October 2008 Commit Log

Number of Commits:
67
Number of Active Developers:
6
rambaut 2008-10-31 03:43 Rev.: 1266

Was finding that for pure R/Y encoded data the empirical frequency estimation was getting stuck in an iteration that never converged. Added a maximum number of iterations. Also added the MrBayes estimator (as opposed to the current one which matches PAUP) but this is not on by default.

101 lines of code changed in 5 files:

msuchard 2008-10-30 09:22 Rev.: 1265

Reads GPU info correctly

60 lines of code changed in 2 files:

bloomquist 2008-10-30 08:33 Rev.: 1264

Changed the parser so it adds the weight.

6 lines of code changed in 1 file:

msuchard 2008-10-30 04:33 Rev.: 1263

Removed GPU-related files from dr.evomodel.treelikelihood to cut down on confusion; GPU now only supported in dr.evomodel.newtreelikelihood

1 lines of code changed in 7 files:

msuchard 2008-10-29 13:57 Rev.: 1262

Making stateTipCount compatible with GPU code

44 lines of code changed in 2 files:

rambaut 2008-10-29 13:10 Rev.: 1261

Added the optimization of using fixed states at tips.

599 lines of code changed in 13 files:

msuchard 2008-10-29 08:33 Rev.: 1260

Added back in partialsScaling for debug scaling on GPU

86 lines of code changed in 1 file:

msuchard 2008-10-28 05:24 Rev.: 1259

Modified GPULikelihoodCore wrapped to pass padded state information to native code

20 lines of code changed in 1 file:

rambaut 2008-10-28 00:28 Rev.: 1258

Added some generalizations to the path sampling code.

65 lines of code changed in 2 files:

msuchard 2008-10-25 06:06 Rev.: 1257

Need to manually convert double[] freqs -> float[] freqs; array-copy does not work.

35 lines of code changed in 1 file:

rambaut 2008-10-25 05:52 Rev.: 1256

Alex and I have been experimenting with a path sampling approach to estimating marginal likelihoods. See eXML in examples/testPathSampling.xml. Not sure it works.

707 lines of code changed in 10 files:

alexei.drummond 2008-10-25 01:01 Rev.: 1255

preparation for implementation of birth-death-sampling prior

56 lines of code changed in 2 files:

alexei.drummond 2008-10-24 23:08 Rev.: 1254

uncommented Andrew's comments :-) Please add options.jar to your classpath.

177 lines of code changed in 1 file:

rambaut 2008-10-24 22:25 Rev.: 1253

Unresolved import: ml.*

177 lines of code changed in 1 file:

rambaut 2008-10-24 05:00 Rev.: 1252

14 lines of code changed in 3 files:

alexei.drummond 2008-10-24 03:11 Rev.: 1251

improved speed by factor of 8 by using binary search and caching intensities, and added ability to do multiple replicates.

296 lines of code changed in 8 files:

jheled 2008-10-23 06:54 Rev.: 1250

Add handling of constant intervals in Piecewise linear. Those can happen demographic is explicitly set for simulation purposes.

17 lines of code changed in 1 file:

bloomquist 2008-10-23 06:08 Rev.: 1249

Added some extra names for the xml parser.

6 lines of code changed in 1 file:

bloomquist 2008-10-23 06:08 Rev.: 1248

Rewrote for easiser use.

31 lines of code changed in 1 file:

alexei.drummond 2008-10-23 03:54 Rev.: 1247

build script and usage instructions for Variable Coalescent Simulator version 0.1

600 lines of code changed in 11 files:

alexei.drummond 2008-10-22 23:40 Rev.: 1246

fixed bone-headed intensity and inverse-intensity functions. The previous functions were piecewise-constant with population size being set to the mean over the interval! This is now properly piecewise linear.

12 lines of code changed in 1 file:

jheled 2008-10-22 21:51 Rev.: 1245

Added 5'th optional argument - file name to log the demographic

42 lines of code changed in 1 file:

Michael.DefoinPLatel 2008-10-22 14:19 Rev.: 1244

Missing option for object file in Linux

3 lines of code changed in 1 file:

alexei.drummond 2008-10-22 10:56 Rev.: 1243

simulation of trees from piecewise linear populations

245 lines of code changed in 3 files:

rambaut 2008-10-22 09:45 Rev.: 1242

Created a likelihood core that uses floats to test precision management techniques.

408 lines of code changed in 3 files:

rambaut 2008-10-20 00:35 Rev.: 1241

Made some improvements to TreeStat

643 lines of code changed in 19 files:

msuchard 2008-10-13 14:11 Rev.: 1240

I promise; it works this time

1 lines of code changed in 1 file:

msuchard 2008-10-13 14:09 Rev.: 1239

Forgot to set the compiler directive -- the most important part

4 lines of code changed in 2 files:

msuchard 2008-10-13 14:05 Rev.: 1238

Added Makefile for new native cores

43 lines of code changed in 2 files:

rambaut 2008-10-13 11:28 Rev.: 1237

A few adjustments about what is passed from the Eigen decomposition to the likelihood core.

22 lines of code changed in 1 file:

msuchard 2008-10-13 11:08 Rev.: 1236

Wrote Java portion of GPULikelihoodCore.

151 lines of code changed in 4 files:

rambaut 2008-10-13 10:28 Rev.: 1235

A few adjustments about what is passed from the Eigen decomposition to the likelihood core.

68 lines of code changed in 8 files:

rambaut 2008-10-13 08:12 Rev.: 1234

NewNativeLikelihood now works.

24 lines of code changed in 3 files:

rambaut 2008-10-13 06:09 Rev.: 1233

NewNativeLikelihood now runs but gives a NaN. Onwards and upwards...

36 lines of code changed in 4 files:

msuchard 2008-10-13 05:15 Rev.: 1232

1. Refactored newtreelikelihood.GPUMemoryLikelihoodCore to GPULikelihoodCore for naming consistency and to avoid confusion with the old (and working) treelikelihood.GPUMemoryLikelihoodCore

2. Added 64-state GeneticCode to YangCodonModel. Why are there so many different GeneticCode parsers?

171 lines of code changed in 3 files:

rambaut 2008-10-12 23:17 Rev.: 1231

Added the native code for the newtreelikelihood's native likelihood core. This compiles but doesn't work yet.

524 lines of code changed in 3 files:

rambaut 2008-10-12 23:14 Rev.: 1230

Simplified the SiteModel interface so it is no longer a wrapper for a substitution model to get transition probability matrix.

1653 lines of code changed in 23 files:

rambaut 2008-10-12 11:54 Rev.: 1229

New TreeLikelihood seems to be running. New example xml, testNewTreeLikelihoodMCMC.xml gives exactly the same sequence using the seed -666 (the seed of the BEAST) as the old TreeLikelihood.

3 lines of code changed in 2 files:

rambaut 2008-10-12 11:33 Rev.: 1228

MCMC is running with GeneralLikelihoodCore. The new TreeLikelihood has a parser called 'crazyTreeLikelihood'. Not sure whether it is giving the right answer yet.

54 lines of code changed in 4 files:

msuchard 2008-10-12 11:33 Rev.: 1227

Added "spawn" attribute to MCMC. When spawn="false", the MCMC runs in the same thread as the parser, otherwise the parsers spawns a new thread in which to run the MCMC. Keeping everything in one thread is important for GPU profiling (until I learn how to get contexts to work correctly).

24 lines of code changed in 2 files:

rambaut 2008-10-12 10:12 Rev.: 1226

Now calculates likelihoods correctly. Next step to test MCMC run.

21 lines of code changed in 1 file:

rambaut 2008-10-12 09:06 Rev.: 1225

Working towards a working new likelihood core.

492 lines of code changed in 6 files:

rambaut 2008-10-12 08:34 Rev.: 1224

Added a native 'husk' for the new likelihoodcore

32 lines of code changed in 2 files:

rambaut 2008-10-12 08:14 Rev.: 1223

Undid my last change on further consideration. I intend to write a simple 'NativeLikelihoodCore' so I want to avoid confusion.

1020 lines of code changed in 4 files:

rambaut 2008-10-12 08:06 Rev.: 1222

Renamed the native likelihood cores in the newtreelikelihood package removing the word 'Memory' as in this implementation, all native LCs will be doing the memory on the native side.

1106 lines of code changed in 4 files:

rambaut 2008-10-12 08:01 Rev.: 1221

Added an 'updateSiteModel' method to the LikelihoodCore interface and storing and restoring of local copies of state frequencies, category rates and proportions.

This is part of an effort to put more of the likelihood calculations on the native side to facilitate the use of cool hardware like GPUs and Cell processors (I wonder if you can get them as PCI cards?).

86 lines of code changed in 4 files:

rambaut 2008-10-11 21:17 Rev.: 1220

Improved the comments in the interface

24 lines of code changed in 2 files:

rambaut 2008-10-11 21:11 Rev.: 1219

Split the dependency information into a seperate array for clarity.

26 lines of code changed in 4 files:

msuchard 2008-10-11 12:35 Rev.: 1218

Some work on a likelihood core registry and factory

1180 lines of code changed in 4 files:

msuchard 2008-10-11 09:32 Rev.: 1217

Fixed ConvertAlignmentParser to return the correct codon type.

14 lines of code changed in 2 files:

msuchard 2008-10-11 08:02 Rev.: 1216

64 state codon model for testing purposes

75 lines of code changed in 6 files:

msuchard 2008-10-10 13:07 Rev.: 1215

Missing interface components fixed.

24 lines of code changed in 4 files:

Michael.DefoinPLatel 2008-10-10 09:52 Rev.: 1214

Started to integrate the autocorrelated relaxed clock in Beauti. Not happy yet with the intial priors. Some commented code will be removed later.

1749 lines of code changed in 8 files:

msuchard 2008-10-09 11:37 Rev.: 1213

Move complicated parsing of dataType and available JNI libraries into a factory class

19 lines of code changed in 1 file:

msuchard 2008-10-09 11:33 Rev.: 1212

Working on codon support for the GPU

117 lines of code changed in 5 files:

rambaut 2008-10-08 21:57 Rev.: 1211

Compiling - ready to start testing...

newtreelikelihood is a new approach to the likelihood core to minimize
communication between Java and native implementations. This should allow faster native code and use of GPUs. This is just a temporary parallel package whilst this is developed.

1002 lines of code changed in 7 files:

msuchard 2008-10-08 04:56 Rev.: 1210

Fixed the final (?) thread migration issue with the GPU. Someday I will learn how to use context-dependent GPU addresses and avoid this whole issue all together.

41 lines of code changed in 4 files:

msuchard 2008-10-07 12:57 Rev.: 1209

Fixed thread migration issue in GPU/NativeMemoryLikelihoodCore.

54 lines of code changed in 2 files:

msuchard 2008-10-07 11:27 Rev.: 1208

Little tweaks to GPU/native memory stuff

90 lines of code changed in 4 files:

rambaut 2008-10-07 11:12 Rev.: 1207

newtreelikelihood is a new approach to the likelihood core to minimize communication between Java and native implementations. This should allow faster native code and use of GPUs. This is just a temporary parallel package whilst this is developed.

1143 lines of code changed in 5 files:

msuchard 2008-10-06 03:46 Rev.: 1206

Missed one line of code! I really suck sometimes.

1 lines of code changed in 1 file:

msuchard 2008-10-06 03:40 Rev.: 1205

Reverted TreeLikelihood to state before my hack. Renamed ExperimentalTL into PrecisionTestTL and copied hack into new ExperiementalTL.

1012 lines of code changed in 4 files:

msuchard 2008-10-05 16:23 Rev.: 1204

As usual, I forgot the C source files

31 lines of code changed in 3 files:

msuchard 2008-10-05 16:21 Rev.: 1203

Adding NativeSubstitutionModel that computes the finite-time transition probabilities (matrix-multiplication, not eigendecomposition) in native memory cache. This is in intermediate step to porting these calculations onto the GPU. Small example shows 2x overall Beast speed-up doing matrix multiplication in native memory over copying results from Java to native stuff. Be warned! I hacked TreeLikelihood and this is going to make you unhappy.

919 lines of code changed in 7 files:

rambaut 2008-10-03 10:50 Rev.: 1202

Fixed a null pointer error

14 lines of code changed in 1 file:

msuchard 2008-10-01 10:58 Rev.: 1201

32 lines of code changed in 1 file:

msuchard 2008-10-01 05:01 Rev.: 1200

Added GPUMemoryLikelihoodCore from which Dat will rewrite the GPU code to hold partials/matrices/states in the GPU global memory

154 lines of code changed in 5 files:

September 2008 »

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