Preventing “soft” failures due to memory fragmentation in Linux

A previous post documented that a Linux server running a pre-2.6.24 kernel can fail to allocate large chunks of memory after its memory has been fragmented by a "thrashing" incident. In this post, I will point out some ways to prevent this problem. Use a Newer Kernel We have some servers running RHEL 5.9 with … Continue reading Preventing “soft” failures due to memory fragmentation in Linux

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Memory fragmentation degrades performance in Linux kernels < 2.6.24 (RHEL 5.4)

I have data from the STOKES High Performance Compute Cluster which definitively shows that kernel versions prior to 2.6.24 can suffer significant performance degradation due to memory fragmentation. I noticed the problem on servers running Red Hat Enterprise Linux (RHEL) 5.4 with kernel version 2.6.18-164.el5. This post will document my findings. The graphs were taken … Continue reading Memory fragmentation degrades performance in Linux kernels < 2.6.24 (RHEL 5.4)

Insert an EPS file into an Asymptote Vector Graphics document

It's surprisingly difficult to find out whether it is possible to include an image from an Encapsulated PostScript (EPS) file into an Asymptote vector graphics document. It turns out that it is easy, but difficult to find in the Asymptote docs (I finally found the answer, via Google, in the FAQ). It turns out that … Continue reading Insert an EPS file into an Asymptote Vector Graphics document

Using the MATLAB Distributed/Parallel Computing Toolbox without modifying your cluster

This post shows how I set up MATLAB to perform parallel calculations on a multi-core server which is part of an existing cluster that is managed using Torque and Moab. I did this without making any changes to the cluster submission system. The installation documentation for the MATLAB Parallel Computing Toolbox and Distributed Computing Server … Continue reading Using the MATLAB Distributed/Parallel Computing Toolbox without modifying your cluster

How to plot .xvg files from GROMACS on Windows

GROMACS produces graphical output in the form of .xvg files. These are designed to be viewed with a classic UNIX/Linux plotting program called Grace. If you happen to be using Linux and you have Grace installed, it is very easy to plot the data with the command xmgrace my_file.xvg If you aren't using Linux, plotting .xvg files … Continue reading How to plot .xvg files from GROMACS on Windows

Opportunity for postdoctoral research associate in high performance computing

My current employer, the STOKES Advanced Research Computing Center (STOKES ARCC), is hiring a postdoctoral research associate to conduct research in high performance computing with an emphasis on next-generation networking technologies. The ARCC has internal funding that will be used to upgrade our research network to the Internet2 Innovation Platform standard. We are also seeking … Continue reading Opportunity for postdoctoral research associate in high performance computing

Updated GROMACS tutorials

I have published up-to-date versions of two classic GROMACS tutorials on GitHub. The Getting Started section of the GROMACS online documentation contains some helpful tutorials.  Unfortunately, these tutorials have not been updated in a while. They also don't explain how to set up an efficient workflow to run large molecular dynamics simulations on a shared cluster … Continue reading Updated GROMACS tutorials

Installing Lumerical FDTD on a linux cluster

Most of the time, RPM (especially in conjunction with yum) is a decent package management solution. However, I can think of two common circumstances when you don't want to let RPM install a package: You don't have root permissions on a system such as a shared cluster You are an administrator on a shared cluster … Continue reading Installing Lumerical FDTD on a linux cluster

OpenMPI, Intel Compilers and RedHat 5: cannot find -lnuma

I found an interesting quirk when trying to build an OpenMPI application on a visualization node with a "stock" version of Red Hat Enterprise Linux 5.8.  I used mpicc to compile the application and got the following error: $ mpicc hello_world_mpi.c -o hello_world /usr/bin/ld: cannot find -lnuma This was rather surprising, since this node mounts … Continue reading OpenMPI, Intel Compilers and RedHat 5: cannot find -lnuma

Building NumPy and SciPy with Intel Composer 2013 and the MKL

Since Python is widely used as a high-productivity language for scientific computing, Intel has created a page showing how to build NumPy with Intel compilers and the Math Kernel Library (MKL). I would like to clarify a few items regarding building NumPy on a 64-bit Red Hat Enterprise Linux 5.4 system. Since this is a … Continue reading Building NumPy and SciPy with Intel Composer 2013 and the MKL