Useful Repositories for CentOS 5

RPMForge - This repository is a collaboration of Dag
i386

# wget
http://packages.sw.be/rpmforge-release/rpmforge-release-0.5.2-2.el5.rf.i386.rpm

x86_64

# wget
http://packages.sw.be/rpmforge-release/rpmforge-release-0.5.2-2.el5.rf.x86_64.rpm

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Extra Packages for Enterprise Linux Repository (EPEL)
Architecture-independent

# wget 
http://dl.fedoraproject.org/pub/epel/5/i386/epel-release-5-4.noarch.rpm

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IUS Community Repository -
IUS is a new third party repo for RHEL that provides the "latest upstream versions of PHP, Python, MySQL.

# wget
http://dl.iuscommunity.org/pub/ius/stable/Redhat/5/x86_64/ius-release-1.0-10.ius.el5.noarch.rpm

For a full-listing, see

• Available Repositories for CentOS

General run-time tuning for Open MPI 1.4 and later (Part1)

Taken from 17. How do I tell Open MPI to use processor and/or memory affinity in Open MPI v1.4.x? (How do I use the –by* and –bind-to-* options?)
During the mpirun, you can put in the parameter of the Open MPI 1.4 and above to improve performance

1. –bind-to-none: Do not bind processes (Default)
2. –bind-to-core: Bind each MPI process to a core
3. –bind-to-socket: Bind each MPI process to a processor socket
4. –report bindings: Report how the launches processes are bound by Open MPI

If the hardware has multiple hardware threads like those belonging to Hyperthreading, only the first thread of each core is used with the -bind-to-*. According to the article, it is supposed to be fixed in v1.5
The following options below is to be used with –bind-to-*

1. –byslot: Alias for –bycore
2. –bycore: When laying out processes, put sequential MPI processes on adjacent processor cores. (Default)
3. –bysocket: When laying out processes, put sequential MPI processes on adjacent processor sockets.
4. –bynode: When laying out processes, put sequential MPI processes on adjacent nodes.

Finally you can use the –cpus-per-procs which binds ncpus OS processor IDS to each MPI process. If there is a machine with 4 cores and 4 cores, hence 16 cores in total.

$ mpirun -np 8 --cupus-per-proc 2 my_mpi_process

The command will bind each MPI process to ncpus=2 cores. All cores on the machine will be used.

Unable to restart pbs_mom on nodes

I was unable to restart the pbs_mom from one of the compute node. A look at the log file at /var/spool/torque/mom_logs shows

 # less /var/spool/torque/mom_logs

pbs_mom;Svr;pbs_mom;LOG_ERROR::pbs_mom, 
Unable to get my full hostname for grapefruit.local.spms.ntu.edu.sg error -1

 Once you have this type of error, torque server will not be able to manage pbs_mom on the node which have this error

To solve the issues, it is very simple, you have to resolve the hostname discrepancy client hostname information between what the Torque Server has and what Torque Client. Check that the /etc/hostname or /etc/resolv.conf have the necessary information. Look at the Changing the hostname on CentOS on how to change hostname.

Data ONTAP Cluster-Mode Vsim Tutorial

10 steps to a 2-node Data ONTAP 8.1.1 Cluster-Mode Vsim cluster. See https://www.youtube.com/watch?feature=player_embedded&v=prEf5J0wvi0

Unable to SSH due to failure of authentication with GSSAPI

I have a very slow or failed ssh connection due to failure with authentication with GSSAPI. See below my error

.....
debug1: Authentications that can continue: publickey,gssapi-with-mic,password
debug1: Next authentication method: gssapi-with-mic
debug1: Unspecified GSS failure.  Minor code may provide more information Unknown code krb5 195
debug1: Unspecified GSS failure.  Minor code may provide more information Unknown code krb5 195
debug1: Unspecified GSS failure.  Minor code may provide more information Unknown code krb5 195
debug1: Next authentication method: publickey
debug1: Trying private key: /home/user1/.ssh/identity
.....

It seems that when the ssh connection first try to authenticate with GSSAPI and when it failed, it switched to the publickey.

To change the ssh at user level

$ vim ~/.ssh/config

GSSAPIAuthentication no 

To change at global level

# /etc/ssh/sshd_config

GSSAPIAuthentication no 

More Information

1. Slow SSH connections – hanging at GSSAPI auth