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64 lines
2.2 KiB
Markdown
64 lines
2.2 KiB
Markdown
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<!--
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Time-stamp: "Last modified 2020-02-01 18:14:13 delucia"
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-->
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# install libraries from MDL
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library(devtools)
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devtools::install_git("https://gitext.gfz-potsdam.de/delucia/RedModRphree.git")
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devtools::install_git("https://gitext.gfz-potsdam.de/delucia/Rmufits.git")
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# USAGE
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mpirun ./kin <OPTIONS> <simfile.R> <DIRECTORY>
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OPTIONS:
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--work-package-size=<1-n> ... size of work packages (default 5)
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--ignore-result ... disables store of simulation resuls
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DHT:
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--dht ... enable dht (default is off)
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--dht-nolog ... enable logarithm application before rounding (default is off)
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--dht-signif=<1-n> ... set rounding to number of significant digits (default 5)
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(only used if no vector is given in setup file)
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(for individual values per column use R vector "signif_vector" in setup file)
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--dht-strategy=<0-1> ... change dht strategy, not implemented yet (default 0, dht on workers)
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--dht-size=<1-n> ... size of dht per process involved (see dht-strategy) in byte (default 1GiB)
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--dht-snaps=<0-2> ... enable or disable storage of DHT snapshots
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0 = snapshots are disabled
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1 = only stores snapshot at the end of the simulation with name <DIRECTORY>.dht
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2 = stores snapshot at the end and after each iteration
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iteration snapshot files are stored in <DIRECTORY>/iter<n>.dht
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--dht-file=<snapshot> ... initializes DHT with the given snapshot file
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###############################################################################
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# about the usage of MPI_Wtime()
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From the OpenMPI Man Page:
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For example, on platforms that support it, the clock_gettime() function will be used
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to obtain a monotonic clock value with whatever precision is supported on that platform (e.g., nanoseconds).
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# External Libraries
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Cmdline Parsing -> https://github.com/adishavit/argh
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# Examples included (more to come)
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1) SimDol2D.R ... simple chemistry (Calcite/Dolomite) on a 50x50 2D grid, 20 time steps
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2) SimDolKtz.R ... simple chemistry (Calcite/Dolomite) on Ketzin grid (~650k elements), 20 time steps
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The flow snapshots are NOT INCLUDED in svn but must be provided separately
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