MUSIC Tutorial

Running the Pmap

You are now ready to start your first music simulation. There is only one more thing to do: you have to create the executable. To do this follow the steps decribed in " Compiling music programs " with the music_mapmaker.F90 driver.

You should now have the following:

A-A-interaction file
M-M-interaction file
Environment variables file
Intra-molecular file
A Link to compiled musicmap executable
A control file for the map program
All the atom and molecule files in the directories specified in your environment file

You can download a tar-file containing all the necessary files to create a pmap for Methane in IRMOF1 with the UFF force field here.

You are now ready to start your first music simulation. Before you start your simulation, you must tell MUSIC where to look for the atom and molecule files:
>source [environment file]

Now start the simulation:
>./[map executable link] [map control file]

Clusters

If you are using a computer cluster such as gladiator at Edinburgh University you are not allowed to run simulations on the front end but you have to submit the job to the queue. Repeat the above to check it works (there is nothing more annoying than to find out that your simulation wasn't able to start properly becuase you made a mistake in setting up one of your files). Then after about 10-20 seconds press control-c to stop it. Remove the (empty) *.pmap file that was created.

To submit a job to the cluster, you have to write a shell script. The following script can be used on gladiator. For other systems, contact your system administrator about how to adopt it.

 
#!/bin/sh
#
#PBS -l nodes=1:ppn=1	
#PBS -l cput=10:00:00 		 See ** below
#PBS -j oe
#PBS -m bea	 		requests an email at the start and the end of your job. For security reasons, this function is disabled at the moment. 
#PBS -M [email address]		email address 

 (The next 3 lines tells the processor what to do) 

cd /home/[Pmap folder]				Go to the directory with the files in it.
source ./[environment file]				Source your other files
./[map executable link]  [map control file] > logfile.meta 	Run the simulation 


 to submit it, type in the shell window:

 >qsub [above filename]

**This is the amount of time that you want the cluster to give to your simulation, the longer the time the lower priority it gets in the queue but if not enough time the simulation will be cut off and will have to be started from where it stopped. 10 hrs is more than enough for basic Pmap creation. If you have over your limit of submitted jobs they will be put in another queue until one of your jobs are done.