Commit 0ae247b2 authored by TURPIN Laurent's avatar TURPIN Laurent
Browse files

Remove Aevol6

parent 692a063a
......@@ -16,67 +16,16 @@ add_definitions(-DVERSION="${PROJECT_VERSION}")
set(CMAKE_CXX_STANDARD 17)
set(AUTHORIZED_MTPERIOD 607 1279 2281 4253 11213 19937 44497 86243 132049 216091)
set(with-post-treatments ON CACHE BOOL "Whether to build post-treatments")
set(with-x OFF CACHE BOOL "Whether to enable graphical outputs")
set(with-omp ON CACHE BOOL "Whether to enable OpenMP parallelization")
set(enable-profiling OFF CACHE BOOL "Whether to enable profiling")
set(with-tracing OFF CACHE BOOL "Whether to use tracing")
set(enable-perflog OFF CACHE BOOL "Whether to active performance log")
set(enable-normalized-fitness OFF CACHE BOOL "With this option, the NORMALIZED_FITNESS flag is defined, allowing a different fitness calculation")
set(enable-mtperiod 607 CACHE STRING "Period of the Mersen Twister. Autorized values are : 607 1279 2281 4253 11213 19937 44497 86243 132049 216091")
set(enable-trivialjumps OFF CACHE STRING "When this option is set, a trivial jump algorithm will be used instead of the polynomial-based method")
set(enable-mpi OFF CACHE BOOL "When this option is set, the MPI interface is set")
set(enable-omp-sort "" CACHE STRING "Which sorting algorithm to use for sorting mutant individual before processing them (by default, no sorting)")
set(disable-multi-promoters "" CACHE STRING "Forbid that a gene is translated by multiple RNAs: MAX keep only the RNA with maximum production rate (e) or FAREST keep only the RNA which is the farest from the protein")
set(dna-factory-alg "FIRSTFIT" CACHE STRING "Which memory allocation algorithm to use for managing the DnaFactory pool of DNAs")
set(with-triangle OFF CACHE BOOL "Whether to enable triangle phenotypic target (else Gaussian)")
set(with-raevol OFF CACHE BOOL "Whether to enable R-Aevol (Gene regulation) version")
set(with-detectclone ON CACHE BOOL "Whether to enable clones and not recompute them")
set(with-floatconcentration OFF CACHE BOOL "Whether to enable the encoding of concentration has float (and not double)")
set(with-perf-traces OFF CACHE BOOL "Whether to activate performance traces of (R-)Aevol")
set(with-indiv-perf-traces OFF CACHE BOOL "Whether to activate performance traces (per individual) of (R-)Aevol")
set(search-type "OLD" CACHE STRING "Which SIMD pattern search version of (R-)Aevol")
set(with-opt-diff-search OFF CACHE BOOL "Activate the optimize version of differential search for motifs (RNA and Genes)")
set(without-stats ON CACHE BOOL "Activate (or not) stats (best individuals) for each generation")
set(with-progeny-stats OFF CACHE BOOL "Activate (or not) stats for progeny (should generate a lot of data)")
set(nb-bp "2" CACHE STRING "How many BPs to be used (2 = binary DNA, 4 = classical DNA)")
if ( ${with-indiv-perf-traces} )
add_definitions(-DWITH_PERF_TRACES_PER_INDIV)
endif ()
if ( ${with-progeny-stats} )
add_definitions(-DPROGENY_STATS)
endif ()
if ( ${enable-mpi} )
add_definitions(-DHAVE_MPI)
endif ()
if ( ${with-x} )
FIND_PACKAGE(X11 REQUIRED)
if ( X11_FOUND )
add_definitions(-D__X11)
INCLUDE_DIRECTORIES(${X11_INCLUDE_DIR})
LINK_LIBRARIES(${X11_LIBRARIES})
message("graphical output enable")
endif ( X11_FOUND )
else ()
add_definitions(-D__NO_X)
message("graphical output disable")
endif ()
if(APPLE)
# X11 headers
include_directories(AFTER "/opt/X11/include")
# OpenMP stuff for Clang
if(CMAKE_C_COMPILER_ID STREQUAL "Clang" OR
......@@ -120,35 +69,10 @@ if ( ${with-omp} )
endif ()
endif ()
if ( ${enable-profiling} )
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pg")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
endif ()
if ( ${with-tracing} )
add_definitions(-D__TRACING__)
endif ()
if ( ${without-stats} )
add_definitions(-DAEVOL_NO_STATS)
endif ()
if ( ${enable-perflog} )
add_definitions(-D__PERF_LOG__)
endif ()
if ( ${with-perf-traces} )
add_definitions(-DWITH_PERF_TRACES)
endif ()
if ( ${with-opt-diff-search} )
add_definitions(-DWITH_OPTIMIZE_DIFF_SEARCH)
endif ()
if ( ${enable-normalized-fitness} )
add_definitions(-DNORMALIZED_FITNESS)
endif ()
if ( DEFINED enable-mtperiod )
list(FIND AUTHORIZED_MTPERIOD ${enable-mtperiod} _index)
if ( ${_index} GREATER -1 )
......@@ -168,30 +92,6 @@ if ( ${enable-trivialjumps} )
endif ()
endif ()
if ( ${with-triangle} )
add_definitions(-DPHENOTYPIC_TARGET_TRIANGLE)
endif ()
if ( ${with-raevol} )
add_definitions(-D__REGUL)
endif ()
if ( ${with-detectclone} )
add_definitions(-D__DETECT_CLONE)
endif ()
if ( ${with-floatconcentration} )
add_definitions(-D__FLOAT_CONCENTRATION)
endif ()
if ( NOT ${enable-omp-sort} STREQUAL "" )
if ( ${enable-omp-sort} STREQUAL "LDNA" )
add_definitions(-D__OMP_LIST_SORT=0)
elseif( ${enable-omp-sort} STREQUAL "SHUFFLE" )
add_definitions(-D__OMP_LIST_SORT=1)
endif ()
endif ()
if ( NOT ${disable-multi-promoters} STREQUAL "" )
if ( ${disable-multi-promoters} STREQUAL "MAX" )
add_definitions(-D__MULTI_PROMOTERS=0)
......@@ -200,16 +100,6 @@ if ( NOT ${disable-multi-promoters} STREQUAL "" )
endif ()
endif ()
if ( ${dna-factory-alg} STREQUAL "FIRST" )
add_definitions(-D__DNA_FACTORY_ALG=0)
elseif ( ${dna-factory-alg} STREQUAL "FIRSTFIT" )
add_definitions(-D__DNA_FACTORY_ALG=1)
elseif ( ${dna-factory-alg} STREQUAL "L2G" )
add_definitions(-D__DNA_FACTORY_ALG=2)
elseif ( ${dna-factory-alg} STREQUAL "ALLOCATE" )
add_definitions(-D__DNA_FACTORY_ALG=3)
endif ()
if ( ${nb-bp} STREQUAL "2" )
add_definitions(-DBASE_2=1)
elseif ( ${nb-bp} STREQUAL "4" )
......@@ -221,15 +111,6 @@ endif ()
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
# ===========================================================================
# Look for Boost
# ===========================================================================
set(Boost_USE_STATIC_LIBS OFF)
set(Boost_USE_MULTITHREADED ON)
set(Boost_USE_STATIC_RUNTIME OFF)
find_package(Boost 1.65.0 COMPONENTS filesystem)
# ============================================================================
# Look for Zlib
# ============================================================================
......
Generation,Coalescence
0,0
1,52
2,51
3,50
4,49
5,48
6,47
7,46
8,45
9,44
10,43
11,42
12,41
13,40
14,51
15,50
16,49
17,48
18,47
19,46
20,45
21,44
22,43
23,42
24,41
25,40
26,39
27,38
28,37
29,36
30,35
31,34
32,33
33,32
34,31
35,30
36,29
37,28
38,27
39,26
40,25
41,24
42,23
43,22
44,21
45,20
46,49
47,48
48,47
49,46
50,45
51,44
52,43
53,42
54,41
55,40
56,39
57,38
58,37
59,36
60,35
61,34
62,33
63,32
64,31
65,30
66,29
67,28
68,27
69,54
70,53
71,52
72,51
73,50
74,49
75,48
76,47
77,46
78,45
79,44
80,43
81,42
82,41
83,40
84,39
85,38
86,37
87,36
88,35
89,34
90,33
91,32
92,31
93,30
94,29
95,28
96,27
97,26
98,25
99,24
100,60
101,59
102,58
103,57
104,56
105,55
106,54
107,53
108,52
109,51
110,50
111,49
112,48
113,47
114,46
115,45
116,44
117,43
118,42
119,41
120,40
121,39
122,38
123,37
124,36
125,35
126,34
127,33
128,32
129,31
130,30
131,65
132,64
133,63
134,62
135,61
136,60
137,59
138,58
139,57
140,56
141,55
142,54
143,53
144,52
145,51
146,50
147,49
148,48
149,47
150,46
151,45
152,44
153,43
154,42
155,41
156,40
157,39
158,38
159,37
160,36
161,35
162,34
163,41
164,45
165,44
166,43
167,42
168,41
169,40
170,39
171,38
172,37
173,57
174,56
175,55
176,54
177,53
178,52
179,51
180,64
181,63
182,62
183,61
184,60
185,59
186,58
187,57
188,56
189,55
190,54
191,53
192,52
193,51
194,50
195,49
196,48
197,47
198,46
199,45
200,44
201,43
202,42
203,41
204,40
205,39
206,58
207,57
208,56
209,55
210,54
211,53
212,52
213,51
214,50
215,49
216,48
217,47
218,46
219,45
220,44
221,43
222,42
223,41
224,40
225,39
226,38
227,37
228,36
229,35
230,34
231,33
232,32
233,31
234,30
235,29
236,90
237,89
238,88
239,98
240,97
241,96
242,95
243,94
244,93
245,92
246,91
247,90
248,89
249,88
250,87
251,86
252,85
253,84
254,83
255,82
256,81
257,80
258,79
259,78
260,77
261,76
262,75
263,74
264,73
265,72
266,71
267,70
268,69
269,68
270,67
271,66
272,65
273,64
274,63
275,62
276,61
277,60
278,59
279,58
280,57
281,56
282,55
283,54
284,53
285,52
286,51
287,50
288,49
289,48
290,47
291,46
292,45
293,44
294,43
295,42
296,41
297,40
298,39
299,38
300,59
301,58
302,57
303,56
304,55
305,54
306,53
307,52
308,51
309,65
310,64
311,63
312,62
313,61
314,60
315,59
316,58
317,57
318,56
319,55
320,54
321,53
322,52
323,51
324,50
325,49
326,48
327,47
328,46
329,45
330,44
331,43
332,42
333,41
334,40
335,39
336,38
337,37
338,36
339,35
340,34
341,33
342,32
343,31
344,30
345,29
346,28
347,27
348,163
349,162
350,161
351,160
352,159
353,158
354,157
355,156
356,155
357,154
358,153
359,152
360,151
361,150
362,149
363,148
364,147
365,146
366,145
367,144
368,143
369,142
370,141
371,140
372,139
373,138
374,137
375,136
376,135
377,134
378,133
379,132
380,131
381,130
382,129
383,128
384,127
385,126
386,125
387,124
388,123
389,122
390,121
391,120
392,119
393,118
394,117
395,116
396,115
397,114
398,113
399,112
400,111
401,110
402,109
403,108
404,107
405,106
406,105
407,104
408,103
409,102
410,101
411,100
412,99
413,98
414,97
415,96
416,95
417,94
418,93
419,92
420,91
421,90
422,89
423,88
424,87
425,86
426,85
427,84
428,83
429,82
430,81
431,80
432,79
433,78
434,77
435,76
436,75
437,74
438,73
439,72
440,71
441,70
442,69
443,68
444,67
445,66
446,65
447,64
448,63
449,62
450,61
451,60
452,59
453,58
454,57
455,56
456,55
457,54
458,53
459,52
460,51
461,50
462,49
463,48
464,47
465,47
466,46
467,45
468,44
469,43
470,42
471,41
472,40
473,39
474,38
475,37
476,36
477,108
478,107