git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5413 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Changed messages from Tree balancing.
Changed few BEB message formats.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5328 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Changed C style include to C++ style
Fixed few doxygen comments


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5191 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Upgraded doxygen and fixed doxygen comments
Fixed bug in write results
Changed computation order. First H1 then H0
Changed option init H1 from H0 to init H0 from H1
Added maximization forced stop if result does not already pass the LRT
Added MPI trace level and fixed messages
Added testing hooks to BEB.
Passed scale values from H1 to BEB
Fixed relative error default
Added initial map of internal to external site numbers
Changed iterator initialization


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4924 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Cleaned code
Started fixing design problem in MPI part


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4834 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Cosmetic changes (variable names, variables access rights)
Added routines to support BEB
More validity controls on command line parameters


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4829 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Removed dependencies computation from Forest and created a standalone class
Added accessors to Forest
Removed unneeded methods
Write results do nothing if file not defined
Adjusted member visibility to various variables
Removed custom code for memalign
Added more tasking


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4784 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added write results into file for database loading
Fixed various MPI problems


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4737 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added initial routine to output results in a form suitable for automatic load into the database
Inital work on BEB


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4719 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Removed unneeded piece of code
Added special case for compute likelihood for gradient
Changed var order
Removed switch for S matrix usage (now it is permanently set when using lapack)
Corrected doxygen comments


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4603 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added missing ifdef
Add shortcut to recursive likelihood computation
Ordered correctly member initialization
Started implementing reuse in gradient computation
Precomputed few array access
Aligned Timer implementation between Linux and Windows
Removed unneeded includes


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4580 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Reordered class members
No effort computation if not run multithread


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4560 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added new option to set the maximum number of MKL threads
Check for invalid times in file
Added definition for dsyevd
Added explanation for codon classes
Removed invalid test on parameters


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4537 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Parallelized eigendecomposition
Simplified dependencies pass to parallel computation to reduce overhead
Fixed MPI init for pure mpi
Added temporary print to count the number of eigendecompositions, P matrix computation and CPV computation


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4204 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Fixed missing initialization in BranchSiteModelAltHyp.
Removed hardcoded value for relative error value.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4099 95c5a404-1f88-0410-a6b0-c3f062b6f34a

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4004 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Changed interface to BrancSiteModel.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4003 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Clarified Verbose levels.
Disabled balancing if run serial.
Move various initialization to be constructor initialization lists.
Fixed storage of results in MPI run.
All messages now go to cerr.
Different initialization of proportions. Now all classes have the same value.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3700 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Removed few return pointer to return reference


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3693 95c5a404-1f88-0410-a6b0-c3f062b6f34a

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3509 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Put const in end value for iteration
Made loadTreeFromString private
Changed to C++ casts


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3504 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Optimized elementWiseMult for PGI compiler
Added restrict attriute for PGI compiler
Changed few loops in old ming2 optimizer to memcpy calls


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3503 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added initial support for intra-class balancing
Removed obsolete functions


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3501 95c5a404-1f88-0410-a6b0-c3f062b6f34a

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3500 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Updated Doxygen and Doxyfile to 1.7.6.1
Removed warning at level 4 on Windows
Removed unused operations in ProbabilityMatrixSet
Fixed Doxygen comments


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3493 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Simplified Forest removing methods that pertain to othere classes
Corrected set of matrices name from Transition to Probability


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3490 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Removed unneeded parameter from CodeML optimizer


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3470 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Corrected include file placement in Timer
Rationalized choice of Likelihood computation modes in CMAKE


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3452 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added comments for typedef.
More tests for eigendecomposition added.
Move isDifferent to MathSupport.
Removed unneeded include.
Overloaded computeMatrixSet.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3380 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added margin for points lying on the boundaries
Fixed typo in LoadTreeFromString
Added BLAS function used by new optimizer


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3264 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added command line switch to change the delta for the gradient computation.
Changed list of available optimization algorithms.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3247 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Tested different optimizers
Forced sequential MKL usage


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3129 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added option to have always the same starting point for optimization.
Added support for testing of variable h values.
Better check for parameters validity.
Small fixes.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3061 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added schedule(static) to prepare NUMA support
Removed unused computeNEB routine
New structure for the MPI layer


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3054 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Changed MPI structure
Aligned arrays
Added support for BLAS/LAPACK on windows.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3053 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Remove unused code and compilation options
Added USE_OLD_PROPORTIONS option
Streamlined Dependency between site classes computation
Correctly reinitialized BranchSiteModel variables



git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3043 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Simplified BranchSiteModel invocation.
Fixed OpenMP calls in main.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3007 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Fixed few doxygen comments


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@2925 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Cleaned comments (for doxygen)
Changed few size_t into unsigned int
Moved preprocessing fields into anothed structure linked to ForestNode
Print active options improved
Moved to NLopt 2.2.4
Added RESTRICT keyword
Unrolled few loops for efficiency
Added new method to balance execution in the by-tree likelihood computation


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@2892 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Use MKL VML functions
Better log messages formatting
Changed access method to children
New implementation of the 'same tree' flag
Fixed MKL directory and compilation line
Removed alignment for PGI compiler
Set slot (matrix and vector) length by experiment
Removed inline keywords
Added explicit to constructors
Aligned eigen decomposed matrices
Removed reversing of mD
Using STL map to convert codons to numbers
Reordered access to big vectors



git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@2872 95c5a404-1f88-0410-a6b0-c3f062b6f34a