HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0

Hdf-forum archives
1

I am building HDF5 version 1.8.14 with Intel compiler version 15. My system is OS X 10.10. My build configuration is:

CC=icc FC=ifort CXX=icpc ./configure --prefix=/somelocation/hdf5_1814 --enable-fortran --enable-fortran2003 --enable-cxx --enable-production --enable-hl --with-zlib=somelocation

The build proceeds correct, but I encounter a problem in the check process. When the check reaches fortranlib_test the test just hangs. When I kill the running process from activity monitor I get an endless sequence of identical message printed to the terminal. The message is:

HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
  #000: H5S.c line 392 in H5Sclose(): not a dataspace
    major: Invalid arguments to routine
    minor: Inappropriate type
h5sclose_f FAILED
file name obtained from the dataset id is incorrect

Any advise on what I should do? Does this issue reflect a problem with the test script or a problem with the compiled library?

Thanks,
Deepak

2

Hi Deepak,

This is a known issue for HDF5 with the Intel 15 compiler. We hope to address it for HDF5 1.8.15. For now, please try the following workaround: use the "-assume nostd_value" compilation flag with fort.

Please let us know if the workaround works for you.

Elena

···

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Jan 19, 2015, at 12:49 PM, Deepak Chandan <chandand@yahoo.com> wrote:

I am building HDF5 version 1.8.14 with Intel compiler version 15. My system is OS X 10.10. My build configuration is:

CC=icc FC=ifort CXX=icpc ./configure --prefix=/somelocation/hdf5_1814 --enable-fortran --enable-fortran2003 --enable-cxx --enable-production --enable-hl --with-zlib=somelocation

The build proceeds correct, but I encounter a problem in the check process. When the check reaches fortranlib_test the test just hangs. When I kill the running process from activity monitor I get an endless sequence of identical message printed to the terminal. The message is:

HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
#000: H5S.c line 392 in H5Sclose(): not a dataspace
   major: Invalid arguments to routine
   minor: Inappropriate type
h5sclose_f FAILED
file name obtained from the dataset id is incorrect

Any advise on what I should do? Does this issue reflect a problem with the test script or a problem with the compiled library?

Thanks,
Deepak
_______________________________________________
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Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

3

Hi Elena,
Thanks for the solution. After reporting the issue I tried to compile while taking out the “—enable-fortran2003” flag. This solved the problem. Since I didn’t need Fortran 2003 anyway everything worked out for me. I do not know whether or not you are aware the taking the flag out resolves the problem.

Cheers,
Deepak

···

On Jan 19, 2015, at 5:48 PM, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Hi Deepak,

This is a known issue for HDF5 with the Intel 15 compiler. We hope to address it for HDF5 1.8.15. For now, please try the following workaround: use the "-assume nostd_value" compilation flag with fort.

Please let us know if the workaround works for you.

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Jan 19, 2015, at 12:49 PM, Deepak Chandan <chandand@yahoo.com> wrote:

I am building HDF5 version 1.8.14 with Intel compiler version 15. My system is OS X 10.10. My build configuration is:

CC=icc FC=ifort CXX=icpc ./configure --prefix=/somelocation/hdf5_1814 --enable-fortran --enable-fortran2003 --enable-cxx --enable-production --enable-hl --with-zlib=somelocation

The build proceeds correct, but I encounter a problem in the check process. When the check reaches fortranlib_test the test just hangs. When I kill the running process from activity monitor I get an endless sequence of identical message printed to the terminal. The message is:

HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
#000: H5S.c line 392 in H5Sclose(): not a dataspace
  major: Invalid arguments to routine
  minor: Inappropriate type
h5sclose_f FAILED
file name obtained from the dataset id is incorrect

Any advise on what I should do? Does this issue reflect a problem with the test script or a problem with the compiled library?

Thanks,
Deepak
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

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

4

Deepak,

Hi Elena,
Thanks for the solution. After reporting the issue I tried to compile while taking out the “—enable-fortran2003” flag. This solved the problem. Since I didn’t need Fortran 2003 anyway everything worked out for me. I do not know whether or not you are aware the taking the flag out resolves the problem.

Yes, we are aware, thank you! We are not compliant with the Fortran2003 standard. Disabling the feature solves the problem :slight_smile:

Elena

···

On Jan 19, 2015, at 4:57 PM, Deepak Chandan <chandand@yahoo.com> wrote:

Cheers,
Deepak

On Jan 19, 2015, at 5:48 PM, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Hi Deepak,

This is a known issue for HDF5 with the Intel 15 compiler. We hope to address it for HDF5 1.8.15. For now, please try the following workaround: use the "-assume nostd_value" compilation flag with fort.

Please let us know if the workaround works for you.

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Jan 19, 2015, at 12:49 PM, Deepak Chandan <chandand@yahoo.com> wrote:

I am building HDF5 version 1.8.14 with Intel compiler version 15. My system is OS X 10.10. My build configuration is:

CC=icc FC=ifort CXX=icpc ./configure --prefix=/somelocation/hdf5_1814 --enable-fortran --enable-fortran2003 --enable-cxx --enable-production --enable-hl --with-zlib=somelocation

The build proceeds correct, but I encounter a problem in the check process. When the check reaches fortranlib_test the test just hangs. When I kill the running process from activity monitor I get an endless sequence of identical message printed to the terminal. The message is:

HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
#000: H5S.c line 392 in H5Sclose(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type
h5sclose_f FAILED
file name obtained from the dataset id is incorrect

Any advise on what I should do? Does this issue reflect a problem with the test script or a problem with the compiled library?

Thanks,
Deepak
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

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

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