HDF5 and Hadoop

Andrew_Nguyen1 · May 6, 2010, 3:39pm

Hello all,

I've been starting to do some research and searches on the web but haven't really found anything. I was wondering if anyone is aware of any existing work on combining Hadoop (and their MapReduce implementation) with HDF5.

Thanks!

--Andrew

Cyril_Giraudon · May 26, 2010, 3:57pm

Hello,

I have a problem with h5tget_size under windows.
The compiler is ifort 11.1 and I use a the latest precompiled version of
HDF5 :
hdf5-1.8.4-patch1-win32-vs2008-iv101-enc

The following little program works under linux (ubuntu 32bit & centos5.4
64bit) but does'nt under windowsXP :

"""
program test

use hdf5

integer :: hdferr
integer(hid_t) :: real_type_id
integer(size_t) :: type_size

print *, "Test starting ..."

call h5open_f(hdferr)

call h5tget_size_f(H5T_NATIVE_REAL, type_size, hdferr)
if (hdferr<0) then
print *, "Get size failed"
endif
print *, "Real's size : ", type_size

print *, "End."

call h5close_f(hdferr)

end program test
"""

Under windows, the program stops with :
"""
Test starting ...
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0:
  #000: ../../../src/H5T.c line 2071 in H5Tget_size(): not a datatype
    major: Invalid arguments to routine
    minor: Inapproriate type
Get size failed.
"""

Do I something wrong ?

Thanks a lot,

Cyril.

epourmal · May 26, 2010, 4:52pm

Cyril,

Your program looks fine. We will need to look into the issue. To my knowledge all tests passed with Intel 10 compiler (and function has been tested :-). I will file a bug report.

Elena

···

On May 26, 2010, at 10:57 AM, Giraudon Cyril wrote:

Hello,

I have a problem with h5tget_size under windows.
The compiler is ifort 11.1 and I use a the latest precompiled version of
HDF5 :
hdf5-1.8.4-patch1-win32-vs2008-iv101-enc

The following little program works under linux (ubuntu 32bit & centos5.4
64bit) but does'nt under windowsXP :

"""
program test

use hdf5

integer :: hdferr
integer(hid_t) :: real_type_id
integer(size_t) :: type_size

print *, "Test starting ..."

call h5open_f(hdferr)

call h5tget_size_f(H5T_NATIVE_REAL, type_size, hdferr)
if (hdferr<0) then
   print *, "Get size failed"
endif
print *, "Real's size : ", type_size

print *, "End."

call h5close_f(hdferr)

end program test
"""

Under windows, the program stops with :
"""
Test starting ...
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0:
#000: ../../../src/H5T.c line 2071 in H5Tget_size(): not a datatype
   major: Invalid arguments to routine
   minor: Inapproriate type
Get size failed.
"""

Do I something wrong ?

Thanks a lot,

Cyril.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

Cyril_Giraudon · May 28, 2010, 8:39am

Elena,

Is there any way to follow the ticket status ?

Thanks a lot,

Cyril.

Le 26/05/2010 18:52, Elena Pourmal a �crit :

···

Cyril,

Your program looks fine. We will need to look into the issue. To my knowledge all tests passed with Intel 10 compiler (and function has been tested :-). I will file a bug report.

Elena

On May 26, 2010, at 10:57 AM, Giraudon Cyril wrote:

Hello,

I have a problem with h5tget_size under windows.
The compiler is ifort 11.1 and I use a the latest precompiled version of
HDF5 :
hdf5-1.8.4-patch1-win32-vs2008-iv101-enc

The following little program works under linux (ubuntu 32bit & centos5.4
64bit) but does'nt under windowsXP :

"""
program test

use hdf5

integer :: hdferr
integer(hid_t) :: real_type_id
integer(size_t) :: type_size

print *, "Test starting ..."

call h5open_f(hdferr)

call h5tget_size_f(H5T_NATIVE_REAL, type_size, hdferr)
if (hdferr<0) then
   print *, "Get size failed"
endif
print *, "Real's size : ", type_size

print *, "End."

call h5close_f(hdferr)

end program test
"""

Under windows, the program stops with :
"""
Test starting ...
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0:
#000: ../../../src/H5T.c line 2071 in H5Tget_size(): not a datatype
   major: Invalid arguments to routine
   minor: Inapproriate type
Get size failed.
"""

Do I something wrong ?

Thanks a lot,

Cyril.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

epourmal · May 31, 2010, 8:35pm

Hi Cyril and All,

We have been thinking about opening our ticket system (read-only), but we are not there yet. We need to finish some clean-up work before we can make it freely accessible by the HDF community.

We will definitely let everyone know when the system is set up for browsing. For now, if your reported a bug, please feel free to contact help@hdfgroup.org for the status of your bug. We also will be very happy to accept any bug fixes along with the appropriate tests (failed before the fix, passed after).

Thank you for your contributions to HDF and for your patience!

Elena

···

On May 28, 2010, at 3:39 AM, Giraudon Cyril wrote:

Elena,

Is there any way to follow the ticket status ?

Thanks a lot,

Cyril.

Le 26/05/2010 18:52, Elena Pourmal a écrit :

Cyril,

Your program looks fine. We will need to look into the issue. To my knowledge all tests passed with Intel 10 compiler (and function has been tested :-). I will file a bug report.

Elena

On May 26, 2010, at 10:57 AM, Giraudon Cyril wrote:

Hello,

I have a problem with h5tget_size under windows.
The compiler is ifort 11.1 and I use a the latest precompiled version of
HDF5 :
hdf5-1.8.4-patch1-win32-vs2008-iv101-enc

The following little program works under linux (ubuntu 32bit & centos5.4
64bit) but does'nt under windowsXP :

"""
program test

use hdf5

integer :: hdferr
integer(hid_t) :: real_type_id
integer(size_t) :: type_size

print *, "Test starting ..."

call h5open_f(hdferr)

call h5tget_size_f(H5T_NATIVE_REAL, type_size, hdferr)
if (hdferr<0) then
  print *, "Get size failed"
endif
print *, "Real's size : ", type_size

print *, "End."

call h5close_f(hdferr)

end program test
"""

Under windows, the program stops with :
"""
Test starting ...
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0:
#000: ../../../src/H5T.c line 2071 in H5Tget_size(): not a datatype
  major: Invalid arguments to routine
  minor: Inapproriate type
Get size failed.
"""

Do I something wrong ?

Thanks a lot,

Cyril.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

Cyril_Giraudon · June 21, 2010, 12:26pm

Hello,

I tries the little test program with the latest release of HDF5 (1.8.5)
and the same H5Tget_size function fails.
The binary package is compiled with ifort 10 and I compile the program
with ifort 11.1.06.

Are binaries, created with ifort 10, 100% compatible with ifort 11 ?

I can't compile HDF5 under windows since i have not Visual Studio 2008,
only the Express Edition with which the CMake 2.8.1 FortranCInterface
seems broken.

Is there any windows binaries compiled with ifort 11.1 that I could try ?

Thank a lot,

Regards,

Cyril.

···

Le 26/05/2010 18:52, Elena Pourmal a �crit :


Cyril,

Your program looks fine. We will need to look into the issue. To my knowledge all tests passed with Intel 10 compiler (and function has been tested :-). I will file a bug report.

Elena

On May 26, 2010, at 10:57 AM, Giraudon Cyril wrote:

Hello,

I have a problem with h5tget_size under windows.
The compiler is ifort 11.1 and I use a the latest precompiled version of
HDF5 :
hdf5-1.8.4-patch1-win32-vs2008-iv101-enc

The following little program works under linux (ubuntu 32bit & centos5.4
64bit) but does'nt under windowsXP :

"""
program test

use hdf5

integer :: hdferr
integer(hid_t) :: real_type_id
integer(size_t) :: type_size

print *, "Test starting ..."

call h5open_f(hdferr)

call h5tget_size_f(H5T_NATIVE_REAL, type_size, hdferr)
if (hdferr<0) then
  print *, "Get size failed"
endif
print *, "Real's size : ", type_size

print *, "End."

call h5close_f(hdferr)

end program test
"""

Under windows, the program stops with :
"""
Test starting ...
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0:
#000: ../../../src/H5T.c line 2071 in H5Tget_size(): not a datatype
  major: Invalid arguments to routine
  minor: Inapproriate type
Get size failed.
"""

Do I something wrong ?

Thanks a lot,

Cyril.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

epourmal · June 21, 2010, 2:00pm

Cyril,

We have binaries packed with CPack (as part of our CMake effort). Do you think you can test it for us?

If so, we will send you a link to the binaries, and if they work, we will post binaries on the Web site.

Thank you!

Elena

···

On Jun 21, 2010, at 7:26 AM, Giraudon Cyril wrote:

Hello,

I tries the little test program with the latest release of HDF5 (1.8.5)
and the same H5Tget_size function fails.
The binary package is compiled with ifort 10 and I compile the program
with ifort 11.1.06.

Are binaries, created with ifort 10, 100% compatible with ifort 11 ?

I can't compile HDF5 under windows since i have not Visual Studio 2008,
only the Express Edition with which the CMake 2.8.1 FortranCInterface
seems broken.

Is there any windows binaries compiled with ifort 11.1 that I could try ?

Thank a lot,

Regards,

Cyril.

Le 26/05/2010 18:52, Elena Pourmal a écrit :

Cyril,

Your program looks fine. We will need to look into the issue. To my knowledge all tests passed with Intel 10 compiler (and function has been tested :-). I will file a bug report.

Elena

On May 26, 2010, at 10:57 AM, Giraudon Cyril wrote:

Hello,

I have a problem with h5tget_size under windows.
The compiler is ifort 11.1 and I use a the latest precompiled version of
HDF5 :
hdf5-1.8.4-patch1-win32-vs2008-iv101-enc

The following little program works under linux (ubuntu 32bit & centos5.4
64bit) but does'nt under windowsXP :

"""
program test

use hdf5

integer :: hdferr
integer(hid_t) :: real_type_id
integer(size_t) :: type_size

print *, "Test starting ..."

call h5open_f(hdferr)

call h5tget_size_f(H5T_NATIVE_REAL, type_size, hdferr)
if (hdferr<0) then
print *, "Get size failed"
endif
print *, "Real's size : ", type_size

print *, "End."

call h5close_f(hdferr)

end program test
"""

Under windows, the program stops with :
"""
Test starting ...
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0:
#000: ../../../src/H5T.c line 2071 in H5Tget_size(): not a datatype
major: Invalid arguments to routine
minor: Inapproriate type
Get size failed.
"""

Do I something wrong ?

Thanks a lot,

Cyril.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

Cyril_Giraudon · June 21, 2010, 2:12pm

Elena,

Yes yes with a link toward ifort 11.1 binaries I will do the test.

Regards,

Cyril.

Le 21/06/2010 16:00, Elena Pourmal a �crit :

···

Cyril,

We have binaries packed with CPack (as part of our CMake effort). Do you think you can test it for us?

If so, we will send you a link to the binaries, and if they work, we will post binaries on the Web site.

Thank you!

Elena
On Jun 21, 2010, at 7:26 AM, Giraudon Cyril wrote:

Hello,

I tries the little test program with the latest release of HDF5 (1.8.5)
and the same H5Tget_size function fails.
The binary package is compiled with ifort 10 and I compile the program
with ifort 11.1.06.

Are binaries, created with ifort 10, 100% compatible with ifort 11 ?

I can't compile HDF5 under windows since i have not Visual Studio 2008,
only the Express Edition with which the CMake 2.8.1 FortranCInterface
seems broken.

Is there any windows binaries compiled with ifort 11.1 that I could try ?

Thank a lot,

Regards,

Cyril.

Le 26/05/2010 18:52, Elena Pourmal a �crit :

Cyril,

Your program looks fine. We will need to look into the issue. To my knowledge all tests passed with Intel 10 compiler (and function has been tested :-). I will file a bug report.

Elena

On May 26, 2010, at 10:57 AM, Giraudon Cyril wrote:

Hello,

I have a problem with h5tget_size under windows.
The compiler is ifort 11.1 and I use a the latest precompiled version of
HDF5 :
hdf5-1.8.4-patch1-win32-vs2008-iv101-enc

The following little program works under linux (ubuntu 32bit & centos5.4
64bit) but does'nt under windowsXP :

"""
program test

use hdf5

integer :: hdferr
integer(hid_t) :: real_type_id
integer(size_t) :: type_size

print *, "Test starting ..."

call h5open_f(hdferr)

call h5tget_size_f(H5T_NATIVE_REAL, type_size, hdferr)
if (hdferr<0) then
print *, "Get size failed"
endif
print *, "Real's size : ", type_size

print *, "End."

call h5close_f(hdferr)

end program test
"""

Under windows, the program stops with :
"""
Test starting ...
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0:
#000: ../../../src/H5T.c line 2071 in H5Tget_size(): not a datatype
major: Invalid arguments to routine
minor: Inapproriate type
Get size failed.
"""

Do I something wrong ?

Thanks a lot,

Cyril.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

Cyril_Giraudon · June 23, 2010, 4:39pm

Hello,

I've tested the program against the latest binary release (downloaded today)

When I link the program against dll/lib libraries contained in
HDF5-1.8.5-win32/dll, the test fails.
When I link the program agains libraries contained in
HDF5-1.8.5-win32/lib, I have to add the following options to the linker :

- NODEFAULTLIB:MSVCRT.lib
- NODEFAULTLIB:libifcoremt.lib

but the test passes.

Hope this helps.

Best regards,

Cyril.

Le 21/06/2010 16:12, Giraudon Cyril a �crit :

···

Elena,

Yes yes with a link toward ifort 11.1 binaries I will do the test.

Regards,

Cyril.

Le 21/06/2010 16:00, Elena Pourmal a �crit :


Cyril,

We have binaries packed with CPack (as part of our CMake effort). Do you think you can test it for us?

If so, we will send you a link to the binaries, and if they work, we will post binaries on the Web site.

Thank you!

Elena
On Jun 21, 2010, at 7:26 AM, Giraudon Cyril wrote:

Hello,

I tries the little test program with the latest release of HDF5 (1.8.5)
and the same H5Tget_size function fails.
The binary package is compiled with ifort 10 and I compile the program
with ifort 11.1.06.

Are binaries, created with ifort 10, 100% compatible with ifort 11 ?

I can't compile HDF5 under windows since i have not Visual Studio 2008,
only the Express Edition with which the CMake 2.8.1 FortranCInterface
seems broken.

Is there any windows binaries compiled with ifort 11.1 that I could try ?

Thank a lot,

Regards,

Cyril.

Le 26/05/2010 18:52, Elena Pourmal a �crit :

Cyril,

Your program looks fine. We will need to look into the issue. To my knowledge all tests passed with Intel 10 compiler (and function has been tested :-). I will file a bug report.

Elena

On May 26, 2010, at 10:57 AM, Giraudon Cyril wrote:

Hello,

I have a problem with h5tget_size under windows.
The compiler is ifort 11.1 and I use a the latest precompiled version of
HDF5 :
hdf5-1.8.4-patch1-win32-vs2008-iv101-enc

The following little program works under linux (ubuntu 32bit & centos5.4
64bit) but does'nt under windowsXP :

"""
program test

use hdf5

integer :: hdferr
integer(hid_t) :: real_type_id
integer(size_t) :: type_size

print *, "Test starting ..."

call h5open_f(hdferr)

call h5tget_size_f(H5T_NATIVE_REAL, type_size, hdferr)
if (hdferr<0) then
print *, "Get size failed"
endif
print *, "Real's size : ", type_size

print *, "End."

call h5close_f(hdferr)

end program test
"""

Under windows, the program stops with :
"""
Test starting ...
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0:
#000: ../../../src/H5T.c line 2071 in H5Tget_size(): not a datatype
major: Invalid arguments to routine
minor: Inapproriate type
Get size failed.
"""

Do I something wrong ?

Thanks a lot,

Cyril.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org


_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

epourmal · June 23, 2010, 11:10pm

Hi Cyril,

Do you mean binaries from http://www.hdfgroup.org/HDF5/release/obtain5.html ?

If yes, could you please send the errors you got and did you use Vista or XP?

Thank you!

Elena

···

On Jun 23, 2010, at 11:39 AM, Giraudon Cyril wrote:

Hello,

I've tested the program against the latest binary release (downloaded today)

When I link the program against dll/lib libraries contained in
HDF5-1.8.5-win32/dll, the test fails.
When I link the program agains libraries contained in
HDF5-1.8.5-win32/lib, I have to add the following options to the linker :

- NODEFAULTLIB:MSVCRT.lib
- NODEFAULTLIB:libifcoremt.lib

but the test passes.

Hope this helps.

Best regards,

Cyril.

Le 21/06/2010 16:12, Giraudon Cyril a écrit :

Elena,

Yes yes with a link toward ifort 11.1 binaries I will do the test.

Regards,

Cyril.

Le 21/06/2010 16:00, Elena Pourmal a écrit :

Cyril,

We have binaries packed with CPack (as part of our CMake effort). Do you think you can test it for us?

If so, we will send you a link to the binaries, and if they work, we will post binaries on the Web site.

Thank you!

Elena
On Jun 21, 2010, at 7:26 AM, Giraudon Cyril wrote:

Hello,

I tries the little test program with the latest release of HDF5 (1.8.5)
and the same H5Tget_size function fails.
The binary package is compiled with ifort 10 and I compile the program
with ifort 11.1.06.

Are binaries, created with ifort 10, 100% compatible with ifort 11 ?

I can't compile HDF5 under windows since i have not Visual Studio 2008,
only the Express Edition with which the CMake 2.8.1 FortranCInterface
seems broken.

Is there any windows binaries compiled with ifort 11.1 that I could try ?

Thank a lot,

Regards,

Cyril.

Le 26/05/2010 18:52, Elena Pourmal a écrit :

Cyril,

Your program looks fine. We will need to look into the issue. To my knowledge all tests passed with Intel 10 compiler (and function has been tested :-). I will file a bug report.

Elena

On May 26, 2010, at 10:57 AM, Giraudon Cyril wrote:

Hello,

I have a problem with h5tget_size under windows.
The compiler is ifort 11.1 and I use a the latest precompiled version of
HDF5 :
hdf5-1.8.4-patch1-win32-vs2008-iv101-enc

The following little program works under linux (ubuntu 32bit & centos5.4
64bit) but does'nt under windowsXP :

"""
program test

use hdf5

integer :: hdferr
integer(hid_t) :: real_type_id
integer(size_t) :: type_size

print *, "Test starting ..."

call h5open_f(hdferr)

call h5tget_size_f(H5T_NATIVE_REAL, type_size, hdferr)
if (hdferr<0) then
print *, "Get size failed"
endif
print *, "Real's size : ", type_size

print *, "End."

call h5close_f(hdferr)

end program test
"""

Under windows, the program stops with :
"""
Test starting ...
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0:
#000: ../../../src/H5T.c line 2071 in H5Tget_size(): not a datatype
major: Invalid arguments to routine
minor: Inapproriate type
Get size failed.
"""

Do I something wrong ?

Thanks a lot,

Cyril.

_______________________________________________
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Cyril_Giraudon · June 25, 2010, 10:48am

Hi,

I make the test again today 2010 06 23, 10h paris
I use windows XP 32bits
My system is updated regularly and automatically.
Ifort 11.1 under VS 2008
CMake 2.8.1

As for the static libraries use :
Only NODEFAULTLIB:msvcrt.lib is necessary to link against HDF5-1.8.5-win32/lib librairies.
ifort output is :

···

####################################################
......
zlib.lib(zutil.obj):warning : locally defined symbol __imp__malloc imported

zlib.lib(zutil.obj):warning : locally defined symbol __imp__free imported

LINK : test.exe non trouv� ou non g�n�r� par la derni�re �dition de liens incr�mentielle ; �dition de liens compl�te en cours

LINK : warning LNK4068: /MACHINE non sp�cifi� ; X86 pris par d�faut

zlib.lib(zutil.obj) : warning LNK4217: symbole d�fini localement _malloc import� dans la fonction _zcalloc

libszip.lib(sz_api.obj) : warning LNK4049: symbole d�fini localement _malloc import�

libszip.lib(rice.obj) : warning LNK4217: symbole d�fini localement _malloc import� dans la fonction _fix_last_scanline

zlib.lib(zutil.obj) : warning LNK4217: symbole d�fini localement _free import� dans la fonction _zcfree

libszip.lib(sz_api.obj) : warning LNK4049: symbole d�fini localement _free import�

libszip.lib(rice.obj) : warning LNK4217: symbole d�fini localement _free import� dans la fonction _encode_scanline
.......
######################################################

Albeit ifort output is (without NODEFAULTLIB:MSVCDT.lib) :

############################################################
"C:\Program Files\CMake 2.8\bin\cmake.exe" -HC:\xxx\yyy\zzz\src -BC:\xxx\yyy\zzz\build --check-build-system CMakeFiles\Makefile.cmake 0
"C:\Program Files\CMake 2.8\bin\cmake.exe" -E cmake_progress_start C:\xxx\yyy\zzz\build\CMakeFiles C:\xxx\yyy\zzz\build\CMakeFiles\progress.marks
C:/dev/programs/MinGW/bin/mingw32-make -f CMakeFiles\Makefile2 all
mingw32-make[1]: Entering directory `C:/dev/projects/test_ifort_hdf5/build'
C:/dev/programs/MinGW/bin/mingw32-make -f CMakeFiles\test.dir\build.make CMakeFiles/test.dir/depend
mingw32-make[2]: Entering directory `C:/dev/projects/test_ifort_hdf5/build'
"C:\Program Files\CMake 2.8\bin\cmake.exe" -E cmake_depends "MinGW Makefiles" C:\xxx\yyy\zzz\src C:\xxx\yyy\zzz\src C:\xxx\yyy\zzz\build C:\xxx\yyy\zzz\build C:\xxx\yyy\zzz\build\CMakeFiles\test.dir\DependInfo.cmake --color=
mingw32-make[2]: Leaving directory `C:/dev/projects/test_ifort_hdf5/build'
C:/dev/programs/MinGW/bin/mingw32-make -f CMakeFiles\test.dir\build.make CMakeFiles/test.dir/requires
mingw32-make[2]: Entering directory `C:/dev/projects/test_ifort_hdf5/build'
mingw32-make[2]: Nothing to be done for `CMakeFiles/test.dir/requires'.
mingw32-make[2]: Leaving directory `C:/dev/projects/test_ifort_hdf5/build'
C:/dev/programs/MinGW/bin/mingw32-make -f CMakeFiles\test.dir\build.make CMakeFiles/test.dir/build
mingw32-make[2]: Entering directory `C:/dev/projects/test_ifort_hdf5/build'
"C:\Program Files\CMake 2.8\bin\cmake.exe" -E cmake_progress_report C:\xxx\yyy\zzz\build\CMakeFiles 1
[100%] Building Fortran object CMakeFiles/test.dir/test.f90.obj
C:\PROGRA~1\Intel\Compiler\11.1\060\bin\ia32\ifort.exe /fpp /FoCMakeFiles\test.dir\test.f90.obj /W1 /nologo /fpp /libs:dll /threads /O1 /D NDEBUG -IC:\aaa\bbb\HDF5-1.8.5-win32\mods -c C:\xxx\yyy\zzz\src\test.f90
Linking Fortran executable test.exe
"C:\Program Files\CMake 2.8\bin\cmake.exe" -E cmake_link_script CMakeFiles\test.dir\link.txt --verbose=1
"C:\Program Files\CMake 2.8\bin\cmake.exe" -E vs_link_exe C:\PROGRA~1\Intel\Compiler\11.1\060\bin\ia32\ifort.exe @CMakeFiles\test.dir\objects1.rsp /W1 /nologo /fpp /libs:dll /threads /O1 /D NDEBUG /Fetest.exe -link /implib:libtest.dll.a /INCREMENTAL:YES /subsystem:console C:\aaa\bbb\HDF5-1.8.5-win32\lib\hdf5.lib C:\aaa\bbb\HDF5-1.8.5-win32\lib\hdf5_fortran.lib C:\aaa\bbb\HDF5-1.8.5-win32\lib\hdf5_f90cstub.lib C:\aaa\bbb\HDF5-1.8.5-win32\lib\zlib.lib C:\aaa\bbb\HDF5-1.8.5-win32\lib\libszip.lib user32.lib
LINK : test.exe non trouv� ou non g�n�r� par la derni�re �dition de liens incr�mentielle ; �dition de liens compl�te en cours

LINK : warning LNK4068: /MACHINE non sp�cifi� ; X86 pris par d�faut

libifcoremt.lib(for_reentrancy.obj) : error LNK2005: _for_set_reentrancy d�j� d�fini(e) dans libifcoremd.lib(libifcoremd.dll)

LIBCMT.lib(crt0dat.obj) : error LNK2005: __amsg_exit d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(crt0dat.obj) : error LNK2005: __initterm_e d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(crt0dat.obj) : error LNK2005: _exit d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(crt0dat.obj) : error LNK2005: __exit d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(crt0dat.obj) : error LNK2005: __cexit d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(_ctype.obj) : error LNK2005: _isgraph d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(invarg.obj) : error LNK2005: __invoke_watson d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(tidtable.obj) : error LNK2005: __encode_pointer d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(tidtable.obj) : error LNK2005: __decode_pointer d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(winxfltr.obj) : error LNK2005: __XcptFilter d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(crt0init.obj) : error LNK2005: ___xi_a d�j� d�fini(e) dans MSVCRT.lib(cinitexe.obj)

LIBCMT.lib(crt0init.obj) : error LNK2005: ___xi_z d�j� d�fini(e) dans MSVCRT.lib(cinitexe.obj)

LIBCMT.lib(crt0init.obj) : error LNK2005: ___xc_a d�j� d�fini(e) dans MSVCRT.lib(cinitexe.obj)

LIBCMT.lib(crt0init.obj) : error LNK2005: ___xc_z d�j� d�fini(e) dans MSVCRT.lib(cinitexe.obj)

LIBCMT.lib(hooks.obj) : error LNK2005: "void __cdecl terminate(void)" (?terminate@@YAXXZ) d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(setlocal.obj) : error LNK2005: __configthreadlocale d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(crt0.obj) : error LNK2005: _mainCRTStartup d�j� d�fini(e) dans MSVCRT.lib(crtexe.obj)

LIBCMT.lib(mlock.obj) : error LNK2005: __unlock d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(mlock.obj) : error LNK2005: __lock d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LIBCMT.lib(errmode.obj) : error LNK2005: ___set_app_type d�j� d�fini(e) dans MSVCRT.lib(MSVCR90.dll)

LINK : warning LNK4098: conflit entre la biblioth�que par d�faut 'MSVCRT' et les autres biblioth�ques ; utilisez /NODEFAULTLIB:library

LINK : warning LNK4098: conflit entre la biblioth�que par d�faut 'LIBCMT' et les autres biblioth�ques ; utilisez /NODEFAULTLIB:library

test.exe : fatal error LNK1169: un ou plusieurs symboles d�finis � diff�rentes reprises ont �t� rencontr�s

LINK Pass 1 failed. with 1169
mingw32-make[2]: Leaving directory `C:/dev/projects/test_ifort_hdf5/build'
mingw32-make[1]: Leaving directory `C:/dev/projects/test_ifort_hdf5/build'
#####################################################"""

With the dynamic library, the test wites :
HDF5-DIAG: Error detected in HDF5 (1.8.5) thread 0:
   #000: ..\..\..\src\H5T.c line 2102 in H5Tget_size(): not a datatype
     major: Invalid arguments to routine
     minor: Inappropriate type

With static library, the test write :
  Starting tests ...
  Real's size : 4
  End.

In addition, some hacks were necessary to link against the new hdf5_f90cstub.lib.

Test Program CMakeLists.txt
###########################################################
cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
enable_language(Fortran)

PROJECT(test)

SET(HDF5_MODULE_DIR /usr CACHE PATH "Path to HDF5 fortran modules library")
SET(SZIP_LIB /usr CACHE PATH "Path to SZIP library")

FIND_PACKAGE(ZLIB REQUIRED)
FIND_PACKAGE(HDF5 REQUIRED)

INCLUDE_DIRECTORIES(${HDF5_MODULE_DIR})

ADD_EXECUTABLE(test test.f90)
TARGET_LINK_LIBRARIES(test ${HDF5_hdf5_LIBRARY} ${HDF5_hdf5_fortran_LIBRARY}
${HDF5_LIB_DIR}/hdf5_f90cstub.lib ${ZLIB_LIBRARY}
${SZIP_LIB}/libszip.lib)

MESSAGE( STATUS "C library : ${HDF5_hdf5_LIBRARY}" )
MESSAGE( STATUS "C includes : ${HDF5_INCLUDE_DIRS}")
MESSAGE( STATUS "Fortran modules : ${HDF5_MODULE_DIR}" )
MESSAGE( STATUS "Fortran library : ${HDF5_hdf5_fortran_LIBRARY}" )
MESSAGE( STATUS "Fortran stub library : ${HDF5_LIB_DIR}/hdf5_f90cstub.lib" )
###########################################################

Best regards,

Cyril.

Le 24/06/2010 01:10, Elena Pourmal a �crit :

Hi Cyril,

Do you mean binaries from http://www.hdfgroup.org/HDF5/release/obtain5.html ?

If yes, could you please send the errors you got and did you use Vista or XP?

Thank you!

Elena
On Jun 23, 2010, at 11:39 AM, Giraudon Cyril wrote:

Hello,

I've tested the program against the latest binary release (downloaded today)

When I link the program against dll/lib libraries contained in
HDF5-1.8.5-win32/dll, the test fails.
When I link the program agains libraries contained in
HDF5-1.8.5-win32/lib, I have to add the following options to the linker :

- NODEFAULTLIB:MSVCRT.lib
- NODEFAULTLIB:libifcoremt.lib

but the test passes.

Hope this helps.

Best regards,

Cyril.

Le 21/06/2010 16:12, Giraudon Cyril a �crit :

Elena,

Yes yes with a link toward ifort 11.1 binaries I will do the test.

Regards,

Cyril.

Le 21/06/2010 16:00, Elena Pourmal a �crit :

Cyril,

We have binaries packed with CPack (as part of our CMake effort). Do you think you can test it for us?

If so, we will send you a link to the binaries, and if they work, we will post binaries on the Web site.

Thank you!

Elena
On Jun 21, 2010, at 7:26 AM, Giraudon Cyril wrote:

Hello,

I tries the little test program with the latest release of HDF5 (1.8.5)
and the same H5Tget_size function fails.
The binary package is compiled with ifort 10 and I compile the program
with ifort 11.1.06.

Are binaries, created with ifort 10, 100% compatible with ifort 11 ?

I can't compile HDF5 under windows since i have not Visual Studio 2008,
only the Express Edition with which the CMake 2.8.1 FortranCInterface
seems broken.

Is there any windows binaries compiled with ifort 11.1 that I could try ?

Thank a lot,

Regards,

Cyril.

Le 26/05/2010 18:52, Elena Pourmal a �crit :

Cyril,

Your program looks fine. We will need to look into the issue. To my knowledge all tests passed with Intel 10 compiler (and function has been tested :-). I will file a bug report.

Elena

On May 26, 2010, at 10:57 AM, Giraudon Cyril wrote:

Hello,

I have a problem with h5tget_size under windows.
The compiler is ifort 11.1 and I use a the latest precompiled version of
HDF5 :
hdf5-1.8.4-patch1-win32-vs2008-iv101-enc

The following little program works under linux (ubuntu 32bit& centos5.4
64bit) but does'nt under windowsXP :

"""
program test

use hdf5

integer :: hdferr
integer(hid_t) :: real_type_id
integer(size_t) :: type_size

print *, "Test starting ..."

call h5open_f(hdferr)

call h5tget_size_f(H5T_NATIVE_REAL, type_size, hdferr)
if (hdferr<0) then
print *, "Get size failed"
endif
print *, "Real's size : ", type_size

print *, "End."

call h5close_f(hdferr)

end program test
"""

Under windows, the program stops with :
"""
Test starting ...
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0:
#000: ../../../src/H5T.c line 2071 in H5Tget_size(): not a datatype
major: Invalid arguments to routine
minor: Inapproriate type
Get size failed.
"""

Do I something wrong ?

Thanks a lot,

Cyril.

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Cyril_Giraudon · July 5, 2010, 2:29pm

Hello,

Just a little question : is there any way to create scalar attributes
with hdfview ?

Thanks a lot,

Best regards,

Cyril.

Peter_Cao · July 7, 2010, 2:27pm

You can create an attribute with a single value in HDFView but it will treat the value as single
point of 1D not scalar.

Thanks
--pc

Giraudon Cyril wrote:

···

Hello,

Just a little question : is there any way to create scalar attributes
with hdfview ?

Thanks a lot,

Best regards,

Cyril.

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