Memory corruption problems with a dynamic filter in jhdf5

Hdf-forum archives
1

Hi,

I'm working on a compression filter for HDF5, but I had some problems with
jhdf5 opening the filtered datasets.

I managed to trace down the problem to this: the filter plugin is found,
starts execution, but when it wants to free the original buffer, the
program exits with a memory heap corruption error. This is a minimal
version of the filter that reproduces the error:

size_t H5Z_dummy_filter(unsigned int flags, size_t cd_nelmts, const
unsigned int cd_values[], size_t nbytes, size_t *buf_size, void **buf)
{
    int* outbuf = (int*)malloc(*buf_size);
    memcpy(outbuf, *buf, *buf_size);
    free(*buf); // error occurs here
    *buf = outbuf;
    return nbytes;
}

This (dummy) filter works from C++, from the command line with h5dump, and
also with HDFView. I only had a problem when using it with Fiji, which uses
the jhdf5 library (14.12.2).

I compiled the dll with Visual Studio 2013 on Windows 7 64 bit, and use the
64 bit version of Java 8 with Fiji.

Thanks in advance for the help!
Cheers,
Balint

2

Hi,

You could try using the H5allocate_memory and H5free_memory functions in the filter, instead of regular malloc and free.

Dan.

···

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Bálint Balázs
Sent: 08 January 2016 13:51
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Memory corruption problems with a dynamic filter in jhdf5

Hi,
I'm working on a compression filter for HDF5, but I had some problems with jhdf5 opening the filtered datasets.

I managed to trace down the problem to this: the filter plugin is found, starts execution, but when it wants to free the original buffer, the program exits with a memory heap corruption error. This is a minimal version of the filter that reproduces the error:

size_t H5Z_dummy_filter(unsigned int flags, size_t cd_nelmts, const unsigned int cd_values[], size_t nbytes, size_t *buf_size, void **buf)
{
    int* outbuf = (int*)malloc(*buf_size);
    memcpy(outbuf, *buf, *buf_size);
    free(*buf); // error occurs here
    *buf = outbuf;
    return nbytes;
}

This (dummy) filter works from C++, from the command line with h5dump, and also with HDFView. I only had a problem when using it with Fiji, which uses the jhdf5 library (14.12.2).
I compiled the dll with Visual Studio 2013 on Windows 7 64 bit, and use the 64 bit version of Java 8 with Fiji.

Thanks in advance for the help!
Cheers,
Balint

3

Hi Dan,

Thanks for the tip, I didn't realize these functions existed.
Unfortunately, however, this didn't fix the problem...

Balint

···

2016-01-08 15:03 GMT+01:00 Daniel Tetlow <daniel.tetlow@optasense.com>:

Hi,

You could try using the H5allocate_memory and H5free_memory functions in
the filter, instead of regular malloc and free.

Dan.

*From:* Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] *On
Behalf Of *Bálint Balázs
*Sent:* 08 January 2016 13:51
*To:* hdf-forum@lists.hdfgroup.org
*Subject:* [Hdf-forum] Memory corruption problems with a dynamic filter
in jhdf5

Hi,

I'm working on a compression filter for HDF5, but I had some problems with
jhdf5 opening the filtered datasets.

I managed to trace down the problem to this: the filter plugin is found,
starts execution, but when it wants to free the original buffer, the
program exits with a memory heap corruption error. This is a minimal
version of the filter that reproduces the error:

size_t H5Z_dummy_filter(unsigned int flags, size_t cd_nelmts, const
unsigned int cd_values, size_t nbytes, size_t *buf_size, void **buf)
{
    int* outbuf = (int*)malloc(*buf_size);
    memcpy(outbuf, *buf, *buf_size);
    free(*buf); // error occurs here
    *buf = outbuf;
    return nbytes;
}

This (dummy) filter works from C++, from the command line with h5dump, and
also with HDFView. I only had a problem when using it with Fiji, which uses
the jhdf5 library (14.12.2).

I compiled the dll with Visual Studio 2013 on Windows 7 64 bit, and use
the 64 bit version of Java 8 with Fiji.

Thanks in advance for the help!

Cheers,

Balint

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