git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5413 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

Changed timer to return time_t
Added more catch cases
Different interface to BEB
Fixed warnings on windows
Changed BEB constructor
Partial porting to XMT
Fixed bug for testing


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4970 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Changed nul pointers from 0 to NULL (readability)
Fixed datatypes


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4896 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

Fixed check for MPI threading type
Used posix_memalign on linux


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4779 95c5a404-1f88-0410-a6b0-c3f062b6f34a

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4751 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Switched to posix_memalign for Linux


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4750 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Changed various unsigned to size_t
For MPI passed the entire command line
Fixed local variable names
Added casts
Put save to Octave routines for testing


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3754 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added support for XMT compilation


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3716 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

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

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

Split aligned malloc/free from allocator. Used bitmap to see if subtree in the same tree. added option USE_MKL_VML to select vector routines if available. Preallocated arrays when needed.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@2692 95c5a404-1f88-0410-a6b0-c3f062b6f34a

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@2624 95c5a404-1f88-0410-a6b0-c3f062b6f34a