hdf5 dependency

[Steve Berg]

Not sure if this is the right place to ask but here goes...

I've got a collection of SciLinux 7.2 systems at work that all need the hdf5 packages
and lately updating those packages has been failing.

Error: Package: hdf5-openmpi-1.8.12-8.el7.x86_64 (epel)
           Requires: libmpi_usempi.so.5()(64bit)

Normally my systems update from a locally rsync'd mirror, but I've tried using the
regular repos/mirrors and still see the error.  Tried using "yum whatprovides
*/libmpi_usempi.so.5" and that didn't find any package to provide the
dependency.

How do I get the hdf5 packages updated if a dependency isn't available?

[Anssi Johansson]

11.1.2017, 13.24, Steve Berg kirjoitti:
>  Not sure if this is the right place to ask but here goes...
>
>  I've got a collection of SciLinux 7.2 systems at work that all need the hdf5 packages
> and lately updating those packages has been failing.
>
>  Error: Package: hdf5-openmpi-1.8.12-8.el7.x86_64 (epel)
>             Requires: libmpi_usempi.so.5()(64bit)
>
>  Normally my systems update from a locally rsync'd mirror, but I've tried using
> the regular repos/mirrors and still see the error.  Tried using "yum whatprovides
> */libmpi_usempi.so.5" and that didn't find any package to provide the
> dependency.
>
>  How do I get the hdf5 packages updated if a dependency isn't available? 
On a CentOS 7.3.1611 system:

# yum provides 'libmpi_usempi.so.5()(64bit)'
...
openmpi-1.10.3-3.el7.x86_64 : Open Message Passing Interface
Repo        : base
Matched from:
Provides    : libmpi_usempi.so.5()(64bit)

openmpi-1.10.0-10.el7.x86_64.rpm in 7.2 provides only 
libmpi_usempi.so.1()(64bit), so you will need to upgrade to 7.3 to use 
hdf5-openmpi-1.8.12-8.el7.x86_64 from EPEL.

[Steve Berg]

I'm working on setting up my 7.3 mirror locally now so that'll get me a fix,
thanks.  But I am curious why the updated rpm's for hdf5 are available in 7.2 if
there's a known dependency error with openmpi.  Is it just a matter of waiting for
openmpi in 7.2 to get an update or will this error continue to exist?

[Anssi Johansson]

11.1.2017, 15.31, Steve Berg kirjoitti:
>  I'm working on setting up my 7.3 mirror locally now so
> that'll get me a fix, thanks.  But I am curious why the updated rpm's for hdf5 are
> available in 7.2 if there's a known dependency error with openmpi.  Is it just a
> matter of waiting for openmpi in 7.2 to get an update or will this error continue to
> exist? 
EPEL does not have different repositories for 7.0, 7.1, 7.2, 7.3 etc, 
it's only "7". Whenever RHEL gets an update that breaks dependencies 
with EPEL (such as in this case), the EPEL package will need to be 
rebuilt against the newest RHEL package. This will unfortunately mean 
that the newest EPEL package will be installable only with the newest 
dependant RHEL package. RHEL does try to keep these breakages to the 
minimum, but sometimes these library version bumps are required.

As for whether there will be an updated openmpi in SciLinux's 7.2, I 
don't know. You would need to ask them, but I'd guess the answer would 
be "no". Upgrading to 7.3 would be your best bet.