallel I/O access is only available in library build which support
parallel I/O. To support parallel I/O, netCDF must be built with
netCDF-4 enabled, and with a HDF5 library that supports parallel I/O,
or with support for the parallel-netcdf library via the
enable-pnetcdf option.
or with support for the PnetCDF library via the enable-pnetcdf option.
It is not necessary to pass any information about the format of the
file being opened. The file type will be detected automatically by the
@ -139,7 +137,7 @@ errors, it simply stops their display to the user through stderr.
\param mode The mode flag may include NC_WRITE (for read/write
access), NC_MPIIO or NC_MPIPOSIX (not both) for parallel netCDF-4 I/O,
or NC_PNETCDF for parallel-netcdf parallel I/O access for a netCDF
or NC_PNETCDF for PnetCDF parallel I/O access for a netCDF
classic or CDF5 file.
\param comm the MPI communicator to be used.
@ -205,7 +203,7 @@ integers.
\param mode The mode flag may include NC_WRITE (for read/write
access), NC_MPIIO or NC_MPIPOSIX (not both) for parallel netCDF-4 I/O,
or NC_PNETCDF for parallel-netcdf parallel I/O access for a netCDF
or NC_PNETCDF for PnetCDF parallel I/O access for a netCDF
classic or CDF5 file.
\param comm the MPI communicator to be used.