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 and pnetcdf . -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
How do I test if PIO is installed and working correctly?
-
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.
+
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.
*/ diff --git a/docs/_c_a_mexample.html b/docs/_c_a_mexample.html index 91aecb86dc7..68c288eaa7c 100644 --- a/docs/_c_a_mexample.html +++ b/docs/_c_a_mexample.html @@ -107,7 +107,7 @@

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-Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
diff --git a/docs/api.html b/docs/api.html index 97525a227e0..425fccd849b 100644 --- a/docs/api.html +++ b/docs/api.html @@ -149,7 +149,7 @@

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diff --git a/docs/contributing_code.html b/docs/contributing_code.html index 9e35b709902..0e578e94e05 100644 --- a/docs/contributing_code.html +++ b/docs/contributing_code.html @@ -94,7 +94,7 @@

Indentation and Spacing

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Other Examples

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How do I test if PIO is installed and working correctly?
-

The PIO Library distribution contains a testpio subdirectory with a number of programs to test the PIO library. Please see the Examples page for details.

+

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.

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- x -

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    -Generated on Fri Apr 19 2019 14:00:18 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
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    -Generated on Fri Apr 19 2019 14:00:18 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
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    -Generated on Fri Apr 19 2019 14:00:18 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
    diff --git a/docs/group__iodesc__generate.html b/docs/group__iodesc__generate.html index 0a52003d2e4..37541d182e7 100644 --- a/docs/group__iodesc__generate.html +++ b/docs/group__iodesc__generate.html @@ -71,7 +71,7 @@
    -Generated on Fri Apr 19 2019 14:00:18 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
    diff --git a/docs/index.html b/docs/index.html index 36f13004ce8..da212039423 100644 --- a/docs/index.html +++ b/docs/index.html @@ -71,9 +71,9 @@ Mariana Vertenstein
    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.

    -

    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.

    -

    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.

    +

    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.

    +

    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 watch the PIO GitHub site [https://github.com/NCAR/ParallelIO] for announcements and new releases.

    • Introduction
    • Installing PIO
      • @@ -89,7 +89,7 @@
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      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 @@

      The PIO code is currently stored on github at https://github.com/PARALLELIO/ParallelIO. For questions about downloading or developing this code, consult the CIME Git Wiki or email jedwa.nosp@m.rds@.nosp@m.ucar..nosp@m.edu.

      Dependencies

      -

      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.

      +

      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.

      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
@@ -110,7 +110,7 @@ 
      Examples
      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
      diff --git a/docs/intro.html b/docs/intro.html index fc28df52ef3..3c9a6f2f962 100644 --- a/docs/intro.html +++ b/docs/intro.html @@ -66,18 +66,18 @@

      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 netcdf and pnetcdf .

      Basic description of how to optimize IO in a parallel environment...

      -

      PIO calls are collective. A MPI communicator is set in a call to 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 communicators.

      -

      Begin by checking out a copy from gitHub and installing on your system as per the instructions in the Installation document. Take a look at examples of PIO usage in both complex and simple test programs in the Examples document. Finally, read through the FAQ to see if any remaining questions can be answered.

      +

      PIO calls are collective. A MPI communicator is set in a call to 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 communicators.

      +

      Begin by getting and unpacking the most recent release of PIO from gitHub and installing on your system as per the instructions in the Installation document. Take a look at examples of PIO usage in both complex and simple test programs in the [Examples](Examples) document. Finally, read through the FAQ to see if any remaining questions can be answered.

      Using PIO has three basic steps.

      1. Your program should call the 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 PIO_createfile or 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. -
      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 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?)
        4. +
      4. 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 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.
      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
      diff --git a/docs/mach_walkthrough.html b/docs/mach_walkthrough.html index 59131960365..416c22af0ce 100644 --- a/docs/mach_walkthrough.html +++ b/docs/mach_walkthrough.html @@ -491,7 +491,7 @@
      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
      diff --git a/docs/modules.html b/docs/modules.html index c43ce20211d..2202ff55e2b 100644 --- a/docs/modules.html +++ b/docs/modules.html @@ -129,7 +129,7 @@
      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
      diff --git a/docs/pages.html b/docs/pages.html index 5e3c8e6746f..7e8f21284cc 100644 --- a/docs/pages.html +++ b/docs/pages.html @@ -84,7 +84,7 @@
      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
      diff --git a/docs/pio__types_8_f90.html b/docs/pio__types_8_f90.html index 3366e7c6f38..2022449d665 100644 --- a/docs/pio__types_8_f90.html +++ b/docs/pio__types_8_f90.html @@ -197,7 +197,7 @@
      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
      diff --git a/docs/pionfput__mod_8_f90.html b/docs/pionfput__mod_8_f90.html index b69f5d4c4a5..1f84a0221f8 100644 --- a/docs/pionfput__mod_8_f90.html +++ b/docs/pionfput__mod_8_f90.html @@ -389,7 +389,7 @@
      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
      diff --git a/docs/structpio__types_1_1decompmap__t-members.html b/docs/structpio__types_1_1decompmap__t-members.html index 444bcad3a63..1880d53be24 100644 --- a/docs/structpio__types_1_1decompmap__t-members.html +++ b/docs/structpio__types_1_1decompmap__t-members.html @@ -76,7 +76,7 @@
      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
      diff --git a/docs/structpio__types_1_1file__desc__t-members.html b/docs/structpio__types_1_1file__desc__t-members.html index 7465a904ec2..d5ab0032a4d 100644 --- a/docs/structpio__types_1_1file__desc__t-members.html +++ b/docs/structpio__types_1_1file__desc__t-members.html @@ -76,7 +76,7 @@
      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
      diff --git a/docs/structpio__types_1_1file__desc__t.html b/docs/structpio__types_1_1file__desc__t.html index 565fe77a674..19a8874358c 100644 --- a/docs/structpio__types_1_1file__desc__t.html +++ b/docs/structpio__types_1_1file__desc__t.html @@ -100,7 +100,7 @@
      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
      diff --git a/docs/structpio__types_1_1io__desc__t-members.html b/docs/structpio__types_1_1io__desc__t-members.html index cb367471646..5605653bdfe 100644 --- a/docs/structpio__types_1_1io__desc__t-members.html +++ b/docs/structpio__types_1_1io__desc__t-members.html @@ -75,7 +75,7 @@
      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
      diff --git a/docs/structpio__types_1_1io__desc__t.html b/docs/structpio__types_1_1io__desc__t.html index 0a323de62dc..a51b1bd27a1 100644 --- a/docs/structpio__types_1_1io__desc__t.html +++ b/docs/structpio__types_1_1io__desc__t.html @@ -89,7 +89,7 @@
      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
      diff --git a/docs/structpio__types_1_1iosystem__desc__t-members.html b/docs/structpio__types_1_1iosystem__desc__t-members.html index 3a36d8374a1..49256470a0f 100644 --- a/docs/structpio__types_1_1iosystem__desc__t-members.html +++ b/docs/structpio__types_1_1iosystem__desc__t-members.html @@ -75,7 +75,7 @@
      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:19 for PIO by   +Generated on Tue Apr 30 2019 10:14:36 for PIO by   doxygen 1.8.13
      diff --git a/docs/test.html b/docs/test.html index 78f74a00b30..bd5994a3e9e 100644 --- a/docs/test.html +++ b/docs/test.html @@ -130,7 +130,7 @@

      PIO2 Unit Tests

      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13
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      -Generated on Fri Apr 19 2019 14:00:17 for PIO by   +Generated on Tue Apr 30 2019 10:14:35 for PIO by   doxygen 1.8.13