hdf5-1.8.2 make check fails looking for shared file

Mark_V · January 15, 2009, 6:35am

Hi,

I'm trying to build HDF from the source files.
So far configure and make have proceeded without error.
Some system details:

# lsb_release -a
LSB Version:
core-2.0-noarch:core-3.0-noarch:core-2.0-ia32:core-3.0-ia32:desktop-3.1-ia32:desktop-3.1-noarch:graphics-2.0-ia32:graphics-2.0-noarch:graphics-3.1-ia32:graphics-3.1-noarch
Distributor ID: SUSE LINUX
Description: openSUSE 11.0 (i586)
Release: 11.0
Codename: n/a

# rpm -qa|grep -i gcc
gcc-info-4.3-39.1
gcc-gij-4.3-39.1
gcc43-gij-4.3.1_20080507-9.1
gcc-java-4.3-39.1
gcc43-4.3.1_20080507-6.1
libgcc43-4.3.1_20080507-6.1
gcc-c++-4.3-39.1
gcc43-java-4.3.1_20080507-9.1
gcc43-info-4.3.1_20080507-6.1
gcc43-c++-4.3.1_20080507-6.1
gcc-4.3-39.1

When I get to `make check`, the test log indicates a file couldn't be found.
The `make check` log is here:

http://www.pastie.org/361266

I've followed the install file instructions, and the commands run have been:

http://www.pastie.org/361269

I'd appreciate any suggestions.

Regards
Mark

···

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Mark_V · January 15, 2009, 9:47am

An update...

Hi,

I'm trying to build HDF from the source files.
So far configure and make have proceeded without error.
Some system details:

# lsb_release -a
LSB Version:
core-2.0-noarch:core-3.0-noarch:core-2.0-ia32:core-3.0-ia32:desktop-3.1-ia32:desktop-3.1-noarch:graphics-2.0-ia32:graphics-2.0-noarch:graphics-3.1-ia32:graphics-3.1-noarch
Distributor ID: SUSE LINUX
Description: openSUSE 11.0 (i586)
Release: 11.0
Codename: n/a

# rpm -qa|grep -i gcc
gcc-info-4.3-39.1
gcc-gij-4.3-39.1
gcc43-gij-4.3.1_20080507-9.1
gcc-java-4.3-39.1
gcc43-4.3.1_20080507-6.1
libgcc43-4.3.1_20080507-6.1
gcc-c++-4.3-39.1
gcc43-java-4.3.1_20080507-9.1
gcc43-info-4.3.1_20080507-6.1
gcc43-c++-4.3.1_20080507-6.1
gcc-4.3-39.1

When I get to `make check`, the test log indicates a file couldn't be found.
The `make check` log is here:

http://www.pastie.org/361266

I've followed the install file instructions, and the commands run have been:

http://www.pastie.org/361269

I now run this configuration:

# ./configure --prefix=$HDF5_DIR \
            --with-szlib=$SZIP_DIR/include,$SZIP_DIR/lib \
            --with-zlib=/usr/include,/usr/lib \
            --with-pthread=/usr/include,/usr/lib \
            --with-default-api-version=v16 \
            --enable-production \
            --enable-threadsafe \
            --enable-build-all

Then `make check` stops with

make[1]: *** No rule to make target `gen_bad_ohdr.o', needed by
`gen_bad_ohdr'. Stop.

The full log was too large to pastie, so final fragment is here:

http://www.pastie.org/361310

Let me know if you want the full log file.

Mark

···

On Thu, Jan 15, 2009 at 5:35 PM, Mark V <mvyver@gmail.com> wrote:

I'd appreciate any suggestions.

Regards
Mark

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

Quincey_Koziol · January 15, 2009, 12:29pm

Hi Mark,

An update...

Hi,

I'm trying to build HDF from the source files.
So far configure and make have proceeded without error.
Some system details:

# lsb_release -a
LSB Version:
core-2.0-noarch:core-3.0-noarch:core-2.0-ia32:core-3.0-ia32:desktop-3.1-ia32:desktop-3.1-noarch:graphics-2.0-ia32:graphics-2.0-noarch:graphics-3.1-ia32:graphics-3.1-noarch
Distributor ID: SUSE LINUX
Description: openSUSE 11.0 (i586)
Release: 11.0
Codename: n/a

# rpm -qa|grep -i gcc
gcc-info-4.3-39.1
gcc-gij-4.3-39.1
gcc43-gij-4.3.1_20080507-9.1
gcc-java-4.3-39.1
gcc43-4.3.1_20080507-6.1
libgcc43-4.3.1_20080507-6.1
gcc-c++-4.3-39.1
gcc43-java-4.3.1_20080507-9.1
gcc43-info-4.3.1_20080507-6.1
gcc43-c++-4.3.1_20080507-6.1
gcc-4.3-39.1

When I get to `make check`, the test log indicates a file couldn't be found.
The `make check` log is here:

http://www.pastie.org/361266

I've followed the install file instructions, and the commands run have been:

http://www.pastie.org/361269

I now run this configuration:

# ./configure --prefix=$HDF5_DIR \
           --with-szlib=$SZIP_DIR/include,$SZIP_DIR/lib \
           --with-zlib=/usr/include,/usr/lib \
           --with-pthread=/usr/include,/usr/lib \
           --with-default-api-version=v16 \
           --enable-production \
           --enable-threadsafe \
           --enable-build-all

Then `make check` stops with

make[1]: *** No rule to make target `gen_bad_ohdr.o', needed by
`gen_bad_ohdr'. Stop.

Hmm, try without the --enable-build-all (which builds some executables only needed to generate test files).

Quincey

···

On Jan 15, 2009, at 3:47 AM, Mark V wrote:

On Thu, Jan 15, 2009 at 5:35 PM, Mark V <mvyver@gmail.com> wrote:

The full log was too large to pastie, so final fragment is here:

http://www.pastie.org/361310

Let me know if you want the full log file.

Mark

I'd appreciate any suggestions.

Regards
Mark

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

Mark_V · January 17, 2009, 12:26am

Hi Mark,

An update...

Hi,

I'm trying to build HDF from the source files.
So far configure and make have proceeded without error.
Some system details:

# lsb_release -a
LSB Version:

core-2.0-noarch:core-3.0-noarch:core-2.0-ia32:core-3.0-ia32:desktop-3.1-ia32:desktop-3.1-noarch:graphics-2.0-ia32:graphics-2.0-noarch:graphics-3.1-ia32:graphics-3.1-noarch
Distributor ID: SUSE LINUX
Description: openSUSE 11.0 (i586)
Release: 11.0
Codename: n/a

# rpm -qa|grep -i gcc
gcc-info-4.3-39.1
gcc-gij-4.3-39.1
gcc43-gij-4.3.1_20080507-9.1
gcc-java-4.3-39.1
gcc43-4.3.1_20080507-6.1
libgcc43-4.3.1_20080507-6.1
gcc-c++-4.3-39.1
gcc43-java-4.3.1_20080507-9.1
gcc43-info-4.3.1_20080507-6.1
gcc43-c++-4.3.1_20080507-6.1
gcc-4.3-39.1

When I get to `make check`, the test log indicates a file couldn't be
found.
The `make check` log is here:

http://www.pastie.org/361266

I've followed the install file instructions, and the commands run have
been:

http://www.pastie.org/361269

I now run this configuration:

# ./configure --prefix=$HDF5_DIR \
          --with-szlib=$SZIP_DIR/include,$SZIP_DIR/lib \
          --with-zlib=/usr/include,/usr/lib \
          --with-pthread=/usr/include,/usr/lib \
          --with-default-api-version=v16 \
          --enable-production \
          --enable-threadsafe \
          --enable-build-all

Then `make check` stops with

make[1]: *** No rule to make target `gen_bad_ohdr.o', needed by
`gen_bad_ohdr'. Stop.

       Hmm, try without the --enable-build-all (which builds some
executables only needed to generate test files).

When I disable --enable-build-all, the make proceeds
However, `make check` seems to terminate complaining about library and
header version mismatch:

http://www.pastie.org/362975

Is this expected?
The quick installation section of the install document does not
mention setting LD_LIBRARY_PATH or HDF5_DISABLE_VERSION_CHECK

Appreciate any suggestions.

Mark

···

On Thu, Jan 15, 2009 at 11:29 PM, Quincey Koziol <koziol@hdfgroup.org> wrote:

On Jan 15, 2009, at 3:47 AM, Mark V wrote:

On Thu, Jan 15, 2009 at 5:35 PM, Mark V <mvyver@gmail.com> wrote:

Quincey

The full log was too large to pastie, so final fragment is here:

http://www.pastie.org/361310

Let me know if you want the full log file.

Mark

I'd appreciate any suggestions.

Regards
Mark

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to
hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

Mark_V · January 17, 2009, 1:00am

Hi Mark,

An update...

Hi,

I'm trying to build HDF from the source files.
So far configure and make have proceeded without error.
Some system details:

# lsb_release -a
LSB Version:

core-2.0-noarch:core-3.0-noarch:core-2.0-ia32:core-3.0-ia32:desktop-3.1-ia32:desktop-3.1-noarch:graphics-2.0-ia32:graphics-2.0-noarch:graphics-3.1-ia32:graphics-3.1-noarch
Distributor ID: SUSE LINUX
Description: openSUSE 11.0 (i586)
Release: 11.0
Codename: n/a

# rpm -qa|grep -i gcc
gcc-info-4.3-39.1
gcc-gij-4.3-39.1
gcc43-gij-4.3.1_20080507-9.1
gcc-java-4.3-39.1
gcc43-4.3.1_20080507-6.1
libgcc43-4.3.1_20080507-6.1
gcc-c++-4.3-39.1
gcc43-java-4.3.1_20080507-9.1
gcc43-info-4.3.1_20080507-6.1
gcc43-c++-4.3.1_20080507-6.1
gcc-4.3-39.1

When I get to `make check`, the test log indicates a file couldn't be
found.
The `make check` log is here:

http://www.pastie.org/361266

I've followed the install file instructions, and the commands run have
been:

http://www.pastie.org/361269

I now run this configuration:

# ./configure --prefix=$HDF5_DIR \
          --with-szlib=$SZIP_DIR/include,$SZIP_DIR/lib \
          --with-zlib=/usr/include,/usr/lib \
          --with-pthread=/usr/include,/usr/lib \
          --with-default-api-version=v16 \
          --enable-production \
          --enable-threadsafe \
          --enable-build-all

Then `make check` stops with

make[1]: *** No rule to make target `gen_bad_ohdr.o', needed by
`gen_bad_ohdr'. Stop.

       Hmm, try without the --enable-build-all (which builds some
executables only needed to generate test files).

When I disable --enable-build-all, the make proceeds
However, `make check` seems to terminate complaining about library and
header version mismatch:

http://www.pastie.org/362975

Is this expected?

AGGGH, my mistake. apologies. I had mixed-up src directories.

Mark

···

On Sat, Jan 17, 2009 at 11:26 AM, Mark V <mvyver@gmail.com> wrote:

On Thu, Jan 15, 2009 at 11:29 PM, Quincey Koziol <koziol@hdfgroup.org> wrote:

On Jan 15, 2009, at 3:47 AM, Mark V wrote:

On Thu, Jan 15, 2009 at 5:35 PM, Mark V <mvyver@gmail.com> wrote:

The quick installation section of the install document does not
mention setting LD_LIBRARY_PATH or HDF5_DISABLE_VERSION_CHECK

Appreciate any suggestions.

Mark

Quincey

The full log was too large to pastie, so final fragment is here:

http://www.pastie.org/361310

Let me know if you want the full log file.

Mark

I'd appreciate any suggestions.

Regards
Mark

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to
hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.