diff --git a/configure.ac b/configure.ac index 2578f109266..caa4b983301 100644 --- a/configure.ac +++ b/configure.ac @@ -253,6 +253,7 @@ AC_OUTPUT(Makefile tests/general/util/Makefile tests/performance/Makefile doc/Makefile + doc/source/Makefile examples/Makefile examples/c/Makefile scripts/Makefile) diff --git a/doc/Makefile.am b/doc/Makefile.am index 295f98602c2..0b028f7c496 100644 --- a/doc/Makefile.am +++ b/doc/Makefile.am @@ -2,13 +2,16 @@ # Ed Hartnett 4/1/19 -EXTRA_DIST = CMakeLists.txt customdoxygen.css Doxyfile.in \ -DoxygenLayout.xml doxygen.sty - # Run doxygen, then confirm warning log file is empty. check: all all: doxygen Doxyfile + cat doxywarn.log [ ! -s doxywarn.log ] +SUBDIRS = source + CLEANFILES = *.log + +EXTRA_DIST = CMakeLists.txt customdoxygen.css Doxyfile.in \ +DoxygenLayout.xml doxygen.sty diff --git a/doc/source/Makefile.am b/doc/source/Makefile.am new file mode 100644 index 00000000000..74fbc779139 --- /dev/null +++ b/doc/source/Makefile.am @@ -0,0 +1,8 @@ +# This is part of PIO. It creates the doc/source Makefile. + +# Ed Hartnett 5/20/19 + +EXTRA_DIST = api.txt CAMexample.txt Decomp.txt faq.txt Installing.txt \ +Testing.txt base.txt c_api.txt contributing_code.txt Error.txt \ +Examples.txt GettingStarted.txt mach_walkthrough.txt \ +testpio_example.txt diff --git a/doc/source/api.txt b/doc/source/api.txt index a97161b7261..72420cffb7e 100644 --- a/doc/source/api.txt +++ b/doc/source/api.txt @@ -1,14 +1,14 @@ - /*! \page api PIO user interface + /*! \page api PIO Fortran Interface This is a list of all user interface routines: + \section api_system PIO startup and shutdown routines + - \ref PIO_init + - \ref PIO_finalize \section api_fileops PIO file Operations - \ref PIO_openfile - \ref PIO_createfile - \ref PIO_syncfile - \ref PIO_closefile - \section api_system PIO startup and shutdown routines - - \ref PIO_init - - \ref PIO_finalize \section api_decomp PIO decomposition routines - \ref PIO_initdecomp - \ref PIO_freedecomp diff --git a/doc/source/base.txt b/doc/source/base.txt index 674155493de..68908c477d7 100644 --- a/doc/source/base.txt +++ b/doc/source/base.txt @@ -50,5 +50,6 @@ releases. - \ref examp - \ref faq - \ref api + - \ref c_api - \ref contributing_code */ diff --git a/doc/source/c_api.txt b/doc/source/c_api.txt new file mode 100644 index 00000000000..be71cb9d2dc --- /dev/null +++ b/doc/source/c_api.txt @@ -0,0 +1,44 @@ + /*! \page c_api PIO C Interface + This is a list of all user interface routines: + + \section api_system_c PIO Startup and Shutdown + - \ref PIO_init_c + - \ref PIO_finalize_c + \section api_fileops_c PIO File Operations + - \ref PIO_open_file_c + - \ref PIO_create_file_c + - \ref PIO_sync_file_c + - \ref PIO_close_file_c + \section api_decomp_c PIO Decompositions + - \ref PIO_initdecomp_c + - \ref PIO_freedecomp_c + \section readwrite_c Reading and Writing Distributed Arrays + - \ref PIO_read_darray_c + - \ref PIO_write_darray_c + - \ref PIO_setframe_c + \section utility_c Utility + - \ref PIO_set_hint_c + - \ref PIO_error_method_c + - \ref PIO_get_local_array_size_c + - \ref PIO_getnumiotasks_c + - \ref PIO_set_blocksize_c + \section netcdf_c NetCDF-Like Functions + Also see: http://www.unidata.ucar.edu/software/netcdf/docs/ + \subsection utilnc_c File Operations + - \ref PIO_enddef_c + - \ref PIO_redef_c + \subsection write_metadata_c Writing Metadata + - \ref PIO_def_dim_c + - \ref PIO_def_var_c + - \ref PIO_put_att_c + \subsection putget_c Reading/Writing Data + - \ref PIO_get_var_c + - \ref PIO_put_var_c + \subsection inqnc_c Learn about Files and Metadata + - \ref PIO_inq_c + - \ref PIO_get_att_c + - \ref PIO_inq_att_c + - \ref PIO_inq_var_c + - \ref PIO_inq_dim_c + +*/ diff --git a/docs/_c_a_mexample.html b/docs/_c_a_mexample.html index 80f951426bd..b9f00626885 100644 --- a/docs/_c_a_mexample.html +++ b/docs/_c_a_mexample.html @@ -107,7 +107,7 @@

-Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
diff --git a/docs/annotated.html b/docs/annotated.html index 42263ba5bde..2e7837f2af3 100644 --- a/docs/annotated.html +++ b/docs/annotated.html @@ -79,47 +79,33 @@  CPIOc_write_darray_multi  ▼Npioexample  CpioexampleclassA class to hold example code and data - ▼Npionfatt_mod - CPIOc_get_att_double - CPIOc_get_att_float - CPIOc_get_att_int - CPIOc_get_att_text - CPIOc_put_att_double - CPIOc_put_att_float - CPIOc_put_att_int - CPIOc_put_att_textWrite a netCDF text attribute - ▼Npionfget_mod - CPIOc_get_var_double - CPIOc_get_var_float - CPIOc_get_var_int - CPIOc_get_vara_double - CPIOc_get_vara_float - CPIOc_get_vara_int - CPIOc_get_vara_text - ▼Npionfput_mod - CPIOc_put_vara_double - CPIOc_put_vara_float - CPIOc_put_vara_int - CPIOc_put_vara_text - Cfile_desc_tFile descriptor structure - Cio_desc_tIO descriptor structure - Cio_regionIO region structure - Ciosystem_desc_tIO system descriptor structure - CmapsortUsed to sort map points in the subset rearranger - Cpio_swapm_defaultsSwapm defaults - Crearr_comm_fc_optRearranger comm flow control options - Crearr_optRearranger options - CUT_hash_bucketHash bucket - CUT_hash_handleHash handle - CUT_hash_tableHash table - Cvar_desc_tVariable description structure - Cwmulti_bufferThe multi buffer holds data from one or more variables + ▼Npionfget_mod + CPIOc_get_var_double + CPIOc_get_var_float + CPIOc_get_var_int + CPIOc_get_vara_double + CPIOc_get_vara_float + CPIOc_get_vara_int + CPIOc_get_vara_text + ▼Npionfput_mod + CPIOc_put_vara_double + CPIOc_put_vara_float + CPIOc_put_vara_int + CPIOc_put_vara_text + Cfile_desc_tFile descriptor structure + Cio_desc_tIO descriptor structure + Cio_regionIO region structure + Ciosystem_desc_tIO system descriptor structure + Crearr_comm_fc_optRearranger comm flow control options + Crearr_optRearranger options + Cvar_desc_tVariable description structure + Cwmulti_bufferThe multi buffer holds data from one or more variables
-Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
diff --git a/docs/api.html b/docs/api.html index 0c2ee26dde5..3d4eb5316da 100644 --- a/docs/api.html +++ b/docs/api.html @@ -5,7 +5,7 @@ -PIO: PIO user interface +PIO: PIO Fortran Interface @@ -61,10 +61,16 @@
-
PIO user interface
+
PIO Fortran Interface

This is a list of all user interface routines:

+

+PIO startup and shutdown routines

+

PIO file Operations

-

-PIO startup and shutdown routines

-

PIO decomposition routines

-Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
diff --git a/docs/contributing_code.html b/docs/contributing_code.html index 508f7fa0b90..9d1f97601f8 100644 --- a/docs/contributing_code.html +++ b/docs/contributing_code.html @@ -89,12 +89,209 @@

Indentation and Spacing

  • Indentation as defined by the "linux" style in emacs (see below).
  • -Use spaces around most operators (=+-
    • +Use spaces around most operators (= + - * /) not pointer or prefix/postfile (* ++ –) +
  • +Spaces after most keywords (if, for, while, etc.)
    • +
  • +No spaces after function name.
    • + +

    Braces

    +

    Put braces on their own line, avoiding their use if possible.

    +

    Documentation

    + +

    Emacs

    +

    Put this in your .emacs file:

    +
    +(setq c-default-style "linux"
+          c-basic-offset 4)
+

    The tab key (used anywhere on the line) will indent a line correctly. M-x indent-region will indent a selected region of code.

    +

    M-x untabify will convert all the tabs in a file to spaces.

    +

    Code Review

    + +

    Merge Proceedure

    + +

    Formatting Example

    +
    +/** 
+   @ingroup PIOc_inq_attname
+   The PIO-C interface for the NetCDF function nc_inq_attname.
       This routine is called collectively by all tasks in the communicator 
+   ios.union_comm. For more information on the underlying NetCDF commmand
+   please read about this function in the NetCDF documentation at: 
+   http://www.unidata.ucar.edu/software/netcdf/docs/group__attributes.html
       @param ncid the ncid of the open file, obtained from
+   PIOc_openfile() or PIOc_createfile().
+   @param varid the variable ID.
+   @param attnum the attribute ID.
+   @return PIO_NOERR for success, error code otherwise.  See PIOc_Set_File_Error_Handling
+ */
+int PIOc_inq_attname(int ncid, int varid, int attnum, char *name) 
+{
+    iosystem_desc_t *ios;  /* Pointer to io system information. */
+    file_desc_t *file;     /* Pointer to file information. */
+    int ierr = PIO_NOERR;  /* Return code from function calls. */
+    int mpierr = MPI_SUCCESS, mpierr2;  /* Return code from MPI function codes. */
        LOG((1, "PIOc_inq_attname ncid = %d varid = %d attnum = %d", ncid, varid,
+         attnum));
        /* Find the info about this file. */
+    if (!(file = pio_get_file_from_id(ncid)))
+        return PIO_EBADID;
+    ios = file->iosystem;
        /* If async is in use, and this is not an IO task, bcast the parameters. */
+    if (ios->async_interface)
+    {
+        if (!ios->ioproc)
+        {
+            int msg = PIO_MSG_INQ_ATTNAME;
+            char name_present = name ? true : false;
                if(ios->compmaster) 
+                mpierr = MPI_Send(&msg, 1,MPI_INT, ios->ioroot, 1, ios->union_comm);
                if (!mpierr)
+                mpierr = MPI_Bcast(&ncid, 1, MPI_INT, ios->compmaster, ios->intercomm);
+            if (!mpierr)
+                mpierr = MPI_Bcast(&varid, 1, MPI_INT, ios->compmaster, ios->intercomm);
+            if (!mpierr)
+                mpierr = MPI_Bcast(&attnum, 1, MPI_INT, ios->compmaster, ios->intercomm);
+            if (!mpierr)
+                mpierr = MPI_Bcast(&name_present, 1, MPI_CHAR, ios->compmaster, ios->intercomm);
+        }
            /* Handle MPI errors. */
+        if ((mpierr2 = MPI_Bcast(&mpierr, 1, MPI_INT, ios->comproot, ios->my_comm)))
+            check_mpi(file, mpierr2, __FILE__, __LINE__);
+        if (mpierr)
+            return check_mpi(file, mpierr, __FILE__, __LINE__);
+    }
        /* If this is an IO task, then call the netCDF function. */
+    if (ios->ioproc)
+    {
+#ifdef _PNETCDF
+        if (file->iotype == PIO_IOTYPE_PNETCDF)
+            ierr = ncmpi_inq_attname(file->fh, varid, attnum, name);
+#endif /* _PNETCDF */
+#ifdef _NETCDF
+        if (file->iotype != PIO_IOTYPE_PNETCDF && file->do_io)
+            ierr = nc_inq_attname(file->fh, varid, attnum, name);
+#endif /* _NETCDF */
+        LOG((2, "PIOc_inq_attname netcdf call returned %d", ierr));
+    }
        /* Broadcast and check the return code. */
+    if ((mpierr = MPI_Bcast(&ierr, 1, MPI_INT, ios->ioroot, ios->my_comm)))
+    {
+        check_mpi(file, mpierr, __FILE__, __LINE__);            
+        return PIO_EIO;
+    }
+    check_netcdf(file, ierr, __FILE__, __LINE__);
        /* Broadcast results to all tasks. Ignore NULL parameters. */
+    if (!ierr)
+        if (name)
+        {
+            int namelen = strlen(name);
+            if ((mpierr = MPI_Bcast(&namelen, 1, MPI_INT, ios->ioroot, ios->my_comm)))
+                check_mpi(file, mpierr, __FILE__, __LINE__);
+            if ((mpierr = MPI_Bcast((void *)name, namelen + 1, MPI_CHAR, ios->ioroot,
+                                    ios->my_comm)))
+                check_mpi(file, mpierr, __FILE__, __LINE__);
+        }
        return ierr;
+}
+

    Further Information

    +

    For style issues not already covered in this document, see this style guide.

    +

    Last updated: 05-16-2016

    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/decomp.html b/docs/decomp.html index 4a722c44cf9..76894244a99 100644 --- a/docs/decomp.html +++ b/docs/decomp.html @@ -94,7 +94,7 @@

    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/deprecated.html b/docs/deprecated.html index de98206a3e6..2c3cb114b35 100644 --- a/docs/deprecated.html +++ b/docs/deprecated.html @@ -77,7 +77,7 @@
    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/dir_105b7c361203833ef447ec1f3c9e0fde.html b/docs/dir_105b7c361203833ef447ec1f3c9e0fde.html index a100b91d357..1c63e588576 100644 --- a/docs/dir_105b7c361203833ef447ec1f3c9e0fde.html +++ b/docs/dir_105b7c361203833ef447ec1f3c9e0fde.html @@ -83,26 +83,26 @@ file  pio_types.F90  Derived datatypes and constants for PIO Fortran API.
      -file  piodarray.F90 - Read and write routines for decomposed data.
    +file  piodarray.f90 + Read and write routines for decomposed data.
      -file  piolib_mod.F90 - Initialization Routines for PIO.
    +file  piolib_mod.f90 + Initialization Routines for PIO.
      -file  pionfatt_mod.F90 - NetCDF attribute interface to PIO.
    +file  pionfatt_mod_2.f90 + NetCDF attribute interface to PIO.
      -file  pionfget_mod.F90 - Read Routines for non-decomposed NetCDF data.
    +file  pionfget_mod_2.f90 + Read Routines for non-decomposed NetCDF data.
      -file  pionfput_mod.F90 - Write routines for non-decomposed NetCDF data.
    +file  pionfput_mod.f90 + Write routines for non-decomposed NetCDF data.
     
    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/dir_209baab7a174f8da935e472521be6c82.html b/docs/dir_209baab7a174f8da935e472521be6c82.html index a7e344148fb..bf3b283aea5 100644 --- a/docs/dir_209baab7a174f8da935e472521be6c82.html +++ b/docs/dir_209baab7a174f8da935e472521be6c82.html @@ -78,7 +78,7 @@
    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html b/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html index 14f5a71d502..a4a3fe9a4ed 100644 --- a/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html +++ b/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html @@ -75,7 +75,7 @@
    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/dir_6df6542b1223c38c3752260fabab64d0.html b/docs/dir_6df6542b1223c38c3752260fabab64d0.html index d6fe959bbfb..3591a3eaa6f 100644 --- a/docs/dir_6df6542b1223c38c3752260fabab64d0.html +++ b/docs/dir_6df6542b1223c38c3752260fabab64d0.html @@ -75,7 +75,7 @@ - + @@ -95,7 +95,7 @@
    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/dir_d28a4824dc47e487b107a5db32ef43c4.html b/docs/dir_d28a4824dc47e487b107a5db32ef43c4.html index 98bb3c5f23e..1c59415bd00 100644 --- a/docs/dir_d28a4824dc47e487b107a5db32ef43c4.html +++ b/docs/dir_d28a4824dc47e487b107a5db32ef43c4.html @@ -75,7 +75,7 @@ - + @@ -87,7 +87,7 @@
    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/dir_fbdd47254eba6596566cfbbd6768a55d.html b/docs/dir_fbdd47254eba6596566cfbbd6768a55d.html index 38fc1f32752..3992d8b299b 100644 --- a/docs/dir_fbdd47254eba6596566cfbbd6768a55d.html +++ b/docs/dir_fbdd47254eba6596566cfbbd6768a55d.html @@ -77,26 +77,11 @@ file  pio_darray.c  Public functions that read and write distributed arrays in PIO.
      -file  pio_darray_int.c - Private functions to help read and write distributed arrays in PIO.
    -  file  pio_file.c  PIO File Handling.
      file  pio_get_nc.c - PIO functions to get data (excluding varm functions).
    -  -file  pio_getput_int.c - Internal PIO functions to get and put attributes and data.
    -  -file  pio_internal.h [code] - Private headers and defines for the PIO C interface.
    -  -file  pio_lists.c - PIO list functions.
    -  -file  pio_msg.c - PIO async message handling.
    + PIO functions to get data.
      file  pio_nc.c  PIO interfaces to NetCDF support functions.
    @@ -107,18 +92,9 @@ file  pio_put_nc.c  PIO functions to write data.
      -file  pio_rearrange.c - Code to map IO to model decomposition.
    -  -file  pio_spmd.c - Algorithms modeled after spmd_utils in the Community Atmosphere Model; C translation.
    -  file  pioc.c  Some initialization and support functions.
      -file  pioc_sc.c - Compute start and count arrays for the box rearranger.
    -  file  pioc_support.c  Support functions for the PIO library.
      @@ -126,7 +102,7 @@
    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/error.html b/docs/error.html index e8df5324ce6..4f0ab7d2652 100644 --- a/docs/error.html +++ b/docs/error.html @@ -83,7 +83,7 @@
    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/examp.html b/docs/examp.html index 66994255e65..934e4e4e037 100644 --- a/docs/examp.html +++ b/docs/examp.html @@ -87,7 +87,7 @@

    Other Examples

    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/example1_8c.html b/docs/example1_8c.html index a8580b36b22..d59830b487f 100644 --- a/docs/example1_8c.html +++ b/docs/example1_8c.html @@ -87,8 +87,7 @@
    - - +
    @@ -429,10 +428,10 @@

    PIOc_Init_Intracomm(). It references an internal structure containing the general IO subsystem data and MPI structure. It is passed to PIOc_finalize() to free associated resources, after all I/O, but before MPI_Finalize is called.

    +

    The ID for the parallel I/O system. It is set by PIOc_Init_Intracomm(). It references an internal structure containing the general IO subsystem data and MPI structure. It is passed to PIOc_finalize() to free associated resources, after all I/O, but before MPI_Finalize is called.

    The ncid of the netCDF file created in this example.

    The ID of the netCDF varable in the example file.

    -

    The I/O description ID as passed back by PIOc_InitDecomp() and freed in PIOc_freedecomp().

    +

    The I/O description ID as passed back by PIOc_InitDecomp() and freed in PIOc_freedecomp().

    A buffer for sample data. The size of this array will vary depending on how many processors are involved in the execution of the example code. It's length will be the same as elements_per_pe.

    A 1-D array which holds the decomposition mapping for this example. The size of this array will vary depending on how many processors are involved in the execution of the example code. It's length will be the same as elements_per_pe.

    Test filename.

    @@ -479,7 +478,7 @@

    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/example1_8c__incl.map b/docs/example1_8c__incl.map index 7285a033775..e29ed1d6ea9 100644 --- a/docs/example1_8c__incl.map +++ b/docs/example1_8c__incl.map @@ -1,4 +1,3 @@ - - + diff --git a/docs/example1_8c__incl.md5 b/docs/example1_8c__incl.md5 index 06a473b0587..be64f8a9a9a 100644 --- a/docs/example1_8c__incl.md5 +++ b/docs/example1_8c__incl.md5 @@ -1 +1 @@ -7153758fb231a546cd9562782b0185b0 \ No newline at end of file +f609d836a72fdfa9a66def7629912d00 \ No newline at end of file diff --git a/docs/example1_8c__incl.png b/docs/example1_8c__incl.png index 9dbfa5d6223..addb3d17bcd 100644 Binary files a/docs/example1_8c__incl.png and b/docs/example1_8c__incl.png differ diff --git a/docs/example2_8c.html b/docs/example2_8c.html index a67c5b4e4e6..9c213bc326d 100644 --- a/docs/example2_8c.html +++ b/docs/example2_8c.html @@ -87,8 +87,7 @@
    - - +

    @@ -611,10 +610,10 @@

    PIOc_Init_Intracomm(). It references an internal structure containing the general IO subsystem data and MPI structure. It is passed to PIOc_finalize() to free associated resources, after all I/O, but before MPI_Finalize is called.

    +

    The ID for the parallel I/O system. It is set by PIOc_Init_Intracomm(). It references an internal structure containing the general IO subsystem data and MPI structure. It is passed to PIOc_finalize() to free associated resources, after all I/O, but before MPI_Finalize is called.

    The ncid of the netCDF file created in this example.

    The ID of the netCDF varable in the example file.

    -

    The I/O description ID as passed back by PIOc_InitDecomp() and freed in PIOc_freedecomp().

    +

    The I/O description ID as passed back by PIOc_InitDecomp() and freed in PIOc_freedecomp().

    A buffer for sample data. The size of this array will vary depending on how many processors are involved in the execution of the example code. It's length will be the same as elements_per_pe.

    A buffer for reading data back from the file. The size of this array will vary depending on how many processors are involved in the execution of the example code. It's length will be the same as elements_per_pe.

    A 1-D array which holds the decomposition mapping for this example. The size of this array will vary depending on how many processors are involved in the execution of the example code. It's length will be the same as elements_per_pe.

    @@ -707,7 +706,7 @@

    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/example2_8c__incl.map b/docs/example2_8c__incl.map index 5a1e0f365fc..22542cebbcf 100644 --- a/docs/example2_8c__incl.map +++ b/docs/example2_8c__incl.map @@ -1,4 +1,3 @@ - - + diff --git a/docs/example2_8c__incl.md5 b/docs/example2_8c__incl.md5 index 2f029e414ad..586734102a6 100644 --- a/docs/example2_8c__incl.md5 +++ b/docs/example2_8c__incl.md5 @@ -1 +1 @@ -3097b62480407e15ec602b6af990f9a4 \ No newline at end of file +97a8b2d2062567d8481d6e563993bdb3 \ No newline at end of file diff --git a/docs/example2_8c__incl.png b/docs/example2_8c__incl.png index 876c09d4ea7..1d02190c04d 100644 Binary files a/docs/example2_8c__incl.png and b/docs/example2_8c__incl.png differ diff --git a/docs/example_pio_8c.html b/docs/example_pio_8c.html index 6bd66e27822..f251fd22898 100644 --- a/docs/example_pio_8c.html +++ b/docs/example_pio_8c.html @@ -86,8 +86,7 @@
    - - +

    @@ -173,7 +172,7 @@

    Clean up allocated resources.

    -

    This function frees the memory used in this example. It calls the ParallelIO library function PIOc_freedecomp() to free decomposition resources. Then calles PIOc_finalize() and MPI_finalize() to free library resources.

    +

    This function frees the memory used in this example. It calls the ParallelIO library function PIOc_freedecomp() to free decomposition resources. Then calles PIOc_finalize() and MPI_finalize() to free library resources.

    Parameters

    @@ -206,7 +205,7 @@

    Closes the netCDF file.

    -

    Uses the PIOc_closefile() function to close the netCDF sample file written by this example.

    +

    Uses the PIOc_closefile() function to close the netCDF sample file written by this example.

    Parameters

    [in]thisPointer to self.
    @@ -240,7 +239,7 @@

    PIOc_InitDecomp() to initalize the decomposition for this example. The arguments are:

    [in]thisPointer to self.
    @@ -397,7 +396,7 @@

    Error handling function.

    -

    On error, process with rank zero will print error message, the netCDF file will be closed with PIOc_closefile(), and MPI_Abort is called to end the example execution on all processes.

    +

    On error, process with rank zero will print error message, the netCDF file will be closed with PIOc_closefile(), and MPI_Abort is called to end the example execution on all processes.

    Parameters

    [in]thisPointer to self.
    @@ -434,7 +433,7 @@

    PIOc_Init_Intracomm(). This call takes the following parameters:

    +

    The ParallelIO communicator is set up with a call to PIOc_Init_Intracomm(). This call takes the following parameters:

    [in]thisPointer to self.
    @@ -544,7 +543,7 @@

    PIOc_write_darray() function. After the write is complete, ensure the file is synced for all processes after the write.

    +

    The data are written with the PIOc_write_darray() function. After the write is complete, ensure the file is synced for all processes after the write.

    Parameters

    [in]thisPointer to self.
    @@ -628,7 +627,7 @@

    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/example_pio_8c__incl.map b/docs/example_pio_8c__incl.map index 11e4d47bbb4..53afcd3f026 100644 --- a/docs/example_pio_8c__incl.map +++ b/docs/example_pio_8c__incl.map @@ -1,4 +1,3 @@ - - + diff --git a/docs/example_pio_8c__incl.md5 b/docs/example_pio_8c__incl.md5 index b1116fa8f53..b9bdf52ddde 100644 --- a/docs/example_pio_8c__incl.md5 +++ b/docs/example_pio_8c__incl.md5 @@ -1 +1 @@ -16d22277ef70521f625639276c29f987 \ No newline at end of file +2c39d687bcb067eaa76aa2b04df48f7b \ No newline at end of file diff --git a/docs/example_pio_8c__incl.png b/docs/example_pio_8c__incl.png index d5271a78686..72eab304db7 100644 Binary files a/docs/example_pio_8c__incl.png and b/docs/example_pio_8c__incl.png differ diff --git a/docs/example_pio_8f90.html b/docs/example_pio_8f90.html index c85bcdb93bb..00bc6c3c11a 100644 --- a/docs/example_pio_8f90.html +++ b/docs/example_pio_8f90.html @@ -149,7 +149,7 @@

    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/faq.html b/docs/faq.html index 2e7e01ebf4d..59f4b73d027 100644 --- a/docs/faq.html +++ b/docs/faq.html @@ -81,7 +81,7 @@
    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/files.html b/docs/files.html index 2047eeea840..1667c581288 100644 --- a/docs/files.html +++ b/docs/files.html @@ -66,45 +66,34 @@
    Here is a list of all documented files with brief descriptions:

    [in]thisPointer to self.
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + +
     bget.h
     dtypes.h
     example1.cA simple C example for the ParallelIO Library
     example2.cA simple C example for the ParallelIO Library
     examplePio.cA simple C example for the ParallelIO Library
     examplePio.f90A simple Fortran example for the ParallelIO Library
     pio.F90User interface Module for PIO, this is the only file a user program should 'use'
     pio.hPublic headers for the PIO C interface
     pio_darray.cPublic functions that read and write distributed arrays in PIO
     pio_darray_int.cPrivate functions to help read and write distributed arrays in PIO
     pio_file.cPIO File Handling
     pio_get_nc.cPIO functions to get data (excluding varm functions)
     pio_getput_int.cInternal PIO functions to get and put attributes and data
     pio_internal.hPrivate headers and defines for the PIO C interface
     pio_kinds.F90Basic data types
     pio_lists.cPIO list functions
     pio_msg.cPIO async message handling
     pio_nc.cPIO interfaces to NetCDF support functions
     pio_nc4.cFunctions to wrap netCDF-4 functions for PIO
     pio_put_nc.cPIO functions to write data
     pio_rearrange.cCode to map IO to model decomposition
     pio_spmd.cAlgorithms modeled after spmd_utils in the Community Atmosphere Model; C translation
     pio_support.F90Internal code for compiler workarounds, aborts and debug functions
     pio_types.F90Derived datatypes and constants for PIO Fortran API
     pioc.cSome initialization and support functions
     pioc_sc.cCompute start and count arrays for the box rearranger
     pioc_support.cSupport functions for the PIO library
     piodarray.F90Read and write routines for decomposed data
     piolib_mod.F90Initialization Routines for PIO
     pionfatt_mod.F90NetCDF attribute interface to PIO
     pionfget_mod.F90Read Routines for non-decomposed NetCDF data
     pionfput_mod.F90Write routines for non-decomposed NetCDF data
     uthash.h
     example1.cA simple C example for the ParallelIO Library
     example2.cA simple C example for the ParallelIO Library
     examplePio.cA simple C example for the ParallelIO Library
     examplePio.f90A simple Fortran example for the ParallelIO Library
     pio.F90User interface Module for PIO, this is the only file a user program should 'use'
     pio.hPublic headers for the PIO C interface
     pio_darray.cPublic functions that read and write distributed arrays in PIO
     pio_file.cPIO File Handling
     pio_get_nc.cPIO functions to get data
     pio_kinds.F90Basic data types
     pio_nc.cPIO interfaces to NetCDF support functions
     pio_nc4.cFunctions to wrap netCDF-4 functions for PIO
     pio_put_nc.cPIO functions to write data
     pio_support.F90Internal code for compiler workarounds, aborts and debug functions
     pio_types.F90Derived datatypes and constants for PIO Fortran API
     pioc.cSome initialization and support functions
     pioc_support.cSupport functions for the PIO library
     piodarray.f90Read and write routines for decomposed data
     piolib_mod.f90Initialization Routines for PIO
     pionfatt_mod_2.f90NetCDF attribute interface to PIO
     pionfget_mod_2.f90Read Routines for non-decomposed NetCDF data
     pionfput_mod.f90Write routines for non-decomposed NetCDF data
    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/globals.html b/docs/globals.html index 4f07bcfd55c..333f308d8eb 100644 --- a/docs/globals.html +++ b/docs/globals.html @@ -63,28 +63,14 @@
    Here is a list of all documented file members with links to the documentation:

    - a -

    -Generated on Sun May 19 2019 07:57:01 for PIO by   +Generated on Wed May 22 2019 15:09:23 for PIO by   doxygen 1.8.13
    diff --git a/docs/globals_defs.html b/docs/globals_defs.html index ae57fc15687..c7d9aa38328 100644 --- a/docs/globals_defs.html +++ b/docs/globals_defs.html @@ -117,9 +117,6 @@

    - d -