Haijun,
Did do a 'make clean' or (even better) 'make distclean' before
recompiling your code? Make is supposed to determine that the source
files are newer than the object files and build all the object files
that depend on those source files and so on, but it's possible that the
dependency tree broke down somewhere.
I would recommend deleting your entire HDF5 source directory, unzipping
HDF again, applying the patch, and the going through the configure and
make process again.
Prentice
On 07/27/2016 08:24 AM, Dana Robinson wrote:
Hi Haijun,
If you are still getting a flock error, I'd be suspicious that you
aren't linking to the patched HDF5 library. The source patch
completely removes flock so you shouldn't be seeing file locking errors.
Dana Robinson
Software Engineer
The HDF Group
*From:*Hdf-forum [mailto:[email protected]] *On
Behalf Of *???
*Sent:* Wednesday, July 27, 2016 2:16 AM
*To:* HDF Users Discussion List <[email protected]>
*Subject:* Re: [Hdf-forum] Error detected in HDF5 (1.10.0) thread 0:
/home/hdftest/snapshots-hdf5_1_10_alpha/current/src
Hi Dana,
Thanks for your response.
I've tried with your method to patch and compile
hdf5-1.10.0-patch1 source code. Patch and compile have no error.
Unfortunately when run my code the error still exist. And error
information is the same as before.
What should I do? Please help me.
Thank you again for your effort!
Haijun Yu
At 2016-07-26 13:47:39, "Dana Robinson" <[email protected]
<mailto:[email protected]>> wrote:
Hi,
It looks like flock() is not implemented on your filesystem, which
is causing the create call to fail. flock() file locking is used
by the HDF5 1.10.0 to help enforce single-writer/multiple-readers
(SWMR) semantics, but is not necessary for correct operation of
the library. A fix for this problem should be available in HDF5
1.10.1, but in the meantime you can apply a source patch found here:
https://www.hdfgroup.org/HDF5/release/obtainsrc5110.html#conf
under "Patch to Disable File Locking" at the bottom of the page.
Cheers,
Dana Robinson
Software Engineer
The HDF Group
*From:*Hdf-forum [mailto:[email protected]
<mailto:[email protected]>] *On Behalf Of *???
*Sent:* Tuesday, July 26, 2016 1:35 AM
*To:* [email protected]
<mailto:[email protected]>
*Subject:* [Hdf-forum] Error detected in HDF5 (1.10.0) thread 0:
/home/hdftest/snapshots-hdf5_1_10_alpha/current/src
Hi,
I have met an obscure failure, and not find a good solution for
two days. Could you help me? Thanks!
(Using: hdf5-1.10.0-patch1-linux-centos6-x86_64-gcc447-shared.tar.gz)
(Environment: redhat6.4-Intel-X64-g++4.4.7)
The error information:
HDF5-DIAG: Error detected in HDF5 (1.10.0) thread 0:
#000: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src/H5F.c
line 491 in H5Fcreate(): unable to create file
major: File accessibilty
minor: Unable to open file
#001: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src/H5Fint.c
line 1168 in H5F_open(): unable to lock the file or initialize
file structure
major: File accessibilty
minor: Unable to open file
#002: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src/H5FD.c
line 1821 in H5FD_lock(): driver lock request failed
major: Virtual File Layer
minor: Can't update object
#003:
/home/hdftest/snapshots-hdf5_1_10_alpha/current/src/H5FDsec2.c
line 939 in H5FD_sec2_lock(): unable to flock file, errno = 38,
error message = 'Function not implemented'
major: File accessibilty
minor: Bad file ID accessed
HDF5-DIAG: Error detected in HDF5 (1.10.0) thread 0:
#000: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src/H5F.c
line 749 in H5Fclose(): not a file ID
major: Invalid arguments to routine
minor: Inappropriate type
compile no error: g++ -c packageHdf5.cpp -I ../latest/include -L
../latest/lib -lhdf5 -lhdf5_cpp
link no error: g++ -o packageHdf5Run packageHdf5.o -I
../latest/include -L ../latest/lib -lhdf5 -lhdf5_cpp
run error: ./packageHdf5Run (error information as above)
My code:
#include <stdio.h>
#include <iostream>
#include <string>
#include "H5Cpp.h"
#include <H5File.h>
#include "hdf5.h"
#ifndef H5_NO_NAMESPACE
using namespace H5;
#endif
using namespace std;
int main(int argc, char* argv[])
{
hid_t file_id =
H5Fcreate("/home/tg2hpps/tg2hpps_main/src/packageHdf5/dsetddd.h5",
H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
H5Fclose(file_id);
}
Thanks!
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
