Bug 872781

Ugh, looks like this is something we forgot to take into account in the MPI guidelines.

It seems that you have installed the MPICH2 flavor of hdf5, but don't have the serial version installed. RPM then deems that the library dependencies are fulfilled, since libhdf5.so.6 is provided by hdf5-mpich2.

Just remove your workaround and install the hdf5 package.

Thanks, I think I understand what you are suggesting, but I'm not getting it to work. I removed my symlink and installed the hdf5 package from Redhat:

================================================================================
 Package       Arch            Version                  Repository         Size
================================================================================
Installing:
 hdf5          x86_64          1.8.7-1.el6.rf           rpmforge          3.4 M

Result: octave fails again, can't find libhdf5.so.6

I enabled epel and removed the mpich2 version of hdf5, but it insisted that octave depended on it, so I let it remove both.

================================================================================
 Package            Arch          Version                    Repository    Size
================================================================================
Removing:
 hdf5-mpich2        x86_64        1.8.5.patch1-7.el6         @epel        6.8 M
Removing for dependencies:
 octave             x86_64        6:3.4.3-1.el6              @epel         43 M

then reinstalled octave, which again installed hdf5-mpich2:

# yum --enablerepo=epel install octave
...
================================================================================
 Package            Arch          Version                     Repository   Size
================================================================================
Installing:
 octave             x86_64        6:3.4.3-1.el6               epel        9.1 M
Installing for dependencies:
 hdf5-mpich2        x86_64        1.8.5.patch1-7.el6          epel        1.4 M

and again octave failed to launch.

I now seem to have libhdf5.so.7 installed in /usr/lib64/, and libhdf5.so.6  installed in /usr/lib64/mpich2/lib/:

# find / -name *hdf5*
/var/lib/yum/yumdb/h/aa6c7365147a16e317183eb4fc5d0d5395bc27f4-hdf5-mpich2-1.8.5.patch1-7.el6-x86_64
/var/lib/yum/yumdb/h/b260bb88c29aa2427182b78eee259f9ce1697371-hdf5-1.8.7-1.el6.rf-x86_64
/usr/lib64/libhdf5hl_fortran.so.7
/usr/lib64/libhdf5_hl.so.7.0.1
/usr/lib64/libhdf5.so.7.0.1
/usr/lib64/libhdf5.so.7
/usr/lib64/libhdf5_hl.so.7
/usr/lib64/libhdf5_cpp.so.7.0.1
/usr/lib64/libhdf5_fortran.so.7.0.1
/usr/lib64/libhdf5hl_fortran.so.7.0.1
/usr/lib64/mpich2/lib/libhdf5hl_fortran.so.6.0.4
/usr/lib64/mpich2/lib/libhdf5_hl.so.6.0.4
/usr/lib64/mpich2/lib/libhdf5_fortran.so.6
/usr/lib64/mpich2/lib/libhdf5.so.6
/usr/lib64/mpich2/lib/libhdf5_hl.so.6
/usr/lib64/mpich2/lib/libhdf5.so.6.0.4
/usr/lib64/mpich2/lib/libhdf5_fortran.so.6.0.4
/usr/lib64/mpich2/lib/libhdf5hl_fortran.so.6
/usr/lib64/libhdf5_cpp.so.7
/usr/lib64/libhdf5_hl_cpp.so.7
/usr/lib64/libhdf5_hl_cpp.so.7.0.1
/usr/lib64/libhdf5_fortran.so.7
/usr/share/doc/hdf5-1.8.7
/usr/share/doc/hdf5-mpich2-1.8.5.patch1

but octave doesn't seem to be looking in any of these places:

$ strace octave 2>&1 | grep open.*libhdf5.*ENOENT | sed 's/^.*(\"//;s/\".*$//'
/usr/lib64/octave/3.4.3/libhdf5.so.6
/lib64/tls/x86_64/libhdf5.so.6
/lib64/tls/libhdf5.so.6
/lib64/x86_64/libhdf5.so.6
/lib64/libhdf5.so.6
/usr/lib64/tls/x86_64/libhdf5.so.6
/usr/lib64/tls/libhdf5.so.6
/usr/lib64/x86_64/libhdf5.so.6
/usr/lib64/libhdf5.so.6

So here's a new workaround that works:
# ln -s /usr/lib64/libhdf5.so.7 /usr/lib64/libhdf5.so.6
# ls -l /usr/lib64/libhdf5.so*
lrwxrwxrwx. 1 root root      23 Nov  3 12:39 /usr/lib64/libhdf5.so.6 -> /usr/lib64/libhdf5.so.7
lrwxrwxrwx. 1 root root      16 Nov  3 09:52 /usr/lib64/libhdf5.so.7 -> libhdf5.so.7.0.1
-rwxr-xr-x. 1 root root 9646932 Aug  9  2011 /usr/lib64/libhdf5.so.7.0.1

Can you make sense of this, or am I off in the wrong direction? Thanks for taking the time.

--Steve

(In reply to comment #2)
> Thanks, I think I understand what you are suggesting, but I'm not getting it
> to work. I removed my symlink and installed the hdf5 package from Redhat:
> 
> =============================================================================
> ===
>  Package       Arch            Version                  Repository        
> Size
> =============================================================================
> ===
> Installing:
>  hdf5          x86_64          1.8.7-1.el6.rf           rpmforge         
> 3.4 M
> 
> Result: octave fails again, can't find libhdf5.so.6

You're using the rpmforge repository, which results in you having a Frankenstein system. Unlike Fedora EPEL, rpmforge updates system core packages. The problems you are having are probably a symptom of this.

Closing as NOTABUG.

Oops, I think you're right. I didn't realize I had left rpmforge enabled. 

Thought Halloween was over, but here I am with a Frankensystem. Can't say I wasn't warned. Thanks again and sorry to be a bother.

--Steve

I run following codes and succeed:
sudo yum install mpich2
cd /usr/lib64/octave/3.4.3/
ln -s /usr/lib64/libhdf5.so.7
mv libhdf5.so.7 libhdf5.so.6

Because I find libhdf5.so.7 in /usr/lib64

(In reply to gengli from comment #5)
> I run following codes and succeed:
> sudo yum install mpich2
> cd /usr/lib64/octave/3.4.3/
> ln -s /usr/lib64/libhdf5.so.7
> mv libhdf5.so.7 libhdf5.so.6
> 
> Because I find libhdf5.so.7 in /usr/lib64

That's just wrong. Libraries with different sonames are incompatible.

I'll say the same thing to you: remove all third-party packages and use the ones from RHEL and Fedora EPEL. Those work and don't mess up your system, like yours has been messed up as well.

(In reply to Susi Lehtola from comment #6)
> (In reply to gengli from comment #5)
> > I run following codes and succeed:
> > sudo yum install mpich2
> > cd /usr/lib64/octave/3.4.3/
> > ln -s /usr/lib64/libhdf5.so.7
> > mv libhdf5.so.7 libhdf5.so.6
> > 
> > Because I find libhdf5.so.7 in /usr/lib64
> 
> That's just wrong. Libraries with different sonames are incompatible.
> 
> I'll say the same thing to you: remove all third-party packages and use the
> ones from RHEL and Fedora EPEL. Those work and don't mess up your system,
> like yours has been messed up as well.

Action speaks louder than words, I just know after I do that, it works.

(In reply to gengli from comment #7)
> (In reply to Susi Lehtola from comment #6)
> > (In reply to gengli from comment #5)
> > > I run following codes and succeed:
> > > sudo yum install mpich2
> > > cd /usr/lib64/octave/3.4.3/
> > > ln -s /usr/lib64/libhdf5.so.7
> > > mv libhdf5.so.7 libhdf5.so.6
> > > 
> > > Because I find libhdf5.so.7 in /usr/lib64
> > 
> > That's just wrong. Libraries with different sonames are incompatible.
> > 
> > I'll say the same thing to you: remove all third-party packages and use the
> > ones from RHEL and Fedora EPEL. Those work and don't mess up your system,
> > like yours has been messed up as well.
> 

I wrote comment6
reply comment7
> Action speaks louder than words, I just know after I do that, it works.

(In reply to gengli from comment #8)
> (In reply to gengli from comment #7)
> > (In reply to Susi Lehtola from comment #6)
> > > (In reply to gengli from comment #5)
> > > > I run following codes and succeed:
> > > > sudo yum install mpich2
> > > > cd /usr/lib64/octave/3.4.3/
> > > > ln -s /usr/lib64/libhdf5.so.7
> > > > mv libhdf5.so.7 libhdf5.so.6
> > > > 
> > > > Because I find libhdf5.so.7 in /usr/lib64
> > > 
> > > That's just wrong. Libraries with different sonames are incompatible.
> > > 
> > > I'll say the same thing to you: remove all third-party packages and use the
> > > ones from RHEL and Fedora EPEL. Those work and don't mess up your system,
> > > like yours has been messed up as well.
> > 
> 
> I wrote comment5
> reply comment7
> > Action speaks louder than words, I just know after I do that, it works.

(In reply to gengli from comment #7)
> Action speaks louder than words, 

Indeed. Hacking the compatibility checks in the shared library dependency system beats fixing the problem that you have installed incompatible software which could be easily fixed by installing the distribution package, or if it does not suit your needs, compiling the software from sources.

This is not Windows, where you had to Altavista for missing DLLs.