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build.xml
View file @ 0e8c4814
......@@ -83,6 +83,7 @@
<include name="dr/app/beagle/**"/>
<include name="dr/app/seqgen/**"/>
<include name="dr/app/plugin/**"/>
<include name="dr/app/realtime/**"/>
<include name="dr/app/tools/**"/>
<include name="dr/app/util/**"/>
<include name="dr/app/treestat/**"/>
......@@ -129,6 +130,7 @@
<include name="dr/app/gui/**/*.class"/>
<include name="dr/app/seqgen/**"/>
<include name="dr/app/plugin/**"/>
<include name="dr/app/realtime/**"/>
<include name="dr/app/util/**/*.class"/>
<include name="dr/app/tools/**/*.class"/>
<include name="dr/app/treestat/**/*.class"/>
......@@ -319,10 +321,10 @@
<!--
<property name="version" value="1.9"/>
-->
<property name="version" value="1.10.2"/>
<property name="version" value="1.10.4"/>
<property name="jvm_version" value="1.7+"/>
<property name="version_number" value="1.10.2"/>
<property name="version_number" value="1.10.4"/>
<property name="copyright" value="Copyright 2002-2018"/>
<property name="release_dir" value="release"/>
......@@ -401,14 +403,6 @@
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<!-- BEAST v?.?.?.exe -->
<launch4j configFile="${Windows_dir}/BEAST_launch4j.xml"
outfile="${Windows_package_dir}/${BEAST_name} v${version}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}"/>
<!-- TreeAnnotator v?.?.?.exe -->
<launch4j configFile="${Windows_dir}/TreeAnnotator_launch4j.xml"
jar="${dist}/beast.jar"
......
build_bss.xml
View file @ 0e8c4814
......@@ -43,6 +43,7 @@
<include name="dr/inference/loggers/**/*.class" />
<include name="dr/inference/distribution/**/*.class" />
<include name="dr/evomodel/branchratemodel/**/*.class" />
<include name="dr/evomodel/branchmodel/**/*.class" />
<include name="dr/evomodel/substmodel/**/*.class" />
<include name="dr/app/beagle/evomodel/substmodel/**/*.class" />
<include name="dr/app/beagle/evomodel/branchmodel/**/*.class" />
......@@ -107,6 +108,7 @@
<include name="dr/inference/loggers/**" />
<include name="dr/inference/distribution/**" />
<include name="dr/evomodel/branchratemodel/**" />
<include name="dr/evomodel/branchmodel/**" />
<include name="dr/evomodel/substmodel/**" />
<include name="dr/app/beagle/evomodel/substmodel/**" />
<include name="dr/app/beagle/evomodel/branchmodel/**" />
......@@ -149,7 +151,7 @@
<echo message="Successfully compiled." />
</target>
<property name="version" value="1.0" />
<property name="version" value="1.4" />
<property name="release_dir" value="release_pibuss" />
<property name="name" value="piBUSS" />
......@@ -200,6 +202,7 @@
<delete dir="${Linux_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Linux_package_dir}" />
<mkdir dir="${Linux_dir}/lib" />
<copy todir="${Linux_package_dir}/bin">
<fileset dir="${Linux_dir}/scripts"/>
......
build_tempest.xml
View file @ 0e8c4814
......@@ -6,6 +6,10 @@
<description>
Build file for TempEst release versions.
</description>
<property name="JDK_SOURCE_VERSION" value="1.6"/>
<property name="JDK_TARGET_VERSION" value="1.6"/>
<!-- set global properties for this build -->
<property name="src" location="src"/>
<property name="build" location="build"/>
......@@ -33,7 +37,7 @@
<target name="compile" depends="init">
<!-- Compile the java code from ${src} into ${build} -->
<javac source="1.6" target="1.6" srcdir="${src}" destdir="${build}" classpathref="classpath">
<javac source="${JDK_SOURCE_VERSION}" target="${JDK_TARGET_VERSION}" srcdir="${src}" destdir="${build}" classpathref="classpath">
<include name="dr/app/tempest/**"/>
<include name="dr/app/beauti/**"/>
<include name="dr/app/tools/**"/>
......@@ -95,7 +99,7 @@
</jar>
</target>
<property name="version" value="1.5.2" />
<property name="version" value="1.5.3" />
<property name="packaging_tools" value="packaging_tools" />
<property name="release_dir" value="release_tempest" />
<property name="name" value="TempEst" />
......@@ -193,6 +197,7 @@
name="${name} v${version}"
mainclass="dr.app.tempest.TempEstApp"
stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
useJavaXKey="true"
icon="${Mac_dir}/icons/TempEst.icns"
jvmversion="1.6+"
arguments=""
......
debian/beast-mcmc-doc.install deleted 100644 → 0
View file @ f3152232
doc/*.pdf usr/share/doc/beast-mcmc
doc/*/*.pdf usr/share/doc/beast-mcmc
debian/beast-mcmc-examples.install
View file @ 0e8c4814
examples/release/* usr/share/doc/beast-mcmc/examples
examples/* usr/share/doc/beast-mcmc/examples
debian/beast-mcmc.docs
View file @ 0e8c4814
debian/README.test
debian/tests/run-unit-test
README*
debian/beast-mcmc.install
View file @ 0e8c4814
debian/bin usr
debian/*.xpm usr/share/pixmaps
build/dist/*.jar usr/share/beast-mcmc
dist/*.jar usr/share/beast-mcmc
debian/changelog
View file @ 0e8c4814
beast-mcmc (1.10.2+dfsg-1) UNRELEASED; urgency=medium
beast-mcmc (1.10.4+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
* Exclude Latex doc creation
* New Build-Depends: libejml-java
* New versioned Build-Depends: libhmsbeagle-java (>= 3.0.2)
* New upstream version
* Standards-Version: 4.2.1
* Do not try to install mac and windows build
[ Jelmer Vernooij ]
* Use secure copyright file specification URI.
* Trim trailing whitespace.
-- Andreas Tille <tille@debian.org> Tue, 16 Oct 2018 20:54:48 +0200
[ Andreas Tille ]
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
* Tracer is not build in separate build_tracer.xml any more
* Upstream does not ship PDF docs any more thus drop -doc package
* Versioned (Build-)Depends: libhmsbeagle-java (>= 3.1.2~)
-- Andreas Tille <tille@debian.org> Tue, 18 Dec 2018 15:52:51 +0100
beast-mcmc (1.8.4+dfsg.1-3) unstable; urgency=medium
......
debian/control
View file @ 0e8c4814
......@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
libjam-java (>= 0.1.20140824),
figtree,
liboptions-java,
libhmsbeagle-java (>= 3.0.2),
libhmsbeagle-java (>= 3.1.2~),
libcolt-free-java,
libmpj-java,
r-cran-rjava,
......@@ -33,13 +33,12 @@ Package: beast-mcmc
Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends},
libhmsbeagle-java (>= 1.1r1092),
libhmsbeagle-java (>= 3.1.2~),
${java:Depends},
default-jre | java6-runtime,
libnucleotidelikelihoodcore0 (>= ${source:Version}),
libnucleotidelikelihoodcore0 (<< ${source:Version}.1~),
libnetlib-java
Suggests: beast-mcmc-doc
Description: Bayesian MCMC phylogenetic inference
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
......@@ -91,22 +90,3 @@ Description: Bayesian MCMC phylogenetic inference - example data
analyses and a suit of programs for analysing the results.
.
This package contains the example data.
Package: beast-mcmc-doc
Architecture: all
Section: doc
Depends: ${shlibs:Depends},
${misc:Depends}
Enhances: beast-mcmc
Description: Bayesian MCMC phylogenetic inference - documentation
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
phylogenies inferred using strict or relaxed molecular clock models. It
can be used as a method of reconstructing phylogenies but is also a
framework for testing evolutionary hypotheses without conditioning on a
single tree topology. BEAST uses MCMC to average over tree space, so that
each tree is weighted proportional to its posterior probability. Included
is a simple to use user-interface program for setting up standard
analyses and a suit of programs for analysing the results.
.
This package contains the documentation.
debian/patches/ignore_mac_install.patch 0 → 100644
View file @ 0e8c4814
Description: Do not try to install mac and windows build
Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 16 Oct 2018 20:54:48 +0200
--- a/build.xml
+++ b/build.xml
@@ -816,6 +816,6 @@
<echo message="Mac version release is finished."/>
</target>
- <target name="build" depends="mac, windows, linux" description="build all the executables" />
+ <target name="build" depends="linux" description="build all the executables" />
</project>
debian/patches/series
View file @ 0e8c4814
......@@ -2,3 +2,4 @@ enable_hardening.patch
fix_classpath_in_build_xml.patch
create_soname.patch
fix_encoding.patch
ignore_mac_install.patch
debian/rules
View file @ 0e8c4814
......@@ -48,7 +48,8 @@ override_dh_auto_build:
# CLASSPATH=$(CLASS_PATH)
mkdir -p lib
ant build
ant -buildfile build_tracer.xml dist
# FIXME: There is no such file build_tracer.xml any more
# ant -buildfile build_tracer.xml dist
# native/compileNativeLinux.sh does not create dynamic libraries
cd native ; $(MAKE) -f Makefile.linux JAVA_HOME=$(JAVA_HOME)
# gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o ; \
......@@ -67,6 +68,7 @@ ifeq ($(HASTEXDOC),yes)
endif
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
#####################################################################
## Run test suite ##
## -------------- ##
......@@ -75,6 +77,4 @@ override_dh_auto_test:
#####################################################################
#
# $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml junit
override_dh_compress:
dh_compress --exclude=.pdf
endif
release/common/README.txt
View file @ 0e8c4814
BEAST v1.10.2 2002-2018
BEAST v1.10.4 2002-2018
Bayesian Evolutionary Analysis Sampling Trees
by
Alexei J. Drummond, Andrew Rambaut & Marc Suchard
......@@ -16,7 +16,7 @@
msuchard@ucla.edu
Last updated: a.rambaut@ed.ac.uk - 6th October 2018
Last updated: a.rambaut@ed.ac.uk - 9th November 2018
Contents:
1) INTRODUCTION
......
release/common/VERSION HISTORY.txt
View file @ 0e8c4814
BEAST v1.10.2 2002-2018
BEAST v1.10.4 2002-2018
Bayesian Evolutionary Analysis Sampling Trees
by
Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard
......@@ -17,11 +17,30 @@
Version History
Last updated: a.rambaut@ed.ac.uk - 6th October 2018
Last updated: a.rambaut@ed.ac.uk - 9th November 2018
All issues can be viewed at https://github.com/beast-dev/beast-mcmc/issues
================================================================================
Version 1.10.4 released 9th November 2018
New Features:
Command-line option to turn off operator adaptation.
Command-line option to limit BEAGLE 3 thread usage.
Bug Fixes:
Issue 1038: Issue specifying burnin in the command-line LogCombiner.
================================================================================
Version 1.10.3 released 28th October 2018
Bug Fixes:
Issue 1037: Likelihood computation performance reduced with BEAGLE 3 on CPU.
Issue 1036: Truncated normals not working as priors.
================================================================================
Version 1.10.2 released 6th October 2018
Bug Fixes:
......
src/dr/app/beagle/tools/Partition.java
View file @ 0e8c4814
......@@ -106,7 +106,8 @@ public class Partition {
FrequencyModel freqModel, //
int from, //
int to, //
int every //
int every, //
DataType dType
) {
this.treeModel = treeModel;
......@@ -119,7 +120,11 @@ public class Partition {
this.to = to;
this.every = every;
if(dType == null) {
dataType = freqModel.getDataType();
}else{
dataType = dType;
}
partitionSiteCount = getPartitionSiteCount();
setBufferHelpers();
......@@ -131,6 +136,18 @@ public class Partition {
}// END: Constructor
public Partition(TreeModel treeModel, //
BranchModel branchModel, //
GammaSiteRateModel siteModel, //
BranchRateModel branchRateModel, //
FrequencyModel freqModel, //
int from, //
int to, //
int every //
){
this(treeModel, branchModel, siteModel, branchRateModel, freqModel, from, to, every, null);
}
private void setSubstitutionModelDelegate() {
substitutionModelDelegate = new SubstitutionModelDelegate(treeModel,
branchModel);
......
src/dr/app/beagle/tools/parsers/PartitionParser.java
View file @ 0e8c4814
......@@ -32,9 +32,11 @@ import dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.app.beagle.tools.Partition;
import dr.evolution.sequence.Sequence;
import dr.evolution.datatype.DataType;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.evomodel.branchratemodel.DefaultBranchRateModel;
import dr.evomodel.tree.TreeModel;
import dr.evoxml.util.DataTypeUtils;
import dr.xml.AbstractXMLObjectParser;
import dr.xml.AttributeRule;
import dr.xml.ElementRule;
......@@ -43,6 +45,9 @@ import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
import dr.xml.XORRule;
import java.util.ArrayList;
import java.util.List;
/**
* @author Filip Bielejec
* @version $Id$
......@@ -53,6 +58,7 @@ public class PartitionParser extends AbstractXMLObjectParser {
public static final String FROM = "from";
public static final String TO = "to";
public static final String EVERY = "every";
public static final String DATA_TYPE = "dataType";
@Override
public String getParserName() {
......@@ -75,6 +81,7 @@ public class PartitionParser extends AbstractXMLObjectParser {
int from = 0;
int to = -1;
int every = xo.getAttribute(EVERY, 1);
DataType dataType = null;
if (xo.hasAttribute(FROM)) {
from = xo.getIntegerAttribute(FROM) - 1;
......@@ -101,10 +108,40 @@ public class PartitionParser extends AbstractXMLObjectParser {
"Illegal 'every' attribute in patterns element");
}// END: every check
if (xo.hasAttribute(DATA_TYPE)){
dataType = DataTypeUtils.getDataType(xo);
}
TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
GammaSiteRateModel siteModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
FrequencyModel freqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
//FrequencyModel freqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
FrequencyModel freqModel;
List<FrequencyModel> freqModels = new ArrayList<FrequencyModel>();
for (int i = 0; i < xo.getChildCount(); i++) {
Object cxo = xo.getChild(i);
if (cxo instanceof FrequencyModel) {
freqModels.add((FrequencyModel) cxo);
}
}
if(freqModels.size()==1){
freqModel = freqModels.get(0);
}else{
double [] freqParameter = new double[freqModels.size()*freqModels.get(0).getFrequencyCount()];
int index = 0;
for(int i = 0; i < freqModels.size(); i++){
for(int j = 0; j < freqModels.get(i).getFrequencyCount(); j++){
freqParameter[index] = (freqModels.get(i).getFrequency(j))/freqModels.size();
index++;
}
}
freqModel = new FrequencyModel(dataType, freqParameter);
}
Sequence rootSequence = (Sequence) xo.getChild(Sequence.class);
BranchRateModel rateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
......@@ -120,7 +157,7 @@ public class PartitionParser extends AbstractXMLObjectParser {
}
Partition partition = new Partition(tree, branchModel, siteModel, rateModel, freqModel, from, to, every);
Partition partition = new Partition(tree, branchModel, siteModel, rateModel, freqModel, from, to, every, dataType);
if (rootSequence != null) {
partition.setRootSequence(rootSequence);
......@@ -145,12 +182,13 @@ public class PartitionParser extends AbstractXMLObjectParser {
"Determines how many sites are selected. A value of 3 will select every third site starting from <b>"
+ FROM
+ "</b>, default is 1 (every site)"), //
AttributeRule.newStringRule(DataType.DATA_TYPE, true),
new ElementRule(TreeModel.class), //
new XORRule(new ElementRule(BranchModel.class),
new ElementRule(SubstitutionModel.class), false), //
new ElementRule(GammaSiteRateModel.class), //
new ElementRule(BranchRateModel.class, true), //
new ElementRule(FrequencyModel.class), //
new ElementRule(FrequencyModel.class, 1, Integer.MAX_VALUE), //
new ElementRule(Sequence.class, true) //
};
......
src/dr/app/beast/BeastMain.java
View file @ 0e8c4814
......@@ -339,14 +339,21 @@ public class BeastMain {
new Arguments.LongOption("tests", "The number of full evaluation tests to perform (default 1000)"),
new Arguments.RealOption("threshold", 0.0, Double.MAX_VALUE, "Full evaluation test threshold (default 0.1)"),
new Arguments.Option("adaptation_off", "Don't adapt operator sizes"),
new Arguments.RealOption("adaptation_target", 0.0, 1.0, "Target acceptance rate for adaptive operators (default 0.234)"),
new Arguments.Option("beagle", "Use BEAGLE library if available (default on)"),
new Arguments.Option("beagle_info", "BEAGLE: show information on available resources"),
new Arguments.StringOption("beagle_order", "order", "BEAGLE: set order of resource use"),
new Arguments.IntegerOption("beagle_instances", "BEAGLE: divide site patterns amongst instances"),
new Arguments.StringOption("beagle_multipartition", new String[]{"auto", "on", "off"},
false, "BEAGLE: use multipartition extensions if available (default auto)"),
new Arguments.Option("beagle_CPU", "BEAGLE: use CPU instance"),
new Arguments.Option("beagle_GPU", "BEAGLE: use GPU instance if available"),
new Arguments.Option("beagle_SSE", "BEAGLE: use SSE extensions if available"),
new Arguments.Option("beagle_SSE_off", "BEAGLE: turn off use of SSE extensions"),
new Arguments.Option("beagle_threading_off", "BEAGLE: turn off auto threading for a CPU instance"),
new Arguments.IntegerOption("beagle_thread_count", 1, Integer.MAX_VALUE, "BEAGLE: manually set number of threads for a CPU instance"),
new Arguments.Option("beagle_cuda", "BEAGLE: use CUDA parallization if available"),
new Arguments.Option("beagle_opencl", "BEAGLE: use OpenCL parallization if available"),
new Arguments.Option("beagle_single", "BEAGLE: use single precision if available"),
......@@ -358,16 +365,19 @@ public class BeastMain {
new Arguments.LongOption("beagle_rescale", "BEAGLE: frequency of rescaling (dynamic scaling only)"),
new Arguments.Option("mpi", "Use MPI rank to label output"),
new Arguments.StringOption("particles", "FOLDER", "Specify a folder of particle start states"),
new Arguments.IntegerOption("mc3_chains", 1, Integer.MAX_VALUE, "number of chains"),
new Arguments.RealOption("mc3_delta", 0.0, Double.MAX_VALUE, "temperature increment parameter"),
new Arguments.RealArrayOption("mc3_temperatures", -1, "a comma-separated list of the hot chain temperatures"),
new Arguments.IntegerOption("mc3_swap", 1, Integer.MAX_VALUE, "frequency at which chains temperatures will be swapped"),
new Arguments.StringOption("load_dump", "FILENAME", "Specify a filename to load a dumped state from"),
new Arguments.LongOption("dump_state", "Specify a state at which to write a dump file"),
new Arguments.LongOption("dump_every", "Specify a frequency to write a dump file"),
new Arguments.StringOption("save_dump", "FILENAME", "Specify a filename to save a dumped state to"),
new Arguments.Option("force_resume", "Force resuming from a dumped state"),
new Arguments.StringOption("load_state", "FILENAME", "Specify a filename to load a saved state from"),
new Arguments.StringOption("save_stem", "FILENAME", "Specify a stem for the filenames to save states to"),
new Arguments.LongOption("save_at", "Specify a state at which to save a state file"),
new Arguments.LongOption("save_every", "Specify a frequency to save the state file"),
new Arguments.StringOption("save_state", "FILENAME", "Specify a filename to save state to"),
new Arguments.Option("force_resume", "Force resuming from a saved state"),
new Arguments.StringOption("citations_file", "FILENAME", "Specify a filename to write a citation list to"),
......@@ -428,8 +438,6 @@ public class BeastMain {
}
final boolean strictXML = arguments.hasOption("strict");
final boolean window = arguments.hasOption("window");
final boolean options = arguments.hasOption("options") || (argumentCount == 0);
final boolean working = arguments.hasOption("working");
String fileNamePrefix = null;
boolean allowOverwrite = arguments.hasOption("overwrite");
......@@ -438,6 +446,26 @@ public class BeastMain {
long seed = MathUtils.getSeed();
boolean useJava = false;
int threadCount = -1;
boolean usingSMC = false;
boolean usingMC3 = false;
double[] chainTemperatures = null;
int swapChainsEvery = DEFAULT_SWAP_CHAIN_EVERY;
if (arguments.hasOption("particles")) {
System.setProperty("smc.particle_folder", arguments.getStringOption("particles"));
usingSMC = true;
System.setProperty("mcmc.evaluation.count", Long.toString(0));
}
// smc option is always run without GUI.
final boolean window = !usingSMC && arguments.hasOption("window");
final boolean options = !usingSMC && (arguments.hasOption("options") || (argumentCount == 0));
if (!usingSMC) {
if (arguments.hasOption("tests")) {
long fullEvaluationCount = arguments.getLongOption("tests");
System.setProperty("mcmc.evaluation.count", Long.toString(fullEvaluationCount));
......@@ -448,8 +476,6 @@ public class BeastMain {
System.setProperty("mcmc.evaluation.threshold", Double.toString(fullEvaluationThreshold));
}
int threadCount = -1;
if (arguments.hasOption("java")) {
useJava = true;
}
......@@ -478,7 +504,7 @@ public class BeastMain {
delta = arguments.getRealOption("mc3_delta");
}
double[] chainTemperatures = new double[chainCount];
chainTemperatures = new double[chainCount];
chainTemperatures[0] = 1.0;
if (arguments.hasOption("mc3_temperatures")) {
double[] hotChainTemperatures = arguments.getRealArrayOption("mc3_temperatures");
......@@ -491,12 +517,12 @@ public class BeastMain {
}
}
int swapChainsEvery = DEFAULT_SWAP_CHAIN_EVERY;
if (arguments.hasOption("mc3_swap")) {
swapChainsEvery = arguments.getIntegerOption("mc3_swap");
}
boolean useMC3 = chainCount > 1;
usingMC3 = chainCount > 1;
}
// ============= BEAGLE settings =============
long beagleFlags = 0;
......@@ -523,6 +549,21 @@ public class BeastMain {
}
if (!arguments.hasOption("beagle_SSE_off")) {
beagleFlags |= BeagleFlag.VECTOR_SSE.getMask();
} else {
beagleFlags |= BeagleFlag.VECTOR_NONE.getMask();
}
if (arguments.hasOption("beagle_threading_off")) {
beagleFlags |= BeagleFlag.THREADING_NONE.getMask();
} else {
beagleFlags |= BeagleFlag.THREADING_CPP.getMask();
}
if (arguments.hasOption("beagle_thread_count")) {
int beagleThreadCount = arguments.getIntegerOption("beagle_thread_count");
if (beagleThreadCount == 1) {
beagleFlags &= ~BeagleFlag.THREADING_CPP.getMask();
beagleFlags |= BeagleFlag.THREADING_NONE.getMask();
}
System.setProperty("beagle.thread.count", Integer.toString(arguments.getIntegerOption("beagle_thread_count")));
}
// if (arguments.hasOption("beagle_double")) {
// beagleFlags |= BeagleFlag.PRECISION_DOUBLE.getMask();
......@@ -556,6 +597,15 @@ public class BeastMain {
System.setProperty("beagle.rescale", Long.toString(arguments.getLongOption("beagle_rescale")));
}
if (arguments.hasOption("beagle_multipartition")) {
// attempt to force the use/non-use of the multipartition extensions, otherwise auto
if (arguments.getStringOption("beagle_multipartition").toLowerCase().equals("on")) {
System.setProperty("beagle.multipartition.extensions", Boolean.TRUE.toString());
} else if (arguments.getStringOption("beagle_multipartition").toLowerCase().equals("off")) {
System.setProperty("beagle.multipartition.extensions", Boolean.FALSE.toString());
}
}
// ============= Other settings =============
if (arguments.hasOption("threads")) {
// threadCount defaults to -1 unless the user specifies an option
......@@ -576,24 +626,40 @@ public class BeastMain {
}
}
if (arguments.hasOption("load_dump")) {
String debugStateFile = arguments.getStringOption("load_dump");
System.setProperty(BeastCheckpointer.LOAD_STATE_FILE, debugStateFile);
if (arguments.hasOption("adaptation_off")) {
System.setProperty("mcmc.use_adaptation", Boolean.FALSE.toString());
}
if (arguments.hasOption("adaptation_target")) {
System.setProperty("adaptation_target",
Double.toString(arguments.getRealOption("mcmc.adaptation_target")));
}
if (arguments.hasOption("dump_state")) {
long debugWriteState = arguments.getLongOption("dump_state");
System.setProperty(BeastCheckpointer.SAVE_STATE_AT, Long.toString(debugWriteState));
if (!usingSMC) {
// ignore these other options
if (arguments.hasOption("load_state")) {
String stateFile = arguments.getStringOption("load_state");
System.setProperty(BeastCheckpointer.LOAD_STATE_FILE, stateFile);
}
if (arguments.hasOption("save_at")) {
long saveAt = arguments.getLongOption("save_at");
System.setProperty(BeastCheckpointer.SAVE_STATE_AT, Long.toString(saveAt));
}
if (arguments.hasOption("dump_every")) {
long debugWriteEvery = arguments.getLongOption("dump_every");
System.setProperty(BeastCheckpointer.SAVE_STATE_EVERY, Long.toString(debugWriteEvery));
if (arguments.hasOption("save_every")) {
long saveEvery = arguments.getLongOption("save_every");
System.setProperty(BeastCheckpointer.SAVE_STATE_EVERY, Long.toString(saveEvery));
}
if (arguments.hasOption("save_dump")) {
String debugStateFile = arguments.getStringOption("save_dump");
System.setProperty(BeastCheckpointer.SAVE_STATE_FILE, debugStateFile);
if (arguments.hasOption("save_state")) {
String stateFile = arguments.getStringOption("save_state");
System.setProperty(BeastCheckpointer.SAVE_STATE_FILE, stateFile);
}
if (arguments.hasOption("save_stem")) {
String stemName = arguments.getStringOption("save_stem");
System.setProperty(BeastCheckpointer.SAVE_STEM, stemName);
}
if (arguments.hasOption("force_resume")) {
......@@ -622,6 +688,7 @@ public class BeastMain {
int rank = Integer.valueOf(rankProp);
seed = updateSeedByRank(seed, rank);
}
}
int maxErrorCount = 0;
if (arguments.hasOption("errors")) {
......@@ -736,9 +803,13 @@ public class BeastMain {
if (BeagleInfo.getVersion().startsWith("1.")) {
System.err.println("WARNING: You are currenly using BEAGLE v1.x. For best performance and compatibility\n" +
"with models in BEAST, please upgrade to BEAGLE v2.x at http://github.com/beagle-dev/beagle-lib/\n");
"with models in BEAST, please upgrade to BEAGLE v3.x at http://github.com/beagle-dev/beagle-lib/\n");
} else if (BeagleInfo.getVersion().startsWith("2.")) {
System.err.println("WARNING: You are currenly using BEAGLE v2.x. For best performance and compatibility\n" +
"with models in BEAST, please upgrade to BEAGLE v3.x at http://github.com/beagle-dev/beagle-lib/\n");
}
if (beagleShowInfo) {
BeagleInfo.printResourceList();
return;
......@@ -809,7 +880,8 @@ public class BeastMain {
System.out.println("Random number seed: " + seed);
try {
new BeastMain(inputFile, consoleApp, maxErrorCount, verbose, warnings, strictXML, additionalParsers, useMC3, chainTemperatures, swapChainsEvery);
new BeastMain(inputFile, consoleApp, maxErrorCount, verbose, warnings, strictXML, additionalParsers,
usingMC3, chainTemperatures, swapChainsEvery);
} catch (RuntimeException rte) {
// The stack trace here is not useful
// rte.printStackTrace(System.err);
......
src/dr/app/beast/BeastVersion.java
View file @ 0e8c4814
......@@ -53,14 +53,14 @@ public class BeastVersion implements Version, Citable {
/**
* Version string: assumed to be in format x.x.x
*/
private static final String VERSION = "1.10.2";
private static final String VERSION = "1.10.4";
private static final String DATE_STRING = "2002-2018";
private static final boolean IS_PRERELEASE = false;
private static final boolean IS_PRERELEASE = true;
// this is now being manually updated since the move to GitHub. 7 digits of GitHub hash.
private static final String REVISION = "4db633b";
private static final String REVISION = "bc6cbd9";
public String getVersion() {
return VERSION;
......
src/dr/app/beast/development_parsers.properties
View file @ 0e8c4814
......@@ -46,10 +46,6 @@ dr.evomodel.coalescent.structure.ConstantMigrationModel
dr.evomodel.coalescent.structure.ColourSamplerModel
dr.evomodel.coalescent.structure.TreeColouringOperator
dr.evomodel.coalescent.structure.MetaPopulationModel
dr.evomodel.operators.ColouredExchangeOperator
dr.evomodel.operators.ColouredSubtreeSlideOperator
dr.evomodel.operators.ColouredOperator
dr.evomodel.operators.FixedColouredOperator
# TREE OPERATORS
dr.inference.operators.hmc.deprecated.LatentFactorHamiltonianMCParser
......
src/dr/app/beast/release_parsers.properties
View file @ 0e8c4814
......@@ -308,6 +308,7 @@ dr.evomodelxml.operators.RandomWalkIntegerSetSizeWeightedOperatorParser
dr.evoxml.MicrosatellitePatternStatisticParser
dr.evomodelxml.operators.FixedHeightSubtreePruneRegraftOperatorParser
dr.evomodelxml.operators.SubtreeJumpOperatorParser
dr.evomodelxml.operators.SubtreeLeapOperatorParser
......@@ -382,7 +383,6 @@ dr.inferencexml.model.ThreadedCompoundLikelihoodParser
dr.inferencexml.operators.RandomWalkIntegerOperatorParser
dr.inferencexml.operators.RandomWalkOperatorParser
dr.inferencexml.operators.ScaleOperatorParser
dr.inferencexml.operators.LogRandomWalkOperatorParser
dr.inferencexml.operators.UniformOperatorParser
dr.inferencexml.operators.UniformIntegerOperatorParser
dr.inferencexml.operators.UpDownOperatorParser
......