Skip to content

Commit 49164a3

Browse files
wangpatrick57wangpatrick57
committed
initial commit
0 parents  commit 49164a3

File tree

311 files changed

+2080438
-0
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

311 files changed

+2080438
-0
lines changed

‎Dockerfile

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
FROM ubuntu:22.04
2+
RUN apt-get update
3+
RUN apt-get install -y python3
4+
RUN apt-get install -y python3-pip
5+
RUN python3 -m pip install networkx
6+
RUN ["/bin/bash", "-c", "echo 'ulimit -s unlimited' >> /root/.bashrc"]

‎Makefile

Lines changed: 228 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,228 @@
1+
# Number of cores to use when invoking parallelism
2+
#ifndef CORES
3+
CORES := 1 # temporarily set to 1 since I broke threading. :-(
4+
#endif
5+
ifndef PAUSE
6+
PAUSE := 100
7+
endif
8+
# Uncomment either of these to remove them (removing 7 implies removing 8)
9+
EIGHT := 8
10+
SEVEN := 7
11+
ifdef NO8
12+
EIGHT :=
13+
endif
14+
ifdef NO7
15+
SEVEN :=
16+
EIGHT := # can't have 8 without 7
17+
endif
18+
19+
ifdef DEBUG
20+
ifdef PROFILE
21+
SPEED=-O0 -ggdb -pg
22+
LIB_OPT=-g-pg
23+
else
24+
SPEED=-O0 -ggdb
25+
LIB_OPT=-g
26+
endif
27+
else
28+
ifdef PROFILE
29+
SPEED=-O3 -pg
30+
LIB_OPT=-pg
31+
else
32+
SPEED=-O3
33+
LIB_OPT=
34+
endif
35+
endif
36+
37+
# Waywe needs gcc-6 on MacOS:
38+
GCC_VER=$(shell echo $(ARCH) $(HOME) | awk '/Darwin/&&/Users.wayne/{V="-6"}END{if(V)print V;else{printf "using default gcc: " > "/dev/null"; exit 1}}')
39+
GCC=gcc$(GCC_VER)
40+
CXX=g++
41+
42+
# Some architectures, eg CYGWIN 32-bit and MacOS("Darwin") need an 80MB stack.
43+
export LIBWAYNE_HOME=$(shell dirname $(realpath $(firstword $(MAKEFILE_LIST))))/libwayne
44+
ARCH=$(shell uname -a | awk '{if(/CYGWIN/){V="CYGWIN"}else if(/Darwin/){V="Darwin"}else if(/Linux/){V="Linux"}}END{if(V){print V;exit}else{print "unknown OS" > "/dev/stderr"; exit 1}}')
45+
46+
# Darwin needs gcc-6 ever since a commit on 22 May 2022:
47+
#GCC= $(shell $(CC) -v 2>&1 | awk '/gcc/{++gcc}{V=$$3}END{if(gcc && (V ~ /[0-9]\.[0-9]\.[0-9]*/))print "$(ARCH).gcc"V; else exit 1}')
48+
STACKSIZE=$(shell ($(GCC) -v 2>&1; uname -a) | awk '/CYGWIN/{print "-Wl,--stack,83886080"}/gcc-/{actualGCC=1}/Darwin/&&actualGCC{print "-Wl,-stack_size -Wl,0x5000000"}')
49+
CC=$(GCC) $(SPEED) -Wall -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wstrict-prototypes -Wshadow $(PG) $(STACKSIZE)
50+
LIBWAYNE_COMP=-I $(LIBWAYNE_HOME)/include $(STACKSIZE) $(SPEED)
51+
LIBWAYNE_LINK=-L $(LIBWAYNE_HOME) -lwayne$(LIB_OPT) -lm $(STACKSIZE) $(SPEED)
52+
LIBWAYNE_BOTH=$(LIBWAYNE_COMP) $(LIBWAYNE_LINK)
53+
54+
# Name of BLANT source directory
55+
SRCDIR = src
56+
# Put all c files in SRCDIR below.
57+
BLANT_SRCS = blant.c \
58+
blant-output.c \
59+
blant-utils.c
60+
61+
OBJDIR = _objs
62+
OBJS = $(addprefix $(OBJDIR)/, $(BLANT_SRCS:.c=.o))
63+
64+
### Generated File Lists ###
65+
K := 3 4 5 6 $(SEVEN) $(EIGHT)
66+
canon_txt := canon_maps/canon_map canon_maps/canon_list canon_maps/canon-ordinal-to-signature canon_maps/orbit_map canon_maps/alpha_list_nbe canon_maps/alpha_list_mcmc
67+
canon_bin := canon_maps/canon_map canon_maps/perm_map
68+
canon_all := $(foreach k, $(K), $(addsuffix $(k).txt, $(canon_txt)) $(addsuffix $(k).bin, $(canon_bin)))
69+
subcanon_txts := $(if $(EIGHT),canon_maps/subcanon_map8-7.txt) $(if $(SEVEN),canon_maps/subcanon_map7-6.txt) canon_maps/subcanon_map6-5.txt canon_maps/subcanon_map5-4.txt canon_maps/subcanon_map4-3.txt
70+
71+
#canon_map_bins := $(foreach k,$(K), canon_maps/canon_map$(k).bin)
72+
#perm_map_bins := $(foreach k,$(K), canon_maps/perm_map$(k).bin)
73+
#canon_map_txts := $(foreach k,$(K), canon_maps/canon_map$(k).txt)
74+
#canon_list_txts := $(foreach k,$(K), canon_maps/canon_list$(k).txt)
75+
#canon_ordinal_to_signature_txts := $(foreach k,$(K), canon_maps/canon-ordinal-to-signature$(k).txt)
76+
#orbit_map_txts := $(foreach k,$(K), canon_maps/orbit_map$(k).txt)
77+
#canon_map_files := $(canon_map_bins) $(perm_map_bins) $(canon_map_txts) $(canon_list_txts) $(canon_ordinal_to_signature_txts) $(orbit_map_txts)
78+
79+
# ehd takes up too much space and isn't used anywhere yet
80+
#ehd_txts := $(foreach k,$(K), canon_maps/EdgeHammingDistance$(k).txt)
81+
#alpha_nbe_txts := $(foreach k, $(K), canon_maps/alpha_list_nbe$(k).txt)
82+
#alpha_mcmc_txts := $(foreach k, $(K), canon_maps/alpha_list_mcmc$(k).txt)
83+
magic_table_txts := $(foreach k,$(K), orca_jesse_blant_table/UpperToLower$(k).txt)
84+
85+
#base: show-gcc-ver ./.notpristine libwayne $(alpha_nbe_txts) $(alpha_mcmc_txts) magic_table $(canon_map_files) blant
86+
base: show-gcc-ver ./.notpristine libwayne $(canon_all) magic_table blant
87+
88+
show-gcc-ver:
89+
$(GCC) -v
90+
91+
./.notpristine:
92+
@echo '****************************************'
93+
@echo "If you haven't already, you should read the README at"
94+
@echo " https://github.com/waynebhayes/BLANT#readme"
95+
@echo "BLANT can sample graphlets of up to k=8 nodes. The lookup table for k=8 can take"
96+
@echo "up to an hour to generate, but is needed if you want BLANT-seed to work, and so"
97+
@echo "we make it by default; set NO8=1 to turn it off."
98+
@echo "The fastest way to get started is to skip k=8 graphlets:"
99+
@echo " PAUSE=0 NO8=1 make base"
100+
@echo "which will make everything needed to get started sampling up to k=7 graphlets".
101+
@echo "You will only see this message once on a 'pristine' repo. Pausing $(PAUSE) seconds..."
102+
@echo '****************************************'
103+
sleep $(PAUSE)
104+
@touch .notpristine
105+
106+
most: base Draw subcanon_maps
107+
108+
all: most $(ehd_txts)
109+
110+
gcc-version:
111+
@if ls $(SRCDIR)/*.gz | fgrep -q "$(GCC)"; then :; else echo "WARNING: gcc version not supported; prediction disabled" >&2; fi
112+
113+
canon_maps: base $(canon_all) subcanon_maps
114+
115+
.PHONY: all most pristine clean_canon_maps
116+
117+
### Executables ###
118+
119+
fast-canon-map: libwayne $(SRCDIR)/fast-canon-map.c | $(SRCDIR)/blant.h $(OBJDIR)/libblant.o
120+
$(CC) '-std=c99' -O3 -o $@ $(OBJDIR)/libblant.o $(SRCDIR)/fast-canon-map.c $(LIBWAYNE_BOTH)
121+
122+
slow-canon-maps: libwayne $(SRCDIR)/slow-canon-maps.c | $(SRCDIR)/blant.h $(OBJDIR)/libblant.o
123+
$(CC) -o $@ $(OBJDIR)/libblant.o $(SRCDIR)/slow-canon-maps.c $(LIBWAYNE_BOTH)
124+
125+
make-orbit-maps: libwayne $(SRCDIR)/make-orbit-maps.c | $(SRCDIR)/blant.h $(OBJDIR)/libblant.o
126+
$(CC) -o $@ $(OBJDIR)/libblant.o $(SRCDIR)/make-orbit-maps.c $(LIBWAYNE_BOTH)
127+
128+
blant: gcc-version libwayne $(OBJS) $(OBJDIR)/convert.o $(OBJDIR)/libblant.o | $(LIBWAYNE_HOME)/MT19937/mt19937.o
129+
$(CXX) -o $@ $(OBJDIR)/libblant.o $(OBJS) $(OBJDIR)/convert.o $(LIBWAYNE_HOME)/MT19937/mt19937.o $(LIBWAYNE_LINK)
130+
131+
$(OBJDIR)/%.o: $(SRCDIR)/%.c
132+
@mkdir -p $(dir $@)
133+
$(CC) -c -o $@ $< $(LIBWAYNE_COMP)
134+
135+
synthetic: libwayne $(SRCDIR)/synthetic.c $(SRCDIR)/syntheticDS.h $(SRCDIR)/syntheticDS.c | $(OBJDIR)/libblant.o
136+
$(CC) -c $(SRCDIR)/syntheticDS.c $(SRCDIR)/synthetic.c $(LIBWAYNE_COMP)
137+
$(CXX) -o $@ syntheticDS.o $(OBJDIR)/libblant.o synthetic.o $(LIBWAYNE_LINK)
138+
139+
CC: libwayne $(SRCDIR)/CC.c $(OBJDIR)/convert.o | $(SRCDIR)/blant.h $(OBJDIR)/libblant.o
140+
$(CXX) -o $@ $(OBJDIR)/libblant.o $(SRCDIR)/CC.c $(OBJDIR)/convert.o $(LIBWAYNE_LINK)
141+
142+
makeEHD: $(OBJDIR)/makeEHD.o
143+
$(CXX) -o $@ $(OBJDIR)/libblant.o $(OBJDIR)/makeEHD.o $(LIBWAYNE_LINK)
144+
145+
compute-alphas-NBE: libwayne $(SRCDIR)/compute-alphas-NBE.c | $(OBJDIR)/libblant.o
146+
$(CC) -Wall -O3 -o $@ $(SRCDIR)/compute-alphas-NBE.c $(OBJDIR)/libblant.o $(LIBWAYNE_BOTH)
147+
148+
compute-alphas-MCMC: libwayne $(SRCDIR)/compute-alphas-MCMC.c | $(OBJDIR)/libblant.o
149+
$(CC) -Wall -O3 -o $@ $(SRCDIR)/compute-alphas-MCMC.c $(OBJDIR)/libblant.o $(LIBWAYNE_BOTH)
150+
151+
Draw: Draw/graphette2dot
152+
153+
Draw/graphette2dot: libwayne Draw/DrawGraphette.cpp Draw/Graphette.cpp Draw/Graphette.h Draw/graphette2dotutils.cpp Draw/graphette2dotutils.h | $(SRCDIR)/blant.h $(OBJDIR)/libblant.o
154+
$(CXX) Draw/DrawGraphette.cpp Draw/graphette2dotutils.cpp Draw/Graphette.cpp $(OBJDIR)/libblant.o -o $@ -std=c++11 $(LIBWAYNE_BOTH)
155+
156+
make-subcanon-maps: libwayne $(SRCDIR)/make-subcanon-maps.c | $(OBJDIR)/libblant.o
157+
$(CC) -Wall -o $@ $(SRCDIR)/make-subcanon-maps.c $(OBJDIR)/libblant.o $(LIBWAYNE_BOTH)
158+
159+
make-orca-jesse-blant-table: libwayne $(SRCDIR)/magictable.cpp | $(OBJDIR)/libblant.o
160+
$(CXX) -Wall -o $@ $(SRCDIR)/magictable.cpp $(OBJDIR)/libblant.o -std=c++11 $(LIBWAYNE_BOTH)
161+
162+
### Object Files/Prereqs ###
163+
164+
$(OBJDIR)/convert.o: $(SRCDIR)/convert.cpp
165+
@mkdir -p $(dir $@)
166+
$(CXX) -c $(SRCDIR)/convert.cpp -o $@ -std=c++11
167+
168+
$(LIBWAYNE_HOME)/MT19937/mt19937.o: libwayne
169+
cd $(LIBWAYNE_HOME)/MT19937 && $(MAKE)
170+
171+
$(OBJDIR)/libblant.o: libwayne $(SRCDIR)/libblant.c
172+
@mkdir -p $(dir $@)
173+
$(CC) -c $(SRCDIR)/libblant.c -o $@ $(LIBWAYNE_COMP)
174+
175+
$(OBJDIR)/makeEHD.o: libwayne $(SRCDIR)/makeEHD.c | $(OBJDIR)/libblant.o
176+
@mkdir -p $(dir $@)
177+
$(CC) -c $(SRCDIR)/makeEHD.c -o $@ $(LIBWAYNE_COMP)
178+
179+
libwayne: $(LIBWAYNE_HOME)/Makefile $(LIBWAYNE_HOME)/made
180+
181+
$(LIBWAYNE_HOME)/made:
182+
cd $(LIBWAYNE_HOME) && $(MAKE) all
183+
184+
### Generated File Recipes ###
185+
186+
canon_maps/canon_map%.bin canon_maps/perm_map%.bin canon_maps/orbit_map%.txt canon_maps/alpha_list_mcmc%.txt: libwayne $(SRCDIR)/create-bin-data.c | $(OBJDIR)/libblant.o $(SRCDIR)/blant.h canon_maps/canon_list%.txt canon_maps/canon_map%.txt make-orbit-maps compute-alphas-MCMC
187+
$(CC) '-std=c99' "-Dkk=$*" "-DkString=\"$*\"" -o create-bin-data$* $(SRCDIR)/libblant.c $(SRCDIR)/create-bin-data.c $(LIBWAYNE_BOTH)
188+
[ -f canon_maps/canon_map$*.bin -a -f canon_maps/perm_map$*.bin ] || ./create-bin-data$*
189+
./make-orbit-maps $* > canon_maps/orbit_map$*.txt
190+
@if [ -f canon_maps.correct/alpha_list_mcmc$*.txt ]; then echo "computing MCMC alphas for k=$* takes days, so just copy it"; cp canon_maps.correct/alpha_list_mcmc$*.txt canon_maps/ && touch $@; else ./compute-alphas-MCMC $* > canon_maps/alpha_list_mcmc$*.txt; fi
191+
192+
canon_maps/canon_map%.txt canon_maps/canon_list%.txt canon_maps/canon-ordinal-to-signature%.txt: fast-canon-map
193+
mkdir -p canon_maps
194+
# It's cheap to make all but k=8 canon maps, so make all but skip 8 if it already exists
195+
[ $* -eq 8 -a '(' -f canon_maps/canon_map$*.txt -o -f canon_maps/canon_map$*.txt.gz ')' ] || ./fast-canon-map $* | tee canon_maps/canon_map$*.txt | awk -F ' ' 'BEGIN{n=0}!seen[$$1]{seen[$$1]=$$0;map[n++]=$$1}END{print n;for(i=0;i<n;i++)print seen[map[i]]}' | cut -f1,3- | tee canon_maps/canon_list$*.txt | awk 'NR>1{print NR-2, $$1}' > canon_maps/canon-ordinal-to-signature$*.txt
196+
if [ $* -eq 8 -a -f canon_maps/canon_map$*.txt -a ! -f canon_maps/canon_map$*.txt.gz ]; then gzip canon_maps/canon_map$*.txt & fi
197+
198+
canon_maps/EdgeHammingDistance%.txt: makeEHD | canon_maps/canon_list%.txt canon_maps/canon_map%.bin
199+
@if [ ! -f canon_maps.correct/EdgeHammingDistance$*.txt.xz ]; then ./makeEHD $* > $@; cmp canon_maps.correct/EdgeHammingDistance$*.txt $@; else echo "EdgeHammingDistance8.txt takes weeks to generate; uncompressing instead"; unxz < canon_maps.correct/EdgeHammingDistance$*.txt.xz > $@ && touch $@; fi
200+
#(cd canon_maps.correct && ls EdgeHammingDistance$*.txt*) | awk '{printf "cmp canon_maps.correct/%s canon_maps/%s\n",$$1,$$1}' | sh
201+
202+
canon_maps/alpha_list_nbe%.txt: compute-alphas-NBE canon_maps/canon_list%.txt
203+
./compute-alphas-NBE $* > $@
204+
205+
.INTERMEDIATE: .created-subcanon-maps
206+
subcanon_maps: $(subcanon_txts) ;
207+
$(subcanon_txts): .created-subcanon-maps
208+
.created-subcanon-maps: make-subcanon-maps | $(canon_all) #$(canon_list_txts) $(canon_map_bins)
209+
# only do it for k > 3 since it's 4-3, 5-4, etc.
210+
for k in $(K); do if [ $$k -gt 3 ]; then ./make-subcanon-maps $$k > canon_maps/subcanon_map$$k-$$(($$k-1)).txt; fi; done
211+
212+
magic_table: $(magic_table_txts) ;
213+
$(magic_table_txts): make-orca-jesse-blant-table | $(canon_all) #$(canon_list_txts) $(canon_map_bins)
214+
./make-orca-jesse-blant-table $(if $(EIGHT),8,$(if $(SEVEN),7,6))
215+
216+
### Cleaning ###
217+
218+
clean:
219+
@/bin/rm -f *.[oa] blant canon-sift fast-canon-map make-orbit-maps compute-alphas-MCMC compute-alphas-NBE makeEHD make-orca-jesse-blant-table Draw/graphette2dot make-subcanon-maps create-bin-data*
220+
@/bin/rm -rf $(OBJDIR)/*
221+
222+
pristine: clean clean_canon_maps
223+
@cd $(LIBWAYNE_HOME); $(MAKE) clean
224+
@/bin/rm -f canon_maps/* .notpristine .firsttime # .firsttime is the old name but remove it anyway
225+
226+
clean_canon_maps:
227+
@/bin/rm -f canon_maps/*[3-7].* # don't remove 8 since it takes too long to create
228+
@/bin/rm -f orca_jesse_blant_table/UpperToLower*.txt

0 commit comments

Comments
 (0)