We are organizing a 1-day workshop on GPU computing for biomedical research. This is organized jointly by the NSF-funded New England Bio-Grid initiative based at HMS, and Prof. David Kaeli of Northeastern. The workshop will be held at Countway Library, HMS, on Thursday October 22nd. Registration is now open. Space is limited.
We have speakers from industry, academia, and several hospital research computing groups.
Abstract, Speaker List, and Registration Form available on the NEBioGrid website.
Dear Consortium Members and Affiliates,
What's new with you? This month we procured and tested the Zalman ZM-M220W Stereo 3d LCD. This is a 22" passive 3d display priced at about $275 USD from online retailers. The cool thing about this LCD is that it does not require a special graphics driver or specific operating system support; the 3d feature can be supported directly in the software package. This means the monitor works with OS X and linux without any special configuration provided that it's supported by your visualization software. At this point in time, Coot, PyMOL, CCP4mg and Chimera all claim support for the Zalman monitor, and we have successfully tested Coot, PyMOL and Chimera. Alwyn Jones has a rough beta of O that should support the Zalman monitor as well, which will be in place for the next update.
The quality of the stereo image is quite good, with very little flickering and nice depth of field. The sweet spot for the stereo image is relatively small; you have to sit directly in front of the monitor, and the monitor has to angle toward you to get the best picture, but given its low price, good image quality and increasing support in the major visualization applications for crystallography, the Zalman LCD is a very good deal. If you like to do your model building in 3d, this is our recommended solution for right now. Our experience was so good that Piotr is buying one for his home office.
In other news, the third installment of the annual structural biology computing school will be sponsored by the European Molecular Biology Laboratory (EMBL) and held in Heidelberg, Germany in May 2010. The conference website has the complete schedule and registration information. Registration is limited to 45 people and is heavily geared toward classroom time focusing on using and developing structural biology software. Molecular visualization, programing in python and OSX programming classes are being offered. Students from European SBGrid labs are encouraged to apply.
Finally I am going to stop building and testing the software for Fedora Core 3 through 5. There are only a handful of machines still running those old, unsupported versions of Fedora, so the impact of this should be fairly minor. If you want to check your operating system, you can use the /programs/share/bin/os utility to make sure you are running a recent distribution.
This update is a pretty large, and it includes PHENIX, Coot, CCP4mg, Chimera, several software packages from the Grigorieff Lab, LABELIT, RNAVIEW, Rosetta and a couple of PyMOL plugins. Due to the large size of the download, I started the site installations updating last night, and I'm sending the email a day later. Details on the various updates are below.
Y'all take care now.
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
PHENIX has been updated to version 1.5-2, which is the latest full release version. The PHENIX documentation has been updated for this version. I'm not sure if the PHENIX team plans on keeping up its frenetic development pace, but if so, we'll probably have a new nightly build up in a few weeks. Requested by everybody.
Frealign has been updated to version 8.08 and there are both 32 and 64-bit versions in the software tree. The NN1 and NNBIG parameters are now set automatically at run time. The Readme.txt file in the Frealign directory contains a few additional details. Requested by Harrison Lab at Harvard Medical School.
Along with Frealign, I have also updated various utilities provided by the Grigorieff Lab including bfactor, ctffind, ctftilt, crop, rmeasure and diffmap. ctftilt requires two extra parameters for expected tilt angle and angle uncertainty.
LABELIT has been updated to version 1.1.5. The PHENIX project is including LABELIT in their installation now; you can differentiate between the versions because the PHENIX versions are all suffixed with the PHENIX version number (e.g. labelit.index_1.5-2). The LABELIT download page has a version history at the bottom with some notes on the changes in the new version, and the user manual is in the usual place. Requested by NECAT at Argonne National Labs.
CCP4mg has been updated to version 1.114.1. This version is supposed to support the Zalman LCD, but it still has some issues on our linux boxes. We are following up with the developers.
Chimera has been updated to version 1.4. This is a major update with many new features detailed in the release notes including support for the Zalman LCD.
RNAVIEW is a new addition to the software tree. This program generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions and is useful for working with nuccyl. The README file in the RNAVIEW directory has some usage information. Requested by D'Souza Lab at Harvard University.
The eMovie and Mole plugins have been installed for PyMOL for linux and both OS X branches. If you have a favorite PyMOL plugin you would like to see included with the software tree, email us at firstname.lastname@example.org to request it. To support the Zalman stereo mode I mentioned above in PyMOL, use the new aliases 'pymol-zalman' or 'macpymol-zalman'.
Linux and Mac OS X Intel
Coot has been updated to 0.6-pre-1-r2439 for the linux branch and 0.6-pre-1-r2425 for the OS X Intel branches. The PowerPC build is giving me problems, but I hope to have it in place for the next update. The usual slew of bug fixes and enhancements are documented in the Coot commit log hosted on Google Code.
Rosetta has been updated to version 3.1. This is a fairly major update as Rosetta has moved from a single application primarily aimed at docking to a suite of applications for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. The Rosetta manual has details on how to use the new features. The Rosetta team has stopped supporting OS X PowerPC for the new version. Requested by Leschziner Lab at Harvard University.
I have seen a few tickets recently that involve problems that affect the software, but are somewhat out of my control. Here's a heads up on some common problems.
TCSH and "Word too long"
TCSH version 6.14 and older has a hard-coded maximum PATH length of 4096 characters. With the large PATH of the linux software tree and some local customizations, sites will occasionally exceed that maximum PATH length resulting in a "Word too long" error. The best fix for this problem is to grab the latest TCSH sources from tcsh.org and compile your own version, since the latest sources have a much larger default PATH setting.
SELinux and Scientific Software
It has been our experience that there are quite a few software packages in the suite that will not run under SELinux. As a general rule, we disable SELinux on the research workstations we administer. I have filed bug reports with developers on this issue occasionally, but it's a low priority for most scientific software developers to address. If you see odd error messages relating to permissions (but not usually file permissions) and you have SELinux enabled, you may want to try disabling it during troubleshooting.
Scripts and $prompt
The $prompt variable is unset for non-interactive shell use (e.g. in a shell script or for an scp/sftp connection). The labcshrc checks for the presence of $prompt before running, so if you have this in your ~/.cshrc:
set prompt="[%n@%m][%/] " source /programs/labcshrc
The labcshrc will always be sourced, which will dump the shell message into your script output and will break scp/sftp transfers. The proper way to set a (t)csh prompt is like this:
if ($?prompt) then set prompt="[%n@%m][%/] " endif source /programs/labcshrc
That way you are checking to see if $prompt exists before setting it. If it exists, then the shell is interactive, and you can set your custom prompt, otherwise you should bail.
Are any of the site admins interested in a technical mailing list for discussion related to integration and deployment of the scientific software? Email me, email@example.com, if you think that would be useful. Thanks.