- 17 Dec, 2013 1 commit
-
-
akalantz authored
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@7105 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
- 29 May, 2013 1 commit
-
-
mvalle authored
Added maximization stop after given number of iterations. Added new cmd line options to define maximum number of iterations. git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6593 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
- 15 May, 2013 1 commit
-
-
mvalle authored
Removed possible race in variable initialization. Don't change vars if they come from H1. git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6553 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
- 26 Apr, 2013 2 commits
-
-
mvalle authored
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6468 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
mvalle authored
Same for constraining variables inside search domain. git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6467 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
- 14 Feb, 2013 1 commit
-
-
mvalle authored
Corrected help line for the -m option For the global optimizer set the timeout to 24 hours git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5926 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
- 05 Feb, 2013 2 commits
-
-
mvalle authored
Started adding code for CPV scaling to avoid under/overflow Added new option in CMake to enable local scaling git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5867 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
mvalle authored
Added print of no pre stop switch Fixed global scaling code git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5861 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
- 28 Jan, 2013 1 commit
-
-
mvalle authored
Implemented initialize h0 from h1 also for MPI. git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5831 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
- 24 Jan, 2013 1 commit
-
-
mvalle authored
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5812 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
- 12 Dec, 2012 1 commit
-
-
mvalle authored
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5413 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
- 04 Dec, 2012 1 commit
-
-
mvalle authored
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
-
- 24 Nov, 2012 1 commit
-
-
mvalle authored
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
-
- 18 Oct, 2012 1 commit
-
-
mvalle authored
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
-
- 10 Oct, 2012 1 commit
-
-
mvalle authored
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
-
- 09 Oct, 2012 1 commit
-
-
mvalle authored
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
-
- 02 Oct, 2012 1 commit
-
-
mvalle authored
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
-
- 25 Sep, 2012 1 commit
-
-
mvalle authored
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
-
- 24 Sep, 2012 1 commit
-
-
mvalle authored
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
-
- 10 Sep, 2012 1 commit
-
-
mvalle authored
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
-
- 04 Sep, 2012 1 commit
-
-
mvalle authored
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
-
- 28 Aug, 2012 1 commit
-
-
mvalle authored
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
-
- 21 Aug, 2012 1 commit
-
-
mvalle authored
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
-
- 12 Jul, 2012 1 commit
-
-
mvalle authored
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
-
- 03 Jul, 2012 1 commit
-
-
mvalle authored
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
-
- 19 Jun, 2012 2 commits
-
-
mvalle authored
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4004 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
mvalle authored
Changed interface to BrancSiteModel. git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4003 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
- 02 Apr, 2012 1 commit
-
-
mvalle authored
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
-
- 26 Mar, 2012 1 commit
-
-
mvalle authored
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
-
- 21 Feb, 2012 3 commits
-
-
mvalle authored
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3509 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
mvalle authored
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
-
mvalle authored
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
-
- 19 Feb, 2012 1 commit
-
-
mvalle authored
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
-
- 17 Feb, 2012 1 commit
-
-
mvalle authored
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3500 95c5a404-1f88-0410-a6b0-c3f062b6f34a
-
- 15 Feb, 2012 2 commits
-
-
mvalle authored
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
-
mvalle authored
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
-
- 13 Feb, 2012 1 commit
-
-
mvalle authored
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
-
- 10 Feb, 2012 1 commit
-
-
mvalle authored
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
-
- 26 Jan, 2012 1 commit
-
-
mvalle authored
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
-
- 11 Jan, 2012 1 commit
-
-
mvalle authored
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
-