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" <[email protected]> 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:[email protected]] On Behalf Of
Prentice Bisbal
Sent: Friday, July 29, 2016 9:43 AM
To:[email protected]
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" <[email protected]> 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:[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]> 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]] On Behalf Of ???
Sent: Tuesday, July 26, 2016 1:35 AM
To:[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
_______________________________________________
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
