2. Start an interactive session on Odyssey

Using the `interactive` script to launch an interactive session

To compile the MITgcm, you will have to start an interactive session on Odyssey. For your convenience, we have provided a script that will make it easier to start an interactive session. This script, named interactive , was installed with the environment scripts in Section 1. To start an Odyssey interactive session, type:

interactive 13 1 4000 60 interact

The arguments to the interactive script are as follows:

`13`	Number of CPUs. Q. Why should I ask for 13 CPUs? A. This will let you ruin short MITgcm debug simulations (which require 13 CPUs instead of the 96 CPUs normally used for science runs.)
`1`	Number of nodes on which the CPUs are located
`4000`	Total amount of memory in MB (4000 MB = 1 GB)
`60`	Amount of time requested in minutes (You can of course increase the amount of time that the interactive session runs (consider 480 minutes = 8 hours = 1 work day)
`interact`	Name of the interactive partition on Odyssey where your session will run

Once your interactive session starts up, you need to run 2 more scripts:

awake.sh & source ~/.bashrc_mitgcm

where:

awake.sh

Prints a null character (“”) to the screen every 10 minutes. This will keep the interactive session occupied.

A SLURM bug can cause an Odyssey interactive session to hang if you step away from the computer for an extended period (more than 30 minutes).
Using awake.sh will prevent your interactive session from hanging.

.bashrc_mitgcm

Customizes your bash Unix environment for the MITgcm. It loads the proper modules needed to run the MITgcm,
as well as defining environment variables and other necessary settings. It will also print out a list of the modules that were loaded:

Currently Loaded Modules:
1) git/2.1.0-fasrc01 3) openmpi/1.8.1-fasrc05 5) hdf5/1.8.12-fasrc09
2) intel/13.0.079-fasrc01 4) zlib/1.2.8-fasrc02 6) netcdf/4.1.3-fasrc06

To build the MITgcm, we shall use the Intel compilers (13.1), OpenMPI (v1.8.1), and netCDF-4.1.3.
We determined that these library versions were compatible by using the RC Portal modules application: https://portal.rc.fas.harvard.edu/apps/modules.

Next steps

Once you have started an interactive session, you will need to do the following steps:

Make a working directory where you can compile and run MITgcm
1. This step only has to be done once for each simulation type (Hg, PFOS, PCB).
  1. Or, when you wish start a simulation with a fresh run directory.
2. NOTE: We recommend creating working directories within your interactive session because the file copying process is very CPU-intensive. This should not be done on an Odyssey login node.
Build the MITgcm executable
Run a MITgcm simulation.

2. Start an interactive session on Odyssey

Using the interactive script to launch an interactive session

Next steps

Using the `interactive` script to launch an interactive session