Hi Dana and Prentice,
Thanks for your help.
My problem has been solved perfectly. I use the h5c++ compiler to compile the code, and it works. Wonderful!
Maybe I linked to the error libraries when I linked mannually.
Thanks again for your help!
Haijun Yu
At 2016-07-29 23:40:52, "Dana Robinson" <derobins@hdfgroup.org> wrote:
Hi all,
The source patch removes all references to flock() so this error
should not be occurring, regardless of the permissions. If you are
still seeing errors, I suspect that you are linking to a different
HDF5 library than the one you patched.
One thing I would try is, instead of using g++ directly, try using
the h5c++ compiler wrapper that should be located in the bin
directory of the HDF5 install. That will ensure that you are
linking to the correct libraries. When you use h5c++, you won't
need to include the -I, -L, and -l flags for HDF5 paths and
libraries since h5c++ sets that up for you.
Dana Robinson
Software Engineer
The HDF Group
*From:*Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org
<mailto:hdf-forum-bounces@lists.hdfgroup.org>] *On Behalf Of
*Prentice Bisbal
*Sent:* Friday, July 29, 2016 9:43 AM
*To:* hdf-forum@lists.hdfgroup.org
<mailto:hdf-forum@lists.hdfgroup.org>
*Subject:* Re: [Hdf-forum] Error detected in HDF5 (1.10.0) thread
0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src
I know this may sound like a stupid question, but I have to ask,
because I've learned never to assume things: Are you sure you have
write access where you're trying to create this file? Have you
confirmed this by going the directory where you are trying to
create the directory and doing 'touch test', which will create an
empty file named "test"?
Prentice
On 07/28/2016 11:24 PM, 于海军 wrote:
Hi Dana and Prentice,
Thanks for your response.
I've tried with your method to repatch and recompile
hdf5-1.10.0-patch1 source code. And I also checked the three
files H5private.h, H5system.c and swmr.c. They were actually
changed after run patch. Unfortunately when run my code the
error still exist. And error information is the same as before.
I compile the hdf5 code as follows:
patch -p0 < file-lock-removal.diff
./configure --prefix=/home/duc001/3dtools/hdf5-1.10.0
--enable-cxx --with-zlib=/home/duc001/zlib-1.2.8/
make
make clean
make check
make install
make check-install
echo $PATH as follows:
/home/duc001/3dtools/hdf5-1.10.0/bin
I compile my code as follows:
g++ -c test.cpp
-I /home/duc001/3dtools/hdf5-1.10.0/include
-L /home/duc001/3dtools/hdf5-1.10.0/lib -lhdf5 -lhdf5_cpp
//no error
g++ -o testRun test.o
-I /home/duc001/3dtools/hdf5-1.10.0/include
-L /home/duc001/3dtools/hdf5-1.10.0/lib -lhdf5 -lhdf5_cpp
//no error
./testRun // with error
Are there any questions in the above operation?
Thanks again for your effort!
Haijun Yu
At 2016-07-27 21:46:43, "Prentice Bisbal" <pbisbal@pppl.gov> > <mailto:pbisbal@pppl.gov>wrote:
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:hdf-forum-bounces@lists.hdfgroup.org] *On
Behalf Of *???
*Sent:* Wednesday, July 27, 2016 2:16 AM
*To:* HDF Users Discussion List
<hdf-forum@lists.hdfgroup.org>
<mailto:hdf-forum@lists.hdfgroup.org>
*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" > <derobins@hdfgroup.org <mailto:derobins@hdfgroup.org>> > 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:hdf-forum-bounces@lists.hdfgroup.org
<mailto:hdf-forum-bounces@lists.hdfgroup.org>] *On
Behalf Of *???
*Sent:* Tuesday, July 26, 2016 1:35 AM
*To:* hdf-forum@lists.hdfgroup.org
<mailto:hdf-forum@lists.hdfgroup.org>
*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!
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<mailto:Hdf-forum@lists.hdfgroup.org>
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Twitter:https://twitter.com/hdf5
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org <mailto:Hdf-forum@lists.hdfgroup.org>
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter:https://twitter.com/hdf5
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
