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-fixed bug in BFGS optimization

-improved error handling
latest commit 297bc55146
@stamatak authored
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WindowsExecutables_v8.1.20 added windowns executables for version 8.1.20
manual updated manual
usefulScripts use more portabel perl shebangs
Makefile.AVX.HYBRID.gcc fixed some typos in the printouts, made the makefiles debian compliant
Makefile.AVX.MPI.gcc fixed some typos in the printouts, made the makefiles debian compliant
Makefile.AVX.PTHREADS.gcc fixed some typos in the printouts, made the makefiles debian compliant
Makefile.AVX.PTHREADS.mac Fixed Makefiles for Macintosh using clang compiler.
Makefile.AVX.gcc fixed some issues with undetermined sites supression
Makefile.AVX.mac some code cleanup for removing warnings generated by clang
Makefile.AVX2.HYBRID.gcc updated Makefiles and version number
Makefile.AVX2.MPI.gcc updated Makefiles and version number
Makefile.AVX2.PTHREADS.gcc updated Makefiles and version number
Makefile.AVX2.PTHREADS.mac updated Makefiles and version number
Makefile.AVX2.gcc updated Makefiles and version number
Makefile.AVX2.mac updated Makefiles and version number
Makefile.HYBRID.gcc fixed some typos in the printouts, made the makefiles debian compliant
Makefile.MPI.gcc fixed some typos in the printouts, made the makefiles debian compliant
Makefile.PTHREADS.gcc fixed some typos in the printouts, made the makefiles debian compliant
Makefile.PTHREADS.mac Fixed Makefiles for Macintosh using clang compiler.
Makefile.QuartetMPI.gcc fixed some typos in the printouts, made the makefiles debian compliant
Makefile.SSE3.HYBRID.gcc fixed some typos in the printouts, made the makefiles debian compliant
Makefile.SSE3.MPI.gcc fixed some typos in the printouts, made the makefiles debian compliant
Makefile.SSE3.PTHREADS.gcc fixed some typos in the printouts, made the makefiles debian compliant
Makefile.SSE3.PTHREADS.mac Fixed Makefiles for Macintosh using clang compiler.
Makefile.SSE3.QuartetMPI.gcc fixed some typos in the printouts, made the makefiles debian compliant
Makefile.SSE3.gcc added expliciit offendimng site printout for invariable sites that ar…
Makefile.SSE3.mac added expliciit offendimng site printout for invariable sites that ar…
Makefile.gcc fixed some typos in the printouts, made the makefiles debian compliant
README -fixed bug in BFGS optimization
Release-Notes -fixed bug in BFGS optimization
ancestralStates.c -added ancestral state computation for LG4X and LG4M models
avxLikelihood.c 1. updated the manual
axml.c -fixed bug in BFGS optimization
axml.h -fixed bug in BFGS optimization
bipartitionList.c improved parser error handling
classify.c -added some additional error checking for partitions and the EPA algo…
eigen.c -put eigenvalue/eigenvector decomposition into separate file that is …
evaluateGenericSpecial.c -added flags for computing JC69 and K80 DNA models
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 flags for computing JC69 and K80 DNA models
mem_alloc.c added better error reporting for cases where RAxML runs out of memory
models.c -added flags for computing JC69 and K80 DNA models
multiple.c -added ancestral state computation for LG4X and LG4M models
newviewGenericSpecial.c -added flags for computing JC69 and K80 DNA models
optimizeModel.c -fixed bug in BFGS optimization
parsePartitions.c -added ancestral state computation for LG4X and LG4M models
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 updated manual

README

Standard RAxML version 8.1.21

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" 
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