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Created with Raphaël 2.2.024Nov22201725Oct2220191815118630Sep29282423222120171526Aug25512Jul928Jun128723May29Apr2827262220191615137630Mar252219171615982125Feb221110943127Jan2221181413126418Dec1716108743230Nov272625191813129654330Oct282622211413129765130Sep2524232217161514111098743227Aug24201965331Jul302927242317103230Jun29272624232219171554327May262526158730Apr29282221201410930Mar2726232221201817[Aevol8][4B] Fix an error in is_promoter for 4b in Aevol6 implementation[Aevol8][2_4_BASE] Both version are compiling (but at least a bug with 2BASE)[Aevol_8][4_BASE] Add the support of Aevol_4b (from Romain and Marco) for Aevol_7/8 implementation, the code should be completed but not tested[Aevol_8][4_BASE] Add the support of Aevol_4b (from Romain and Marco) for CMake (default : 2b)[Aevol_8][4_BASE] Add the support of Aevol_4b (from Romain and Marco) for management classes (run/create/io/mutation/...)[Aevol_8][4_BASE] Add the support of Aevol_4b (from Romain and Marco) for Aevol_6 implementation, the rest will come in next commits[Aevol7][DnaFactory] Add a new policy for pool cleanup (max pool size)aevol_8_tmpaevol_8_tmp[Aevol8][DnaFactory_ALG] Add ALLOCATE (malloc/free) option in CMakeList, Add a function to cleanup the DnaFactory pool to avoid using too much memory[Aevol8][ANC Stats 7] Fix missing value in header when computing non_coding stats[Aevol8][ANC Stats 7] Fix missing value in header when computing non_coding stats[Aevol_8][Stats] Change the name of the NO_STATS flag, fix writing stats during evolution for Aevol_8[Aevol8][Traces] Add nb clones in performance traces[Aevol8][ancestor_stats_7] Fix missing variable[Aevol8][DnaFactory] Fix typo[Aevol7] Fix stats file error with ancestor_stats_7, Fix issue with L2G memory allocator and ancestor stats, Add a new option with ancestor_stats_7 to support manually defined parallelism, Add an option in cmake to choose the memory allocation algorithm of DnaFactory (FIRST, FIRSTFIT, L2G)[Aevol8] Fix reproductibility issues[Aevol8] Switching the custom strncmp with the classical STL one for start_protein[Aevol8] Add a new Dna memory allocator: ALLOCATE which remove any interesting feature of using a custom memory allocator[Aevol7] Fix non-coding stats[Aevol7] Improved and fixed new Dna memory allocator policy[Aevol8] A new DnaFactory policy with less lock[Aevol7] Protect omp simd aligned with #ifdef for ICC and CLANG OneAPI only[Aevol 7][Gantt Trace] Add allocate (or reallocate) Dna and metadata memory tracesmerge conflictaevol_8aevol_8merge conflictmerge conflictmerge conflict[Aevol 7] Write non-coding stats when requested[Aevol 7] Fix CLang (Intel OneAPI + AMD CC) for aligned data assume_aligned[Aevol_7] Add the capability to compute non-coding variables[Aevol 7] Add a new FUNC step in gantt traces[Aevol8] Fix activation of diff RNA optimization + modify vectorized functions to support Intel Clang (OneAPI)[Aevol8][Compute_RNA] Working on fixing searching diff rna options[Aevol8][OMP_LIST_SORT] Add the compilation options to choose between 3 differents algorithms for sorting the list of mutant before processing them + [GANTT] Add per function start/stop counter[Aevol8] Add the new Intel Compiler (from OneAPI and a patched version of Clang) to the list of compiler allowing advanced vectorized optimisation[Aevol8][DnaMutator] Incorrect compute of post mutation DNA length for large deletion event[Aevol 8][Traces] Move some performance counter to be closer to reality[Aevol 8][LDNA] Use pre-computed post-computed DNA length[Aevol 8][LDNA] Before mutation compute the post-mutation DNA Length[Aevol 8][Gantt Chart Traces] Increase details (RNA, Proteins Count and Pre/Post mutation DNA size) (typo fixed)