Scientific computing, mathematical modeling, and computer simulation
This post will take you through the installation and configuration of an Infiniband card on a server running Red Hat Enterprise Linux 5.4. These steps are applicable to any version of Red Hat 5, and will probably work with version 6 as well. It has been surprisingly hard to find all of these steps in […]
Installing and configuring Infiniband on a Red Hat system Read More »
xCAT is the eXtreme Cloud Administration Toolkit from IBM. It’s a suite of tools that IBM has developed to manage large groups of servers, such as a cloud infrastructure or a high-performance computing cluster (HPCC). I have only used xCAT to administer a mid-sized compute cluster (about 140 compute nodes totaling about 1400 cores running
Managing an HPC cluster or cloud infrastructure: alternatives to xCAT Read More »
OpenFOAM is a notoriously difficult piece of software to compile, install and run. OpenCFD (the authors of OpenFOAM) have chosen to require the use of recent versions of gcc that are not available on most stable enterprise-class systems (ie Red Hat Enterprise Linux). To make things worse, until recently, OpenCFD also bundled a large number
An Improved Ebuild for OpenFOAM on Gentoo Linux Read More »
CFD-ACE+ is a multiphysics and computational fluid dynamics (CFD) simulation tool that was originally developed by CFD Research Corp. and is now distributed by ESI Software. The only platforms officially supported by CFD-ACE+ are Red Hat Enterprise Linux, SUSE Linux and Windows. Fortunately, it seems that ACE+ runs on other Linux distributions with only a
Hack of the Day: running CFD-ACE+ on Gentoo Linux Read More »
This is a follow-up to my earlier post about building NumPy with Intel compilers and the Intel MKL on CentOS 5. I will now explain how to build SciPy (which requires NumPy). First, download and unpack the SciPy source tarball. The following command can be used to build SciPy: LDFLAGS=”” FFLAGS=”-fPIC -openmp” python2.7 setup.py build
Building SciPy with Intel compilers and MKL on 64bit RHEL 5 Read More »
I recently installed ATLAS on my new workstation and I’ve been wondering what kind of performance gain I would get compared to the reference BLAS. After some searching, I finally found a BLAS benchmarking tool called BLASbench, which is part of the LLCbench suite. This tool has a rather strange build process, so follow the
Benchmarking BLAS Part 1: Building BLASbench with gcc Read More »
In a previous post I described how to build an optimized version of NumPy using the Intel compilers and Math Kernel Library (MKL). This post will update those instructions, since it has been a few years and I am now using NumPy 1.6.1, MKL 10.0.1.014 and Red Hat 4.1.1 (kernel 2.6.18-8.el5). First, copy the file
Building NumPy on a 64-bit Red Hat Cluster with Intel MKL Read More »
Prerequisites: boost-devel, openmpi-devel, valgrind-devel I installed PETSc and libMesh in my user directory, since I have a single-user workstation. Installing PETSc for use with libMesh First, ensure that OpenMPI is installed and the system paths have been configured correctly. You will need to add the directory containing OpenMPI binaries to your $PATH, and the directory
Installing PETSc and libMesh on CentOS 5 Read More »
I finally got around to installing Paraview on my CentOS 5 box. There are no official RPMS for CentOS 5, so I was expecting a painful build process. To my great surprise, I was able to download the Paraview binary for Linux (64-bit) from Kitware, unpack the archive, and run it! As root, I placed
Paraview 3.12 on 64-bit CentOS 5.7 Read More »
I recently upgraded my desktop workstation from an old 32-bit version of Gentoo to 64-bit CentOS 5. I downloaded and installed the latest version of Sage, and the process went smoothly. If you find this post helpful, please check out the Sage Beginner’s Guide at Packt Publishing. Since I don’t use Sage every day, I
Installing Sage 4.7 on CentOS 5 Read More »