Unable to detect bamlib libraries (version or higher) when installing cufflinks

If you are installing Cufflinks according to the instructions as given by http://cufflinks.cbcb.umd.edu/tutorial.html. 

The compiling of the components below are quite expected.
boost,
eigen,
samtools

But when finally compiling cufflinks, you might encounter errors

.....
..... 
checking for bamlib... configure: error: We could not detect the bam libraries 
(version    or higher). If you have a staged bam library (still not installed) 
please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option.  
If you are sure you have bam installed, then check your version number looking in......... 
See http://randspringer.de/bam for more documentation. 

The source of the error is somehow the cufflinks is not able to find the libraires and binaries found by samtools. This is especially true if you compiled the components into distinct directories and not into standard directories like /usr/local/bin and /usr/local/lib /usr/local/include

To ensure that the cufflinks detects the samtools libraries, you might want to do the following.

# mkdir -p /usr/local/include/bam
# cp ${SAMTOOLS}/libbam.a /usr/local/lib/
# cp ${SAMTOOLS}/*.h /usr/local/include/bam
# cp ${SAMTOOLS}/samtools /usr/local/bin/

Try compiling again. It should work

Uninstalling and reinstalling Intel XE 2013

I installed a non-commercial version of Intel XE 2013 and realise that I wanted to change the installation directory. I realise that for Intel XE 2013 does not have an uninstall script (install-dir/bin/uninstall.sh) like previous version.

A simple removal of the intel directory does not allow me to have a good clean installation like choosing installation directory.It is likely due to the presence of rpm information still remaining in the rpm database.

To solve the issue, I use the command 

# for i in `rpm -qa | grep intel` ; do rpm -e $i ; done

You may need to run the command 2-3 times to ensure all the dependencies and intel packages are totally cleaned up

US-Cert Alert - Oracle has released multiple updates for Java SE

US Cert has released the alert to patch the Java SE

Here is the excerpts of the alert.

Overview
Oracle has released a Critical Patch Update (CPU) for Java SE. Oracle strongly recommends that customers apply CPU fixes as soon as possible.

Description
Oracle Java SE Critical Patch Update Advisory - April 2013 describes the update as:
A Critical Patch Update is a collection of patches for multiple security vulnerabilities. The Critical Patch Update for Java SE also includes non-security fixes. Critical Patch Updates are cumulative and each advisory describes only the security fixes added since the previous Critical Patch Update and Security Alert. Thus, prior Critical Patch Update and Security Alert advisories should be reviewed for information regarding earlier accumulated security fixes.

Impact
A remote, unauthenticated attacker could execute arbitrary code, cause a denial of service, or gain unauthorized access to your files or system.

Solution
Apply Updates

Oracle Java SE Critical Patch Update Advisory - April 2013 includes the following information:

1. Developers can download the latest release from http://www.oracle.com/technetwork/java/javase/downloads/index.html.
2. Users running Java SE with a browser can download the latest release from http://java.com.
3. Users on the Windows and Mac OS X platforms can also use automatic updates to get the latest release.
4. The latest JavaFX release is included with the latest update of JDK and JRE 7. For JDK and JRE 6 users, the latest Java FX release is available from http://www.oracle.com/technetwork/java/javafx/

References
 * Oracle Java SE Critical Patch Update Advisory - April 2013

Starting VNC server: no displays configured on CentOS 6

One of the issue I faced when starting VNC for the first time can be found at Unable to launch VNCServer due to fontpath issues on CentOS 6

Another issue I faced when starting up ie

# service vncserver restart 

You might see this error

Starting VNC server: no displays configured  on CentOS 6

To solve the issues, you have to look at the CentOS Howto for VNC (Virtual Networking Computing)
The portion that helped me was
.....
.....
Edit /etc/sysconfig/vncservers, and add the following to the end of the file.

VNCSERVERARGS[1]="-geometry 640x480"
VNCSERVERARGS[2]="-geometry 640x480"
VNCSERVERARGS[3]="-geometry 800x600"

.....
.....

After editing the vncserver, start the vncserver. You should eliminate the error

# service vncserver start 

Encounter E437: terminal capability "cm" required Press ENTER or type command to continue on CentOS 6

When one of the researcher typed vi, vim, you might encounter an error 

Encounter E437: terminal capability "cm" required 
Press ENTER or type command to continue

# yum install ncurses-term

To verify

# ls /usr/share/terminfo/d  

shows lots of entries


Reference from:

1.  E437: terminal capability “cm” required in Redhat or Centos 6

Disabling the virbr0 NAT Interface

Taken from Linux KVM: Disable virbr0 NAT Interface

 If you accidentally install the KVM components and you do not wish to use the interface, you will notice when you do ifconfig, you will see the "virbro"

virbr0    Link encap:Ethernet  HWaddr 00:00:00:00:00:00
          inet addr:192.168.1.1  Bcast:192.168.122.255  Mask:255.255.255.0
          inet6 addr: fe80::202:c9ff:fee5:70b0/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:0 errors:0 dropped:0 overruns:0 frame:0
          TX packets:6885 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:0
          RX bytes:17192337 (16.3 MiB)  TX bytes::1107966 (1.0 MiB)

If you use the follow command

# virsh net-list

Name                 State      Autostart
-----------------------------------------
default              active     yes

# virsh net-destroy default
# virsh net-undefine default
# service libvirtd restart

Clearing memory cache

First thing you need is kernel 2.6.16
The command to clear the memory cache.

# sync
# echo 3 > /proc/sys/vm/drop_caches

sync -> refers to the tells the kernel that you want the data written to the disk
echo 3 > /proc/sys/vm/drop_caches -> "To free pagecache, dentries and inodes:"

From the article Invalidating the Linux buffer cache ,

To free pagecache:    
# echo 1 > /proc/sys/vm/drop_caches

To free dentries and inodes:
# echo 2 > /proc/sys/vm/drop_caches

To free pagecache, dentries and inodes:
# echo 3 > /proc/sys/vm/drop_caches

References:

1. Invalidating the Linux buffer cache 
2. HOWTO: Clear filesystem memory cache
3. drop_caches

Using MOAB mdiag -n to provide state of nodes

mdiag -n command provides detailed information about the state of nodes Moab or MAUi is currently tracking

Name                State  Procs     Memory         Disk          Swap      Speed  Opsys   Arch Par   Load Res Classes                        Network                        Features

Node-c00            Idle   8:8    32161:32161       1:1       62862:64158   2.10  linux [NONE] DEF   0.00 000 [rambutan_8:8][queue_8:8][lemo [DEFAULT]    
.....
.....
Node-c03            Busy   0:8    32161:32161       1:1       62735:64158   2.10  linux [NONE] DEF   8.00 001 [rambutan_8:8][queue_0:8][queue [DEFAULT]
.....
.....

Interesting Columns that I would find especially useful is the STATE, Procs (Available Core), Swap and Load

You can further refine the search

# mdiag -n |grep Busy
# mdiag -n|grep Idle

Chelsio announced Terminator 5 ASIC

 

Spotlight on 40Gb Ethernet with Terminator 5

Chelsio Announced the Terminator 5 ASIC, a highly integrated, hyper-virtualized 10/40GbE controller built around a programmable protocol-processing engine, with full offload of a complete Unified Wire solution.

Key features of T5

·         Ultra low latency and high IOPs

·         Two 40Gb ports

·         Four 10Gb/1Gb ports

·         PCIe Gen3

·         Concurrent offload of iSCSI, TCP/IP and UDP/IP, FCoE, iWARP RDMA, NAT, vSwitch, Traffic Management and PTP applications

·         Added support for PTP, iWARP 2.0, T10 DIX, NAT

·         Same software on Linux, Windows and FBSD as current T4 ASIC

The Terminator 5 ASIC Architecture White Paper

Error encountered when running ant on CentOS 5

Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other.

After yum installing the following packages

# yum install ant javacc

which will install the package ant-1.6.5-2jpp.2.x86_64.rpm, javacc.x86_64 0:4.0-3jpp.3.rpm

When I type ant, I encountered the following error

/usr/bin/build-classpath: error: Could not find xml-commons-apis Java
>> extension for this JVM

Solution:
---------

# yum install xml-commons xml-comms-apis

$ ant
Buildfile: build.xml does not exist!
Build failed

I think you can specify the ants using the ant -f "build_file"

Device eth0 does not seem to be present, delaying initialization on CentOS

When I use the command

# ifup eth3

I received the error

"device eth3 does not seem to be present, delaying initialization"

First thing first, Do check whether the network card is there, do use the command

# lspci |grep Mellanox

If the card is detected, do use this command to show the link. This will give you the clues on

# ip -o link

.....
.....
2: eth3:  mtu 1500 qdisc pfifo_fast qlen 1000\ 
link/ether 00:00:00:00:00:01 brd ff:ff:ff:ff:ff:ff
3: eth4:  mtu 1500 qdisc pfifo_fast qlen 1000\ 
link/ether 00:00:00:00:00:02 brd ff:ff:ff:ff:ff:ff
.....
.....

References:

1. device eth1 does not seem to be present, delaying initialization from AR

Using pam_pbssimpleauth.so to authorise login for users for Torque

For a cluster shared by many users, it is important to prevent errant users from directly ssh into the compute nodes, thus bypassing the scheduler. To implement the pam module, compile the Torque Server based on Installing Torque 2.5 on CentOS 6
Step 1: You should be able to find the pam_pbssimpleauth.so packages at

$TORQUE_HOME/tpackages/pam/lib64/security/pam_pbssimpleauth.a
$TORQUE_HOME/tpackages/pam/lib64/security/pam_pbssimpleauth.la
$TORQUE_HOME/tpackages/pam/lib64/security/pam_pbssimpleauth.so

Step 2: Copy the  pam_pbssimpleauth.so to the compute nodes. Step 2b: DO not put the pam_pbssimpleauth.so in on the Head Node

# scp $TORQUE_HOME/tpackages/pam/lib64/security/pam_pbssimpleauth.so node1:/lib64/security/

Step 3: Verify that the access.so is also present in the /lib64/security/ directory

# ls /lib64/security/access.so

Step 4: Add the access.so and pam_pbssimpleauth.so in the PAM configuration files

# vim /etc/pam.d/sshd

auth       required     pam_sepermit.so
auth       include      password-auth
account    required     pam_nologin.so

account    required     pam_pbssimpleauth.so
account    required     pam_access.so

account    include      password-auth
password   include      password-auth
.....
.....

When a user ssh’s to a node, this module will check the .JB files in $PBS_SERVER_HOME/mom_priv/jobs/ for a matching uid and that the job is running.
You can try the configuration

Unable to launch VNCServer due to fontpath issues on CentOS 6

When trying out VNCServer on both CentOS 6.2 and CentOS 6.3

$ vncserver 

WARNING: The first attempt to start Xvnc failed, possibly because the font
catalog is not properly configured.  Attempting to determine an appropriate
font path for this system and restart Xvnc using that font path ...
Could not start Xvnc.

/usr/bin/Xvnc: symbol lookup error: /usr/bin/Xvnc: undefined symbol: 
pixman_composite_trapezoids
/usr/bin/Xvnc: symbol lookup error: /usr/bin/Xvnc: undefined symbol: 
pixman_composite_trapezoids

The solution is to Install / Update

1. The Pixel manipulation library development package (pixman, pixman-devel)
2. X font handling library for server (libXfont) 

 Interestingly, the default installation of X Windows misses out these packages

# yum install pixman pixman-devel libXfont

Intel Parallel Studio XE 2013 Software Updates

Intel Software has a couple of updates for Compilers, Math Kernel Libraries, Threading Building Blocks that have been released on 28 March

1. Intel® C++ Composer XE for Linux* 2013 Update 3 Eng/Jpn
2. Intel® Fortran Composer XE for Linux* 2013 Update 3 Eng/Jpn
3. Intel® Math Kernel Library for Linux* 11.0 Update 3
4. Intel® Threading Building Blocks for Linux* 4.1 Update 3

For more information, do look at Intel Parallel Studio XE 2013