Center for Computational Molecular Science and Technology Georgia Institute of Technology Center for Computational Molecular Science and Technology School of Chemistry and Biochemistry

CCMST Weekly News, March 9 2012

March 9, 2012 1:37 pm EST

1. Announcements
2. Tip of the Week


Physical Chemistry Seminar Series

March 13, 2012 4:00 pm - 5:00 pm
MoSE 3201A
Prof. Clemens Burda, Case Western Research University
The Contribution of Femtosecond Laser Spectroscopy to the Development of Advanced Optoelectronic Nanomaterials

Cherry Emerson Seminar Series

March 15, 2012 4:00 pm - 5:00 pm
MoSE G011
Prof. Shelley Minteer, Saint Louis University
Utilization of Enzyme Cascades for Biofuel Cells: From Metabolism to Metabolons


By Massimo

Running commands on the compute nodes on egate and fgate

After the reinstall, egate and fgate now are managed by Rocks version 5.4.3. This new version of Rocks does not support anymore the cluster-fork utility that was used in the older version of the system to execute a command on all the compute nodes of the cluster. The new version of rocks instead provides the rocks run host facility that can be used to execute a command of a series of compute nodes. For example, to check the usage of your scratch directory on all the compute nodes you can enter the following command:

rocks run host compute 'du -sk /scratch/${USER}'

Note that the command has to be quoted if it is composed by more than one word, as in the above case. To run the same command, but only on nodes compute-1-4, compute-1-5, compute-1-6 do the following:

rocks run host compute-1-4 compute-1-5 compute-1-6 'du -sk /scratch/${USER}'

The rocks run host facility by default spawns the commands to the hosts all at the same time, thus the order in which they return is random. To have the command executed sequentially on one compute node after the other use the delay modifier:

rocks run host compute 'du -sk /scratch/${USER}' delay=5

In this case rocks will execute the commands sequentially, waiting 5 seconds before issuing the command to the next node. The commands are sent to the nodes in alphabetical order. To have the output of the command collated with the host name use the collate modifier:

rocks run host compute 'du -sk /scratch/${USER}' collate=yes

Note that in this case rocks will wait to collect the output from all the nodes before displaying it in one long list.

To learn more about the rocks run host facility, please consult the Rocks on-line documentation.

Do you have usage tips that you want to share with the other CCMST users? Please send them to Massimo ( for inclusion in the Tip of the Week section.