2.2 KiB
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)
- SimDol2D.R ... simple chemistry (Calcite/Dolomite) on a 50x50 2D grid, 20 time steps
- 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