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Run_Reaktoro.md

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gems3gui { GEMS-Reaktoro project }

Now we are at the end of Stage 1 having the first working variant of GEMS-Reaktoro code. With GEMS-Reaktoro GUI, we can set up a chemical equilibrium problem as usual and compute Systems and Processes using the GEMS3K code as a standalone server.

The accuracy of results and their consistency with the trunk GEM-Selektor version 3.7.0 has been tested on Kaolinite and Solvus projects; more detailed comparisons will be done in the next tasks.

For GEM2MT reactive transport simulations, we use so far the internal TNodeArray class, which will be connected to GEMS3K server in the next tasks. Main focus at Stage 2 will be to modify Reaktoro as a standalone server using ZeroMQ messaging in a similar way as it has been already done with GEMS3K, and arrange a compatible I/O file exchange to be able to run Reaktoro server alternatively to GEMS3K server and compare the results of solving the same test equilibria and processes. This task may be facilitated by using the new JSON format of GEMS3K I/O files, already readable/writable by GEMS3K server and possible to be used by the Reaktoro/Optima server.

How to build and run GEMS-Reaktoro

For more details see README.md

  • If not yet done, copy recursively the "/Docs/build-release" directory from the folder where this file is located to the folder in which the "/gems-gui" folder is located. Typically, you should have the folders at the same level, as shown below.
~/gitGEMS3
    /gems3gui
    /standalone
    /build-release
    /build-debug

We assume that both subfolders /gems3gui and /standalone are under git control and are checked out to "trunk" branch.

  • To switch to GEMS-Reactoro branch, use a git client or open a terminal, cd to ~/gitGEMS3/gems3gui, and type in the command line
git checkout -b GEMS-Reactoro --track origin/GEMS-Reactoro
git pull origin GEMS-Reactoro

or

git checkout GEMS-Reactoro
  • Do the same to ~/gitGEMS3/standalone

Build standalone GEMS3K server

The GEMS-Reactoro library uses ZeroMQ core engine in C++ that implements ZMTP/3.1 and header-only C++ binding for libzmq as a thirdparty dependency. To install the ~/gitGEMS3/standalone/gemserver, go into a terminal, and execute the following commands:

cd ~/gitGEMS3/standalone/gemserver
sudo ./install-dependencies.sh
  • Start Qt Creator and open project ~/gitGEMS3/standalone/gemserver/gems3_server.pro; link build directory to ~gitGEMS3/standalone/gemserver-build and build the executable.

Build GEMS-Reaktoro client

  • In Qt Creator and open a project ~/gitGEMS3/gems3gui/gems3gui.pro and build the executable.

  • Change command line arguments ( add full path to gemserver executable "~gitGEMS3/standalone/gemserver-build"):

-d -s ~/devGEMS/gitGEMS3/gems3gui -g ~/devGEMS/gitGEMS3/standalone/gemserver-build

Run GEMS-Reaktoro

  • run the gems3gui.pro project from QtCreator and try to open/create a project, calculate an equilibrium and/or a process

  • After a crash or after a stop during debugging, if gems3_server was not terminated in terminal, execute a command ( for Linux)

killall gems3_server

Next to be done

  1. Compare/Test equilibria and processes calculations for more projects, perform bugfixing if needed

  2. Research ZeroMQ patterns, use threads and implemented best practices into gems3_server (then take over to Reaktoro/Optima)

http://zguide.zeromq.org/page:all#toc26

  1. Create a separate repository for GEMS-Reaktoro by forking this branch and connecting to Reaktoro/Optima forked repository to implement Reaktoro_server