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1. Integrated fallback for BFGS optimization to Brent-based optimizat…

…ion in case BFGS requires too many parameters.

2. Raised the minimum rate value to 0.0001
latest commit 70c66a06dc
@stamatak authored
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WindowsExecutables_v8.2.0 updated windows binaries
manual updated manual
usefulScripts use more portabel perl shebangs
Makefile.AVX.HYBRID.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.AVX.MPI.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.AVX.PTHREADS.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.AVX.PTHREADS.mac added modified makefiles that will do a clean build (i.e. remove all …
Makefile.AVX.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.AVX.mac added modified makefiles that will do a clean build (i.e. remove all …
Makefile.AVX2.HYBRID.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.AVX2.MPI.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.AVX2.PTHREADS.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.AVX2.PTHREADS.mac added modified makefiles that will do a clean build (i.e. remove all …
Makefile.AVX2.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.AVX2.mac added modified makefiles that will do a clean build (i.e. remove all …
Makefile.HYBRID.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.MPI.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.PTHREADS.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.PTHREADS.mac added modified makefiles that will do a clean build (i.e. remove all …
Makefile.QuartetMPI.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.SSE3.HYBRID.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.SSE3.MPI.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.SSE3.PTHREADS.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.SSE3.PTHREADS.mac added modified makefiles that will do a clean build (i.e. remove all …
Makefile.SSE3.QuartetMPI.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.SSE3.gcc added modified makefiles that will do a clean build (i.e. remove all …
Makefile.SSE3.mac added modified makefiles that will do a clean build (i.e. remove all …
Makefile.gcc added modified makefiles that will do a clean build (i.e. remove all …
README 1. Integrated fallback for BFGS optimization to Brent-based optimizat…
Release-Notes 1. Integrated fallback for BFGS optimization to Brent-based optimizat…
ancestralStates.c -added ancestral state computation for LG4X and LG4M models
avxLikelihood.c 1. updated the manual
axml.c fixed numerical problem in BFGS optimization
axml.h 1. Integrated fallback for BFGS optimization to Brent-based optimizat…
bipartitionList.c added Kassian's code for TC/IC score calculations on partial gene trees
classify.c fixed major bug in likelihood functions for partitioned analyses with…
eigen.c cleaned up the code
evaluateGenericSpecial.c added Kassian's code for TC/IC score calculations on partial gene trees
evaluatePartialGenericSpecial.c added some experimental stuff for bastien to play with
fastDNAparsimony.c changed output tree format for subtree placements for Alexey
fastSearch.c added some experimental stuff for bastien to play with
globalVariables.h added new protein subst model stmtREV, see: http://datadryad.org/reso…
gpl-3.0.txt added GPL license
leaveDropping.c -added an automatic option to compute the SH-like support values (-f …
legacyCode.c some code cleanup
makenewzGenericSpecial.c added Kassian's code for TC/IC score calculations on partial gene trees
mem_alloc.c added better error reporting for cases where RAxML runs out of memory
models.c added Kassian's code for TC/IC score calculations on partial gene trees
multiple.c -added ancestral state computation for LG4X and LG4M models
newviewGenericSpecial.c fixed numerical problem in BFGS optimization
optimizeModel.c 1. Integrated fallback for BFGS optimization to Brent-based optimizat…
parsePartitions.c added an assertion
rapidBootstrap.c added some experimental stuff for bastien to play with
rmq.h changed source file permissions
rmqs.c fixed minor type casting issues and minor bug in error detection outp…
rmqs.h changed source file permissions
rogueEPA.c -fixed some minor compiler issues with the Makefiles and source files
searchAlgo.c added some experimental stuff for bastien to play with
topologies.c Added ultra-fast RELL bootstrapping that can be invoked via -f D as d…
treeIO.c fixed major bug in likelihood functions for partitioned analyses with…

README

Standard RAxML version 8.2.3

Compiling under Linux:

standard, SSE3 or AVX version?

In general you should try to compile the SSE3 version that makes use of capabilities 
on relativiely recent processors (most Intel or AMD chips not older than 3-4 years).
The SSE3 version will run about 40% faster than the non-SSE3 version.

If you have a more recently bought processor (within the last 1-2 years), please also try to compile
the AVX version which once again uses the capabilities of modern processors better and can be 10-30% faster 
than the SSE3 version. AVX will work on the Intel i7 (sandy-bridge) series processors as well as on the very recently 
released AMD Bulldozer systems. 

Compiling should work out of the box with all reasonably recent vesrion of the GNU gcc and Intel icc compilers.
If you want to use icc replace gcc by icc in the Makefiles.

Please direct all your RAxML questions to our google group (and only after 
having used the search function!): 
https://groups.google.com/forum/?hl=de&fromgroups#!forum/raxml

Sequential version:

type:
"make -f Makefile.gcc"
"rm *.o"
or
"make -f Makefile.SSE3.gcc"
"rm *.o"
or
"make -f Makefile.AVX.gcc"
"rm *.o"

Pthreads version:

type: 
"make -f Makefile.PTHREADS.gcc"
"rm *.o"
or
"make -f Makefile.SSE3.PTHREADS.gcc"
"rm *.o"
or
"make -f Makefile.AVX.PTHREADS.gcc"
"rm *.o"

Coarse-grain MPI version:

type:
"make -f Makefile.MPI.gcc"
"rm *.o"
or
"make -f Makefile.SSE3.MPI.gcc"
"rm *.o"
or
"make -f Makefile.AVX.MPI.gcc"                            
"rm *.o"

Hybrid MPI/Pthreads version:

Before using this version, please read this paper here:

http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2010-3.pdf

and look at these slides: 

http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf

type:
"make -f Makefile.HYBRID.gcc" 
"rm *.o"
or  
"make -f Makefile.SSE3.HYBRID.gcc"
"rm *.o"
or
"make -f Makefile.AVX.HYBRID.gcc" 
"rm *.o" 
Something went wrong with that request. Please try again.