Using GrADS2 on Shaheen

Owned by Mohsin Ahmed Shaikh
Last updated: May 23, 2023 by Kadir Akbudak

Introduction

Grid Analysis and Display System or GrADS is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data.

Since it has quite a few dependencies, we found it more suitable to make it available on Shaheen by creating a container image with CentOS 7.4 as Linux operating system of choice and all the dependencies required by GrADS2/2.2.1.

At the moment singularity can only open and display X11 window on login nodes. On compute node however, GrADS functionalities can be called in non-GUI mode.
Please make sure your GUI based computations a not memory hungry because it can compromise other users' experience on that login node.

Get the container image

First get the container image from DockerHub to Shaheen filesystem

cd $HOME mkdir $HOME/tmp export SINGULARITY_TMPDIR=$HOME/tmp module load singularity singularity pull docker://krccl/grads:2.2.1

The above commands will end up grads_2.2.1.sif which is your Singularity image file.

GrADS requires some supplementary data dowloaded and pointed to by a couple of environment variables.

You can download the data from ftp://cola.gmu.edu/grads/data2.tar.gz and untar it in your /project

directory. The other file you will need is you User Defined Plug-in Table (UDPT). Its a text file that tells GrADS where the plugins are located. Since we are using a container, the following file will work for it. Let’s can this file udpt .

gxprint Cairo /software/grads-2.2.1/lib/libgxpCairo.so gxdisplay Cairo /software/grads-2.2.1/lib/libgxdCairo.so

The following two variable will then be set:

export SINGULARITYENV_GAUDPT=/path/to/your/udpt export SINGULARITYENV_GADDIR=/path/to/your/data/directory

Interactive session

To launch it interactively with a command prompt on a compute node:

shaima0d@cdl3> salloc -p debug salloc: Granted job allocation 24441493 shaima0d@gateway1> srun --pty bash shaima0d@nid00009> module load singularity shaima0d@nid00009> export SINGULARITYENV_GAUDPT=/scratch/shaima0d/grads_test/grads_data/udpt shaima0d@nid00009> export SINGULARITYENV_GADDIR=/scratch/shaima0d/grads_test/grads_data shaima0d@nid00009> singularity exec grads_2.2.1.sif grads -bl Grid Analysis and Display System (GrADS) Version 2.2.1 Copyright (C) 1988-2018 by George Mason University GrADS comes with ABSOLUTELY NO WARRANTY See file COPYRIGHT for more information Config: v2.2.1 little-endian readline grib2 netcdf hdf4-sds hdf5 opendap-grids geotiff shapefile Issue 'q config' and 'q gxconfig' commands for more detailed configuration information GX Package Initialization: Size = 11 8.5 Running in Batch mode ga-> open model.ctl Scanning description file: model.ctl Data file model.dat is open as file 1 LON set to 0 360 LAT set to -90 90 LEV set to 1000 1000 Time values set: 1987:1:2:0 1987:1:2:0 E set to 1 1 ga-> set gxout shaded ga-> set display color white ga-> c ga-> d ps Contouring: 500 to 1000 interval 50 ga-> gxprint ps.eps Created EPS file ps.eps ga-> quit GX Package Terminated

Batch job

The command we ran in the interactive session can be coded in grads script for batch processing. Here is an example grads script that is our workload, let’s call it script.gs

'reinit' 'open model.ctl' 'set gxout shaded' 'set display color white' 'c' 'd ps' 'gxprint ps.eps' 'quit'

Here is an example jobscript for submit our workload to SLURM and schedule a job to run on a single node on our behalf:

#!/bin/bash #SBATCH --time=00:30:00 #SBATCH --nodes=1 module load singularity export SINGULARITYENV_GAUDPT=/scratch/shaima0d/grads_test/grads_data/udpt export SINGULARITYENV_GADDIR=/scratch/shaima0d/grads_test/grads_data srun singularity exec grads_2.2.1.sif grads -bcl 'script.gs'

and the output looks similar as above:

shaima0d@cdl3> cat slurm-24441646.out Grid Analysis and Display System (GrADS) Version 2.2.1 Copyright (C) 1988-2018 by George Mason University GrADS comes with ABSOLUTELY NO WARRANTY See file COPYRIGHT for more information Config: v2.2.1 little-endian readline grib2 netcdf hdf4-sds hdf5 opendap-grids geotiff shapefile Issue 'q config' and 'q gxconfig' commands for more detailed configuration information GX Package Initialization: Size = 11 8.5 Running in Batch mode All files closed; all defined objects released; All GrADS attributes have been reinitialized GX Package Terminated