Recent changes to bugs

CGNS fails to create node when using multiple files

2012-11-23T22:09:19Z

When CGNS is configured with HDF5 I am unable to create a new node (e.g., write a base) when working with multiple files. It only occurs if I close one of the files while writing to the other. For example, to repeat the issue:

1. Open (new) file A for writing
2. Open file B as read only
3. Close file B
4. Write base to file A

When attempting the write to file A the following error is obtained: cgio_create_node:H5Gcreate:node group creation failed

This issue is not observed when using the ADF backend.

Attached are a sample code to reproduce the issue along with the file the sample code opens as read only.

pcgns_util.c fails to compile

2012-04-20T15:58:16Z

cgnslib_3.1.3 fails to compile in Ubuntu 11.10 with parallel support.

Compiler gives following error message:

/home/user/cgnslib_3.1.3/pcgns/src/pcgns_util.c: Function ”new_str_attb”:
/home/user/cgnslib_3.1.3/pcgns/src/pcgns_util.c:264:2: error: too many arguments to function ”H5Acreate1”
/usr/include/H5Apublic.h:105:16: note: declared here

and two similar errors follow.

With Ubuntu 11.10 HDF5 library is compiled with option --with-default-api-version=v16 as there are these two lines in libhdf5.settings:

...
Default API Mapping: v16
With Deprecated Public Symbols: yes
...

It seems that pcgns_util.c uses old functions by default even if it should use newer ones. With hard-coded to use function H5Acreate2 compiling finishes without errors.

Expected behaviour: Compiling finishes without errors.
Current behaviour: Wrong version from function seems to be selected for pcgns_util.c and build process fails.

Problem opening files that have the same name

2011-10-06T12:30:27Z

Steps to reproduce:

1. Create two directories (let’s say dir A and dir B).
2. In dir A create two files (say, file 1 and file 2). File 1 is linked to file 2.
3. In dir B create two different files but give them the same name. File 1 is also linked to file 2.
4. Change the current working directory to one of the previously created directories, let’s say dir A.
5. Open dir A/file 1.
6. Try to open dir B/file 2. This step will fail.

File is being opened as read/write when it is not needed

2011-01-04T14:22:22Z

In ADF_interface.c line 1048 of the 2.5.4 version of the CGNS library the files are being opened as r+b when there is no need to write the file. This is causing old files not to be loaded as the previous libraries did not require write permision

-lX11 not included in OS X

2010-09-29T14:49:21Z

The linker does not include the -lX11 on OS X in the definition for OGLLIBS.

Current values are

OGLLIBS = -lGL -lGLU

but should be

OGLLIBS = -lGL -lGLU -lX11

OpenGL includes not included on OS X

2010-09-29T14:14:40Z

After running the ./configure script, the /usr/X11/include directory is not being included on OS X - this results in all OpenGL related files failing to compile. Workaround is to edit the CFLAGS to have -I/usr/X11/include

syntax error in p3dout.c

2010-09-29T14:08:15Z

The multi-line macro beginning on line 22 of p3dout.c is missing an end bracket. It currently reads (ignoring whitespace)

fprintf (stderr, "Fortran unformatted output not supported for %s machine\n", bf_machname (MACH_LOCAL);

but should read

fprintf (stderr, "Fortran unformatted output not supported for %s machine\n", bf_machname (MACH_LOCAL));

Tcl framework not referenced in OS X build

2010-09-29T14:05:13Z

On OS X, in the file make.defs, the definition for the TKLIBS variable begins

TKLIBS = -framework Tk -framework Tk ...

which results in a failed compile. I believe a simple solution is to replace this with

TKLIBS = -framework Tk -framework Tcl

(i.e. the second framework is Tcl, not a repeat of Tk)

ADFI_string_2_C_String oversteps character string size

2010-05-01T21:05:48Z

This isn't a bug in ADFI_String_2_C_String per say, but rather many of the routines that call it. What happens is that this function is being passed character strings which are smaller than the specified string_length parameter and the internal for loop is accessing memory beyond the size of the passed in string argument. In many places you are calling cgi_new_node(...) with a fixed character string of "R4" for instance which is turn may call cgio_set_dimensions(...), eventually calling ADFI_string_2_C_string(...) with a value of string_length equal to ADF_DATA_TYPE_LENGTH, but you passed in a character constant of length 2, so you access memory outside the bounds of string. So to repeat, the call path is:

cgi_new_node -> cgio_set_dimensions -> ADF_Put_Dimension_Information -> ADF_evaluate_datatype -> ADFI_string_2_C_string

If cgi_new_node is called with data_type="R4" or some such, this will be a problem as you will exceed the memory region of string in ADFI_string_2_C_string(...) when performing the copy. An easy fix is to not use a character constant in the actual calls, but to define a ADF_DATA_TYPE_LENGTH length character constant in the header for things such as "I4", "R4", etc... Also, they should be used in the cgi_adf_datatype(...) function as well. Thanks.

Prameters in cg_gopath_f

2008-10-17T13:59:58Z

There is a mismatch in parameters in cg_gopath_f.
Documentation says:
cg_gopath_f(fn, ier, path)

however, the actual (2.5r3) implementation is
cg_gopath_f(fn, path, ier)