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Branch: master
Commits on Mar 4, 2019
  1. updated for 3.4.0 release

    brtnfld committed Mar 4, 2019
  2. Merge pull request #122 from CGNS/develop

    brtnfld committed Mar 4, 2019
    Release v3.4.0
Commits on Mar 1, 2019
  1. fixed link ordering for SunOS

    brtnfld committed Mar 1, 2019
  2. Automatic linking of szip and zlib (if needed by HDF5) (#116)

    brtnfld committed Mar 1, 2019
    * automatic detection of zlib and szip
    
    * Solaris Compiler fixes
    
    * added NAG compiler flags
    
    * fixed issue with NAG detection
    
    * fixed seg fault with gcc 4.8.5,Red Hat 4.8.5-4
    
    * fixed link ordering
  3. Fix for OSX Build (#120)

    gsjaardema authored and brtnfld committed Mar 1, 2019
    On OSX, the XOPEN version needs to be at least 600 to include the function prototype for `readlink` using the following compiler:
    ```
    Apple LLVM version 10.0.0 (clang-1000.11.45.5)
    Target: x86_64-apple-darwin17.7.0
    ```
    The warning is:
    ```
    /Users/gdsjaar/src/seacas/TPL/cgns/CGNS/src/cgns_io.c:229:15: warning: implicit declaration of function 'readlink' is invalid in C99
          [-Wimplicit-function-declaration]
            len = readlink(filename, linkfile, st.st_size + 1);
                  ^
    ```
    When `_XOPEN_SOURCE` is defined to be 500.  Warning goes away when defined to be 600.  
    
    This also happens with gcc-8.3.0 on OSX.
Commits on Feb 28, 2019
  1. Create hdf5-1.8.x compatible files from 1.10.X library (#114)

    gsjaardema authored and brtnfld committed Feb 28, 2019
    If CGNS is built against the new HDF5-1.10.x library versions, the files that are created are not readable by applications which are built against earlier HDF5-1.8.x library versions.  This can cause issues on many systems which are using commercial or externally maintained visualization or other applications (ParaView, Ensight, ...) . 
    
    Adding the command to use the `H5F_LIBVER_V18` option makes the files readable by the older applications.  
    
    Here is some advice from the HDF5 group related to this issue:
    ```
    If an application written for 1.8.* is linked with HDF5 1.10.(i.e., it doesn’t use any new features of 1.10.0), a file created by the application will be readable by HDF5 1.8. (or even earlier versions). The exception to this rule would be an application that uses H5Pset_libver_bounds with H5F_LIBVER_LATEST value for its “low” and “high” parameters.
    
    In this case both parameters should be set to H5F_LIBVER_V18 to create 1.8 compatible file.
    
    File control versioning became available in the HDF5 1.10.3 release. As a safeguard feature, we recommend using H5Pset_libver_bounds function to control file versioning.
    ```
Commits on Feb 27, 2019
  1. Revert "Fixed cmake to build shared library on Windows. Added a matri…

    brtnfld committed Feb 27, 2019
    …x item to test it. (#115)" (#121)
    
    This reverts commit f356dd9.
Commits on Feb 26, 2019
  1. Cgns107 (#118)

    brtnfld committed Feb 26, 2019
    Added compiler flags needed for NAG, CGNS-107
  2. Fixed cmake to build shared library on Windows. Added a matrix item t…

    matmel authored and brtnfld committed Feb 26, 2019
    …o test it. (#115)
    
    At the moment, you cannot build shared and static versions at the same time.
Commits on Feb 25, 2019
  1. Cgns107 (#117)

    brtnfld committed Feb 25, 2019
    CGNS-107
    
    Fixed ISO_C_BINDING "NULL" issue with NAG compiler.
    Moved tests to use free format Fortran.
    Fixed WRITE format statement causing NAG to crash.
    Passes tests with NAG 6.1
Commits on Feb 21, 2019
  1. Merge pull request #113 from CGNS/Rind_Plane_Indexing

    brtnfld committed Feb 21, 2019
    Redo of Rind Plane Indexing with no squash merge
  2. Merge branch 'develop' into Rind_Plane_Indexing

    brtnfld committed Feb 21, 2019
Commits on Feb 20, 2019
  1. Fixed ENUMVS issue in new tests (#110)

    brtnfld committed Feb 20, 2019
    Added missing autotools test.
  2. Order include directives to get correct includes (#109)

    gsjaardema authored and brtnfld committed Feb 20, 2019
    In the current CMake build, the `${CMAKE_CURRENT_BINARY_DIR}` include is the last one on the compilation line.  This directory contains the most up-to-date version of the `cgnstypes.h` include file.  If there is another version of `cgnstypes.h` existing in an install directory, perhaps the same directory containing hdf5 or some other include files, then the older `cgnstypes.h` will be included instead of the more current one.    Here is an example of the include specifications for the PATCHED and ORIGINAL compilation commands:
    ```
    ORIGINAL:
    cd /gpfs1/cgns/CGNS/build/src && mpicc 
    -I/gpfs1/install_dir/include 
    -I/gpfs1/cgns/CGNS/src 
    -I/gpfs1/cgns/CGNS/build/src  
    -I/gpfs1/install_dir/include 
    
    
    PATCHED:
    cd /gpfs1/cgns/CGNS/build/src && mpicc 
    -I/gpfs1/cgns/CGNS/build/src 
    -I/gpfs1/cgns/CGNS/src 
    -I/gpfs1/install_dir/include  
    -I/gpfs1/install_dir/include 
    ```
  3. Eliminate potential integer overflow / undefined behavior (#106)

    gsjaardema authored and brtnfld committed Feb 20, 2019
    The check for open files was summing the `g_files` entry when all that was needed was a yes/no on whether there were any open files.  Depending of the value of `g_files` it was possible for the integer sum to overflow the range of a signed int which gives undefined behavior.  `idx` is an integer and `g_files` is an `hid_t` which is 64-bits on recent HDF5 versions, so overflow is definitely a possibility (and has happened in the wild)
  4. Revert "Allow serial access to file with cpg_open (#105)" (#107)

    brtnfld committed Feb 20, 2019
    This reverts commit 38235b3.
Commits on Feb 18, 2019
  1. Allow serial access to file with cpg_open (#105)

    brtnfld committed Feb 18, 2019
    *Allow serial access to file with cpg_open
     Added new serial open options for cgp_open, used for open a file using a single processes
Commits on Feb 15, 2019
  1. Handle paths with spaces when launching cgnsview on windows (#99)

    sveale authored and brtnfld committed Feb 15, 2019
Commits on Feb 13, 2019
  1. Revert " Fixed compliation error with cc: Sun C 5.12 SunOS_sparc (#100)…

    brtnfld committed Feb 13, 2019
    …" (#101)
    
    This reverts commit ca41bfa.
Commits on Feb 12, 2019
  1. Fixed compliation error with cc: Sun C 5.12 SunOS_sparc (#100)

    brtnfld committed Feb 12, 2019
    * Fixed compliation error with cc: Sun C 5.12 SunOS_sparc 2011/11/16
    
    ifdef #define _XOPEN_SOURCE
    
    is not defined for SunOS compilers.
  2. removed RETURN from main program

    brtnfld committed Feb 12, 2019
Commits on Feb 8, 2019
  1. Changed ADFH_Read_Data and ADFH_Write_Data to honor the cgp_pio_mode …

    brtnfld committed Feb 8, 2019
    …setting. (#98)
    
    Added command line argument setting cgp_pio_mode in benchmark_hdf5.c
Commits on Feb 7, 2019
  1. Fixed szip detection, linking. It was not specifying the correct link…

    brtnfld committed Feb 7, 2019
    … command and include directories for szip.
  2. gnuplot summary of benchmark_hdf5.c results

    brtnfld committed Feb 7, 2019
Commits on Feb 6, 2019
  1. Support for std C on linux (#96)

    smguzik authored and brtnfld committed Feb 6, 2019
  2. Eliminate dead / unreachable code (#93)

    gsjaardema authored and brtnfld committed Feb 6, 2019
    The `data` pointer is never set to any value, so remains NULL throughout.  Remove all code inside `if (data != NULL)`
    This removes all mentions of `data`, so remove its assignment also.
Commits on Feb 5, 2019
  1. Eliminate C99 style for loop -- unneeded (#95)

    gsjaardema authored and brtnfld committed Feb 5, 2019
    Eliminate for loops of the form `for (int n=....` . In this case, the only change needed is to remove the `int` since `n` is already declared in the routines and the `int n` is just causing a shadowing of the previously defined `n`.  Also eliminates need to use C99 or later standard when compiling.
  2. Null check fix (#94)

    gsjaardema authored and brtnfld committed Feb 5, 2019
    * Remove windows-style line endings
    
    * Move pointer access after null check
Commits on Feb 4, 2019
  1. Eliminate use of variable in two nested loops (#91)

    gsjaardema authored and brtnfld committed Feb 4, 2019
    The variable `n` is used as an index in an outer and inner loop.  Use different index for inner loop.
  2. fixed various appveyor HDF5 version issues

    brtnfld committed Feb 4, 2019
  3. updated HDF5 version

    brtnfld committed Feb 4, 2019
  4. updated HDF5 binaries location

    brtnfld committed Feb 4, 2019
Commits on Feb 3, 2019
  1. Rind plane indexing (#90)

    MicK7 authored and brtnfld committed Feb 3, 2019
    * Serial starting point for bug fix and some shaped read/write
    - Supports reading/writing to fields to shaped memory and files through
      cg_field_general_read
      cg_field_general_write
    
    * Created parallel general write interface
    
    * Shaped write for even number of zones
    
    * Fixes to get compilation
    
    * Allow cgnsview to open files marked as pcgns (cgnsview with treat it as standard hdf5)
    
    * Fixed an interface.  Can successfully write shaped data in parallel.
    
    * Should (H5Pget_driver(did) == H5FD_MPIO) be replaced with (pcg_mpi_initialized) as shown here?
    
    * Added some UserGuideCode parallel/shaped examples (not yet ready for release)
    
    * Some fixups after merge
    
    * Adjust test for reading flow solution with rind plane
    
    * Modify cg_coord_* indexing with rind planes
    
    * Add cg_coord_general* function
    
    * Try refactoring cg_coord_* with general path
    
    * Add cgp_coord_general_write_data function
    
    * Add ADF reading back when conversion is needed
    
    - some code formatting with tabulation to spaces
    - Add a small part in the general coordinate reading to allocate and read array of different type
    
    * Add test for Rind Planes functions
    
    - add test for cg_coord_general_read/write
    - add test for cg_field_general_read/write
    - add general interface to fortran API
    
    * Added configure flag to permit obsolete rind-plane indexing
    
    * Add cg_array_general_xxx
    
    - add read/write array
    
    * Add fortran interface to cg_array_general
    
    * Consistent general field_*_read and coord_*_read.
    Grid node removed from cg_coord_general_read.
    
    * Consistent general field_*_write and coord_*_write.
    Grid node removed from cg_coord_general_write.
    
    * fix test for general interface
    
    - remove grid number from cg_coord_general_xxx
    - remove unused variable
    - clean fortran interface
    
    * remove some gcc warnings
    
    - remove a prinf used for debug
    - specify max string length to prevent buffer overflow in sprintf
    
    * reverting change to printing model name in Rind Plane Indexing branch
    
    * Revised all *general_read
    
    * Refactored *general_real to call cgi_array_general_read in cgns_internals
    Memory array can now have up to 12 dimensions
    
    * Partial refactoring of *general_write to call cgi_array_general_write in cgns_internals
    
    * Refactoring of cg_field_*_write complete
    
    * All reads refactored
    
    * Commit that should finish serial general_read/write for coord, field, and data
    
    * Bug fixes for rind plane indexing and minor changes to tests
    
    * Clean up unused variables
    
    * Made C and Fortran test_general_rind look much more similar
    
    * Much more extensive testing of options related to rind-plane indexing in C
    
    * More extensive testing in Fortran
    
    * Serial testing complete
    
    * Bug fixes and user-guide-code for cg_array_general_read/write under the guise of writing discrete data to faces
    
    * Removed some debug printf
    
    * More refactoring so parallel code can call same range checking from internals
    
    * General writes now support changing data type
    
    * Modification of Mickael's suggestions for fixing tests to support 64-bit cgsize_t builds
    
    * More extensive testing of data conversion in general array reads and writes
    
    * Fix parallel write
    
    In parallel writing mode NULL pointer can be used to write node without data
    
    * draft basic parallel test with rind.
    
    * Working approach for parallel field_general_
    
    * Finished general field, coord, and array functions
    
    * Revised parallel test for general read/write
    
    * Grouped all memory-space arguments together in serial cg_*_general_read functions.  This also better matches signature of parallel cgp_*_general_read_data functions.
    
    * Added user guide code example of write structured grid with parallelism over zones
    
    * C_code_parallel read/write strucutred grid examples
    
    * C_code_parallel write flowcentrind example
    
    * C_code_parallel write flowcentrind parallel in zone example
    
    * C_code_parallel read flowcentrind parallel- (in-and-over-zone) examples
Commits on Jan 22, 2019
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