Routing Application for Parallel computatIon of Discharge (RAPID)
Fortran Shell Makefile
ch-m-emery and c-h-david Subroutine rapid_cov_mat.F90 (#12)
* rename downstream covariances array into ZV_riv_tot_cdownQlat

* update non-zeros counting procedure to include symetric elements

* change preallocation routines to those for matrices of type aij

* update population of matrix with symmetric elements

* add PetscPrintf notice at the end of the routine

* new subroutine for data assimilation: compute matrix that maps daily average runoff into daily average discharge

* new subroutine for data assimilation: compute the kalman filter observation operator ZM_H from the runoff-to-discharge matrix and the selection off observed reaches

* new subroutine for data assimilation: compute the control error covariance matrices PbHT and HPbHT used to estimate the Kalman gain from the runoff error covariance matrix and the observation operator

* new subroutine for data assimilation: compute the analysis/updated control vector using Kalman Filter update equation
Latest commit 668458f Jul 10, 2018

README.md

RAPID

DOI

License (3-Clause BSD)

Build Status

Docker Build

The Routing Application for Parallel computatIon of Discharge (RAPID) is a river network routing model. Given surface and groundwater inflow to rivers, this model can compute flow and volume of water everywhere in river networks made out of many thousands of reaches.

For further information on RAPID including peer-reviewed publications, tutorials, sample input/output data, sample processing scripts and animations of model results, please go to: http://rapid-hub.org/.

Installation with Docker

Installing RAPID is by far the easiest with Docker. This document was written and tested using Docker Community Edition which is available for free and can be installed on a wide variety of operating systems. To install it, follow the instructions in the link provided above.

Note that the experienced users may find more up-to-date installation instructions in Dockerfile.

Download RAPID

Downloading RAPID with Docker can be done using:

$ docker pull chdavid/rapid

Install packages

The beauty of Docker is that there is no need to install anymore packages. RAPID is ready to go! To run it, just use:

$ docker run --rm --name rapid -it chdavid/rapid

Testing with Docker

Testing scripts are currently under development.

Note that the experienced users may find more up-to-date testing instructions in docker.test.yml.

Installation on Ubuntu

This document was written and tested on a machine with a clean image of Ubuntu 14.04.0 Desktop 64-bit installed, i.e. no update was performed, and no upgrade either.

Note that the experienced users may find more up-to-date installation instructions in .travis.yml.

Download RAPID

First, make sure that git is installed:

$ sudo apt-get install -y git

Then download RAPID:

$ git clone https://github.com/c-h-david/rapid

Finally, enter the rapid directory:

$ cd rapid/

Install APT packages

Software packages for the Advanced Packaging Tool (APT) are summarized in requirements.apt and can be installed with apt-get. All packages can be installed at once using:

$ sudo apt-get install -y $(grep -v -E '(^#|^$)' requirements.apt)

Alternatively, one may install the APT packages listed in requirements.apt one by one, for example:

$ sudo apt-get install -y gfortran

Install netCDF

The Network Common Data Form (NetCDF) can be installed using:

$ mkdir $HOME/installz
$ cd $HOME/installz
$ wget "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-3.6.3.tar.gz"
$ mkdir netcdf-3.6.3-install
$ tar -xzf netcdf-3.6.3.tar.gz 
$ cd netcdf-3.6.3
$ ./configure CC=gcc CXX=g++ FC=gfortran --prefix=$HOME/installz/netcdf-3.6.3-install
$ make check > check.log
$ make install > install.log

Then, the environment should be updated using:

$ export TACC_NETCDF_DIR=$HOME/installz/netcdf-3.6.3-install
$ export TACC_NETCDF_LIB=$TACC_NETCDF_DIR/lib
$ export TACC_NETCDF_INC=$TACC_NETCDF_DIR/include
$ export PATH=$PATH:$TACC_NETCDF_DIR/bin

Note that these four lines can also be added in ~/.bash_aliases so that the environment variables persist.

Install PETSc

The Portable, Extensible Toolkit for Scientific Computation (PETSc) can be installed using:

$ cd $HOME/installz
$ wget "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.6.2.tar.gz"
$ tar -xzf petsc-3.6.2.tar.gz
$ cd petsc-3.6.2
$ ./configure PETSC_DIR=$PWD PETSC_ARCH=linux-gcc-c --download-fblaslapack=1 --download-mpich=1 --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-clanguage=c --with-debugging=0
$ make all > all.log
$ make test > test.log

Then, the environment should be updated using:

$ export PETSC_DIR=$HOME/installz/petsc-3.6.2
$ export PETSC_ARCH=linux-gcc-c
$ export PATH=$PATH:$PETSC_DIR/$PETSC_ARCH/bin

Note that these three lines can also be added in ~/.bash_aliases so that the environment variables persist.

Build RAPID

$ cd rapid/
$ cd src/
$ make rapid

Testing on Ubuntu

Testing scripts are currently under development.

$ cd rapid/
$ cd rtk/
$ gfortran -o rtk_run_comp rtk_run_comp.f90 -I $TACC_NETCDF_INC -L $TACC_NETCDF_LIB -lnetcdf
$ gfortran -o rtk_run_conv_Qinit rtk_run_conv_Qinit.f90 -I $TACC_NETCDF_INC -L $TACC_NETCDF_LIB -lnetcdf

Note that the experienced users may find more up-to-date testing instructions in .travis.yml.