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dong.w.xie@gmail.com 2012-02-07 14:53 Rev.: 4642

trunk: move confused native files to \deprecated folder

0 lines of code changed in 2 files:

• native: compileNativeLinux.sh (del), compileNativeMacOSX.sh (del)

rambaut 2011-12-21 22:10 Rev.: 4559

Updated MacOSX make file. Notionally makes a fat library containing 32bit, 64bit and PPC code.

16 lines of code changed in 2 files:

• native: Makefile.OSX (new)

rambaut 2011-12-21 22:00 Rev.: 4558

Updated MacOSX make file. Notionally makes a fat library containing 32bit, 64bit and PPC code. Have commented out the PPC version as I can't compile it (on Lion). Will try to make it conditional on PPC compiler being available. Probably a good idea to distribute a full fat version as binary.

41 lines of code changed in 2 files:

• native: Makefile.OSX (+41 -7), Makefile.OSX.icc (del)

dong.w.xie 2011-12-12 12:10 Rev.: 4539

trunk: tidy up native/ folder but it needs Andrew to update all Makefiles before deleting compile scripts

0 lines of code changed in 3 files:

• native: Makefile (del), NewNativeLikelihoodCore.c (del), NewNativeLikelihoodCore.h (del)

dong.w.xie 2011-12-07 11:13 Rev.: 4521

trunk: move the remaining native folder under the root of project for easy finding.

4003 lines of code changed in 11 files:

• native: AminoAcidLikelihoodCore.c (new 2405), AminoAcidLikelihoodCore.h (new 57), GeneralLikelihoodCore.c (new 266), GeneralLikelihoodCore.h (new 52), NativeMemoryLikelihoodCore.c (new 509), NativeMemoryLikelihoodCore.h (new 97), NativeSubstitutionModel.c (new 177), NativeSubstitutionModel.h (new 45), NucleotideLikelihoodCore.c (new 330), NucleotideLikelihoodCore.h (new 61), compileNativeWin32.bat (new 4)

dong.w.xie 2011-12-07 11:07 Rev.: 4520

trunk: delete duplicate native folder

0 lines of code changed in 16 files:

• native: AminoAcidLikelihoodCore.c (del), AminoAcidLikelihoodCore.h (del), GeneralLikelihoodCore.c (del), GeneralLikelihoodCore.h (del), Makefile (del), NativeMemoryLikelihoodCore.c (del), NativeMemoryLikelihoodCore.h (del), NativeSubstitutionModel.c (del), NativeSubstitutionModel.h (del), NewNativeLikelihoodCore.c (del), NewNativeLikelihoodCore.h (del), NucleotideLikelihoodCore.c (del), NucleotideLikelihoodCore.h (del), compileNativeLinux.sh (del), compileNativeMacOSX.sh (del), compileNativeWin32.bat (del)

dong.w.xie 2011-12-06 16:09 Rev.: 4511

more

3 lines of code changed in 1 file:

• native: compileNativeLinux.sh (new 3)

rambaut 2011-11-20 07:28 Rev.: 4456

Refactoring of the robust counting and sequence error model into a new tab ('States') which allows these options to be specified on a per partition basis. These options are still not finished yet but the panel can be hidden using the constant at the top of BeautiFrame.

4 lines of code changed in 1 file:

• native: Makefile (new 4)

msuchard 2011-04-10 03:58 Rev.: 3930

Updated compileNativeMacOSX.sh to work under 10.6 and added a parse class for paired-amino acid evolution

14 lines of code changed in 1 file:

• native: compileNativeMacOSX.sh (new 14)

rambaut 2009-04-01 11:52 Rev.: 1532

Fixed problem with ambiguous states. Removed unneccesary allocation of partials/states.

18 lines of code changed in 1 file:

• native: compileNativeMacOSX.sh (+18 -12)

rambaut 2008-11-02 12:54 Rev.: 1268

Cleaning up and testing

151 lines of code changed in 3 files:

• native: Makefile (+1 -1), NewNativeLikelihoodCore.c (new 148), NewNativeLikelihoodCore.h (new 2)

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

Added the optimization of using fixed states at tips.

176 lines of code changed in 2 files:

• native: NewNativeLikelihoodCore.c (+166 -31), NewNativeLikelihoodCore.h (+10 -2)

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

Missing option for object file in Linux

3 lines of code changed in 1 file:

• native: Makefile (+3 -4)

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

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

3 lines of code changed in 2 files:

• native: Makefile (+2 -2), NewNativeLikelihoodCore.h (+1 -1)

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

I promise; it works this time

1 lines of code changed in 1 file:

• native: Makefile (+1 -1)

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:

• native: Makefile (+4 -2), NewNativeLikelihoodCore.c (-1)

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

Added Makefile for new native cores

43 lines of code changed in 2 files:

• native: Makefile (+40), NewNativeLikelihoodCore.h (+3 -3)

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:

• native: NewNativeLikelihoodCore.c (+22 -23)

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

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

19 lines of code changed in 1 file:

• native: NewNativeLikelihoodCore.c (+19 -8)

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

NewNativeLikelihood now works.

22 lines of code changed in 1 file:

• native: NewNativeLikelihoodCore.c (+22 -8)

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

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

21 lines of code changed in 1 file:

• native: NewNativeLikelihoodCore.c (+21 -25)

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.

523 lines of code changed in 2 files:

• native: NewNativeLikelihoodCore.c (+414), NewNativeLikelihoodCore.h (+109)

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

As usual, I forgot the C source files

31 lines of code changed in 3 files:

• native: NativeSubstitutionModel.c (new), NativeSubstitutionModel.h (new), compileNativeMacOSX.sh (+31 -20)

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.

13 lines of code changed in 2 files:

• native: NativeMemoryLikelihoodCore.c (+13 -2)

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

37 lines of code changed in 3 files:

• native: NativeMemoryLikelihoodCore.c (+33 -9), NativeMemoryLikelihoodCore.h (+4)

msuchard 2008-09-30 09:15 Rev.: 1199

Damn class names. Who had the idea to name the Java classes as NativeX and the C files as X?

25 lines of code changed in 5 files:

• native: GeneralLikelihoodCore.c (new), GeneralLikelihoodCore.h (new), NativeMemoryLikelihoodCore.c (+9 -7)

msuchard 2008-09-30 06:16 Rev.: 1197

Added a native general likelihood core, an experimental likelihood core that holds partials/matrices/states as native pointers (intermediate step to off-loading these to the GPU).

900 lines of code changed in 5 files:

• native: GeneralLikelihoodCore.c (+266), GeneralLikelihoodCore.h (+52), NativeMemoryLikelihoodCore.c (+472), NativeMemoryLikelihoodCore.h (+93), compileNativeMacOSX.sh (+17)

bloomquist 2008-06-17 07:45 Rev.: 957

Unrolled the loops in two of functions. Results in slightly better performance.

1959 lines of code changed in 2 files:

• native: AminoAcidLikelihoodCore.c (+1959 -91)

bloomquist 2008-06-13 11:19 Rev.: 953

Created a native AminoAcidLikelihoodCore to speed up computations when using protein data. Also edited makefiles so that it compiles. I know that the makefile works fine for Linux, but I haven't tested it for MacOSx or Win32.

The native core drops runtime by 45%.

551 lines of code changed in 6 files:

• native: AminoAcidLikelihoodCore.c (+537), AminoAcidLikelihoodCore.h (new), compileNativeLinux.sh (+2), compileNativeMacOSX.sh (+9), compileNativeWin32.bat (new)

jheled 2007-06-26 06:02 Rev.: 327

newline at end to eliminate gcc warning

1 lines of code changed in 2 files:

• native: NucleotideLikelihoodCore.h (new)

sidneym 2007-04-24 17:43 Rev.: 243

build script for Windows version of native library

2 lines of code changed in 1 file:

• native: compileNativeWin32.bat (+2)

sidneym 2007-04-24 15:07 Rev.: 241

remove unused local variables that produced compiler warning

0 lines of code changed in 2 files:

• native: NucleotideLikelihoodCore.c (-1)

rambaut 2006-12-04 09:38 Rev.: 83

Merged some fixes and improvements I made in the 1.4 branch in to the trunk. This includes the fix for Issue 8 in LogCombiner. Also, I have made some interfaces in the TreeColouring stuff so that other sources of TreeColouring (such as the Transmission history stuff) can provide coloured trees for logging.

2 lines of code changed in 1 file:

• native: compileNativeMacOSX.sh (+2 -2)

rambaut 2006-10-18 23:56 Rev.: 37

Updated some benchmarks in the benchmark.xml comments and fixed the Mac OS X native compile script

3 lines of code changed in 1 file:

• native: compileNativeMacOSX.sh (+3 -3)

rambaut 2006-10-12 22:53 Rev.: 22

Updated the "compileNativeMacOSX.sh" script to create a fat dylib that runs on both intel & PPC macs.

12 lines of code changed in 1 file:

• native: compileNativeMacOSX.sh (+12 -2)

rambaut 2006-10-12 21:49 Rev.: 21

This is our native library that helps speed up likelihood calculations for nucleotide sequences. If the compiled JNI dynamic library is found on BEAST start up then it will be used otherwise a pure Java version will be used. The scripts contain the commands to compile the library on Mac & Linux (I have no idea how to do it on Windows). Ideally we would produce a "configure" script so that users can compile a version optimized for their machine.

397 lines of code changed in 4 files:

• native: NucleotideLikelihoodCore.c (+331), NucleotideLikelihoodCore.h (+61), compileNativeLinux.sh (+3), compileNativeMacOSX.sh (+2)