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 holdersRRA
account holdersSC
account holders
Platforms
CIRCE
clusterRRA
clusterSC
cluster
Modules
GMT requires the following module file to run:
apps/gmt/5.4.0
- See Modules for more information.
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
- If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
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
- GMT Home Page:
- GMT User Guide
- /apps/gmt/5.4.0/docs/GMT_Docs.pdf
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