Lamarc on the cluster

Lamarc version 1.2.2 is on the cluster.

You can run Lamarc from a command line. To use it type "qrsh" (this will log you onto a single cluster node) and then type "lamarc". Now use Lamarc as you normally would in interactive mode.

A drawback of using Lamarc this way is that if you log out of your qrsh session (or your cluster session) your Lamarc job will be aborted.

You can get around this by using the "nohup" command. Daniel Cadena has kindly provided instructions for doing this:

First of all, you need to create a text file (with unix line breaks) that contains all the commands that one types in the programs when these are run interactively. Here is an example of a file I created to run a dataset in lamarc:

/home/cdc35b/lamarc/infile
E
G
X


S
S
2
1000
6
100000
.

This file specifies the location of the input file, tells the program to go to the Evolutionary Forces menu (E), then to Growth (X), and then tells it to enable the estimation of growth (X). The two "returns" that follow take you back to the main menu. Then, S tells it to go to the Search and Rearrange Menu, and the second S to go to the Search Strategy submenu. Number 2 tells it to modify the number of steps for the short chains, which is then specified as 1000; then 6 tells it to modify the number of steps for the long chains, which is specified in the next step as 100000. Finally, the period tells the program to start running.

In order to make this work, all that needs to be done is to copy the above file to your home directory in expedition. Once you have logged in to the cluster, you simply need to tell the program to run specifying the above file as the input using the nohup command. For the particular case of Lamarc, assuming we called the file with the commands "lamarc.batch" this is done through the following steps:

qrsh

nohup /home/scripts/lamarc < lamarc.batch


(The syntax of nohup is that on the left hand side of the < symbol you type the command normally used to launch the program and on the right hand side you type the name of the file that has the batch of commands).