GMT

Description

From GMT Home Page: GMT (Generic Mapping Tools) is an open source collection of ~60 tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing encapsulated postscript file (EPS) illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3-D perspective views. GMT supports ~30 map projections and transformations and comes with support data such as GSHHS coastlines, rivers, and political boundaries.

Version

  • 5.4.0

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

GMT requires the following module file to run:

  • apps/gmt/5.4.0

Running GMT on CIRCE/SC

The GMT user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Starting the Application

Establishing a GUI connection to CIRCE/SC

To use GMT, you will need to connect to CIRCE/SC with GUI redirection, either using:

  • CIRCE/SC Desktop Environment
  • SSH with X11 redirection
    • If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
      • [user@localhost ~]$ ssh -X circe.rc.usf.edu
        or
      • [user@localhost ~]$ ssh -X sc.rc.usf.edu

Once connected to CIRCE/SC, you can simply load the GMT module, then execute GMT-related scripts and binaries.

The following submit script is a good starting point for submitting GMT jobs using one of the GMT provided examples:

#!/bin/bash
#
#SBATCH --job-name=gmt_example_04
#SBATCH --output=output.%j.gmt04
#SBATCH --time=00:30:00
#SBATCH --nodes=1 --ntasks-per-node=6
#SBATCH --mem-per-cpu=512

#### SLURM 6 processor GMT test to run on 1 node with 3 GB of total memory. 
#### This GMT example takes less than 30 mins to run.

module purge
module add apps/gmt/5.4.0

### the following script command can be run from your work directory after
###   copying the appropriate example from /apps/gmt/5.4.0/share/doc/examples

./job04.sh

### the following commands will create  eps and png files from the output
###  see the GMT documentation for more info
ps2raster -A -Te *.ps
ps2raster -A -P -Tg *.ps

 
Next, make sure you are in the job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./gmt-example04.sh
  • You can view the status of your job with the “squeue -u <username>” command
  • To view the output postscript files, you can use evince.

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

  • GMT Examples
    • /apps/gmt/5.4.0/share/doc/examples

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with GMT to the IT Help Desk: rc-help@usf.edu