install libraries from MDL

library(devtools)
devtools::install_git("https://gitext.gfz-potsdam.de/delucia/RedModRphree.git")
devtools::install_git("https://gitext.gfz-potsdam.de/delucia/Rmufits.git")

USAGE

mpirun ./kin <simfile.R>

OPTIONS:

--work-package-size=<1-n> ... size of work packages (default 5)

--ignore-result ... disables store of simulation resuls

DHT:

--dht ... enable dht (default is off)

--dht-log ... enable logarithm application before rounding (default is off)

--dht-signif=<1-n> ... set rounding to number of significant digits (default 5) (only used if no vector is given in setup file) (for individual values per column use R vector "signif_vector" in setup file)

--dht-strategy=<0-1> ... change dht strategy, not implemented yet (default 0, dht on workers)

--dht-size=<1-n> ... size of dht per process involved (see dht-strategy) in byte (default 1GiB)

--dht-snaps=<0-2> ... enable or disable storage of DHT snapshots 0 = snapshots are disabled 1 = only stores snapshot at the end of the simulation with name .dht 2 = stores snapshot at the end and after each iteration iteration snapshot files are stored in /iter.dht

--dht-file= ... initializes DHT with the given snapshot file

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about the usage of MPI_Wtime()

From the OpenMPI Man Page:

For example, on platforms that support it, the clock_gettime() function will be used to obtain a monotonic clock value with whatever precision is supported on that platform (e.g., nanoseconds).

External Libraries

Cmdline Parsing -> https://github.com/adishavit/argh

Examples included (more to come)

1. SimDol2D.R ... simple chemistry (Calcite/Dolomite) on a 50x50 2D grid, 20 time steps
2. SimDolKtz.R ... simple chemistry (Calcite/Dolomite) on Ketzin grid (~650k elements), 20 time steps The flow snapshots are NOT INCLUDED in svn but must be provided separately