Bug 750839

Summary:	error while loading shared libraries: libhdf5_hl.so.6
Product:	[Fedora] Fedora EPEL	Reporter:	Fabien Archambault <marbolangos>
Component:	grace	Assignee:	José Matos <jamatos>
Status:	CLOSED NOTABUG	QA Contact:	Fedora Extras Quality Assurance <extras-qa>
Severity:	unspecified	Docs Contact:
Priority:	unspecified
Version:	el6	CC:	dominik, dyilmaz, jamatos, jonathan.underwood, pertusus
Target Milestone:	---
Target Release:	---
Hardware:	Unspecified
OS:	Unspecified
Whiteboard:
Fixed In Version:		Doc Type:	Bug Fix
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2011-12-05 08:11:07 UTC	Type:	---
Regression:	---	Mount Type:	---
Documentation:	---	CRM:
Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:

Description Fabien Archambault 2011-11-02 13:59:00 UTC

Description of problem: after installing grace with yum I have the error:
xmgrace: error while loading shared libraries: libhdf5_hl.so.6: cannot open shared object file: No such file or directory


Version-Release number of selected component (if applicable): grace-5.1.22-7.el6.x86_64


Steps to Reproduce:
1. # yum install grace
Loaded plugins: fastestmirror, refresh-packagekit
Loading mirror speeds from cached hostfile
 * base: mirror.in2p3.fr
 * elrepo: mirrors.coreix.net
 * epel: fr2.rpmfind.net
 * extras: mirror.in2p3.fr
 * rpmforge: fr2.rpmfind.net
 * updates: mirror.in2p3.fr
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package grace.x86_64 0:5.1.22-7.el6 will be installed
--> Processing Dependency: nedit for package: grace-5.1.22-7.el6.x86_64
--> Processing Dependency: libfftw.so.2()(64bit) for package: grace-5.1.22-7.el6.x86_64
--> Processing Dependency: libXbae.so.4()(64bit) for package: grace-5.1.22-7.el6.x86_64
--> Processing Dependency: libnetcdf.so.6()(64bit) for package: grace-5.1.22-7.el6.x86_64
--> Processing Dependency: libXm.so.4()(64bit) for package: grace-5.1.22-7.el6.x86_64
--> Running transaction check
---> Package fftw2.x86_64 0:2.1.5-21.el6 will be installed
---> Package nedit.x86_64 0:5.5-23.el6 will be installed
---> Package netcdf.x86_64 0:4.1.1-3.el6.2 will be installed
---> Package openmotif.x86_64 0:2.3.3-4.el6 will be installed
---> Package xbae.x86_64 0:4.60.4-12.el6 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

=============================================================================================================================================================================================================================================
 Package                                                   Arch                                                   Version                                                         Repository                                            Size
=============================================================================================================================================================================================================================================
Installing:
 grace                                                     x86_64                                                 5.1.22-7.el6                                                    epel                                                 1.1 M
Installing for dependencies:
 fftw2                                                     x86_64                                                 2.1.5-21.el6                                                    epel                                                 395 k
 nedit                                                     x86_64                                                 5.5-23.el6                                                      epel                                                 575 k
 netcdf                                                    x86_64                                                 4.1.1-3.el6.2                                                   epel                                                 4.8 M
 openmotif                                                 x86_64                                                 2.3.3-4.el6                                                     cr                                                   1.4 M
 xbae                                                      x86_64                                                 4.60.4-12.el6                                                   epel                                                 139 k

Transaction Summary
=============================================================================================================================================================================================================================================
Install       6 Package(s)

Total download size: 8.3 M
Installed size: 26 M
Is this ok [y/N]: y
Downloading Packages:
(1/6): fftw2-2.1.5-21.el6.x86_64.rpm                                                                                                                                                                                  | 395 kB     00:00     
(2/6): grace-5.1.22-7.el6.x86_64.rpm                                                                                                                                                                                  | 1.1 MB     00:00     
(3/6): nedit-5.5-23.el6.x86_64.rpm                                                                                                                                                                                    | 575 kB     00:00     
(4/6): netcdf-4.1.1-3.el6.2.x86_64.rpm                                                                                                                                                                                | 4.8 MB     00:00     
(5/6): openmotif-2.3.3-4.el6.x86_64.rpm                                                                                                                                                                               | 1.4 MB     00:02     
(6/6): xbae-4.60.4-12.el6.x86_64.rpm                                                                                                                                                                                  | 139 kB     00:00     
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                                                                                                                        2.3 MB/s | 8.3 MB     00:03     
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing : openmotif-2.3.3-4.el6.x86_64                                                                                                                                                                                              1/6 
  Installing : nedit-5.5-23.el6.x86_64                                                                                                                                                                                                   2/6 
  Installing : xbae-4.60.4-12.el6.x86_64                                                                                                                                                                                                 3/6 
  Installing : netcdf-4.1.1-3.el6.2.x86_64                                                                                                                                                                                               4/6 
  Installing : fftw2-2.1.5-21.el6.x86_64                                                                                                                                                                                                 5/6 
  Installing : grace-5.1.22-7.el6.x86_64                                                                                                                                                                                                 6/6 

Installed:
  grace.x86_64 0:5.1.22-7.el6                                                                                                                                                                                                                

Dependency Installed:
  fftw2.x86_64 0:2.1.5-21.el6                   nedit.x86_64 0:5.5-23.el6                   netcdf.x86_64 0:4.1.1-3.el6.2                   openmotif.x86_64 0:2.3.3-4.el6                   xbae.x86_64 0:4.60.4-12.el6                  

Complete!
2. $ xmgrace
xmgrace: error while loading shared libraries: libhdf5_hl.so.6: cannot open shared object file: No such file or directory

Additional info:
I tried: # yum install hdf5 and # yum install hdf5-openmpi
But I still have the same error. Perhaps is it just a missing dependency?

Comment 1 Fabien Archambault 2011-11-15 09:03:54 UTC

I really need this (I believe I am not alone). Can someone help?

Comment 2 Fabien Archambault 2011-12-02 21:25:53 UTC

Please someone reply. This is like loosing the best software for science!

Comment 3 Fabien Archambault 2011-12-05 08:11:07 UTC

Ok I have found the problem it was a conflict with rpmforge which gives an higher version of hdf5...
I will report it to rpmforge as they do not provide enough tools to rebuild grace against there versions (netcdf missing).

Comment 4 José Matos 2011-12-05 09:59:35 UTC

The work to convert grace to use hdf5 will be done for rawhide first.

Comment 5 Dogan YILMAZ 2012-05-24 10:51:49 UTC

Please try: ( use epel repository! )
-------------------------------
yum erase grace netcdf hdf5*
yum install grace

you will see following packages will be installed:
-------------------------------
hdf5-1.8.5.patch1-7.el6.x86_64
netcdf-4.1.1-3.el6.2.x86_64
grace-5.1.22-7.el6.x86_64