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https://github.com/brenhinkeller/bayezirchron.c
Bayesian eruption age estimation code from Keller, Schoene, and Samperton (2018)
https://github.com/brenhinkeller/bayezirchron.c
Last synced: 19 days ago
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Bayesian eruption age estimation code from Keller, Schoene, and Samperton (2018)
- Host: GitHub
- URL: https://github.com/brenhinkeller/bayezirchron.c
- Owner: brenhinkeller
- License: gpl-3.0
- Created: 2016-06-29T04:49:28.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2021-10-01T19:11:50.000Z (about 3 years ago)
- Last Synced: 2023-02-27T05:17:05.308Z (over 1 year ago)
- Language: C
- Homepage: https://doi.org/10.7185/geochemlet.1826
- Size: 24.9 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# BayeZirChron.c
C version of the Bayesian zircon eruption age estimation code from [Keller, Schoene, and Samperton (2018)](https://doi.org/10.7185/geochemlet.1826)
## Installation from command line
Installation from the command line requires a working C compiler. The default [makefile](src/Makefile) assumes [gcc](https://gcc.gnu.org) (or an alias) is available.
On linux/unix/bsd this is likely already true; on Mac OS the necessary tools for compiling C source can be installed by typing `xcode-select --install` at the command line.
```bash
# Download
git clone https://github.com/brenhinkeller/BayeZirChron.c.git
# Move to folder containing source code
cd BayeZirChron.c/src/
# Compile
make serial
```
To compile the parallel code used for synthetic distribution tests, additionally run:
```bash
make parallel
```
or
```bash
mpicc -std=c11 -O3 -o tzircrystestaccuracy tzircrystestaccuracy.c
```
Compiling and running this parallel version additionally requires a working installation of MPI (either [Open MPI](https://www.open-mpi.org) or [MPICH](https://www.mpich.org)) A sample batchfile is provided in the example folder: [runTest.pbs](examples/synthetic%20dataset%20tests/runTest.pbs)
## Usage
A range of [examples](examples/), including the application Bayesian zircon eruption age estimation code to literature datasets, is provided. A Matlab script to run all literature examples is provided in [examples/literature dataset tests/RunLiteratureExamples.m](examples/literature%20dataset%20tests/RunLiteratureExamples.m)
Basic command-line usage follows the pattern:
```bash
tzircrystmetropolis distribution.tsv sample.tsv > output.tsv
```
where is the length of Markov chain to run, `distribution.tsv` is an ascii file describing a zircon saturation distribution, `sample.tsv` is a tab or comma-separated file containing a list of individual zircon ages and 2-sigma uncertainties; the resulting stationary distributions will be written to `output.tsv`. For example
```bash
tzircrystmetropolis 10000 MeltsTZircDistribution.tsv sample.tsv > metropolisdata.tsv
```
The results of synthetic dataset tests, which compare traditional weighted-mean and youngest-zircon interpretations to Bayesian eruption age estimates (using several different crystallization distributions) are provided in [examples/synthetic dataset tests/](examples/synthetic%20dataset%20tests/). Figures can be re-plotted using a Matlab script [tzircrystestaccuracyPlots.m](examples/synthetic%20dataset%20tests/tzircrystestaccuracyPlots.m).
To reproduce the datafiles provided in this folder, compile the parallel code [tzircrystestaccuracy.c](src/tzircrystestaccuracy.c) as described above (using mpicc), and run using
```bash
mpiexec -np ./tzircrystestaccuracy
```
where is the number of MPI tasks to run (typically you want this to be equal to the number of CPU cores or hardware threads you are running on), is the number of simulations (at each N) to run per MPI task, is the length of Markov chain to run,
for example:
```bash
mpiexec -np 16 ./tzircrystestaccuracy 4 10000 1 MeltsTZircDistribution.tsv > eruptionestimates1.tsv
```
to run on 16 cores with 4 simulations per taks, each 10000 MCMC steps long, with a dt/sigma of 1 and using the crystallization distribution found in [MeltsTZircDistribution.tsv](distributions/MeltsTZircDistribution.tsv). To run on a cluster, you will need a batch file suited to your cluster's workload manager. For instance, the example batchfile [runTest.pbs](examples/synthetic%20dataset%20tests/runTest.pbs):
```bash
#!/bin/bash
#PBS -l nodes=20:ppn=16,walltime=00:40:00
module load openmpi
mpiexec ./tzircrystestaccuracy 4 10000 1 MeltsTZircDistribution.tsv > eruptionestimates1.tsv
```
runs 4 simulations per task on 20 nodes with 16 cores each, for a total of 1280 simulations at each N
## Julia version
[](https://mybinder.org/v2/gh/brenhinkeller/BayeZirChron.c/master?filepath=julia%2Fdemo.ipynb)
See [julia](julia/) folder. Try it out in this [interactive Jupyter notebook](https://mybinder.org/v2/gh/brenhinkeller/BayeZirChron.c/master?filepath=julia%2Fdemo.ipynb) via [Binder](https://mybinder.org)!
For future work, see [Chron.jl](https://github.com/brenhinkeller/Chron.jl), which can be run in [standalone eruption/deposition mode](https://github.com/brenhinkeller/Chron.jl#standalone-age-depth-modelling) using the approach developed here.