From 4e1897e074e7197fe933ee25cebc5253ef870980 Mon Sep 17 00:00:00 2001
From: Ed Hartnett <edwardjameshartnett@gmail.com>
Date: Tue, 30 Apr 2019 09:26:07 -0600
Subject: [PATCH 1/9] fixed docs

---
 doc/source/GettingStarted.txt | 40 +++++++++++++++++++++++++++++------
 1 file changed, 34 insertions(+), 6 deletions(-)

diff --git a/doc/source/GettingStarted.txt b/doc/source/GettingStarted.txt
index 40fe348d534..d2aaaf3603e 100644
--- a/doc/source/GettingStarted.txt
+++ b/doc/source/GettingStarted.txt
@@ -20,21 +20,49 @@
 
 /*! \page intro Introduction 
 
-PIO is a software interface layer designed to encapsolate the complexities of parallel IO and make it easier to replace the lower level software backend.  It currently supports <a href=http://www.unidata.ucar.edu/software/netcdf/docs/html_guide/index.html#user_guide> netcdf </a>  and <a href=http://trac.mcs.anl.gov/projects/parallel-netcdf> pnetcdf </a>.
+PIO is a software interface layer designed to encapsolate the
+complexities of parallel IO and make it easier to replace the lower
+level software backend.  It currently supports <a
+href=http://www.unidata.ucar.edu/software/netcdf/docs/html_guide/index.html#user_guide>
+netcdf </a> and <a
+href=http://trac.mcs.anl.gov/projects/parallel-netcdf> pnetcdf </a>.
 
 Basic description of how to optimize IO in a parallel environment...
 
-PIO calls are collective.  A MPI communicator is set in a call to \ref PIO_init and all tasks associated with that communicator must participate in all subsequent calls to PIO.  An application can make multiple calls to \ref PIO_init in order to support multiple MPI communicators.
+PIO calls are collective.  A MPI communicator is set in a call to \ref
+PIO_init and all tasks associated with that communicator must
+participate in all subsequent calls to PIO.  An application can make
+multiple calls to \ref PIO_init in order to support multiple MPI
+communicators.
 
-Begin by checking out a copy from [gitHub](https://github.com/PARALLELIO/ParallelIO) and installing on your system as per the instructions in the [Installation](@ref install) document. Take a look at examples of PIO usage in both complex and simple test programs in the [Examples](@ref examp) document. Finally, read through the [FAQ](@ref faq) to see if any remaining questions can be answered. 
+Begin by getting and unpacking the most recent release of PIO from
+[gitHub](https://github.com/PARALLELIO/ParallelIO/releases) and
+installing on your system as per the instructions in the
+[Installation](@ref install) document. Take a look at examples of PIO
+usage in both complex and simple test programs in the [Examples](@ref
+examp) document. Finally, read through the [FAQ](@ref faq) to see if
+any remaining questions can be answered.
 
 ### Using PIO has three basic steps. ###
 
-1. Your program should call the \ref PIO_init function, and provide the MPI communicator (and the rank within that communicator) of the calling task. This call initializes an IO system type structure that will be used in subsequent file and decomposition functions.
+1. Your program should call the \ref PIO_init function, and provide
+the MPI communicator (and the rank within that communicator) of the
+calling task. This call initializes an IO system type structure that
+will be used in subsequent file and decomposition functions.
 
-2. You can open a file for reading or writing with a call to \ref PIO_createfile or \ref PIO_openfile. In this call you will specify the file type: pio_iotype_netcdf, pio_iotype_pnetcdf, pio_iotype_netcdf4c or pio_iotype_netcdf4p; along with the file name and optionally the netcdf mode.
+2. You can open a file for reading or writing with a call to \ref
+PIO_createfile or \ref PIO_openfile. In this call you will specify the
+file type: pio_iotype_netcdf, pio_iotype_pnetcdf, pio_iotype_netcdf4c
+or pio_iotype_netcdf4p; along with the file name and optionally the
+netcdf mode.
 
-3. Finally, you can read or write decomposed data to the output file. You must describe the mapping between the organization of data in the file and that same data in the application space.  This is done in a call to \ref PIO_initdecomp. In the simplest call to this function, a one dimensional integer array is passed from each task, the values in the array represent the offset from the beginning of the array on file. (what happens next?)
+3. Finally, you can read or write decomposed data to the output
+file. You must describe the mapping between the organization of data
+in the file and that same data in the application space.  This is done
+in a call to \ref PIO_initdecomp. In the simplest call to this
+function, a one dimensional integer array is passed from each task,
+the values in the array represent the offset from the beginning of the
+array on file.
 
 
 */

From 3f0112f2ccd3d3182bfaed80ee1a11dcf40b67bb Mon Sep 17 00:00:00 2001
From: Ed Hartnett <edwardjameshartnett@gmail.com>
Date: Tue, 30 Apr 2019 09:38:29 -0600
Subject: [PATCH 2/9] updated README

---
 README.md                     | 21 +++++++++++++++++----
 doc/source/GettingStarted.txt |  2 +-
 2 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index c94f5d8c71d..8595e6d5c80 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@ cdash site at [http://my.cdash.org/index.php?project=PIO](http://my.cdash.org/in
 
 ## Dependencies
 
-PIO can use NetCDF (version 4.3.3+) and/or PnetCDF (version 1.6.0+)
+PIO can use NetCDF (version 4.6.1+) and/or PnetCDF (version 1.9.0+)
 for I/O. NetCDF may be built with or without netCDF-4 features. NetCDF
 is required for PIO, PnetCDF is optional.
 
@@ -29,6 +29,19 @@ be linked with an MPI-enabled version of HDF5.  Optionally, NetCDF can be
 built with DAP support, which introduces a dependency on CURL.  Additionally,
 HDF5, itself, introduces dependencies on LIBZ and (optionally) SZIP.
 
+## Building PIO
+
+To build PIO, unpack the distribution tarball and do:
+
+```
+CC=mpicc FC=mpif90 ./configure --enable-fortran && make check install
+```
+
+For a full description of the available options and flags, try:
+```
+./configure --help
+```
+
 ## Configuring with CMake
 
 To configure the build, PIO requires CMake version 2.8.12+.  The typical
@@ -88,7 +101,7 @@ If you wish to install PIO in a safe location for use later with other
 software, you may set the `CMAKE_INSTALL_PREFIX` variable to point to the
 desired install location.
 
-## Building
+### Building
 
 Once you have successfully configured PIO with CMake in a build directory.
 From within the build directory, build PIO with:
@@ -99,7 +112,7 @@ make
 
 This will build the `pioc` and `piof` libraries.
 
-## Testing
+### Testing
 
 If you desire to do testing, and `PIO_ENABLE_TESTS=ON` (which is the default
 setting), you may build the test executables with:
@@ -136,7 +149,7 @@ job submission script.  It is important to understand, however, that `ctest` its
 will preface all of the test executable commands with the appropriate `mpirun`/`mpiexec`/`runjob`/etc.
 Hence, you should not further preface the `ctest` command with these MPI launchers.
 
-## Installing
+### Installing
 
 Once you have built the PIO libraries, you may install them in the location
 specified by the `CMAKE_INSTALL_PREFIX`.  To do this, simply type:
diff --git a/doc/source/GettingStarted.txt b/doc/source/GettingStarted.txt
index d2aaaf3603e..09ea7864ebe 100644
--- a/doc/source/GettingStarted.txt
+++ b/doc/source/GettingStarted.txt
@@ -32,7 +32,7 @@ Basic description of how to optimize IO in a parallel environment...
 PIO calls are collective.  A MPI communicator is set in a call to \ref
 PIO_init and all tasks associated with that communicator must
 participate in all subsequent calls to PIO.  An application can make
-multiple calls to \ref PIO_init in order to support multiple MPI
+multiple calls to PIO_init() in order to support multiple MPI
 communicators.
 
 Begin by getting and unpacking the most recent release of PIO from

From 5030bf3c68592f5387bf19c154639197add3d18e Mon Sep 17 00:00:00 2001
From: Ed Hartnett <edwardjameshartnett@gmail.com>
Date: Tue, 30 Apr 2019 10:17:01 -0600
Subject: [PATCH 3/9] more doc fixes

---
 README.md                                     | 131 +++---------------
 doc/source/GettingStarted.txt                 |   2 +-
 doc/source/Installing.txt                     |   2 +-
 doc/source/base.txt                           |  30 ++--
 doc/source/faq.txt                            |   2 +-
 docs/_c_a_mexample.html                       |   2 +-
 docs/annotated.html                           |   2 +-
 docs/api.html                                 |   2 +-
 docs/contributing_code.html                   |   2 +-
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diff --git a/README.md b/README.md
index 8595e6d5c80..38eacdbf0ca 100644
--- a/README.md
+++ b/README.md
@@ -42,122 +42,31 @@ For a full description of the available options and flags, try:
 ./configure --help
 ```
 
-## Configuring with CMake
-
-To configure the build, PIO requires CMake version 2.8.12+.  The typical
-configuration with CMake can be done as follows:
-
-```
-CC=mpicc FC=mpif90 cmake [-DOPTION1=value1 -DOPTION2=value2 ...] /path/to/pio/source
-```
-
-where `mpicc` and `mpif90` are the appropriate MPI-enabled compiler wrappers
-for your system.
-
-The `OPTIONS` section typically should consist of pointers to the install
-locations for various dependencies, assuming these dependencies are not 
-located in *canonical* search locations.  
-
-For each dependency `XXX`, one can specify the location of its 
-installation path with the CMake variable `XXX_PATH`.  If the `C` and
-`Fortran` libraries for the dependency are installed in different locations
-(such as can be done with NetCDF), then you can specify individually
-`XXX_C_PATH` and `XXX_Fortran_PATH`.  Hence, you can specify the locations
-of both NetCDF-C and NetCDF-Fortran, as well as PnetCDF, with the following
-CMake configuration line:
-
-```
-CC=mpicc FC=mpif90 cmake -DNetCDF_C_PATH=/path/to/netcdf-c \
-                         -DNetCDF_Fortran_PATH=/path/to/netcdf-fortran \
-                         -DPnetCDF_PATH=/path/to/pnetcdf \
-                         /path/to/pio/source
-```
-
-This works for the dependencies: `NetCDF`, `PnetCDF`, `HDF5`, `LIBZ`, `SZIP`.
-
-### Additional CMake Options
-
-Additional configuration options can be specified on the command line.
-
-The `PIO_ENABLE_TIMING` option can be set to `ON` or `OFF` to enable or
-disable the use of GPTL timing in the PIO libraries.  This feature requires
-the GPTL C library for the PIO `C` library and the GPTL Fortran library with
-the `perf_mod.mod` and `perf_utils.mod` interface modules.  If these GPTL
-libraries are already installed on the system, the user can point PIO to the
-location of these libraries with the `GPTL_PATH` variable (or, individually,
-`GPTL_C_PATH` and `GPTL_Fortran_Perf_PATH` variables).  However, if these
-GPTL libraries are not installed on the system, and GPTL cannot be found,
-then PIO will build its own internal version of GPTL.  
-
-If PnetCDF is not installed on the system, the user can disable its use by
-setting `-DWITH_PNETCDF=OFF`.  This will disable the search for PnetCDF on the
-system and disable the use of PnetCDF from within PIO.
-
-If the user wishes to disable the PIO tests, then the user can set the
-variable `-DPIO_ENABLE_TESTS=OFF`.  This will entirely disable the CTest 
-testing suite, as well as remove all of the test build targets.
-
-If you wish to install PIO in a safe location for use later with other
-software, you may set the `CMAKE_INSTALL_PREFIX` variable to point to the
-desired install location.
-
-### Building
-
-Once you have successfully configured PIO with CMake in a build directory.
-From within the build directory, build PIO with:
-
-```
-make
-```
-
-This will build the `pioc` and `piof` libraries.
-
-### Testing
-
-If you desire to do testing, and `PIO_ENABLE_TESTS=ON` (which is the default
-setting), you may build the test executables with:
-
-```
-make tests
-```
-
-Once the tests have been built, you may run tests with:
-
-```
-ctest
-```
-
-If you have not run `make tests` before you run `ctest`, then you will see
-all of the tests fail.
-
-Alternatively, you may build the test executables and then run tests 
-immediately with:
-
-```
+Note that environment variables CC and FC may need to be set to the
+MPI versions of the C and Fortran compiler. Also CPPFLAGS and LDFLAGS
+may need to be set to indicate the locations of one or more of the
+dependent libraries. (If using MPI compilers, the entire set of
+dependent libraries should be built with the same compilers.) For
+example:
+
+```
+export CC=mpicc
+export FC=mpifort
+export CPPFLAGS='-I/usr/local/netcdf-fortran-4.4.5_c_4.6.3_mpich-3.2/include -I/usr/local/netcdf-c-4.6.3_hdf5-1.10.5/include -I/usr/local/pnetcdf-1.11.0_shared/include'
+export LDFLAGS='-L/usr/local/netcdf-c-4.6.3_hdf5-1.10.5/lib -L/usr/local/pnetcdf-1.11.0_shared/lib'
+./configure --prefix=/usr/local/pio-2.4.2 --enable-fortran
 make check
+make install
 ```
 
-(similar to the typical `make check` Autotools target).
+## Building with CMake
 
-**NOTE:** It is important to note that these tests are designed to run in parallel.
-If you are on one of the supported supercomputing platforms (i.e., NERSC, NWSC, ALCF, 
-etc.), then the `ctest` command will assume that the tests will be run in an appropriately
-configured and scheduled parallel job.  This can be done by requesting an interactive
-session from the login nodes and then running `ctest` from within the interactive
-terminal.  Alternatively, this can be done by running the `ctest` command from a
-job submission script.  It is important to understand, however, that `ctest` itself
-will preface all of the test executable commands with the appropriate `mpirun`/`mpiexec`/`runjob`/etc.
-Hence, you should not further preface the `ctest` command with these MPI launchers.
-
-### Installing
-
-Once you have built the PIO libraries, you may install them in the location
-specified by the `CMAKE_INSTALL_PREFIX`.  To do this, simply type:
+The typical configuration with CMake can be done as follows:
 
 ```
-make install
+CC=mpicc FC=mpif90 cmake [-DOPTION1=value1 -DOPTION2=value2 ...] /path/to/pio/source
 ```
 
-If the internal GPTL libraries were built (because GPTL could not be found
-and the `PIO_ENABLE_TIMING` variable is set to `ON`), then these libraries
-will be installed with PIO.
+Full instructions for the cmake build can be found in the installation
+documentation.
+
diff --git a/doc/source/GettingStarted.txt b/doc/source/GettingStarted.txt
index 09ea7864ebe..d2a510d9a8b 100644
--- a/doc/source/GettingStarted.txt
+++ b/doc/source/GettingStarted.txt
@@ -27,7 +27,7 @@ href=http://www.unidata.ucar.edu/software/netcdf/docs/html_guide/index.html#user
 netcdf </a> and <a
 href=http://trac.mcs.anl.gov/projects/parallel-netcdf> pnetcdf </a>.
 
-Basic description of how to optimize IO in a parallel environment...
+Basic description of how to optimize IO in a parallel environment:
 
 PIO calls are collective.  A MPI communicator is set in a call to \ref
 PIO_init and all tasks associated with that communicator must
diff --git a/doc/source/Installing.txt b/doc/source/Installing.txt
index 6f281152248..05aa5d1dd61 100644
--- a/doc/source/Installing.txt
+++ b/doc/source/Installing.txt
@@ -20,7 +20,7 @@ The PIO code is currently stored on github at <https://github.com/PARALLELIO/Par
 
 ### Dependencies ###
 
-PIO can use NetCDF (version 4.3.3+) and/or PnetCDF (version 1.6.1+) for I/O.
+PIO can use NetCDF (version 4.6.1+) and/or PnetCDF (version 1.9.0+) for I/O.
 Ideally, the NetCDF version should be built with MPI, which requires that it
 be linked with an MPI-enabled version of HDF5.  Optionally, NetCDF can be 
 built with DAP support, which introduces a dependency on CURL.  Additionally,
diff --git a/doc/source/base.txt b/doc/source/base.txt
index 210c9bbfbf3..674155493de 100644
--- a/doc/source/base.txt
+++ b/doc/source/base.txt
@@ -16,28 +16,30 @@
  */ 
 /*! 
 
-\mainpage Parallel I/O library (PIO)
+\mainpage Parallel I/O Libraries (PIO)
 
 \author Jim Edwards
 \author John M. Dennis
 \author Mariana Vertenstein
 \author Edward Hartnett
 
-The Parallel I/O (PIO) library has been developed over several years
-to improve the ability of component models of the Community Earth
-System Model (CESM) to perform I/O.  We believe that the interface is
-sufficiently general to be useful to a broader spectrum of
-applications.  The focus of development has been on backend tools that
-use the NetCDF file format.  PIO currently supports NetCDF and PnetCDF
-as backend libraries, both can be linked and used with runtime options
-controlling which is used for a given file.
+The Parallel IO libraries (PIO) are high-level parallel I/O C and
+Fortran libraries for structured grid applications. PIO provides a
+netCDF-like API, and allows users to designate some subset of
+processors to perform IO. Computational code calls netCDF-like
+functions to read and write data, and PIO uses the IO processors to
+perform all necessary IO.
 
-PIO2 represents a significant rewrite of the PIO library and includes
-a C API as well as the original F90 API.  A new decomposition strategy
-has been introduced which gives the user more ability to tune io communications.
+PIO also supports the creation of multiple computation components,
+each containing many processors, and one shared set of IO
+processors. The computational components can perform write operation
+asynchronously, and the IO processors will take care of all storage
+interaction.
 
-This user's guide provides information about the PIO library and examples on how it can be used. 
-Please review the ChangeLog that is included with the distribution for up-to-date release information.
+This user's guide provides information about the PIO library and
+examples on how it can be used. Please watch the PIO GitHub site
+[https://github.com/NCAR/ParallelIO] for announcements and new
+releases.
 
  - \ref intro
  - \ref install
diff --git a/doc/source/faq.txt b/doc/source/faq.txt
index 99d7c46b7a4..dab793d8667 100644
--- a/doc/source/faq.txt
+++ b/doc/source/faq.txt
@@ -25,7 +25,7 @@
 Note that num_iotasks is the maximum number of IO tasks to use for an IO operation.   The size of the field being read or written along with the tunable blocksize parameter, \ref PIO_set_blocksize, determines the actual number of tasks used for a given IO operation.
 </dd>
 <dt>How do I test if PIO is installed and working correctly? </dt> 
-    <dd>The PIO Library distribution contains a testpio subdirectory with a number of programs to test the PIO library. Please see the \ref examp page for details. </dd>
+    <dd>The PIO Library distribution contains tests for PIO. They are run my 'make check'. The tests use mpiexec to run tests on 4, 8, or 16 processors. </dd>
 
 </dl>
 */
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-Generated on Fri Apr 19 2019 14:00:17 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
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 Note that num_iotasks is the maximum number of IO tasks to use for an IO operation. The size of the field being read or written along with the tunable blocksize parameter, <a class="el" href="group___p_i_o__set__blocksize.html">PIO_set_blocksize</a>, determines the actual number of tasks used for a given IO operation.  </dd>
 <dt>How do I test if PIO is installed and working correctly?  </dt>
-<dd><p class="startdd">The PIO Library distribution contains a testpio subdirectory with a number of programs to test the PIO library. Please see the <a class="el" href="examp.html">Examples</a> page for details. </p>
+<dd><p class="startdd">The PIO Library distribution contains tests for PIO. They are run my 'make check'. The tests use mpiexec to run tests on 4, 8, or 16 processors. </p>
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-Generated on Fri Apr 19 2019 14:00:18 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Tue Apr 30 2019 10:14:35 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
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 </a> 1.8.13
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diff --git a/docs/group__iodesc__generate.html b/docs/group__iodesc__generate.html
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--- a/docs/group__iodesc__generate.html
+++ b/docs/group__iodesc__generate.html
@@ -71,7 +71,7 @@
 </div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Fri Apr 19 2019 14:00:18 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Tue Apr 30 2019 10:14:35 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
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 </a> 1.8.13
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--- a/docs/index.html
+++ b/docs/index.html
@@ -71,9 +71,9 @@
 Mariana Vertenstein </dd>
 <dd>
 Edward Hartnett</dd></dl>
-<p>The Parallel I/O (PIO) library has been developed over several years to improve the ability of component models of the Community Earth System Model (CESM) to perform I/O. We believe that the interface is sufficiently general to be useful to a broader spectrum of applications. The focus of development has been on backend tools that use the NetCDF file format. PIO currently supports NetCDF and PnetCDF as backend libraries, both can be linked and used with runtime options controlling which is used for a given file.</p>
-<p>PIO2 represents a significant rewrite of the PIO library and includes a C API as well as the original F90 API. A new decomposition strategy has been introduced which gives the user more ability to tune io communications.</p>
-<p>This user's guide provides information about the PIO library and examples on how it can be used. Please review the ChangeLog that is included with the distribution for up-to-date release information.</p>
+<p>The Parallel IO libraries (PIO) are high-level parallel I/O C and Fortran libraries for structured grid applications. PIO provides a netCDF-like API, and allows users to designate some subset of processors to perform IO. Computational code calls netCDF-like functions to read and write data, and PIO uses the IO processors to perform all necessary IO.</p>
+<p>PIO also supports the creation of multiple computation components, each containing many processors, and one shared set of IO processors. The computational components can perform write operation asynchronously, and the IO processors will take care of all storage interaction.</p>
+<p>This user's guide provides information about the PIO library and examples on how it can be used. Please watch the PIO GitHub site [<a href="https://github.com/NCAR/ParallelIO">https://github.com/NCAR/ParallelIO</a>] for announcements and new releases.</p>
 <ul>
 <li><a class="el" href="intro.html">Introduction</a></li>
 <li><a class="el" href="install.html">Installing PIO</a></li>
@@ -89,7 +89,7 @@
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 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Fri Apr 19 2019 14:00:19 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Tue Apr 30 2019 10:14:36 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.13
 </small></address>
diff --git a/docs/install.html b/docs/install.html
index 73b130eafec..2893a6017f1 100644
--- a/docs/install.html
+++ b/docs/install.html
@@ -66,7 +66,7 @@
 <div class="contents">
 <div class="textblock"><p>The PIO code is currently stored on github at <a href="https://github.com/PARALLELIO/ParallelIO">https://github.com/PARALLELIO/ParallelIO</a>. For questions about downloading or developing this code, consult the <a href="https://github.com/CESM-Development/cime/wiki/CIME-Git-Workflow">CIME Git Wiki</a> or email <a href="#" onclick="location.href='mai'+'lto:'+'jed'+'wa'+'rds'+'@u'+'car'+'.e'+'du'; return false;">jedwa<span style="display: none;">.nosp@m.</span>rds@<span style="display: none;">.nosp@m.</span>ucar.<span style="display: none;">.nosp@m.</span>edu</a>.</p>
 <h3>Dependencies</h3>
-<p>PIO can use NetCDF (version 4.3.3+) and/or PnetCDF (version 1.6.1+) for I/O. Ideally, the NetCDF version should be built with MPI, which requires that it be linked with an MPI-enabled version of HDF5. Optionally, NetCDF can be built with DAP support, which introduces a dependency on CURL. Additionally, HDF5, itself, introduces dependencies on LIBZ and (optionally) SZIP.</p>
+<p>PIO can use NetCDF (version 4.6.1+) and/or PnetCDF (version 1.9.0+) for I/O. Ideally, the NetCDF version should be built with MPI, which requires that it be linked with an MPI-enabled version of HDF5. Optionally, NetCDF can be built with DAP support, which introduces a dependency on CURL. Additionally, HDF5, itself, introduces dependencies on LIBZ and (optionally) SZIP.</p>
 <h3>Configuring with CMake</h3>
 <p>To configure the build, PIO requires CMake version 2.8.12+. The typical configuration with CMake can be done as follows:</p>
 <pre class="fragment">&gt; CC=mpicc FC=mpif90 cmake [-DOPTION1=value1 -DOPTION2=value2 ...] /path/to/pio/source
@@ -110,7 +110,7 @@ <h3>Examples</h3>
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 <img class="footer" src="doxygen.png" alt="doxygen"/>
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diff --git a/docs/intro.html b/docs/intro.html
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 <div class="contents">
 <div class="textblock"><p>PIO is a software interface layer designed to encapsolate the complexities of parallel IO and make it easier to replace the lower level software backend. It currently supports <a href="http://www.unidata.ucar.edu/software/netcdf/docs/html_guide/index.html#user_guide">netcdf </a> and <a href="http://trac.mcs.anl.gov/projects/parallel-netcdf">pnetcdf </a>.</p>
 <p>Basic description of how to optimize IO in a parallel environment...</p>
-<p>PIO calls are collective. A MPI communicator is set in a call to <a class="el" href="group___p_i_o__init.html">PIO_init</a> and all tasks associated with that communicator must participate in all subsequent calls to PIO. An application can make multiple calls to <a class="el" href="group___p_i_o__init.html">PIO_init</a> in order to support multiple MPI communicators.</p>
-<p>Begin by checking out a copy from <a href="https://github.com/PARALLELIO/ParallelIO">gitHub</a> and installing on your system as per the instructions in the <a class="el" href="install.html">Installation</a> document. Take a look at examples of PIO usage in both complex and simple test programs in the <a class="el" href="examp.html">Examples</a> document. Finally, read through the <a class="el" href="faq.html">FAQ</a> to see if any remaining questions can be answered.</p>
+<p>PIO calls are collective. A MPI communicator is set in a call to <a class="el" href="group___p_i_o__init.html">PIO_init</a> and all tasks associated with that communicator must participate in all subsequent calls to PIO. An application can make multiple calls to PIO_init() in order to support multiple MPI communicators.</p>
+<p>Begin by getting and unpacking the most recent release of PIO from <a href="https://github.com/PARALLELIO/ParallelIO/releases">gitHub</a> and installing on your system as per the instructions in the <a class="el" href="install.html">Installation</a> document. Take a look at examples of PIO usage in both complex and simple test programs in the [Examples](<a class="el" href="examp.html">Examples</a>) document. Finally, read through the <a class="el" href="faq.html">FAQ</a> to see if any remaining questions can be answered.</p>
 <h3>Using PIO has three basic steps.</h3>
 <ol type="1">
 <li>Your program should call the <a class="el" href="group___p_i_o__init.html">PIO_init</a> function, and provide the MPI communicator (and the rank within that communicator) of the calling task. This call initializes an IO system type structure that will be used in subsequent file and decomposition functions.</li>
 <li>You can open a file for reading or writing with a call to <a class="el" href="group___p_i_o__createfile.html">PIO_createfile</a> or <a class="el" href="group___p_i_o__openfile.html">PIO_openfile</a>. In this call you will specify the file type: pio_iotype_netcdf, pio_iotype_pnetcdf, pio_iotype_netcdf4c or pio_iotype_netcdf4p; along with the file name and optionally the netcdf mode.</li>
-<li>Finally, you can read or write decomposed data to the output file. You must describe the mapping between the organization of data in the file and that same data in the application space. This is done in a call to <a class="el" href="group___p_i_o__initdecomp.html">PIO_initdecomp</a>. In the simplest call to this function, a one dimensional integer array is passed from each task, the values in the array represent the offset from the beginning of the array on file. (what happens next?) </li>
+<li>Finally, you can read or write decomposed data to the output file. You must describe the mapping between the organization of data in the file and that same data in the application space. This is done in a call to <a class="el" href="group___p_i_o__initdecomp.html">PIO_initdecomp</a>. In the simplest call to this function, a one dimensional integer array is passed from each task, the values in the array represent the offset from the beginning of the array on file. </li>
 </ol>
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--- a/docs/testpio_example.html
+++ b/docs/testpio_example.html
@@ -290,7 +290,7 @@ <h1><a class="anchor" id="Decomposition"></a>
 </pre> </div></div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Fri Apr 19 2019 14:00:17 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Tue Apr 30 2019 10:14:35 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.13
 </small></address>

From 6d7a936b0bf28478e70750bc61bc3055ea3a0f45 Mon Sep 17 00:00:00 2001
From: Ed Hartnett <edwardjameshartnett@gmail.com>
Date: Tue, 30 Apr 2019 10:18:54 -0600
Subject: [PATCH 4/9] more doc fixes

---
 doc/source/GettingStarted.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/GettingStarted.txt b/doc/source/GettingStarted.txt
index d2a510d9a8b..aee7661482b 100644
--- a/doc/source/GettingStarted.txt
+++ b/doc/source/GettingStarted.txt
@@ -32,7 +32,7 @@ Basic description of how to optimize IO in a parallel environment:
 PIO calls are collective.  A MPI communicator is set in a call to \ref
 PIO_init and all tasks associated with that communicator must
 participate in all subsequent calls to PIO.  An application can make
-multiple calls to PIO_init() in order to support multiple MPI
+multiple calls to \ref PIO_init in order to support multiple MPI
 communicators.
 
 Begin by getting and unpacking the most recent release of PIO from

From f395aa9c2506b6bca774265055bb2be51b1365b3 Mon Sep 17 00:00:00 2001
From: Ed Hartnett <edwardjameshartnett@gmail.com>
Date: Wed, 1 May 2019 04:37:08 -0600
Subject: [PATCH 5/9] changed example

---
 examples/c/darray_no_async.c | 73 +++++++++++++++++++++++-------------
 examples/c/run_tests.sh      | 12 +++++-
 src/clib/pio.h               |  2 +-
 3 files changed, 57 insertions(+), 30 deletions(-)

diff --git a/examples/c/darray_no_async.c b/examples/c/darray_no_async.c
index 126adcd5ba0..784612acdcf 100644
--- a/examples/c/darray_no_async.c
+++ b/examples/c/darray_no_async.c
@@ -6,7 +6,7 @@
  * (one unlimited) and one variable. It first writes, then reads the
  * sample file using distributed arrays.
  *
- * This example can be run in parallel for 4 processors.
+ * This example can be run in parallel for 16 processors.
  */
 
 #include "config.h"
@@ -32,10 +32,10 @@
 #define NUM_TIMESTEPS 2
 
 /* The length of our sample data in X dimension.*/
-#define DIM_LEN_X 4
+#define DIM_LEN_X 8
 
 /* The length of our sample data in Y dimension.*/
-#define DIM_LEN_Y 4
+#define DIM_LEN_Y 8
 
 /* The name of the variable in the netCDF output file. */
 #define VAR_NAME "foo"
@@ -48,7 +48,7 @@
 #define START_DATA_VAL 42
 
 /* Number of tasks this example runs on. */
-#define TARGET_NTASKS 4
+#define TARGET_NTASKS 16
 
 /* Logging level. */
 #define LOG_LEVEL -1
@@ -59,6 +59,11 @@ int dim_len[NDIM3] = {NC_UNLIMITED, DIM_LEN_X, DIM_LEN_Y};
 /* Names of dimensions. */
 char dim_name[NDIM3][PIO_MAX_NAME + 1] = {"unlimted", "x", "y"};
 
+/* These are used when writing the decomposition file. */
+#define DECOMP_FILENAME "darray_no_async_decomp.nc"
+#define DECOMP_TITLE "Example Decomposition from darray_no_async.c"
+#define DECOMP_HISTORY "This file is created by the program darray_no_async in the PIO C library"
+
 /* Handle MPI errors. This should only be used with MPI library
  * function calls. */
 #define MPIERR(e) do {                                                  \
@@ -180,25 +185,33 @@ int check_file(int iosysid, int ntasks, char *filename, int iotype,
    has the following contents (as shown by ncdump):
 
    <pre>
-   netcdf darray_no_async_iotype_1 {
-   dimensions:
-   unlimted = UNLIMITED ; // (2 currently)
-   x = 4 ;
-   y = 4 ;
-   variables:
-   int foo(unlimted, x, y) ;
-   data:
-
-   foo =
-   42, 42, 42, 42,
-   43, 43, 43, 43,
-   44, 44, 44, 44,
-   45, 45, 45, 45,
-   142, 142, 142, 142,
-   143, 143, 143, 143,
-   144, 144, 144, 144,
-   145, 145, 145, 145 ;
-   }
+netcdf darray_no_async_iotype_1 {
+dimensions:
+	unlimted = UNLIMITED ; // (2 currently)
+	x = 8 ;
+	y = 8 ;
+variables:
+	int foo(unlimted, x, y) ;
+data:
+
+ foo =
+  42, 42, 42, 42, 43, 43, 43, 43,
+  44, 44, 44, 44, 45, 45, 45, 45,
+  46, 46, 46, 46, 47, 47, 47, 47,
+  48, 48, 48, 48, 49, 49, 49, 49,
+  50, 50, 50, 50, 51, 51, 51, 51,
+  52, 52, 52, 52, 53, 53, 53, 53,
+  54, 54, 54, 54, 55, 55, 55, 55,
+  56, 56, 56, 56, 57, 57, 57, 57,
+  142, 142, 142, 142, 143, 143, 143, 143,
+  144, 144, 144, 144, 145, 145, 145, 145,
+  146, 146, 146, 146, 147, 147, 147, 147,
+  148, 148, 148, 148, 149, 149, 149, 149,
+  150, 150, 150, 150, 151, 151, 151, 151,
+  152, 152, 152, 152, 153, 153, 153, 153,
+  154, 154, 154, 154, 155, 155, 155, 155,
+  156, 156, 156, 156, 157, 157, 157, 157 ;
+}
    </pre>
 
 */
@@ -239,7 +252,7 @@ int main(int argc, char* argv[])
 
     /* Check that a valid number of processors was specified. */
     if (ntasks != TARGET_NTASKS)
-        fprintf(stderr, "Number of processors must be 4!\n");
+        fprintf(stderr, "Number of processors must be 16!\n");
     printf("%d: ParallelIO Library darray_no_async example running on %d processors.\n",
            my_rank, ntasks);
 
@@ -253,7 +266,7 @@ int main(int argc, char* argv[])
 
     /* Initialize the PIO IO system. This specifies how many and
      * which processors are involved in I/O. */
-    if ((ret = PIOc_Init_Intracomm(MPI_COMM_WORLD, 1, ioproc_stride,
+    if ((ret = PIOc_Init_Intracomm(MPI_COMM_WORLD, 4, ioproc_stride,
                                    ioproc_start, PIO_REARR_BOX, &iosysid)))
         ERR(ret);
 
@@ -268,9 +281,15 @@ int main(int argc, char* argv[])
     /* Create the PIO decomposition for this example. Since this
      * is a variable with an unlimited dimension, we want to
      * create a 2-D composition which represents one record. */
-    printf("rank: %d Creating decomposition...\n", my_rank);
+    printf("rank: %d Creating decomposition, elements_per_pe %lld...\n", my_rank,
+           elements_per_pe);
     if ((ret = PIOc_init_decomp(iosysid, PIO_INT, NDIM3 - 1, &dim_len[1], elements_per_pe,
-                                compdof, &ioid, 0, NULL, NULL)))
+                                compdof, &ioid, PIO_REARR_SUBSET, NULL, NULL)))
+        ERR(ret);
+
+    /* Write the decomposition file. */
+    if ((ret = PIOc_write_nc_decomp(iosysid, DECOMP_FILENAME, NC_CLOBBER,
+                                    ioid, DECOMP_TITLE, DECOMP_HISTORY, 0)))
         ERR(ret);
 
     /* The number of favors may change with the build parameters. */
diff --git a/examples/c/run_tests.sh b/examples/c/run_tests.sh
index 1cfb586d292..caf49573aba 100755
--- a/examples/c/run_tests.sh
+++ b/examples/c/run_tests.sh
@@ -11,7 +11,8 @@ trap exit INT TERM
 printf 'running PIO examples...\n'
 
 #PIO_EXAMPLES='examplePio'
-PIO_EXAMPLES='example1 examplePio darray_no_async'
+PIO_EXAMPLES='example1 examplePio'
+PIO_EXAMPLES_16='darray_no_async'
 
 success1=true
 for EXAMPLE in $PIO_EXAMPLES
@@ -20,9 +21,16 @@ do
     echo "running ${EXAMPLE}"
     mpiexec -n 4 ./${EXAMPLE} && success1=true || break
 done
+success2=true
+for EXAMPLE in $PIO_EXAMPLES_16
+do
+    success2=false
+    echo "running ${EXAMPLE}"
+    mpiexec -n 16 ./${EXAMPLE} && success2=true || break
+done
 
 # Did we succeed?
-if test x$success1 = xtrue; then
+if test x$success1 = xtrue -a  x$success2 = xtrue; then
     exit 0
 fi
 exit 1
diff --git a/src/clib/pio.h b/src/clib/pio.h
index d88a4b3f3f6..f5647e364a0 100644
--- a/src/clib/pio.h
+++ b/src/clib/pio.h
@@ -410,7 +410,7 @@ typedef struct iosystem_desc_t
     MPI_Comm comp_comm;
 
     /** This is an MPI inter communicator between IO communicator and
-     * computation communicator. */
+     * computation communicator, only used for async mode. */
     MPI_Comm intercomm;
 
     /** This is a copy (but not an MPI copy) of either the comp (for

From cbf0a485dd240e2878c3f28a27f9577443ff2606 Mon Sep 17 00:00:00 2001
From: Ed Hartnett <edwardjameshartnett@gmail.com>
Date: Wed, 1 May 2019 04:39:30 -0600
Subject: [PATCH 6/9] returned docs directory

---
 docs/_c_a_mexample.html                                   | 2 +-
 docs/annotated.html                                       | 2 +-
 docs/api.html                                             | 2 +-
 docs/contributing_code.html                               | 2 +-
 docs/decomp.html                                          | 2 +-
 docs/deprecated.html                                      | 2 +-
 docs/dir_105b7c361203833ef447ec1f3c9e0fde.html            | 2 +-
 docs/dir_209baab7a174f8da935e472521be6c82.html            | 2 +-
 docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html            | 2 +-
 docs/dir_6df6542b1223c38c3752260fabab64d0.html            | 2 +-
 docs/dir_d28a4824dc47e487b107a5db32ef43c4.html            | 2 +-
 docs/dir_fbdd47254eba6596566cfbbd6768a55d.html            | 2 +-
 docs/error.html                                           | 2 +-
 docs/examp.html                                           | 2 +-
 docs/example1_8c.html                                     | 2 +-
 docs/example2_8c.html                                     | 2 +-
 docs/example_pio_8c.html                                  | 2 +-
 docs/example_pio_8f90.html                                | 2 +-
 docs/faq.html                                             | 4 ++--
 docs/files.html                                           | 2 +-
 docs/globals.html                                         | 2 +-
 docs/globals_defs.html                                    | 2 +-
 docs/globals_func.html                                    | 2 +-
 docs/globals_type.html                                    | 2 +-
 docs/globals_vars.html                                    | 2 +-
 docs/graph_legend.html                                    | 2 +-
 docs/group___p_i_o__advanceframe.html                     | 2 +-
 docs/group___p_i_o__closefile.html                        | 2 +-
 docs/group___p_i_o__createfile.html                       | 2 +-
 docs/group___p_i_o__def__dim.html                         | 2 +-
 docs/group___p_i_o__def__var.html                         | 2 +-
 docs/group___p_i_o__enddef.html                           | 2 +-
 docs/group___p_i_o__error__method.html                    | 2 +-
 docs/group___p_i_o__finalize.html                         | 2 +-
 docs/group___p_i_o__freedecomp.html                       | 2 +-
 docs/group___p_i_o__get__att.html                         | 2 +-
 docs/group___p_i_o__get__local__array__size.html          | 2 +-
 docs/group___p_i_o__get__var.html                         | 2 +-
 docs/group___p_i_o__getnumiotasks.html                    | 2 +-
 docs/group___p_i_o__init.html                             | 2 +-
 docs/group___p_i_o__initdecomp.html                       | 2 +-
 docs/group___p_i_o__inq__att.html                         | 2 +-
 docs/group___p_i_o__inq__attlen.html                      | 2 +-
 docs/group___p_i_o__inq__attname.html                     | 2 +-
 docs/group___p_i_o__inq__dimid.html                       | 2 +-
 docs/group___p_i_o__inq__dimlen.html                      | 2 +-
 docs/group___p_i_o__inq__dimname.html                     | 2 +-
 docs/group___p_i_o__inq__natts.html                       | 2 +-
 docs/group___p_i_o__inq__ndims.html                       | 2 +-
 docs/group___p_i_o__inq__nvars.html                       | 2 +-
 docs/group___p_i_o__inq__unlimdim.html                    | 2 +-
 docs/group___p_i_o__inq__var__deflate.html                | 2 +-
 docs/group___p_i_o__inq__vardimid.html                    | 2 +-
 docs/group___p_i_o__inq__varid.html                       | 2 +-
 docs/group___p_i_o__inq__varname.html                     | 2 +-
 docs/group___p_i_o__inq__varnatts.html                    | 2 +-
 docs/group___p_i_o__inq__varndims.html                    | 2 +-
 docs/group___p_i_o__inq__vartype.html                     | 2 +-
 docs/group___p_i_o__inquire.html                          | 2 +-
 docs/group___p_i_o__inquire__dimension.html               | 2 +-
 docs/group___p_i_o__inquire__variable.html                | 2 +-
 docs/group___p_i_o__iotype.html                           | 2 +-
 docs/group___p_i_o__kinds.html                            | 2 +-
 docs/group___p_i_o__openfile.html                         | 2 +-
 docs/group___p_i_o__put__att.html                         | 2 +-
 docs/group___p_i_o__put__var.html                         | 2 +-
 docs/group___p_i_o__read__darray.html                     | 2 +-
 docs/group___p_i_o__rearr__comm__dir.html                 | 2 +-
 docs/group___p_i_o__rearr__comm__fc__options.html         | 2 +-
 docs/group___p_i_o__rearr__comm__t.html                   | 2 +-
 docs/group___p_i_o__rearr__method.html                    | 2 +-
 docs/group___p_i_o__rearr__options.html                   | 2 +-
 docs/group___p_i_o__redef.html                            | 2 +-
 docs/group___p_i_o__set__blocksize.html                   | 2 +-
 docs/group___p_i_o__set__hint.html                        | 2 +-
 docs/group___p_i_o__set__log__level.html                  | 2 +-
 docs/group___p_i_o__setdebuglevel.html                    | 2 +-
 docs/group___p_i_o__seterrorhandling.html                 | 2 +-
 docs/group___p_i_o__setframe.html                         | 2 +-
 docs/group___p_i_o__strerror.html                         | 2 +-
 docs/group___p_i_o__syncfile.html                         | 2 +-
 docs/group___p_i_o__write__darray.html                    | 2 +-
 docs/group__error__return.html                            | 2 +-
 docs/group__iodesc__generate.html                         | 2 +-
 docs/index.html                                           | 8 ++++----
 docs/install.html                                         | 4 ++--
 ...terfacepiodarray_1_1_p_i_oc__read__darray-members.html | 2 +-
 docs/interfacepiodarray_1_1_p_i_oc__read__darray.html     | 2 +-
 ...iodarray_1_1_p_i_oc__write__darray__multi-members.html | 2 +-
 ...terfacepiodarray_1_1_p_i_oc__write__darray__multi.html | 2 +-
 ...ionfatt__mod_1_1_p_i_oc__get__att__double-members.html | 2 +-
 ...terfacepionfatt__mod_1_1_p_i_oc__get__att__double.html | 2 +-
 ...pionfatt__mod_1_1_p_i_oc__get__att__float-members.html | 2 +-
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 .../interfacepionfatt__mod_1_1_p_i_oc__put__att__int.html | 2 +-
 ...epionfatt__mod_1_1_p_i_oc__put__att__text-members.html | 2 +-
 ...interfacepionfatt__mod_1_1_p_i_oc__put__att__text.html | 2 +-
 ...ionfget__mod_1_1_p_i_oc__get__var__double-members.html | 2 +-
 ...terfacepionfget__mod_1_1_p_i_oc__get__var__double.html | 2 +-
 ...pionfget__mod_1_1_p_i_oc__get__var__float-members.html | 2 +-
 ...nterfacepionfget__mod_1_1_p_i_oc__get__var__float.html | 2 +-
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 .../interfacepionfget__mod_1_1_p_i_oc__get__var__int.html | 2 +-
 ...onfget__mod_1_1_p_i_oc__get__vara__double-members.html | 2 +-
 ...erfacepionfget__mod_1_1_p_i_oc__get__vara__double.html | 2 +-
 ...ionfget__mod_1_1_p_i_oc__get__vara__float-members.html | 2 +-
 ...terfacepionfget__mod_1_1_p_i_oc__get__vara__float.html | 2 +-
 ...epionfget__mod_1_1_p_i_oc__get__vara__int-members.html | 2 +-
 ...interfacepionfget__mod_1_1_p_i_oc__get__vara__int.html | 2 +-
 ...pionfget__mod_1_1_p_i_oc__get__vara__text-members.html | 2 +-
 ...nterfacepionfget__mod_1_1_p_i_oc__get__vara__text.html | 2 +-
 ...onfput__mod_1_1_p_i_oc__put__vara__double-members.html | 2 +-
 ...erfacepionfput__mod_1_1_p_i_oc__put__vara__double.html | 2 +-
 ...ionfput__mod_1_1_p_i_oc__put__vara__float-members.html | 2 +-
 ...terfacepionfput__mod_1_1_p_i_oc__put__vara__float.html | 2 +-
 ...epionfput__mod_1_1_p_i_oc__put__vara__int-members.html | 2 +-
 ...interfacepionfput__mod_1_1_p_i_oc__put__vara__int.html | 2 +-
 ...pionfput__mod_1_1_p_i_oc__put__vara__text-members.html | 2 +-
 ...nterfacepionfput__mod_1_1_p_i_oc__put__vara__text.html | 2 +-
 docs/intro.html                                           | 8 ++++----
 docs/mach_walkthrough.html                                | 2 +-
 docs/modules.html                                         | 2 +-
 docs/pages.html                                           | 2 +-
 docs/pio_8_f90.html                                       | 2 +-
 docs/pio__kinds_8_f90.html                                | 2 +-
 docs/pio__nc4_8c.html                                     | 2 +-
 docs/pio__support_8_f90.html                              | 2 +-
 docs/pio__types_8_f90.html                                | 2 +-
 docs/piodarray_8_f90.html                                 | 2 +-
 docs/piolib__mod_8_f90.html                               | 2 +-
 docs/pionfatt__mod_8_f90.html                             | 2 +-
 docs/pionfget__mod_8_f90.html                             | 2 +-
 docs/pionfput__mod_8_f90.html                             | 2 +-
 docs/structpio__types_1_1decompmap__t-members.html        | 2 +-
 docs/structpio__types_1_1decompmap__t.html                | 2 +-
 docs/structpio__types_1_1file__desc__t-members.html       | 2 +-
 docs/structpio__types_1_1file__desc__t.html               | 2 +-
 docs/structpio__types_1_1io__desc__t-members.html         | 2 +-
 docs/structpio__types_1_1io__desc__t.html                 | 2 +-
 docs/structpio__types_1_1iosystem__desc__t-members.html   | 2 +-
 docs/structpio__types_1_1iosystem__desc__t.html           | 2 +-
 ...io__types_1_1pio__rearr__comm__fc__opt__t-members.html | 2 +-
 .../structpio__types_1_1pio__rearr__comm__fc__opt__t.html | 2 +-
 docs/structpio__types_1_1pio__rearr__opt__t-members.html  | 2 +-
 docs/structpio__types_1_1pio__rearr__opt__t.html          | 2 +-
 docs/structpio__types_1_1var__desc__t-members.html        | 2 +-
 docs/structpio__types_1_1var__desc__t.html                | 2 +-
 docs/structpioexample_1_1pioexampleclass-members.html     | 2 +-
 docs/structpioexample_1_1pioexampleclass.html             | 2 +-
 docs/test.html                                            | 2 +-
 docs/testpio_example.html                                 | 2 +-
 160 files changed, 168 insertions(+), 168 deletions(-)

diff --git a/docs/_c_a_mexample.html b/docs/_c_a_mexample.html
index 68c288eaa7c..91aecb86dc7 100644
--- a/docs/_c_a_mexample.html
+++ b/docs/_c_a_mexample.html
@@ -107,7 +107,7 @@ <h1><a class="anchor" id="Init"></a>
 </div></div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Tue Apr 30 2019 10:14:35 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Fri Apr 19 2019 14:00:17 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.13
 </small></address>
diff --git a/docs/annotated.html b/docs/annotated.html
index 0038650a1ce..20e9b4f9c2d 100644
--- a/docs/annotated.html
+++ b/docs/annotated.html
@@ -106,7 +106,7 @@
 </div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Tue Apr 30 2019 10:14:36 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Fri Apr 19 2019 14:00:19 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.13
 </small></address>
diff --git a/docs/api.html b/docs/api.html
index 425fccd849b..97525a227e0 100644
--- a/docs/api.html
+++ b/docs/api.html
@@ -149,7 +149,7 @@ <h2><a class="anchor" id="inqnc"></a>
 </div></div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Tue Apr 30 2019 10:14:35 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Fri Apr 19 2019 14:00:17 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.13
 </small></address>
diff --git a/docs/contributing_code.html b/docs/contributing_code.html
index 0e578e94e05..9e35b709902 100644
--- a/docs/contributing_code.html
+++ b/docs/contributing_code.html
@@ -94,7 +94,7 @@ <h2>Indentation and Spacing</h2>
 </div></div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Tue Apr 30 2019 10:14:35 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Fri Apr 19 2019 14:00:17 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.13
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 Mariana Vertenstein </dd>
 <dd>
 Edward Hartnett</dd></dl>
-<p>The Parallel IO libraries (PIO) are high-level parallel I/O C and Fortran libraries for structured grid applications. PIO provides a netCDF-like API, and allows users to designate some subset of processors to perform IO. Computational code calls netCDF-like functions to read and write data, and PIO uses the IO processors to perform all necessary IO.</p>
-<p>PIO also supports the creation of multiple computation components, each containing many processors, and one shared set of IO processors. The computational components can perform write operation asynchronously, and the IO processors will take care of all storage interaction.</p>
-<p>This user's guide provides information about the PIO library and examples on how it can be used. Please watch the PIO GitHub site [<a href="https://github.com/NCAR/ParallelIO">https://github.com/NCAR/ParallelIO</a>] for announcements and new releases.</p>
+<p>The Parallel I/O (PIO) library has been developed over several years to improve the ability of component models of the Community Earth System Model (CESM) to perform I/O. We believe that the interface is sufficiently general to be useful to a broader spectrum of applications. The focus of development has been on backend tools that use the NetCDF file format. PIO currently supports NetCDF and PnetCDF as backend libraries, both can be linked and used with runtime options controlling which is used for a given file.</p>
+<p>PIO2 represents a significant rewrite of the PIO library and includes a C API as well as the original F90 API. A new decomposition strategy has been introduced which gives the user more ability to tune io communications.</p>
+<p>This user's guide provides information about the PIO library and examples on how it can be used. Please review the ChangeLog that is included with the distribution for up-to-date release information.</p>
 <ul>
 <li><a class="el" href="intro.html">Introduction</a></li>
 <li><a class="el" href="install.html">Installing PIO</a></li>
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diff --git a/docs/install.html b/docs/install.html
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 <h3>Dependencies</h3>
-<p>PIO can use NetCDF (version 4.6.1+) and/or PnetCDF (version 1.9.0+) for I/O. Ideally, the NetCDF version should be built with MPI, which requires that it be linked with an MPI-enabled version of HDF5. Optionally, NetCDF can be built with DAP support, which introduces a dependency on CURL. Additionally, HDF5, itself, introduces dependencies on LIBZ and (optionally) SZIP.</p>
+<p>PIO can use NetCDF (version 4.3.3+) and/or PnetCDF (version 1.6.1+) for I/O. Ideally, the NetCDF version should be built with MPI, which requires that it be linked with an MPI-enabled version of HDF5. Optionally, NetCDF can be built with DAP support, which introduces a dependency on CURL. Additionally, HDF5, itself, introduces dependencies on LIBZ and (optionally) SZIP.</p>
 <h3>Configuring with CMake</h3>
 <p>To configure the build, PIO requires CMake version 2.8.12+. The typical configuration with CMake can be done as follows:</p>
 <pre class="fragment">&gt; CC=mpicc FC=mpif90 cmake [-DOPTION1=value1 -DOPTION2=value2 ...] /path/to/pio/source
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diff --git a/docs/intro.html b/docs/intro.html
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 <div class="textblock"><p>PIO is a software interface layer designed to encapsolate the complexities of parallel IO and make it easier to replace the lower level software backend. It currently supports <a href="http://www.unidata.ucar.edu/software/netcdf/docs/html_guide/index.html#user_guide">netcdf </a> and <a href="http://trac.mcs.anl.gov/projects/parallel-netcdf">pnetcdf </a>.</p>
 <p>Basic description of how to optimize IO in a parallel environment...</p>
-<p>PIO calls are collective. A MPI communicator is set in a call to <a class="el" href="group___p_i_o__init.html">PIO_init</a> and all tasks associated with that communicator must participate in all subsequent calls to PIO. An application can make multiple calls to PIO_init() in order to support multiple MPI communicators.</p>
-<p>Begin by getting and unpacking the most recent release of PIO from <a href="https://github.com/PARALLELIO/ParallelIO/releases">gitHub</a> and installing on your system as per the instructions in the <a class="el" href="install.html">Installation</a> document. Take a look at examples of PIO usage in both complex and simple test programs in the [Examples](<a class="el" href="examp.html">Examples</a>) document. Finally, read through the <a class="el" href="faq.html">FAQ</a> to see if any remaining questions can be answered.</p>
+<p>PIO calls are collective. A MPI communicator is set in a call to <a class="el" href="group___p_i_o__init.html">PIO_init</a> and all tasks associated with that communicator must participate in all subsequent calls to PIO. An application can make multiple calls to <a class="el" href="group___p_i_o__init.html">PIO_init</a> in order to support multiple MPI communicators.</p>
+<p>Begin by checking out a copy from <a href="https://github.com/PARALLELIO/ParallelIO">gitHub</a> and installing on your system as per the instructions in the <a class="el" href="install.html">Installation</a> document. Take a look at examples of PIO usage in both complex and simple test programs in the <a class="el" href="examp.html">Examples</a> document. Finally, read through the <a class="el" href="faq.html">FAQ</a> to see if any remaining questions can be answered.</p>
 <h3>Using PIO has three basic steps.</h3>
 <ol type="1">
 <li>Your program should call the <a class="el" href="group___p_i_o__init.html">PIO_init</a> function, and provide the MPI communicator (and the rank within that communicator) of the calling task. This call initializes an IO system type structure that will be used in subsequent file and decomposition functions.</li>
 <li>You can open a file for reading or writing with a call to <a class="el" href="group___p_i_o__createfile.html">PIO_createfile</a> or <a class="el" href="group___p_i_o__openfile.html">PIO_openfile</a>. In this call you will specify the file type: pio_iotype_netcdf, pio_iotype_pnetcdf, pio_iotype_netcdf4c or pio_iotype_netcdf4p; along with the file name and optionally the netcdf mode.</li>
-<li>Finally, you can read or write decomposed data to the output file. You must describe the mapping between the organization of data in the file and that same data in the application space. This is done in a call to <a class="el" href="group___p_i_o__initdecomp.html">PIO_initdecomp</a>. In the simplest call to this function, a one dimensional integer array is passed from each task, the values in the array represent the offset from the beginning of the array on file. </li>
+<li>Finally, you can read or write decomposed data to the output file. You must describe the mapping between the organization of data in the file and that same data in the application space. This is done in a call to <a class="el" href="group___p_i_o__initdecomp.html">PIO_initdecomp</a>. In the simplest call to this function, a one dimensional integer array is passed from each task, the values in the array represent the offset from the beginning of the array on file. (what happens next?) </li>
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+Generated on Fri Apr 19 2019 14:00:19 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
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+Generated on Fri Apr 19 2019 14:00:19 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
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+Generated on Fri Apr 19 2019 14:00:19 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
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+Generated on Fri Apr 19 2019 14:00:19 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
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@@ -101,7 +101,7 @@
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+Generated on Fri Apr 19 2019 14:00:19 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
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-Generated on Tue Apr 30 2019 10:14:36 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Fri Apr 19 2019 14:00:19 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
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-Generated on Tue Apr 30 2019 10:14:36 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Fri Apr 19 2019 14:00:19 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
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index 4833842a0e6..847b3b971cb 100644
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+++ b/docs/structpioexample_1_1pioexampleclass-members.html
@@ -102,7 +102,7 @@
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 <hr class="footer"/><address class="footer"><small>
-Generated on Tue Apr 30 2019 10:14:36 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Fri Apr 19 2019 14:00:19 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
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 </a> 1.8.13
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+++ b/docs/structpioexample_1_1pioexampleclass.html
@@ -668,7 +668,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#a7db2a2d4a3a90efb1d15304a
 </div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Tue Apr 30 2019 10:14:36 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Fri Apr 19 2019 14:00:19 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.13
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diff --git a/docs/test.html b/docs/test.html
index bd5994a3e9e..78f74a00b30 100644
--- a/docs/test.html
+++ b/docs/test.html
@@ -130,7 +130,7 @@ <h2>PIO2 Unit Tests</h2>
 </div></div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Tue Apr 30 2019 10:14:35 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Fri Apr 19 2019 14:00:17 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.13
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diff --git a/docs/testpio_example.html b/docs/testpio_example.html
index e01f811c23f..4fce9ecba71 100644
--- a/docs/testpio_example.html
+++ b/docs/testpio_example.html
@@ -290,7 +290,7 @@ <h1><a class="anchor" id="Decomposition"></a>
 </pre> </div></div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Tue Apr 30 2019 10:14:35 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Fri Apr 19 2019 14:00:17 for PIO by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.13
 </small></address>

From 080fe0ae66ee2ac83f9cb320829baa845567602b Mon Sep 17 00:00:00 2001
From: Ed Hartnett <edwardjameshartnett@gmail.com>
Date: Wed, 1 May 2019 05:08:22 -0600
Subject: [PATCH 7/9] fixed codacy warnings

---
 README.md               |  1 -
 examples/c/run_tests.sh | 10 ++++++++--
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 38eacdbf0ca..6e8b263e018 100644
--- a/README.md
+++ b/README.md
@@ -69,4 +69,3 @@ CC=mpicc FC=mpif90 cmake [-DOPTION1=value1 -DOPTION2=value2 ...] /path/to/pio/so
 
 Full instructions for the cmake build can be found in the installation
 documentation.
-
diff --git a/examples/c/run_tests.sh b/examples/c/run_tests.sh
index caf49573aba..0d369bbb53d 100755
--- a/examples/c/run_tests.sh
+++ b/examples/c/run_tests.sh
@@ -19,14 +19,20 @@ for EXAMPLE in $PIO_EXAMPLES
 do
     success1=false
     echo "running ${EXAMPLE}"
-    mpiexec -n 4 ./${EXAMPLE} && success1=true || break
+    mpiexec -n 4 ./${EXAMPLE} && success1=true
+    if test $success1 = false; then
+        break
+    fi
 done
 success2=true
 for EXAMPLE in $PIO_EXAMPLES_16
 do
     success2=false
     echo "running ${EXAMPLE}"
-    mpiexec -n 16 ./${EXAMPLE} && success2=true || break
+    mpiexec -n 16 ./${EXAMPLE} && success2=true
+    if test $success2 = false; then
+        break
+    fi
 done
 
 # Did we succeed?

From 0f9122efa79c8354b6747a372b4a09055aa69236 Mon Sep 17 00:00:00 2001
From: Ed Hartnett <edwardjameshartnett@gmail.com>
Date: Wed, 1 May 2019 07:26:48 -0600
Subject: [PATCH 8/9] fixe codacity warning

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 6e8b263e018..dd1ec51418d 100644
--- a/README.md
+++ b/README.md
@@ -68,4 +68,4 @@ CC=mpicc FC=mpif90 cmake [-DOPTION1=value1 -DOPTION2=value2 ...] /path/to/pio/so
 ```
 
 Full instructions for the cmake build can be found in the installation
-documentation.
+documentation.
\ No newline at end of file

From 59b88bccef6b3c664e4adb73fb052867637c387a Mon Sep 17 00:00:00 2001
From: Ed Hartnett <edwardjameshartnett@gmail.com>
Date: Wed, 1 May 2019 09:36:02 -0600
Subject: [PATCH 9/9] fixed warning

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index dd1ec51418d..6e8b263e018 100644
--- a/README.md
+++ b/README.md
@@ -68,4 +68,4 @@ CC=mpicc FC=mpif90 cmake [-DOPTION1=value1 -DOPTION2=value2 ...] /path/to/pio/so
 ```
 
 Full instructions for the cmake build can be found in the installation
-documentation.
\ No newline at end of file
+documentation.