omouraenko / figuregen

Visualization of ADCIRC Model Data in Raster Formats

FigureGen

This is an updated version of FigureGen. It was modified to work with GMT version 6.0 or higher.

Rerequesites

FigureGen requires the following software:

1. Generic Mapping Tools (GMT) is the software package that plots the contours, contour lines, etc. and produces a PostScript file containing the figure. This version of FigureGen requires GMT 6.0 or higher. Install with command:

   yum install gmt
   

2. GhostScript is the software package that converts PostScript files into different formats, including the raster format used by FigureGen. Install with command:

   yum install ghostscript
   

3. ImageMagick is a software package for the manipulation and conversion of images. This software is optional. It is only required when FigureGen adds background images to the plots. Install with command:

   yum install ImageMagick
   

4. Zip is a compression and file packaging uility. Install with command:

   yum install zip
   

5. Sed is a string processing utility. Install with command:

   yum install sed
   

Installation of GMT on CentOS 8.5

Installation of GMT package on CentOS 8.5 may fail as package with the specific version of libjson-c library is not avaialble from the EPEL repository. The error may look like this (note, that gdal package is required by the gmt package):

[root@node ~]# yum install gdal
Last metadata expiration check: 0:48:50 ago on Thu 11 Apr 2024 01:20:18 PM CDT.
Error:
Problem: package gdal-3.0.4-12.el8.x86_64 requires libgdal.so.26()(64bit), but none of the providers can be installed
  - package gdal-3.0.4-12.el8.x86_64 requires gdal-libs(x86-64) = 3.0.4-12.el8, but none of the providers can be installed
  - conflicting requests
  - nothing provides libjson-c.so.4(JSONC_0.14)(64bit) needed by gdal-libs-3.0.4-12.el8.x86_64
(try to add '--skip-broken' to skip uninstallable packages or '--nobest' to use not only best candidate packages)

The latest version of libjson-c library from the EPEL reposotiry is 0.13.1-2. However, it does not include the required libjson-c.so.4(JSONC_0.14) library:

[root@node ~]# rpm -q --provides json-c
json-c = 0.13.1-2.el8
json-c(x86-64) = 0.13.1-2.el8
libjson-c.so.4()(64bit)

The later version 0.13.1-3 includes the required library and can be downloaded separately. For example, from rpmfind.net download json-c-0.13.1-3.el8.x86_64.rpm and json-c-devel-0.13.1-3.el8.x86_64.rpm.

Then install the packages and verify:

[root@node ~]# yum install json-c-0.13.1-3.el8.x86_64.rpm json-c-devel-0.13.1-3.el8.x86_64.rpm
[root@node ~]# rpm -q --provides json-c
json-c = 0.13.1-3.el8
json-c(x86-64) = 0.13.1-3.el8
libjson-c.so.4()(64bit)
libjson-c.so.4(JSONC_0.14)(64bit)
libjson-c.so.4(JSONC_0.15)(64bit)

After that, the GMT package should install without issues.

Compilation

Below is an example of compilation steps using the Intel compiler. Intel MPI and NetCDF libraries should be available.

cmake -B build \
        -DUSE_MPI=ON \
        -DUSE_NETCDF=ON \
        -DCMAKE_Fortran_COMPILER=ifort \
        -DNETCDF_INCLUDES="$(nc-config --includedir)" \
        -DNETCDF_LIBRARIES="$(nf-config --flibs)" \
        -DNETCDF_LIBRARIES_F90="$(nc-config --libdir)"

cmake --build build

The parallel version executable name is pfiguregen. The serial version executable name is figuregen. The executables are created under build folder.

Input file

Note, that in the input file, names of gmt and gs executables or full paths to executables (if they are not in the PATH) need to be specified:

gmt                                                ! Path to GMT executable.
gs                                                 ! Path to GhostScript executable.

Or

/usr/bin/gmt                                       ! Path to GMT executable.
/usr/bin/gs                                        ! Path to GhostScript executable.

Example script

Below is an example script to run parallel version of FigureGen:

#!/bin/bash

# select executable
exe=pfiguregen

# input file name
inpFile=new.inp

# set environment (load mpi, netcdf, and set path to binaries)
module load mpi
module load netcdf
module load figuregen

# configure gmt.conf, check defaults with 'gmt defaults' command
# '-D' option for FORMAT_GEO_* not working, use '"-D"' instead of -D
gmt set FORMAT_GEO_MAP D
gmt set FORMAT_GEO_OUT D
gmt set FORMAT_FLOAT_OUT %lg
gmt set MAP_FRAME_TYPE fancy
gmt set GMT_HISTORY FALSE
gmt set PS_MEDIA letter
gmt set FONT_TITLE 18p

mpirun -n 2 $exe -I $inpFile > ${exe}.log