The assertion occurs when using the HDF5 v1.8.16 Thread Safe with Zlib and
the H5_term_library() function is called after having closed a file which
contains a chunked, *non-compressed* Armadillo Matrix of doubles (i.e.,
arma::mat).
The assertion *does not occur* when using the HDF5 v1.8.16 Thread Safe *without
Zlib* and the H5_term_library() function is called after having closed a
file which contains a chunked, *non-compressed* Armadillo Matrix of doubles
(i.e., arma::mat).
The H5 file is created with the ‘H5F_CLOSE_STRONG’ property
GDB dump:
Program received signal SIGABRT, Aborted.
0x0000003ca7032625 in raise () from /lib64/libc.so.6
(gdb) up
#1 0x0000003ca7033e05 in abort () from /lib64/libc.so.6
(gdb)
#2 0x0000003ca702b74e in __assert_fail_base () from /lib64/libc.so.6
(gdb)
#3 0x0000003ca702b810 in __assert_fail () from /lib64/libc.so.6
(gdb)
#4 0x00007ffff7584e1c in H5T_conv_struct_free (priv=0xab6e30) at
H5Tconv.c:1845
1845 HDassert(status >= 0);
(gdb)
#5 0x00007ffff7587180 in H5T__conv_struct_opt (src_id=-1, dst_id=-1,
cdata=0xab2410, nelmts=0, buf_stride=0, bkg_stride=0,
_buf=0x0, _bkg=0x0, dxpl_id=167772168) at H5Tconv.c:2458
2458 cdata->priv = H5T_conv_struct_free((H5T_conv_struct_t
*)(cdata->priv));
(gdb)
#6 0x00007ffff7564c0f in H5T_term_interface () at H5T.c:1410
1410 if((path->func)((hid_t)FAIL, (hid_t)FAIL,
&(path->cdata), (size_t)0,
(gdb)
#7 0x00007ffff7279134 in H5_term_library () at H5.c:289
289 pending += DOWN(T);
(gdb)
#8 0x00007ffff727b082 in H5close () at H5.c:859
859 H5_term_library();
(gdb)
#9 0x00007ffff6fffa5f in H5::H5Library::termH5cpp() ()
from
/local/mnt/workspace/pcereck/ra_comp/pensim/ThirdParty/hdf5/hdf5-1.8.16/thread.safe.with.zlib/lib/libhdf5_cpp.so.11
(gdb) up
#10 0x0000003ca7035ebd in __cxa_finalize () from /lib64/libc.so.6
(gdb)
#11 0x00007ffff6ffc1e6 in __do_global_dtors_aux ()
from
/local/mnt/workspace/pcereck/ra_comp/pensim/ThirdParty/hdf5/hdf5-1.8.16/thread.safe.with.zlib/lib/libhdf5_cpp.so.11
(gdb)
Here is the *H5T_conv_struct_free*() function (the assert on line 1845 is
highlighted):
static H5T_conv_struct_t *
*H5T_conv_struct_free*(H5T_conv_struct_t *priv)
{
int *src2dst = priv->src2dst;
hid_t *src_memb_id = priv->src_memb_id,
*dst_memb_id = priv->dst_memb_id;
unsigned i;
FUNC_ENTER_NOAPI_NOINIT_NOERR
for(i = 0; i < priv->src_nmembs; i++)
if(src2dst[i] >= 0) {
int status;
status = *H5I_dec_ref*(src_memb_id[i]);
*HDassert*(status >= 0);
status = *H5I_dec_ref*(dst_memb_id[src2dst[i]]);
*HDassert*(status >= 0);
} */* end if */*
*H5MM_xfree*(src2dst);
*H5MM_xfree*(src_memb_id);
*H5MM_xfree*(dst_memb_id);
*H5MM_xfree*(priv->memb_path);
*FUNC_LEAVE_NOAPI*((H5T_conv_struct_t *)*H5MM_xfree*(priv))
} */* end H5T_conv_struct_free() */*
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