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 […]
Updated GROMACS tutorials Read More »
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
Installing Lumerical FDTD on a linux cluster Read More »
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
OpenMPI, Intel Compilers and RedHat 5: cannot find -lnuma Read More »
Danny Price recently left a comment to let me know about a new Python package he’s developing called hickle. The goal of “hickle” is to create a module that works like Python’s pickle module but stores its data in the HDF5 binary file format. This is a promising approach, because I advocate storing binary data
pickle, hickle and HDF5 Read More »
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
Building NumPy and SciPy with Intel Composer 2013 and the MKL Read More »
This article from Admin Magazine has a handy list of profiling tools.
A list of system and application profiling tools Read More »
3D printers have been getting more attention in the mainstream media in the past few months. 3D printers were mentioned in a story about tech trends on National Public Radio today, and my father showed me a newsletter from a mutual fund company with a short article about 3D printing. You know that something is
A trend for 2013: the democratization of manufacturing Read More »
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 »
Glossary of Infiniband Terminology: GID: Global Identifier GUID: Global Unique Identifiers (also known as Direct Address) HCA: Host Channel Adapter LID: Local Identifier TCA: Target Channel Adapter SM: Subnet Manager Infiniband: The Host Perspective Every host on an Infiniband fabric has three identifiers: GUID, GID, and LID. A GUID is similar in concept to a
The Infiniband troubleshooting quick reference 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 »