Libraries compiled wrong on site?

Hdf-forum archives
1

When I download this, http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-x86_64/hdf5-1.8.7-linux-x86_64-shared.tar.gz

The lib directory contains files that are not recognized by my compiler. Normally objects say (GNU/Linux) when I "file" them; these say "SYSV".

$ uname -a
Linux gemini02 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 x86_64 x86_64 x86_64 GNU/Linux

$ file *
libhdf5.a: current ar archive
libhdf5.la: ASCII English text
libhdf5.settings: ASCII text, with very long lines
libhdf5.so: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_cpp.a: current ar archive
libhdf5_cpp.la: ASCII English text
libhdf5_cpp.so: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_fortran.a: current ar archive
libhdf5_fortran.la: ASCII English text
libhdf5_fortran.so: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl.a: current ar archive
libhdf5_hl.la: ASCII English text
libhdf5_hl.so: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl_cpp.a: current ar archive
libhdf5_hl_cpp.la: ASCII English text, with very long lines
libhdf5_hl_cpp.so: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5hl_fortran.a: current ar archive
libhdf5hl_fortran.la: ASCII English text, with very long lines
libhdf5hl_fortran.so: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libsz.so: symbolic link to `libsz.so.2.0.0'
libsz.so.2: symbolic link to `libsz.so.2.0.0'
libsz.so.2.0.0: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libz.so: symbolic link to `libz.so.1.2.5'
libz.so.1: symbolic link to `libz.so.1.2.5'
libz.so.1.2.5: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

David McCloskey
Lead Programmer Analyst
Software Development
Core Engineering
Nuclear Fuel

Westinghouse Electric Company
Cranberry Headquarters, Building 4
1000 Westinghouse Drive
Suite 451
Cranberry, PA, 16066, USA
Phone: +1 (412) 374-3789
Fax: +1 (724) 720-0853
Email: mcclosdl@westinghouse.com
Home Page: www.westinghousenuclear.com

2

Hello,

Are you using the C library or another one (then, the compiler matters more precisely).
Also, does your system provides hdf5 as a package ? It may be easier.
Finally, can you copy the terminal session showing the error ?

Regards,

Pierre

···

Le 8 août 11 à 11:01, McCloskey, David L. a écrit :

When I download this, http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-x86_64/hdf5-1.8.7-linux-x86_64-shared.tar.gz

The lib directory contains files that are not recognized by my compiler. Normally objects say (GNU/Linux) when I “file” them; these say “SYSV”.

$ uname -a

Linux gemini02 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 x86_64 x86_64 x86_64 GNU/Linux

$ file *

libhdf5.a: current ar archive

libhdf5.la: ASCII English text

libhdf5.settings: ASCII text, with very long lines

libhdf5.so: symbolic link to `libhdf5.so.7.0.1'

libhdf5.so.7: symbolic link to `libhdf5.so.7.0.1'

libhdf5.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

libhdf5_cpp.a: current ar archive

libhdf5_cpp.la: ASCII English text

libhdf5_cpp.so: symbolic link to `libhdf5_cpp.so.7.0.1'

libhdf5_cpp.so.7: symbolic link to `libhdf5_cpp.so.7.0.1'

libhdf5_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

libhdf5_fortran.a: current ar archive

libhdf5_fortran.la: ASCII English text

libhdf5_fortran.so: symbolic link to `libhdf5_fortran.so.7.0.1'

libhdf5_fortran.so.7: symbolic link to `libhdf5_fortran.so.7.0.1'

libhdf5_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

libhdf5_hl.a: current ar archive

libhdf5_hl.la: ASCII English text

libhdf5_hl.so: symbolic link to `libhdf5_hl.so.7.0.1'

libhdf5_hl.so.7: symbolic link to `libhdf5_hl.so.7.0.1'

libhdf5_hl.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

libhdf5_hl_cpp.a: current ar archive

libhdf5_hl_cpp.la: ASCII English text, with very long lines

libhdf5_hl_cpp.so: symbolic link to `libhdf5_hl_cpp.so.7.0.1'

libhdf5_hl_cpp.so.7: symbolic link to `libhdf5_hl_cpp.so.7.0.1'

libhdf5_hl_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

libhdf5hl_fortran.a: current ar archive

libhdf5hl_fortran.la: ASCII English text, with very long lines

libhdf5hl_fortran.so: symbolic link to `libhdf5hl_fortran.so.7.0.1'

libhdf5hl_fortran.so.7: symbolic link to `libhdf5hl_fortran.so.7.0.1'

libhdf5hl_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

libsz.so: symbolic link to `libsz.so.2.0.0'

libsz.so.2: symbolic link to `libsz.so.2.0.0'

libsz.so.2.0.0: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

libz.so: symbolic link to `libz.so.1.2.5'

libz.so.1: symbolic link to `libz.so.1.2.5'

libz.so.1.2.5: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

David McCloskey

Lead Programmer Analyst

Software Development

Core Engineering

Nuclear Fuel

Westinghouse Electric Company

Cranberry Headquarters, Building 4

1000 Westinghouse Drive

Suite 451

Cranberry, PA, 16066, USA

Phone: +1 (412) 374-3789

Fax: +1 (724) 720-0853

Email: mcclosdl@westinghouse.com

Home Page: www.westinghousenuclear.com

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

-----------------------------------------------------------
Pierre de Buyl
Chemical Physics Theory Group - University of Toronto
Physique des Systèmes Complexes et Mécanique Statistique - Université Libre de Bruxelles
web: http://homepages.ulb.ac.be/~pdebuyl/
Tel: +1-416-946-0047
-----------------------------------------------------------

3

This is a C++ library. I use both C and C libraries (as you can see), using Intel compiler.

/usr/local/products/intel/Compiler/11.1/069/bin/intel64/icpc -o libcorestore.so -g -shared -Wl,-soname,libcorestore.120.so -L/vobs/wec/lib/SLES10 -L/opt/wec/lib -L/users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib -L/usr/local/products/intel/Compiler/11.1/069/lib/intel64 [all my .o files] -lxml2 -lcrypto -lhdf5 -lhdf5_cpp -lifcore -openmp
/users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib/libhdf5.so: file not recognized: File format not recognized

However, even outside of compiling, I can get errors. For example:

$ objdump -f libhdf5.so.7.0.1
objdump: libhdf5.so.7.0.1: File format not recognized

David McCloskey
(412) 374-3789

···

From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of Pierre de Buyl
Sent: Monday, August 08, 2011 12:19 PM
To: HDF Users Discussion List
Cc: McDonald, Stuart M.
Subject: Re: [Hdf-forum] Libraries compiled wrong on site?

Hello,

Are you using the C library or another one (then, the compiler matters more precisely).
Also, does your system provides hdf5 as a package ? It may be easier.
Finally, can you copy the terminal session showing the error ?

Regards,

Pierre

Le 8 août 11 à 11:01, McCloskey, David L. a écrit :

When I download this, http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-x86_64/hdf5-1.8.7-linux-x86_64-shared.tar.gz

The lib directory contains files that are not recognized by my compiler. Normally objects say (GNU/Linux) when I "file" them; these say "SYSV".

$ uname -a
Linux gemini02 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 x86_64 x86_64 x86_64 GNU/Linux

$ file *
libhdf5.a: current ar archive
libhdf5.la: ASCII English text
libhdf5.settings: ASCII text, with very long lines
libhdf5.so: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_cpp.a: current ar archive
libhdf5_cpp.la: ASCII English text
libhdf5_cpp.so: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_fortran.a: current ar archive
libhdf5_fortran.la: ASCII English text
libhdf5_fortran.so: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl.a: current ar archive
libhdf5_hl.la: ASCII English text
libhdf5_hl.so: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl_cpp.a: current ar archive
libhdf5_hl_cpp.la: ASCII English text, with very long lines
libhdf5_hl_cpp.so: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5hl_fortran.a: current ar archive
libhdf5hl_fortran.la: ASCII English text, with very long lines
libhdf5hl_fortran.so: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libsz.so: symbolic link to `libsz.so.2.0.0'
libsz.so.2: symbolic link to `libsz.so.2.0.0'
libsz.so.2.0.0: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libz.so: symbolic link to `libz.so.1.2.5'
libz.so.1: symbolic link to `libz.so.1.2.5'
libz.so.1.2.5: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

David McCloskey
Lead Programmer Analyst
Software Development
Core Engineering
Nuclear Fuel

Westinghouse Electric Company
Cranberry Headquarters, Building 4
1000 Westinghouse Drive
Suite 451
Cranberry, PA, 16066, USA
Phone: +1 (412) 374-3789
Fax: +1 (724) 720-0853
Email: mcclosdl@westinghouse.com<mailto:mcclosdl@westinghouse.com>
Home Page: www.westinghousenuclear.com

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

-----------------------------------------------------------
Pierre de Buyl
Chemical Physics Theory Group - University of Toronto
Physique des Systèmes Complexes et Mécanique Statistique - Université Libre de Bruxelles
web: http://homepages.ulb.ac.be/~pdebuyl/
Tel: +1-416-946-0047
-----------------------------------------------------------

4

I just compiled it on my system using the default compilers (gcc/g++). Objdump works. Also, my software links and builds and runs normally. Has anyone verified that the build on the web site works?

See my attached hdf5.settings to see how similar our builds are on paper.

David McCloskey
(412) 374-3789

libhdf5.settings (3.01 KB)

···

From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of McCloskey, David L.
Sent: Monday, August 08, 2011 1:27 PM
To: HDF Users Discussion List
Cc: McDonald, Stuart M.
Subject: Re: [Hdf-forum] Libraries compiled wrong on site?

This is a C++ library. I use both C and C libraries (as you can see), using Intel compiler.

/usr/local/products/intel/Compiler/11.1/069/bin/intel64/icpc -o libcorestore.so -g -shared -Wl,-soname,libcorestore.120.so -L/vobs/wec/lib/SLES10 -L/opt/wec/lib -L/users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib -L/usr/local/products/intel/Compiler/11.1/069/lib/intel64 [all my .o files] -lxml2 -lcrypto -lhdf5 -lhdf5_cpp -lifcore -openmp
/users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib/libhdf5.so: file not recognized: File format not recognized

However, even outside of compiling, I can get errors. For example:

$ objdump -f libhdf5.so.7.0.1
objdump: libhdf5.so.7.0.1: File format not recognized

David McCloskey
(412) 374-3789

From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of Pierre de Buyl
Sent: Monday, August 08, 2011 12:19 PM
To: HDF Users Discussion List
Cc: McDonald, Stuart M.
Subject: Re: [Hdf-forum] Libraries compiled wrong on site?

Hello,

Are you using the C library or another one (then, the compiler matters more precisely).
Also, does your system provides hdf5 as a package ? It may be easier.
Finally, can you copy the terminal session showing the error ?

Regards,

Pierre

Le 8 août 11 à 11:01, McCloskey, David L. a écrit :

When I download this, http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-x86_64/hdf5-1.8.7-linux-x86_64-shared.tar.gz

The lib directory contains files that are not recognized by my compiler. Normally objects say (GNU/Linux) when I "file" them; these say "SYSV".

$ uname -a
Linux gemini02 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 x86_64 x86_64 x86_64 GNU/Linux

$ file *
libhdf5.a: current ar archive
libhdf5.la: ASCII English text
libhdf5.settings: ASCII text, with very long lines
libhdf5.so: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_cpp.a: current ar archive
libhdf5_cpp.la: ASCII English text
libhdf5_cpp.so: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_fortran.a: current ar archive
libhdf5_fortran.la: ASCII English text
libhdf5_fortran.so: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl.a: current ar archive
libhdf5_hl.la: ASCII English text
libhdf5_hl.so: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl_cpp.a: current ar archive
libhdf5_hl_cpp.la: ASCII English text, with very long lines
libhdf5_hl_cpp.so: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5hl_fortran.a: current ar archive
libhdf5hl_fortran.la: ASCII English text, with very long lines
libhdf5hl_fortran.so: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libsz.so: symbolic link to `libsz.so.2.0.0'
libsz.so.2: symbolic link to `libsz.so.2.0.0'
libsz.so.2.0.0: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libz.so: symbolic link to `libz.so.1.2.5'
libz.so.1: symbolic link to `libz.so.1.2.5'
libz.so.1.2.5: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

David McCloskey
Lead Programmer Analyst
Software Development
Core Engineering
Nuclear Fuel

Westinghouse Electric Company
Cranberry Headquarters, Building 4
1000 Westinghouse Drive
Suite 451
Cranberry, PA, 16066, USA
Phone: +1 (412) 374-3789
Fax: +1 (724) 720-0853
Email: mcclosdl@westinghouse.com<mailto:mcclosdl@westinghouse.com>
Home Page: www.westinghousenuclear.com

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

-----------------------------------------------------------
Pierre de Buyl
Chemical Physics Theory Group - University of Toronto
Physique des Systèmes Complexes et Mécanique Statistique - Université Libre de Bruxelles
web: http://homepages.ulb.ac.be/~pdebuyl/
Tel: +1-416-946-0047
-----------------------------------------------------------

5

David,

I just compiled it on my system using the default compilers (gcc/g++). Objdump works. Also, my software links and builds and runs normally. Has anyone verified that the build on the web site works?

I just did. I downloaded the source from ftp, unpacked, then changed h5c++ to use intel icpc and compiled one of the C++ examples. Worked fine with both static and shared libraries.

Have you tried h5c++ (as is) to run create.cpp example (found under share/hdf5_examples/c++) just to check if distribution works on your machine?

Here is the output of objdump
[epourmal@koala lib]$ pwd
/mnt/scr1/epourmal/_tmp_forum/hdf5-1.8.7-linux-x86_64-shared/lib
[epourmal@koala lib]$ objdump -f libhdf5.so.7.0.1

libhdf5.so.7.0.1: file format elf64-x86-64
architecture: i386:x86-64, flags 0x00000150:
HAS_SYMS, DYNAMIC, D_PAGED
start address 0x0000000000034da0
Of course, I am on the same machine where binaries were built, that is why everything works for me :wink:

Thanks,

Elena

···

On Aug 8, 2011, at 12:42 PM, McCloskey, David L. wrote:

See my attached hdf5.settings to see how similar our builds are on paper.

David McCloskey
(412) 374-3789

From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of McCloskey, David L.
Sent: Monday, August 08, 2011 1:27 PM
To: HDF Users Discussion List
Cc: McDonald, Stuart M.
Subject: Re: [Hdf-forum] Libraries compiled wrong on site?

This is a C++ library. I use both C and C libraries (as you can see), using Intel compiler.

/usr/local/products/intel/Compiler/11.1/069/bin/intel64/icpc -o libcorestore.so -g -shared -Wl,-soname,libcorestore.120.so -L/vobs/wec/lib/SLES10 -L/opt/wec/lib -L/users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib -L/usr/local/products/intel/Compiler/11.1/069/lib/intel64 [all my .o files] -lxml2 -lcrypto -lhdf5 -lhdf5_cpp -lifcore -openmp
/users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib/libhdf5.so: file not recognized: File format not recognized

However, even outside of compiling, I can get errors. For example:

$ objdump -f libhdf5.so.7.0.1
objdump: libhdf5.so.7.0.1: File format not recognized

David McCloskey
(412) 374-3789

From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of Pierre de Buyl
Sent: Monday, August 08, 2011 12:19 PM
To: HDF Users Discussion List
Cc: McDonald, Stuart M.
Subject: Re: [Hdf-forum] Libraries compiled wrong on site?

Hello,

Are you using the C library or another one (then, the compiler matters more precisely).
Also, does your system provides hdf5 as a package ? It may be easier.
Finally, can you copy the terminal session showing the error ?

Regards,

Pierre

Le 8 août 11 à 11:01, McCloskey, David L. a écrit :

When I download this, http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-x86_64/hdf5-1.8.7-linux-x86_64-shared.tar.gz

The lib directory contains files that are not recognized by my compiler. Normally objects say (GNU/Linux) when I “file” them; these say “SYSV”.

$ uname -a
Linux gemini02 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 x86_64 x86_64 x86_64 GNU/Linux

$ file *
libhdf5.a: current ar archive
libhdf5.la: ASCII English text
libhdf5.settings: ASCII text, with very long lines
libhdf5.so: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_cpp.a: current ar archive
libhdf5_cpp.la: ASCII English text
libhdf5_cpp.so: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_fortran.a: current ar archive
libhdf5_fortran.la: ASCII English text
libhdf5_fortran.so: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl.a: current ar archive
libhdf5_hl.la: ASCII English text
libhdf5_hl.so: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl_cpp.a: current ar archive
libhdf5_hl_cpp.la: ASCII English text, with very long lines
libhdf5_hl_cpp.so: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5hl_fortran.a: current ar archive
libhdf5hl_fortran.la: ASCII English text, with very long lines
libhdf5hl_fortran.so: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libsz.so: symbolic link to `libsz.so.2.0.0'
libsz.so.2: symbolic link to `libsz.so.2.0.0'
libsz.so.2.0.0: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libz.so: symbolic link to `libz.so.1.2.5'
libz.so.1: symbolic link to `libz.so.1.2.5'
libz.so.1.2.5: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

David McCloskey
Lead Programmer Analyst
Software Development
Core Engineering
Nuclear Fuel

Westinghouse Electric Company
Cranberry Headquarters, Building 4
1000 Westinghouse Drive
Suite 451
Cranberry, PA, 16066, USA
Phone: +1 (412) 374-3789
Fax: +1 (724) 720-0853
Email: mcclosdl@westinghouse.com
Home Page: www.westinghousenuclear.com

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

-----------------------------------------------------------
Pierre de Buyl
Chemical Physics Theory Group - University of Toronto
Physique des Systèmes Complexes et Mécanique Statistique - Université Libre de Bruxelles
web: http://homepages.ulb.ac.be/~pdebuyl/
Tel: +1-416-946-0047
-----------------------------------------------------------

<libhdf5.settings>_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

6

I had to change the prefix in h5c++ but that was all I changed. I tried both the run-c++-ex and just regular h5c++ create.cpp and got the same error.

I downloaded mine from an http URL. Not sure if the FTP and HTTP versions point to the same place.

$ ./run-c++-ex.sh

################# create #################
/users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib/libz.so: file not recognized: File format not recognized
collect2: ld returned 1 exit status
messed up compiling create.cpp
rm: cannot remove `*.h5': No such file or directory

mcclosdl@gemini02 |Thu Aug 11 15:13| c++ $ ../../../bin/h5c++ create.cpp
/users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib/libz.so: file not recognized: File format not recognized
collect2: ld returned 1 exit status

David McCloskey
(412) 374-3789

···

From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of Elena Pourmal
Sent: Monday, August 08, 2011 11:43 PM
To: HDF Users Discussion List
Cc: McDonald, Stuart M.
Subject: Re: [Hdf-forum] Libraries compiled wrong on site?

David,

On Aug 8, 2011, at 12:42 PM, McCloskey, David L. wrote:

I just compiled it on my system using the default compilers (gcc/g++). Objdump works. Also, my software links and builds and runs normally. Has anyone verified that the build on the web site works?

I just did. I downloaded the source from ftp, unpacked, then changed h5c++ to use intel icpc and compiled one of the C++ examples. Worked fine with both static and shared libraries.

Have you tried h5c++ (as is) to run create.cpp example (found under share/hdf5_examples/c++) just to check if distribution works on your machine?

Here is the output of objdump
[epourmal@koala lib]$ pwd
/mnt/scr1/epourmal/_tmp_forum/hdf5-1.8.7-linux-x86_64-shared/lib
[epourmal@koala lib]$ objdump -f libhdf5.so.7.0.1

libhdf5.so.7.0.1: file format elf64-x86-64
architecture: i386:x86-64, flags 0x00000150:
HAS_SYMS, DYNAMIC, D_PAGED
start address 0x0000000000034da0
Of course, I am on the same machine where binaries were built, that is why everything works for me :wink:

Thanks,

Elena
See my attached hdf5.settings to see how similar our builds are on paper.

David McCloskey
(412) 374-3789

From: hdf-forum-bounces@hdfgroup.org<mailto:hdf-forum-bounces@hdfgroup.org> [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of McCloskey, David L.
Sent: Monday, August 08, 2011 1:27 PM
To: HDF Users Discussion List
Cc: McDonald, Stuart M.
Subject: Re: [Hdf-forum] Libraries compiled wrong on site?

This is a C++ library. I use both C and C libraries (as you can see), using Intel compiler.

/usr/local/products/intel/Compiler/11.1/069/bin/intel64/icpc -o libcorestore.so -g -shared -Wl,-soname,libcorestore.120.so -L/vobs/wec/lib/SLES10 -L/opt/wec/lib -L/users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib -L/usr/local/products/intel/Compiler/11.1/069/lib/intel64 [all my .o files] -lxml2 -lcrypto -lhdf5 -lhdf5_cpp -lifcore -openmp
/users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib/libhdf5.so: file not recognized: File format not recognized

However, even outside of compiling, I can get errors. For example:

$ objdump -f libhdf5.so.7.0.1
objdump: libhdf5.so.7.0.1: File format not recognized

David McCloskey
(412) 374-3789

From: hdf-forum-bounces@hdfgroup.org<mailto:hdf-forum-bounces@hdfgroup.org> [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of Pierre de Buyl
Sent: Monday, August 08, 2011 12:19 PM
To: HDF Users Discussion List
Cc: McDonald, Stuart M.
Subject: Re: [Hdf-forum] Libraries compiled wrong on site?

Hello,

Are you using the C library or another one (then, the compiler matters more precisely).
Also, does your system provides hdf5 as a package ? It may be easier.
Finally, can you copy the terminal session showing the error ?

Regards,

Pierre

Le 8 août 11 à 11:01, McCloskey, David L. a écrit :

When I download this, http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-x86_64/hdf5-1.8.7-linux-x86_64-shared.tar.gz

The lib directory contains files that are not recognized by my compiler. Normally objects say (GNU/Linux) when I "file" them; these say "SYSV".

$ uname -a
Linux gemini02 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 x86_64 x86_64 x86_64 GNU/Linux

$ file *
libhdf5.a: current ar archive
libhdf5.la: ASCII English text
libhdf5.settings: ASCII text, with very long lines
libhdf5.so: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_cpp.a: current ar archive
libhdf5_cpp.la: ASCII English text
libhdf5_cpp.so: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_fortran.a: current ar archive
libhdf5_fortran.la: ASCII English text
libhdf5_fortran.so: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl.a: current ar archive
libhdf5_hl.la: ASCII English text
libhdf5_hl.so: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl_cpp.a: current ar archive
libhdf5_hl_cpp.la: ASCII English text, with very long lines
libhdf5_hl_cpp.so: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5hl_fortran.a: current ar archive
libhdf5hl_fortran.la: ASCII English text, with very long lines
libhdf5hl_fortran.so: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libsz.so: symbolic link to `libsz.so.2.0.0'
libsz.so.2: symbolic link to `libsz.so.2.0.0'
libsz.so.2.0.0: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libz.so: symbolic link to `libz.so.1.2.5'
libz.so.1: symbolic link to `libz.so.1.2.5'
libz.so.1.2.5: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

David McCloskey
Lead Programmer Analyst
Software Development
Core Engineering
Nuclear Fuel

Westinghouse Electric Company
Cranberry Headquarters, Building 4
1000 Westinghouse Drive
Suite 451
Cranberry, PA, 16066, USA
Phone: +1 (412) 374-3789
Fax: +1 (724) 720-0853
Email: mcclosdl@westinghouse.com<mailto:mcclosdl@westinghouse.com>
Home Page: www.westinghousenuclear.com<x-msg://1217/www.westinghousenuclear.com>

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

-----------------------------------------------------------
Pierre de Buyl
Chemical Physics Theory Group - University of Toronto
Physique des Systèmes Complexes et Mécanique Statistique - Université Libre de Bruxelles
web: http://homepages.ulb.ac.be/~pdebuyl/
Tel: +1-416-946-0047
-----------------------------------------------------------

<libhdf5.settings>_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org<mailto:Hdf-forum@hdfgroup.org>
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

7

On second check, .o files have GNU/Linux; .so files normally have SYSV. I'm not sure what the problem is then.

The error form the compiler is just: /users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib/libhdf5.so: file not recognized: File format not recognized

David McCloskey
(412) 374-3789

···

From: McCloskey, David L.
Sent: Monday, August 08, 2011 11:01 AM
To: hdf-forum@hdfgroup.org
Cc: McDonald, Stuart M.
Subject: Libraries compiled wrong on site?

When I download this, http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-x86_64/hdf5-1.8.7-linux-x86_64-shared.tar.gz

The lib directory contains files that are not recognized by my compiler. Normally objects say (GNU/Linux) when I "file" them; these say "SYSV".

$ uname -a
Linux gemini02 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 x86_64 x86_64 x86_64 GNU/Linux

$ file *
libhdf5.a: current ar archive
libhdf5.la: ASCII English text
libhdf5.settings: ASCII text, with very long lines
libhdf5.so: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_cpp.a: current ar archive
libhdf5_cpp.la: ASCII English text
libhdf5_cpp.so: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_fortran.a: current ar archive
libhdf5_fortran.la: ASCII English text
libhdf5_fortran.so: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl.a: current ar archive
libhdf5_hl.la: ASCII English text
libhdf5_hl.so: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl_cpp.a: current ar archive
libhdf5_hl_cpp.la: ASCII English text, with very long lines
libhdf5_hl_cpp.so: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5hl_fortran.a: current ar archive
libhdf5hl_fortran.la: ASCII English text, with very long lines
libhdf5hl_fortran.so: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libsz.so: symbolic link to `libsz.so.2.0.0'
libsz.so.2: symbolic link to `libsz.so.2.0.0'
libsz.so.2.0.0: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libz.so: symbolic link to `libz.so.1.2.5'
libz.so.1: symbolic link to `libz.so.1.2.5'
libz.so.1.2.5: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

David McCloskey
Lead Programmer Analyst
Software Development
Core Engineering
Nuclear Fuel

Westinghouse Electric Company
Cranberry Headquarters, Building 4
1000 Westinghouse Drive
Suite 451
Cranberry, PA, 16066, USA
Phone: +1 (412) 374-3789
Fax: +1 (724) 720-0853
Email: mcclosdl@westinghouse.com
Home Page: www.westinghousenuclear.com

8

David,

This is weird....Please view libhdf5.settings file in the lib directory; you should see the system on which the distribution was built:

           SUMMARY OF THE HDF5 CONFIGURATION

···

=================================

General Information:
-------------------
                   HDF5 Version: 1.8.7
                  Configured on: Tue May 10 11:41:44 CDT 2011
                  Configured by: hdftest@koala
                 Configure mode: production
                    Host system: x86_64-unknown-linux-gnu
              Uname information: Linux koala 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:10:13 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
                      Libraries:
             Installation point: /mnt/scr1/release-binary/hdf5/v187/builds/koala

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/bin/gcc ( gcc (GCC) 4.1.2 20080704 )
........

May be compiler finds some other libraries? May be LD_LIBRARY_PATH is not correct?

Elena

On Aug 8, 2011, at 10:03 AM, McCloskey, David L. wrote:

On second check, .o files have GNU/Linux; .so files normally have SYSV. I’m not sure what the problem is then.

The error form the compiler is just: /users/mcclosdl/temp/hdf5-1.8.7-linux-x86_64-shared/lib/libhdf5.so: file not recognized: File format not recognized

David McCloskey
(412) 374-3789

From: McCloskey, David L.
Sent: Monday, August 08, 2011 11:01 AM
To: hdf-forum@hdfgroup.org
Cc: McDonald, Stuart M.
Subject: Libraries compiled wrong on site?

When I download this, http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-x86_64/hdf5-1.8.7-linux-x86_64-shared.tar.gz

The lib directory contains files that are not recognized by my compiler. Normally objects say (GNU/Linux) when I “file” them; these say “SYSV”.

$ uname -a
Linux gemini02 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 x86_64 x86_64 x86_64 GNU/Linux

$ file *
libhdf5.a: current ar archive
libhdf5.la: ASCII English text
libhdf5.settings: ASCII text, with very long lines
libhdf5.so: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7: symbolic link to `libhdf5.so.7.0.1'
libhdf5.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_cpp.a: current ar archive
libhdf5_cpp.la: ASCII English text
libhdf5_cpp.so: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7: symbolic link to `libhdf5_cpp.so.7.0.1'
libhdf5_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_fortran.a: current ar archive
libhdf5_fortran.la: ASCII English text
libhdf5_fortran.so: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7: symbolic link to `libhdf5_fortran.so.7.0.1'
libhdf5_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl.a: current ar archive
libhdf5_hl.la: ASCII English text
libhdf5_hl.so: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7: symbolic link to `libhdf5_hl.so.7.0.1'
libhdf5_hl.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5_hl_cpp.a: current ar archive
libhdf5_hl_cpp.la: ASCII English text, with very long lines
libhdf5_hl_cpp.so: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7: symbolic link to `libhdf5_hl_cpp.so.7.0.1'
libhdf5_hl_cpp.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libhdf5hl_fortran.a: current ar archive
libhdf5hl_fortran.la: ASCII English text, with very long lines
libhdf5hl_fortran.so: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7: symbolic link to `libhdf5hl_fortran.so.7.0.1'
libhdf5hl_fortran.so.7.0.1: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libsz.so: symbolic link to `libsz.so.2.0.0'
libsz.so.2: symbolic link to `libsz.so.2.0.0'
libsz.so.2.0.0: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
libz.so: symbolic link to `libz.so.1.2.5'
libz.so.1: symbolic link to `libz.so.1.2.5'
libz.so.1.2.5: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

David McCloskey
Lead Programmer Analyst
Software Development
Core Engineering
Nuclear Fuel

Westinghouse Electric Company
Cranberry Headquarters, Building 4
1000 Westinghouse Drive
Suite 451
Cranberry, PA, 16066, USA
Phone: +1 (412) 374-3789
Fax: +1 (724) 720-0853
Email: mcclosdl@westinghouse.com
Home Page: www.westinghousenuclear.com

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