1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
|
#!/bin/bash
function run_synthetictest {
(time ../examples/synthetictest/synthetictest $1) &> screen_output
echo >> screen_log
echo "./synthetictest $1" >> screen_log
}
function run_fourtaxon {
(cd ../examples/fourtaxon && time ./fourtaxon $1) &> screen_output
}
function grep_print_synthetictest {
RSRC_NAME=`grep "Rsrc" screen_output | cut -f 2 -d ":"`
RSRC_NAME=`echo $RSRC_NAME`
IMPL_NAME=`grep "Impl" screen_output | cut -f 2 -d ":"`
IMPL_NAME=`echo $IMPL_NAME`
BEST_RUN=`grep "best" screen_output | cut -f 3 -d " " | grep -o [0-9.]*`
MAX_DIFF=0.01
LNL=`grep "logL" screen_output | cut -f 3 -d " "`
LNL_DIFF=`echo \($LNL\) - \($2\) | bc`
LNL_ERROR=`echo "$LNL_DIFF > $MAX_DIFF || $LNL_DIFF < -$MAX_DIFF" | bc`
if (( $LNL_ERROR ))
then
echo -n "*** SCORING ISSUE: LNL_EXP = $2 LNL = $LNL DIFF = $LNL_DIFF" 1>&2;
fi
if [ "$1" == "yes" ]
then
D1=`grep "d1" screen_output | cut -f 6 -d " "`
D2=`grep "d2" screen_output | cut -f 9 -d " "`
D1_DIFF=`echo \($D1\) - \($3\) | bc`
D2_DIFF=`echo \($D2\) - \($4\) | bc`
D1_ERROR=`echo "$D1_DIFF > $MAX_DIFF || $D1_DIFF < -$MAX_DIFF" | bc`
D2_ERROR=`echo "$D2_DIFF > $MAX_DIFF || $D2_DIFF < -$MAX_DIFF" | bc`
if (( $D1_ERROR ))
then
echo -n "*** SCORING ISSUE: D1_EXP = $3 D1 = $D1 DIFF = $D1_DIFF" 1>&2;
fi
if (( $D2_ERROR ))
then
echo -n "*** SCORING ISSUE: D2_EXP = $4 D2 = $D2 DIFF = $D2_DIFF" 1>&2;
fi
else
D1="NA"
D2="NA"
D1_DIFF="NA"
D2_DIFF="NA"
fi
set -v
echo -n ","$RSRC_NAME","$IMPL_NAME","$LNL","$LNL_DIFF","$D1","$D1_DIFF","$D2","$D2_DIFF","$BEST_RUN;
set +v
}
function grep_print_fourtaxon {
RSRC_NAME=`grep "Rsrc" screen_output | cut -f 2 -d ":"`
RSRC_NAME=`echo $RSRC_NAME`
IMPL_NAME=`grep "Impl" screen_output | cut -f 2 -d ":"`
IMPL_NAME=`echo $IMPL_NAME`
LNL=`tail -n 5 screen_output | head -n 1 | grep -o "\-[0-9.]*"`
BEST_RUN="NA"
set -v
echo -n ","$RSRC_NAME","$IMPL_NAME","$LNL","LNL_DIFF","D1","D1_DIFF","D2","D2_DIFF","$BEST_RUN
set +v
}
function grep_print_time {
TIME_REAL_MIN=`grep "real" screen_output | cut -f 1 -d "m" | grep -o [0-9.].*`
TIME_REAL_SEC=`grep "real" screen_output | cut -f 2 -d "m" | grep -o [0-9.]*`
TIME_REAL=`echo $TIME_REAL_MIN*60 + $TIME_REAL_SEC | bc`
TIME_REAL=`printf "%f" $TIME_REAL`
TIME_USER_MIN=`grep "user" screen_output | cut -f 1 -d "m" | grep -o [0-9.].*`
TIME_USER_SEC=`grep "user" screen_output | cut -f 2 -d "m" | grep -o [0-9.]*`
TIME_USER=`echo $TIME_USER_MIN*60 + $TIME_USER_SEC | bc`
TIME_USER=`printf "%f" $TIME_USER`
TIME_SYS_MIN=`grep "sys" screen_output | cut -f 1 -d "m" | grep -o [0-9.].*`
TIME_SYS_SEC=`grep "sys" screen_output | cut -f 2 -d "m" | grep -o [0-9.]*`
TIME_SYS=`echo $TIME_SYS_MIN*60 + $TIME_SYS_SEC | bc`
TIME_SYS=`printf "%f" $TIME_SYS`
set -v; echo -n ","$TIME_REAL","$TIME_USER","$TIME_SYS; set +v
}
function grep_system {
if [ -f /proc/cpuinfo ]
then
CPU_NAME=`cat /proc/cpuinfo | grep "model name" | head -n 1 | cut -f 2 -d ":"`
CPU=`echo $CPU_NAME`
else
CPU_NAME=`system_profiler SPHardwareDataType | grep "Processor Name" | cut -f 2 -d ":"`
CPU_FREQ=`system_profiler SPHardwareDataType | grep "Processor Speed" | cut -f 2 -d ":"`
CPU=`echo $CPU_NAME$CPU_FREQ`
fi
GCC_VERSION=`gcc --version | head -n 1`
REVISION=`(cd .. && svnversion .)`
DATE=`date "+%Y-%m-%d %H:%M:%S"`
}
function print_system {
set -v; echo -n ","$CPU","$GCC_VERSION","$REVISION","$DATE; set +v
}
function run_print_test {
if [ "$1" == "synthetictest" ]
then
CMD_FLAGS="--states $2 --taxa $3 --sites $4 --rates $5 --reps $6 --rsrc $7 --compact-tips ${11} --seed ${12} --rescale-frequency ${13} --eigencount ${20}"
if [ "$8" == "manual" ]
then
CMD_FLAGS="$CMD_FLAGS --manualscale"
fi
if [ "$9" == "double" ]
then
CMD_FLAGS="$CMD_FLAGS --doubleprecision"
fi
if [ "${10}" == "yes" ]
then
CMD_FLAGS="$CMD_FLAGS --SSE"
fi
if [ "${14}" == "no" ]
then
CMD_FLAGS="$CMD_FLAGS --unrooted"
fi
if [ "${15}" == "yes" ]
then
CMD_FLAGS="$CMD_FLAGS --calcderivs"
fi
if [ "${19}" == "yes" ]
then
CMD_FLAGS="$CMD_FLAGS --logscalers"
fi
if [ "${21}" == "yes" ]
then
CMD_FLAGS="$CMD_FLAGS --eigencomplex"
fi
if [ "${22}" == "yes" ]
then
CMD_FLAGS="$CMD_FLAGS --ievectrans"
fi
if [ "${23}" == "yes" ]
then
CMD_FLAGS="$CMD_FLAGS --setmatrix"
fi
run_synthetictest "$CMD_FLAGS"
else
CMD_FLAGS="--niters $6 --rsrc $7"
if [ "$8" == "none" ]
then
CMD_FLAGS="$CMD_FLAGS --scaling 0"
else
CMD_FLAGS="$CMD_FLAGS --scaling 1"
fi
if [ "$9" == "double" ]
then
CMD_FLAGS="$CMD_FLAGS --double"
else
CMD_FLAGS="$CMD_FLAGS --single"
fi
if [ "${10}" == "yes" ]
then
CMD_FLAGS="$CMD_FLAGS --sse"
fi
run_fourtaxon "$CMD_FLAGS"
fi
if [ -n "`grep "Failed" screen_output`" ]
then
echo "*** FAILED: (`grep "Failed" screen_output`)" 1>&2;
elif [ -n "`grep "error" screen_output`" ]
then
echo "*** ERROR: `grep "error" screen_output`" 1>&2;
else
set -v; echo -n $1","$2","$3","$4","$5","$6","$7","$8","$9","${10}","${11}","${12}","${13}","${14}","${15}","${19}","${20}","${21}","${22}","${23}; set +v
if [ "$1" == "synthetictest" ]
then
grep_print_synthetictest ${15} ${16} ${17} ${18}
else
grep_print_fourtaxon
fi
grep_print_time
print_system
set -v; echo; set +v
echo 1>&2;
fi
}
if [ -z "${23}" ];
then
set -v
echo "parse_test.sh requires 23 arguments, as follows:"
echo "parse_test.sh <program> <states> <taxa> <sites> <rates> <reps> <rsrc> <rescaling> <precision> <sse> <compact-tips> <rseed> <rescale-frequency> <rooted> <calc-derivs> <lnl-exp> <d1-exp> <d2-exp> <lscalers> <ecount> <ecomplex> <ievect> <smatrix>"
echo "(see run_tests.sh for examples)"
set +v
else
grep_system
# program states taxa sites rates reps rsrc rescaling precision sse ctips rseed rfreq rooted derivs lnl_exp d1_exp d2_exp lscalers ecount ecomplex ievect smatrix
run_print_test $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18} ${19} ${20} ${21} ${22} ${23}
cat screen_output >> screen_log
rm screen_output
fi
|
