hdf5 fails

[certik]

Now I am at hdf5:

[hdf5] running ['sh', '../configure']
[hdf5] cwd: /panfs/scratch3/vol18/certik/python-hpcmp2/bld/hdf5-n-xvla/src
[hdf5] environment:
[hdf5]   {'ARTIFACT': '/panfs/scratch3/vol18/certik/python-hpcmp2/opt/hdf5/xvla',
[hdf5]    'BUILD': '/panfs/scratch3/vol18/certik/python-hpcmp2/bld/hdf5-n-xvla',
[hdf5]    'HDIST_CFLAGS': '-I/panfs/scratch3/vol18/certik/python-hpcmp2/opt/szip/lw76/include -I/panfs/scratch3/vol18/certik/python-hpcmp2/opt/zlib/usvu/include',
[hdf5]    'HDIST_CONFIG': '{"builder/build-temp":"/panfs/scratch3/vol18/certik/python-hpcmp2/bld","sourcecache/sources":"/panfs/scratch3/vol18/certik/python-hpcmp2/src","builder/artifacts":"/panfs/scratch3/vol18/certik/python-hpcmp2/opt","global/cache":"/panfs/scratch3/vol18/certik/python-hpcmp2/cache","builder/artifact-dir-pattern":"{name}/{shorthash}","global/db":"/panfs/scratch3/vol18/certik/python-hpcmp2/db"}',
[hdf5]    'HDIST_IMPORT': 'szip/lw76qzbljqqjubzv3b5q4bzrbokoogsc launcher/gbaghc5quzejtuyrpawwepqn3tgaawmu zlib/usvubstjijmjryrbgyp47wek77or2o7g',
[hdf5]    'HDIST_IMPORT_PATHS': '/panfs/scratch3/vol18/certik/python-hpcmp2/opt/szip/lw76 /panfs/scratch3/vol18/certik/python-hpcmp2/opt/launcher/gbag /panfs/scratch3/vol18/certik/python-hpcmp2/opt/zlib/usvu',
[hdf5]    'HDIST_LDFLAGS': '-L/panfs/scratch3/vol18/certik/python-hpcmp2/opt/szip/lw76/lib -Wl,-R,/panfs/scratch3/vol18/certik/python-hpcmp2/opt/szip/lw76/lib -L/panfs/scratch3/vol18/certik/python-hpcmp2/opt/zlib/usvu/lib -Wl,-R,/panfs/scratch3/vol18/certik/python-hpcmp2/opt/zlib/usvu/lib',
[hdf5]    'HDIST_VIRTUALS': '',
[hdf5]    'LAUNCHER': '/panfs/scratch3/vol18/certik/python-hpcmp2/opt/launcher/gbag',
[hdf5]    'LAUNCHER_ID': 'launcher/gbaghc5quzejtuyrpawwepqn3tgaawmu',
[hdf5]    'PATH': '/usr/bin:/bin',
[hdf5]    'PYTHONHPC_PREFIX': '/panfs/scratch3/vol18/certik/python-hpcmp2/opt/hdf5/xvla',
[hdf5]    'SZIP': '/panfs/scratch3/vol18/certik/python-hpcmp2/opt/szip/lw76',
[hdf5]    'SZIP_ID': 'szip/lw76qzbljqqjubzv3b5q4bzrbokoogsc',
[hdf5]    'ZLIB': '/panfs/scratch3/vol18/certik/python-hpcmp2/opt/zlib/usvu',
[hdf5]    'ZLIB_ID': 'zlib/usvubstjijmjryrbgyp47wek77or2o7g'}
[hdf5] checking for a BSD-compatible install... /usr/bin/install -c
[hdf5] checking whether build environment is sane... yes
[hdf5] checking for a thread-safe mkdir -p... /bin/mkdir -p
[hdf5] checking for gawk... gawk
[hdf5] checking whether make sets $(MAKE)... yes
[hdf5] checking whether make supports nested variables... yes
[hdf5] checking whether to enable maintainer-specific portions of Makefiles... no
[hdf5] checking build system type... x86_64-unknown-linux-gnu
[hdf5] checking host system type... x86_64-unknown-linux-gnu
[hdf5] checking shell variables initial values... done
[hdf5] checking if basename works... yes
[hdf5] checking if xargs works... yes
[hdf5] checking for cached host... none
[hdf5] checking for config x86_64-unknown-linux-gnu... no
[hdf5] checking for config x86_64-unknown-linux-gnu... no
[hdf5] checking for config unknown-linux-gnu... no
[hdf5] checking for config unknown-linux-gnu... no
[hdf5] checking for config x86_64-linux-gnu... no
[hdf5] checking for config x86_64-linux-gnu... no
[hdf5] checking for config x86_64-unknown... no
[hdf5] checking for config linux-gnu... found
[hdf5] compiler 'gcc' is GNU gcc-4.1.2
[hdf5] CC_BASENAME is gcc.
[hdf5] checking for config ./config/site-specific/host-cj-fe1.lanl.gov... no
[hdf5] checking for config ./config/site-specific/host-lanl.gov... no
[hdf5] checking for config ./config/site-specific/host-gov... no
[hdf5] checking for gcc... gcc
[hdf5] checking whether the C compiler works... yes
[hdf5] checking for C compiler default output file name... a.out
[hdf5] checking for suffix of executables... 
[hdf5] configure: error: in `/panfs/scratch3/vol18/certik/python-hpcmp2/bld/hdf5-n-xvla/src':
[hdf5] configure: error: cannot run C compiled programs.
[hdf5] If you meant to cross compile, use `--host'.
[hdf5] See `config.log' for more details
[hdf5] checking whether we are cross compiling... 
[hdf5 ERROR] Command '['sh', '../configure']' returned non-zero exit status 1
[hdf5 ERROR] command failed (code=1); raising

The relevant part of config.log is:

configure:4494: $? = 0
configure:4483: gcc -v >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --disable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-50)
configure:4494: $? = 0
configure:4483: gcc -V >&5
gcc: '-V' option must have argument
configure:4494: $? = 1
configure:4483: gcc -qversion >&5
gcc: unrecognized option '-qversion'
gcc: no input files
configure:4494: $? = 1
configure:4514: checking whether the C compiler works
configure:4536: gcc  -I/panfs/scratch3/vol18/certik/python-hpcmp2/opt/hdf5/xvla/include    -L/panfs/scratch3/vol18/certik/python-hpcmp2/opt/hdf5/xvla/lib conftest.c -lsz -lz >&5
configure:4540: $? = 0
configure:4588: result: yes
configure:4591: checking for C compiler default output file name
configure:4593: result: a.out
configure:4599: checking for suffix of executables
configure:4606: gcc -o conftest  -I/panfs/scratch3/vol18/certik/python-hpcmp2/opt/hdf5/xvla/include    -L/panfs/scratch3/vol18/certik/python-hpcmp2/opt/hdf5/xvla/lib conftest.c -lsz -lz >&5
configure:4610: $? = 0
configure:4632: result:
configure:4654: checking whether we are cross compiling
configure:4662: gcc -o conftest  -I/panfs/scratch3/vol18/certik/python-hpcmp2/opt/hdf5/xvla/include    -L/panfs/scratch3/vol18/certik/python-hpcmp2/opt/hdf5/xvla/lib conftest.c -lsz -lz >&5
configure:4666: $? = 0
configure:4673: ./conftest
./conftest: error while loading shared libraries: libsz.so.2: cannot open shared object file: No such file or directory
configure:4677: $? = 127
configure:4684: error: in `/panfs/scratch3/vol18/certik/python-hpcmp2/bld/hdf5-n-xvla/src':
configure:4686: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details

[certik]

So it looks like it cannot find the libsz.so --- possibly at runtime, suggesting the need for LD_LIBRARY_PATH...

[certik]

I bet the problem is right in hdf5Config/configure.linux:

./configure LDFLAGS="-L${PYTHONHPC_PREFIX}/lib" LIBS="-lsz -lz" CFLAGS="-I${PYTHONHPC_PREFIX}/include" --with-szlib=${PYTHONHPC_PREFIX} --with-zlib=${PYTHONHPC_PREFIX} --enable-shared --enable-threadsafe -disable-parallel --with-pthread --with-pic --prefix=${PYTHONHPC_PREFIX}

where -lsz will link with /usr/lib and not ours.

[certik]

Yep. This fixed it:

diff --git a/hdf5Config/configure.linux b/hdf5Config/configure.linux
index c150db4..223d993 100755
--- a/hdf5Config/configure.linux
+++ b/hdf5Config/configure.linux
@@ -1 +1 @@
-./configure LDFLAGS="-L${PYTHONHPC_PREFIX}/lib" LIBS="-lsz -lz" CFLAGS="-I${PYTHONHPC_PREFIX}/include" --with-szlib=${PYTHONHPC_PREFIX} --with-zlib=${PYTHONHPC_PREFIX} --enable-shared --enable-threadsafe -disable-parallel --with-pthread --with-pic --prefix=${PYTHONHPC_PREFIX}
+./configure LDFLAGS="-L${PYTHONHPC_PREFIX}/lib" CFLAGS="-I${PYTHONHPC_PREFIX}/include" --with-szlib=${PYTHONHPC_PREFIX} --with-zlib=${PYTHONHPC_PREFIX} --enable-shared --enable-threadsafe -disable-parallel --with-pthread --with-pic --prefix=${PYTHONHPC_PREFIX}

[hamrejr]

Hi there,

You look to have solved this, nice! I am getting the same error,"error while loading shared libraries: libsz.so.2:", over a remote ubuntu server and I use cygwin or putty to remote in. How do I fix this, is it something with the HDF5 install? Any help would be greatly appreciated.

Thanks,

John