Installing Octave with HDF5 on CentOS 6.8 with yum

If you are installing octave on CentOS6 and you wish to install HDF5, you may want to pull HDF5 from EPEL instead of RPMFORGE. You may have both repositories so you have to disable RPMFORGE first

# yum-config-manager --disable rpmforge

Install Octave with HDF5

# yum install octave hdf5 hdf5-devel

Cannot retrieve metalink for repository: epel. Please verify its path and try again

I was doing a yum install and I encountered an error

# yum install libstdc++-4.4.7-16.el6.x86_64
Loaded plugins: fastestmirror, refresh-packagekit, security
Loading mirror speeds from cached hostfile
Error: Cannot retrieve metalink for repository: epel. 
Please verify its path and try again

The correct fix is to update your SSL certificates.

# yum upgrade ca-certificates --disablerepo=epel -y

Yum install again. You should be able to work.

# yum install libstdc++-4.4.7-16.el6.x86_64

Yum giving "Cannot retrieve metalink for repository: epel" Error for CentOS 6

When I was updating yum install or doing yum update on CentOS 6.4, I received an error "Cannot retrieve metalink for repository: epel"

The error is because of the scripts in the epel.repo under the mirrorlist pointing to https instead of http. If you amend it to http, the epel repo will work

 At /etc/yum/repos.d/epel.repo, change to

[epel]
.....
.....
mirrorlist=http://mirrors.fedoraproject.org/metalink?repo=epel-6&arch=$basearch

[epel-debuginfo]
.....
.....
mirrorlist=http://mirrors.fedoraproject.org/metalink?repo=epel-debug-6&arch=$basearch

References:

1. CentOS 6.3 Instance Giving "Cannot retrieve metalink for repository: epel" Error

Install GCC 4.8.1 and other Scientitic Packages via Yum on CentOS

Do take a look at Linux @ CERN for the documentation on how to use yum to install devtoolset which contain the following packages. The latest version for CentOS 6 is devtoolset-2.1. Here is a summary of the Linux @ CERN

CentOS 6 / SL 6

Developer Toolset 2.1 provides following tools:

• gcc/g++/gfortran - GNU Compiler Collection - version 4.8.2
• gdb - GNU Debugger - version 7.6.34
• binutils - A GNU collection of binary utilities - version 2.23.52
• elfutils - A collection of utilities and DSOs to handle compiled objects - version 0.155
• dwz - DWARF optimization and duplicate removal tool - version 0.11
• systemtap - Programmable system-wide instrumentation system - version 2.1
• valgrind - Tool for finding memory management bugs in programs - version 3.8.1
• oprofile - System wide profiler - version 0.9.8
• eclipse - An Integrated Development Environment - version 4.3.1 (Kepler)

CentOS 5 / SL 5

Developer Toolset 1.1 provides following tools:

• gcc/g++/gfortran - GNU Compiler Collection - version 4.7.2
• gdb - GNU Debugger - version 7.5
• binutils - A GNU collection of binary utilities - version 2.23.51
• elfutils - A collection of utilities and DSOs to handle compiled objects - version 0.154
• dwz - DWARF optimization and duplicate removal tool - version 0.7
• systemtap - Programmable system-wide instrumentation system - version 1.8
• valgrind - Tool for finding memory management bugs in programs - version 3.8.1
• oprofile - System wide profiler - version 0.9.7

Installation and Enablement

CentOS 6 / SL 6
Save repository information as /etc/yum.repos.d/slc6-devtoolset.repo on your system:

# cd /etc/yum.repos.d/ 
# wget -O /etc/yum.repos.d/slc6-devtoolset.repo http://linuxsoft.cern.ch/cern/devtoolset/slc6-devtoolset.repo
# yum install devtoolset-2 --nogpgcheck
# scl enable devtoolset-2 bash

CentOS 5 / SL 5
Save repository information as /etc/yum.repos.d/slc5-devtoolset.repo on your system:

# cd /etc/yum.repos.d/
# wget -O /etc/yum.repos.d/slc5-devtoolset.repo http://linuxsoft.cern.ch/cern/devtoolset/slc5-devtoolset.repo
# yum install devtoolset-1.1
# scl enable devtoolset-1.1 bash

Error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory on CentOS 6

If you using gaussview and you encountered this error on CentOS 6 or RH6, 

$ /usr/local/gaussian/gv/gview.exe: error while loading shared libraries: 
libXmu.so.6: cannot open shared object file: No such file or directory

This is due to the missing libXmu libraries and related dependencies. Just simply do a

# yum install libXmu*

or if you wish to check which repo supplies the libXmu

# yum whatprovides libXmu

libXmu-1.1.1-2.el6.i686 : X.Org X11 libXmu/libXmuu runtime libraries
Repo        : base
Matched from:

libXmu-1.1.1-2.el6.x86_64 : X.Org X11 libXmu/libXmuu runtime libraries
Repo        : base
Matched from:

libXmu-1.1.1-2.el6.i686 : X.Org X11 libXmu/libXmuu runtime libraries
Repo        : installed
Matched from:
Other       : Provides-match: libXmu

Error: php53-common conflicts with php-common when installing php53-xml on CentOS 5

I was trying to install php53-xml on CentOS 5.5. But instead I encountered the error instead. I', assuming  you have activated the webtatic repo and install the rest of the php 5.3 components like the How to yum install PHP 5.3 for CentOS 5

php53-common-5.3.3-21.el5.i386 from base has depsolving problems
  --> php53-common conflicts with php-common
Error: php53-common conflicts with php-common
 You could try using --skip-broken to work around the problem
 You could try running: package-cleanup --problems
                        package-cleanup --dupes
                        rpm -Va --nofiles --nodigest
The program package-cleanup is found in the yum-utils package.

The issue of the problem is that the current PHP from webtatic is 5.3.27, but the one from yum php53-xml is 5.3.3 which is higher. To solve the issue, you have to use the php-xml from webtatic

# yum install  php-xml

Conflict when yum install perl-XML-SAX-0.96-7.el6.noarch on CentOS 6

When yum install perl-XML-SAX, you may encounter an error something like this

Transaction Check Error:
  file /usr/share/man/man3/XML::SAX::Base.3pm.gz conflicts between attempted 
installs of perl-XML-SAX-0.96-7.el6.noarch and perl-XML-SAX-Base-1.04-1.el6.rf.noarch
  file /usr/share/man/man3/XML::SAX::Exception.3pm.gz conflicts between attempted 
installs of perl-XML-SAX-0.96-7.el6.noarch and perl-XML-SAX-Base-1.04-1.el6.rf.noarch

The reason for this is due to the conflict of packages between the CentOS base repo (perl-XML-SAX-0.96-7)  and those found at rpmforge (perl-XML-SAX-Base-1.04-1).

The resolution is to disable the perl-XML-SAX-Base-1.04-1 found at rpmforge. You can do it by putting this line at /etc/yum.repos.d/rpmforge.repo

.....
.....
exclude=perl-XML-SAX-Base
.....
.....

Error installing X11 libraries

If you have error installing X11 libraries for CentOS 5 or CentOS 6, you may want to check whether you have already installed the correct group. To do a grouplist,

 Do  yum grouplist

# yum grouplist 
Installed Groups:
   Administration Tools
   Authoring and Publishing
   Development Libraries
   Development Tools
   Editors
   GNOME Desktop Environment
   Graphics
   Legacy Network Server
   Legacy Software Development
   Legacy Software Support
   Mail Server
   MySQL Database
   Network Servers
   Office/Productivity
   OpenFabrics Enterprise Distribution
   Printing Support
   Server Configuration Tools
   System Tools
   X Software Development
   X Window System
Available Groups:
   Cluster Storage
   Clustering
   DNS Name Server
   Engineering and Scientific
   FTP Server
   GNOME Software Development
   Games and Entertainment
   Graphical Internet
   Java Development
   KDE (K Desktop Environment)
   KDE Software Development
   KVM
   News Server
   PostgreSQL Database
   Sound and Video
   Text-based Internet
   Web Server
   Windows File Server
   Xen

Do a yum groupinstall "X Software Development"

 # yum groupinstall "X Software Development"

Installing matplotlib using yum

matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.

Make sure you have EPEL and RPMForge repositories installed. For more information, do look at
Useful Repositories for CentOS 5

To install matplotib using yum, do the following

# yum install python-matplotlib

Solving python-nose depsolving problems using yum

If you have this error below, it is because somehow yum is not able to download and install python-nose package. To resolve it, download manually python-nose package from a machine which is able to. The machine just name a internet connection and of course have the CentOS base repository enabled.

python-nose-0.11.3-2.el5.noarch from epel has depsolving problems
  --> Missing Dependency: python-setuptools is needed by package python-nose                  1.3-2.el5.noarch (epel)
Error: Missing Dependency: python-setuptools is needed by package python-nos                  11.3-2.el5.noarch (epel)
 You could try using --skip-broken to work around the problem
 You could try running: package-cleanup --problems
                        package-cleanup --dupes
                        rpm -Va --nofiles --nodigest
The program package-cleanup is found in the yum-utils package.

Do a yumloader python. For more information on  yumloader, do look at Using yum to download the rpm package that have already been installed

# yumdownloader python-setuptools

Next do a rpm install

# rpm -Uvh python-setuptools-0.6c5-2.el5.noarch.rpm
warning: python-setuptools-0.6c5-2.el5.noarch.rpm: Header V3 DSA signature: 
NOKEY, key ID e8562897
Preparing...                ########################################### [100%]
   1:python-setuptools      ########################################### [100%]

Now you can do a normal yum install 

using yum to manage software groups for CentOS

This is a simple entry and probably you will know already. Just a reminder for me too :)

List the available groups from all yum repos

# yum grouplist

List the description and package list of a group

# yum groupinfo "General Purpose Desktop"

 
 Remove  all  of  the  packages  in  a  group

# yum groupremove  "System administration tools"

Displaying Repository List with yum

If you wish to display a list of configured repositories which are enabled, you can use the command

# yum repolist

repo id        repo name                                                  status
epel           Extra Packages for Enterprise Linux 5 - x86_64              7,242
ius            IUS Community Packages for Enterprise Linux 5 - x86_64        229
rpmforge       Red Hat Enterprise 5 - RPMforge.net - dag                  11,158
xcat-2-core    xCAT 2 Core packages                                           14
xcat-dep       xCAT 2 depedencies                                             38
repolist: 18,681

# yum -v repolist

Repo-id      : epel
Repo-name    : Extra Packages for Enterprise Linux 5 - x86_64
Repo-revision: 1360778202
Repo-tags    : binary-x86_64
Repo-updated : Thu Feb 14 01:59:23 2013
Repo-pkgs    : 7,242
Repo-size    : 5.4 G
Repo-mirrors : http://mirrors.fedoraproject.org/mirrorlist?repo=epel-5&arch=x86_64
Repo-expire  : 3,600 second(s) (last: Sat Feb 16 01:03:31 2013)

Repo-id      : ius
Repo-name    : IUS Community Packages for Enterprise Linux 5 - x86_64
Repo-revision: 1360910159
Repo-updated : Fri Feb 15 14:36:21 2013
Repo-pkgs    : 229
Repo-size    : 441 M
Repo-mirrors : http://dmirr.iuscommunity.org/mirrorlist/?repo=ius-el5&arch=x86_64
Repo-expire  : 3,600 second(s) (last: Sat Feb 16 01:03:35 2013)

Repo-id      : rpmforge
Repo-name    : Red Hat Enterprise 5 - RPMforge.net - dag
Repo-updated : Fri Dec 21 10:44:36 2012
Repo-pkgs    : 11,158
Repo-size    : 5.8 G
Repo-baseurl : http://apt.sw.be/redhat/el5/en/x86_64/rpmforge/
Repo-mirrors : http://apt.sw.be/redhat/el5/en/mirrors-rpmforge
Repo-expire  : 3,600 second(s) (last: Sat Feb 16 01:03:38 2013)

Repo-id      : xcat-2-core
Repo-name    : xCAT 2 Core packages
Repo-updated : Wed Nov 28 11:01:51 2012
Repo-pkgs    : 14
Repo-size    : 3.2 M
Repo-baseurl : https://sourceforge.net/projects/xcat/files/yum/2.7/xcat-core/
Repo-expire  : 3,600 second(s) (last: Sat Feb 16 01:03:44 2013)

Repo-id      : xcat-dep
Repo-name    : xCAT 2 depedencies
Repo-updated : Wed Feb  6 05:37:39 2013
Repo-pkgs    : 38
Repo-size    : 82 M
Repo-baseurl : https://sourceforge.net/projects/xcat/files/yum/xcat-dep/rh5/x86_64/
Repo-expire  : 3,600 second(s) (last: Sat Feb 16 01:03:51 2013)

repolist: 18,681 

Resolving error libthread-2.0.so.0 on Schrodinger

While executing maestro Schrodinger on CentOS 6, I encountered the following error

/usr/local/schrodinger/maestro-v90211/bin/Linux-x86/maestro: error while loading shared libraries: libgthread-2.0.so.0: cannot open shared object file: No such file or directory
Maestro: Could not load shared library

You have to install glib2 libraries first

# yum install glib2

Dependencies Resolved

===============================================================================================
 Package                 Arch               Version                     Repository        Size
===============================================================================================

Updating:
 glib2                   x86_64             2.22.5-7.el6                base             1.1 M

Updating for dependencies:
 glib2-devel             x86_64             2.22.5-7.el6                base             1.3 M

Transaction Summary
===============================================================================================
Upgrade       2 Package(s)

Total download size: 2.4 M
Is this ok [y/N]: Y

Now install libgthread-2.0.so.0 and its dependencies

# yum install libgthread-2.0.so.0

Dependencies Resolved

===============================================================================================
 Package             Arch               Version                       Repository          Size
===============================================================================================

Installing:
 glib2               i686               2.22.5-7.el6                  base               1.1 M
Installing for dependencies:
 gamin               i686               0.1.10-9.el6                  base               120 k

Transaction Summary
===============================================================================================
Install       2 Package(s)

Total download size: 1.2 M
Installed size: 5.4 M
Is this ok [y/N]: N
Exiting on user Command 

Finding yum install for rpmlibs

If you are looking to install rpmlibs, you can do

# yum install rpm-devel

=======================================================================================
 Package         Arch        Version                                Repository    Size
=======================================================================================
Updating:
 rpm-devel       i386        4.4.2.3-28.el5_8                       updates      1.2 M
 rpm-devel       x86_64      4.4.2.3-28.el5_8                       updates      1.3 M
Installing for dependencies:
 xz              x86_64      4.999.9-0.3.beta.20091007git.el5       base         146 k
 xz-libs         x86_64      4.999.9-0.3.beta.20091007git.el5       base          95 k
Updating for dependencies:
 popt            i386        1.10.2.3-28.el5_8                      updates       76 k
 popt            x86_64      1.10.2.3-28.el5_8                      updates       78 k
 rpm             x86_64      4.4.2.3-28.el5_8                       updates      1.2 M
 rpm-build       x86_64      4.4.2.3-28.el5_8                       updates      303 k
 rpm-libs        i386        4.4.2.3-28.el5_8                       updates      929 k
 rpm-libs        x86_64      4.4.2.3-28.el5_8                       updates      925 k
 rpm-python      x86_64      4.4.2.3-28.el5_8                       updates       64 k

Transaction Summary
=======================================================================================
Install      2 Package(s)
Update       9 Package(s)
Remove       0 Package(s)

Total download size: 6.3 M
Is this ok [y/N]:

Yum cannot retrieve repository metadata for CentOS 5

If you encountered this type of errors, do look at your repo configuration at /etc/yum.repos.d. In my situation, I was trying to update a package which falls under Centos-Base.repo

http://mirror.centos.org/centos/5/addons/x86_64/repodata/repomd.xml: [Errno 12] 
Timeout: 
Trying other mirror.
Error: Cannot retrieve repository metadata (repomd.xml) for repository: 
addons. Please verify its path and try again

http://mirror.centos.org/centos/5/addons/x86_64/repodata/primary.sqlite.bz2: 
[Errno 12] Timeout: Trying other mirror.
http://mirror.centos.org/centos/5/addons/x86_64/repodata/primary.sqlite.bz2: 
Errno 12] Timeout: Trying other mirror.
Error: failure: repodata/primary.sqlite.bz2 from addons: 
[Errno 256] No more mirrors to try.
 

3 things you need to do

1. Check that your mirriorlist in /etc/yum.repo.d is uncommented. It should look something like
   mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=updates
2. Check that your baseurl is uncommented. (Usually this is not needed, but this is a last resort
   baseurl=http://mirror.centos.org/centos/$releasever/os/$basearch/
3. Type the parameter in the repo list
   enabled=1

How to fix a broken yum for CentOS

When we type the command yum, we encounter the error such as the one below.

# yum update
Loaded plugins: downloadonly, fastestmirror
Loading mirror speeds from cached hostfile
Traceback (most recent call last):
  File "/usr/bin/yum", line 29, in ?
    yummain.user_main(sys.argv[1:], exit_code=True)
  File "/usr/share/yum-cli/yummain.py", line 309, in user_main
    errcode = main(args)
  File "/usr/share/yum-cli/yummain.py", line 178, in main
    result, resultmsgs = base.doCommands()
  File "/usr/share/yum-cli/cli.py", line 345, in doCommands
    self._getTs(needTsRemove)
  File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 101, in _getTs
    self._getTsInfo(remove_only)
  File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 112, in _getTsIn                                                                             fo
    pkgSack = self.pkgSack
  File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 661, in 
    pkgSack = property(fget=lambda self: self._getSacks(),
  File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 501, in _getSack                                                                             s
    self.repos.populateSack(which=repos)
  File "/usr/lib/python2.4/site-packages/yum/repos.py", line 232, in populateSac                                                                             k
    self.doSetup()
  File "/usr/lib/python2.4/site-packages/yum/repos.py", line 79, in doSetup
    self.ayum.plugins.run('postreposetup')
  File "/usr/lib/python2.4/site-packages/yum/plugins.py", line 179, in run
    func(conduitcls(self, self.base, conf, **kwargs))
  File "/usr/lib/yum-plugins/fastestmirror.py", line 181, in postreposetup_hook
    all_urls = FastestMirror(all_urls).get_mirrorlist()
  File "/usr/lib/yum-plugins/fastestmirror.py", line 333, in get_mirrorlist
    self._poll_mirrors()
  File "/usr/lib/yum-plugins/fastestmirror.py", line 376, in _poll_mirrors
    pollThread.start()
  File "/usr/lib64/python2.4/threading.py", line 416, in start
    _start_new_thread(self.__bootstrap, ())
thread.error: can't start new thread
 

Possible Solution 1: (which solve my problem immediately). Modify the the following.

# yum clean all
# vim /etc/yum/pluginconf.d/fastestmirror.conf

enabled=0

Possible Solution 2: The good old yum clean all. (Clean everything)

# yum clean all
Loaded plugins: downloadonly, fastestmirror
Cleaning up Everything
Cleaning up list of fastest mirrors

Possible Solution 3: Rebuild the yum database

# yum clean all
# rm -f /var/lib/rpm/__db*
# rpm --rebuilddb
# yum update

Hope this help.

Malformed database image issue with yum

Today I was doing a yum install after updating my LVM and I suffered a "malformed database image issue". This error can be easily rectify. Just do a

# yum clean dbcache

Then do a

# yum check

Getting Yum to install from selected repository only

Working from Using Yum to local install without checking Repository, you can use the same principle to install from selected repository while disabling the rest.

# yum --disablerepo=* --enablerepo=dag install (packages)

where dag and update are repositories. If you are not sure the repository names to use, go to /etc/yum.repos.d/xxx.repo. The first line [.....] is the repository names

Using Yum Provides

This is a continuation of Using Yum effectively (Part 1) and Using Yum effectively (Part 2)

I have learned a cool command line "yum provides". "yum provides" help you search for the packages that will install either a file or directory. For example

# yum provides bash

bash-3.2-24.el5.x86_64 : The GNU Bourne Again shell (bash) version 3.2
Repo : base
Matched from:

bash-3.2-24.el5.x86_64 : The GNU Bourne Again shell (bash) version 3.1.
Repo : installed
Matched from:
Other : Provides-match: bash

Installing lapack, blas and atlas on CentOS 5

Installing lapack, blas and atlas on CentOS 5.4 is very simple.Firstly you must enable the follow repositories:

1. atlas package - EPEL (For more information on how to download EPEL, see Red Hat Enterprise Linux / CentOS Linux Enable EPEL Repository
2. blas and lapack packages - RPMForge (For more information on how to download RPMForge, See Install RPMForge

Installing atlas, blas and lapack x86_64 packages

# yum install atlas.x86_64 blas.x86_64 lapack.x86_64