The concept of Processor Equivalent

Learned a new concept of Process Equivalent or PE. It is a measure of the actual impact of a set of requested resources by a job on the total resources system wide.

Taken from MAUI Admin Guide by Cluster Resources

PE =MAX (ProcsRequestedByJob / TotalConfiguredProcs,
MemoryRequestedByJob / TotalConfiguredMemory,
DiskRequestedByJob / TotalConfiguredDisk,
SwapRequestedByJob / TotalConfiguredSwap) * TotalConfiguredProcs

Assume a homogeneous 100 node system with 4 processors and 1 GB of memory per node. A job is submitted requesting 2 processors and 768 MB of memory. The PE for this job would be calculated as:

PE = MAX(2/(100*4), 768/(100*1024)) * (100*4) = 3.

This result makes sense since the job would be consuming 3/4 of the memory on a 4 processor node. The calculation works equally well on homogeneous or heterogeneous systems, uniprocessor or large way SMP systems.

Installing Intel Compiler on a compute node

The Compute Nodes of a HPC are often on a private network and may not have access to the internet and they are often very lean. How do we compile the Intel Compiler on the compute node?

After untaring the Intel Compiler, and running install.sh and registering the serial number, you will notice that there will be a missing essential prequiste. How to know what is the missing important prequiste?

Go to the intel installation log file /tmp/intel.pset.root........, you can see in the log file "missing g++". To install g++, do the following:

# yum install gcc-c++

Problem solved!

Creating a Yum Local Repository at CentOS

Sometimes, you may want a yum local repository for your CentOS 5 Server as yum automatically resolve all the dependency, With a local repo as a resource it will help resolve potential dependencies especially if you do not have internet access

Step 1: You will need an utility, named createrepo.
# yum install createrepo Or
# rpm -Uvh createrepo-0.4.11-3.el5.noarch.rpm

Step 2: Copy the whole CentOS CD to a directory (E.g. /install/centos5.2/x86_64/CentOS)

Step 3: Createrepo
# createrepo /install/centos5.2/x86_64/CentOS
(you will need to run the above command again, so that the repository metadata gets updated)

Step 4: Create a local-repo file
(You may want to remove CentOS-Base.repo, CentOS-Media.repo if you are not connected to network)
# touch install-local.repo

Type the followings:
[localrepo]
name=CentOS $releasever - My Local Repo
baseurl=file:///install/centos5.2/x86_64/
enabled=1
gpgcheck=0
gpgkey=file:///install/centos5.2/x86_64/RPM-GPG-KEY


Further Information:

1. Local YUM Repository by George Notaras
2. Docs/Drafts/SoftwareManagementGuide from Fedora

Tin Hat Distro

Tin Hat is a Linux distribution derived from hardened Gentoo which aims to provide a very secure, stable and fast Desktop environment that lives purely in RAM................

Tin Hat requires about 4 GB to run comfortably, 3 GB for the tmpfs root file system, and 1 GB for paging. If one wants to further reintroduce Gentoo's portage system and/or the kernel source tree, 4GB becomes a very tight squeeze.

For more information, go to Tin Hat

Building OpenMPI with Intel Compiler (Ver 2)

This is a follow up from Thursday, April 2, 2009 Blog Entry Building OpenMPI with Intel Compiler

Step 1: Download the OpenMPI Software from http://www.open-mpi.org/ . The current stable version at point of writing is OpenMPI 1.3.2

Step 2: Download and Install the Intel Compilers from Intel Website. More information can be taken from Free Non-Commercial Intel Compiler Download

Step 3: Add the Intel Directory Binary Path to the Bash Startup
At my ~/.bash_profile directory, I've added

PATH=$PATH:/opt/intel/Compiler/11.0/081/bin/intel64
At command prompt
# source .bashrc

Step 4: Configuration Information

gunzip -c openmpi-1.2.tar.gz tar xf -
# cd openmpi-1.2
#./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort
# make all install

Step 5: Setting PATH environment for OpenMPI
At my ~/.bash_profile directory, I've added.

export PATH=/usr/local/bin:${PATH}  
export LD_LIBRARY_PATH=/opt/intel/Compiler/11.0/081/lib/intel64:${LD_LIBRARY_PATH}

(The LD_LIBRARY_PATH must point to /opt/intel/Compiler/11.0/081/lib/intel64/libimf.so)

Step 6: mpicc ........

Step 7: Repeat the procedures on the Compute Nodes