Merge branch 'master' into master

Author: rbouckaert

README.md

@@ -1,45 +1,3 @@
-# benchmark
+This repo is obsolete
 
-BEAST benchmarking data
-
-run `perl process.pl` to generate XML files in the "generated" directory
-
-It also produces a script `/generated/_experiment.sh`.  This assumes that 
-the root directory of this repository contains scripts for running BEAST 1 & 2,
-named `beast1` and `beast2` respectively.
-
-Example `beast1` script:
-
-```bash
-export LD_LIBRARY_PATH=/usr/local/lib:/usr/local/cuda/lib64:/usr/local/cuda/lib64:/usr/local/cuda/lib
-java -Djava.library.path=/usr/local/lib -jar /home/remco/data/beast/benchmark/beast1.8.3.jar $*
-```
-
-Example `beast2` script:
-```bash
-export LD_LIBRARY_PATH=/usr/local/lib:/usr/local/cuda/lib64:/usr/local/cuda/lib64:/usr/local/cuda/lib
-java -Djava.library.path=/usr/local/lib -jar /home/remco/data/beast/benchmark/beast2.4.0.jar $*
-```
-
-These assume that beast1.8.3.jar and beast2.4.0.jar are in the main folder (change 
-the path to what is appropriate for your computer).
-
-Use `chmod a+x ./generated/_experiment.sh` to make the script executable.  
-
-Timing information will be recorded in files times1.dat and times2.dat within each of the
-generated directories `singleThread`, `doubleThread`, `fourThread` and `GPU`.
-
-Run the perl script `summarise*.pl` specific to your OS to produce the summary.
-
-If you've run the `summariseLinux.pl` script, a table is produced in `data_frame.txt`
-which can be read into R.  This can be visualized using the `plot_summary.R` R script.
-
-
-For Mac OS, run `perl processMac.pl`. Time will be logged in _time.txt_, and screen logs will be in _screen1.dat_ and _screen2.dat_.
-
-To remove noisy texts from _time.txt_ using the script `cleanTimeLogMac.sh` for all files or the following command for a single file:
-```bash
-sed -i.bak '/.*Fail.*/d;/.*line.*/d;/.*ile.*/d;/.*WARN.*/d;/.*Igno.*/d;/.*With.*/d;/.*Using.*/d;/.*End.*/d;/^\s*$/d' time.txt
-```
-
-Use R script `reportTime.R` to plot figures and print tables.
+BEAST benchmarking data are maintained here: https://github.com/CompEvol/benchmark