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Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

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Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

674438511
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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Re: Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

Dana Robinson

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:[hidden email]] On Behalf Of ???
Sent: Tuesday, July 26, 2016 1:35 AM
To: [hidden email]
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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Re: Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

674438511
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" <[hidden email]> 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:[hidden email]] On Behalf Of ???
Sent: Tuesday, July 26, 2016 1:35 AM
To: [hidden email]
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.
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http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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Re: Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

Dana Robinson

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:[hidden email]] On Behalf Of ???
Sent: Wednesday, July 27, 2016 2:16 AM
To: HDF Users Discussion List <[hidden email]>
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" <[hidden email]> 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:[hidden email]] On Behalf Of ???
Sent: Tuesday, July 26, 2016 1:35 AM
To: [hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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Re: Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

Prentice Bisbal
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 [[hidden email]] On Behalf Of ???
Sent: Wednesday, July 27, 2016 2:16 AM
To: HDF Users Discussion List [hidden email]
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" <[hidden email]> 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:[hidden email]] On Behalf Of ???
Sent: Tuesday, July 26, 2016 1:35 AM
To: [hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
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Twitter: https://twitter.com/hdf5
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Re: Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

674438511
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" <[hidden email]> 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 [[hidden email]] On Behalf Of ???
Sent: Wednesday, July 27, 2016 2:16 AM
To: HDF Users Discussion List [hidden email]
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" <[hidden email]> 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:[hidden email]] On Behalf Of ???
Sent: Tuesday, July 26, 2016 1:35 AM
To: [hidden email]
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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Re: Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

Prentice Bisbal

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" [hidden email] 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 [[hidden email]] On Behalf Of ???
Sent: Wednesday, July 27, 2016 2:16 AM
To: HDF Users Discussion List [hidden email]
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" <[hidden email]> 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:[hidden email]] On Behalf Of ???
Sent: Tuesday, July 26, 2016 1:35 AM
To: [hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5



 



_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
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Re: Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

Dana Robinson

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:[hidden email]] On Behalf Of Prentice Bisbal
Sent: Friday, July 29, 2016 9:43 AM
To: [hidden email]
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 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"
[hidden email] 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 [[hidden email]] On Behalf Of ???
Sent: Wednesday, July 27, 2016 2:16 AM
To: HDF Users Discussion List
[hidden email]
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" <
[hidden email]> 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:[hidden email]] On Behalf Of ???
Sent: Tuesday, July 26, 2016 1:35 AM
To:
[hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

 




 




_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

 


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
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Re: Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

674438511

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" <[hidden email]> 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:[hidden email]] On Behalf Of Prentice Bisbal
Sent: Friday, July 29, 2016 9:43 AM
To: [hidden email]
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 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"
[hidden email] 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 [[hidden email]] On Behalf Of ???
Sent: Wednesday, July 27, 2016 2:16 AM
To: HDF Users Discussion List
[hidden email]
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" <
[hidden email]> 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:[hidden email]] On Behalf Of ???
Sent: Tuesday, July 26, 2016 1:35 AM
To:
[hidden email]
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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Re: Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

Dana Robinson

Great! Glad that worked for you.

 

Dana

 

From: Hdf-forum [mailto:[hidden email]] On Behalf Of ???
Sent: Sunday, July 31, 2016 11:15 PM
To: HDF Users Discussion List <[hidden email]>
Subject: Re: [Hdf-forum] Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

 

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" <[hidden email]> 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:[hidden email]] On Behalf Of Prentice Bisbal
Sent: Friday, July 29, 2016 9:43 AM
To: [hidden email]
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 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" [hidden email] 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 [[hidden email]] On Behalf Of ???
Sent: Wednesday, July 27, 2016 2:16 AM
To: HDF Users Discussion List
[hidden email]
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" <[hidden email]> 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:[hidden email]] On Behalf Of ???
Sent: Tuesday, July 26, 2016 1:35 AM
To:
[hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

 



 



_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

 


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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Re: Error detected in HDF5 (1.10.0) thread 0: /home/hdftest/snapshots-hdf5_1_10_alpha/current/src

Prentice Bisbal
In reply to this post by 674438511

Great news! Thanks for letting us know.

Prentice 
On 07/31/2016 11:14 PM, 于海军 wrote:

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" [hidden email] 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:[hidden email]] On Behalf Of Prentice Bisbal
Sent: Friday, July 29, 2016 9:43 AM
To: [hidden email]
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 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"
[hidden email] 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 [[hidden email]] On Behalf Of ???
Sent: Wednesday, July 27, 2016 2:16 AM
To: HDF Users Discussion List
[hidden email]
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" <
[hidden email]> 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:[hidden email]] On Behalf Of ???
Sent: Tuesday, July 26, 2016 1:35 AM
To:
[hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

 




 




_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

 



_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
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Twitter: https://twitter.com/hdf5
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