Crash on multiple file opens in HDF5 prior to 1.8.7

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1

Hi there,

with PyTables we encountered a problem where HDF5 seg faults when opening a
file multiple times (but without doing any IO!). You can read the reported
issue here https://github.com/PyTables/PyTables/issues/326. These older
versions of HDF5 are relevant because current Ubuntu LTS (long term
support) distribution ships with 1.8.4.

I managed to reduce the problem down to the following program. It opens a
file in read-only twice obtaining two handles and simply close them both in
a stacked order.

#include "stdio.h"
#include "hdf5.h"

const char *name = "/tmp/scalar.h5";

int main(int argc, char const *argv[])
{
printf("=============== before outer open\n");
hid_t file1_id = H5Fopen(name, H5F_ACC_RDONLY, H5P_DEFAULT);
hid_t group1_id = H5Gopen(file1_id, "/", H5P_DEFAULT);

{
printf("=============== before inner open\n");
hid_t file2_id = H5Fopen(name, H5F_ACC_RDONLY, H5P_DEFAULT);
hid_t group2_id = H5Gopen(file2_id, "/", H5P_DEFAULT);

printf("=============== before inner close\n");
H5Gclose(group2_id);
H5Fclose(file2_id);
}

H5L_info_t linfo;
H5Lget_info(group1_id, "/foo", &linfo, H5P_DEFAULT);

printf("=============== before outer close\n");
H5Gclose(group1_id);
H5Fclose(file1_id);

return 0;
}

HDF5 produces the following trace

=============== before outer open
H5Fopen(filename=0x10888bef2, flags=0, fapl=H5P_DEFAULT) = 16777216 (file);
H5Gopen2(loc=16777216 (file), name=0x10888bf24, gapl=H5P_DEFAULT) =
33554432 (group);
=============== before inner open
H5check_version(majnum=1, minnum=8, relnum=6) = SUCCEED;
H5Fopen(filename=0x10888bef2, flags=0, fapl=H5P_DEFAULT) = 16777217 (file);
H5Gopen2(loc=16777217 (file), name=0x10888bf24, gapl=H5P_DEFAULT) =
33554433 (group);
=============== before inner close
H5Gclose(group=33554433 (group)) = SUCCEED;
H5Fclose(file=16777217 (file)) = SUCCEED;
H5Lget_info(loc=33554432 (group), name=0x10888bf6d, linfo=0x7fff573747b0,
lapl=H5P_DEFAULT)
*Assertion failed: (f->shared), function H5AC_protect, file H5AC.c, line
1262.*
Abort trap: 6

Is this a know bug? I can't reproduce it with any version after 1.8.6 but I
can't find anything relevant in the release notes.

Cheers,
Andrea

ยทยทยท

--
Andrea Bedini <andrea.bedini@gmail.com>