Month: April 2012

by

Building LAPACK 3.4 with Intel and GNU Compiler

The reference resource can be found from Building LAPACK library from Netlib. The current latest version of LAPACK is dated 11th November 2011. The current latest version is lapack-3.4.0.tgz.

LAPACK relied on BLAS. See Building BLAS Library using Intel and GNU Compiler

# mkdir -p ~/src
# wget http://www.netlib.org/lapack/lapack-3.4.0.tgz
# tar -zxvf lapack-3.4.0.tgz
# cd lapack-3.4.0.tgz
# cp INSTALL/make.inc.ifort make.inc
# make lapacklib
# make clean
# mkdir -p /usr/local/lapack
# mv liblapack.a /usr/local/lapack/
# export LAPACK=/usr/local/lapack/liblapack.a

For gfortran 64-bits compiler

# cp INSTALL/make.inc.gfortran make.inc

Edit the make.inc

PLAT = _LINUX
OPTS = -O2 -m64 -fPIC
NOOPT = -m64 -fPIC
# make lapacklib
# make clean
# mkdir -p /usr/local/lapack
# mv liblapack.a /usr/local/lapack/
# export LAPACK=/usr/local/lapack/liblapack.a

For more information on LAPACK, see LAPACK — Linear Algebra PACKage

by

Building BLAS Library using Intel and GNU Compiler

The reference resource can be found from Building BLAS library from Netlib. The current latest version of BLAS is dated 14th April 2011.

1. For Intel XE Compiler

# mkdir -p ~/src/
# cd ~/src/
# wget http://www.netlib.org/blas/blas.tgz
# tar -zxvf blas.tgz
# cd BLAS
# ifort -FI -w90 -w95 -cm -O3 -unroll -c *.f
# ar r libfblas.a *.o
# ranlib libfblas.a
# rm -rf *.o
# export BLAS=~/src/BLAS/libfblas.a
# ln -s libfblas.a libblas.a
# mv ~/src/BLAS /usr/local/

2. For 64-bits gfortran Compiler. Replace ” ifort -FI -w90 -w95 -cm -O3 -unroll -c *.f ” with

.........
# gfortran -O3 -std=legacy -m64 -fno-second-underscore -fPIC -c *.f
.........

The rest remains the same.

3. For 64-bits g77 Compiler. Replace ” ifort -FI -w90 -w95 -cm -O3 -unroll -c *.f ” with

............
# g77 -O3 -m64 -fno-second-underscore -fPIC -c *.f
............

The rest remains the same.

by

Installing Chelsio driver CD on an ESX 4.x host

This article is taken and modified from Installing the VMware ESX/ESXi 4.x driver CD on an ESX 4.x host (VMware Knowledge Base)

Step 1: Download the Chelsio Drivers for ESX

Download from relevant drivers for your sepcific cards from  Chelsio Download Centre

Step 2: Follow the instruction from VMware

Note: This procedure requires you to place the host in Maintenance Mode, which requires downtime and a reboot to complete installation. Ensure that any virtual machines that need to stay live are migrated, or plan for proper down time if migration is not possible.
  1. Download the driver CD from the vSphere Download Center.
  2. Extract the ISO on your local workstation using an third-party ISO reader (such as WinISO). Alternatively, you can mount the ISO via SSH with the command:

    mkdir /mnt/iso mount -o loop filename.iso /mnt/iso

    Note: Microsoft operating systems after Windows Vista include a built-in ISO reader.

  3. Use the Data Browser in the vSphere Client to upload the ZIP file that was extracted from the ISO to your ESX host.

    Alternatively, you can use a program like WinSCP to upload the file directly to your ESX host. However, you require root privileges to the host to perform the upload.

  4. Log in to the ESX host as root directly from the Service Console or through an SSH client such as Putty.
  5. Place the ESX host in Maintenance Mode from the vSphere Client.
  6. Run this command from the Service Console or your SSH Client to install the bundled package:

    esxupdate –bundle=<name of bundled zip> update

  7. When the package has been installed, reboot the ESX host by typing reboot from the Service Console.

Note: VMware does not endorse or recommend any particular third party utility, nor are the above suggestions meant to be exhaustive.

by

Enabling Torque for email notification

Step 1:

  1. Do look at the article Configuring CentOS 5 as an SMTP Mail Client with sendmail for configuring your Torque Server to become a SMTP Mail Client.

Step 2:

Ensure the Torque Server has this line

  1. “set server mail_from = adm”(You can replace adm with another useird of your choice). You may want to take a look at Setting up Torque Server on xCAT 2.x from Linux Toolkit

Step 3:

Finally, to ensure that the batch system can send an email to the user when the job start, end or abort, you have to set 2 options

  1. -m switch which define wh information send
  2. -M switch on where the information will be send

For example,

# Send notification when job starts.
#PBS -m b
# Send notification when job finishes and aborts.
#PBS -m ea
# Send notification when job starts, finishes and aborts.
#PBS -m bea

A typical submission script will be

#!/bin/bash
#PBS -N jobname
#PBS -j oe
#PBS -V
#PBS -m bea
#PBS -M kittycool@linucluster.wordpress.com
#PBS -l nodes=2:ppn=8

## pre-processing script
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS