patflick / psac Goto Github PK

I've compiled the code and try it out on some data I have. However, I get the error:

[ERROR]: Assertion failed in /tmp/psac/include/check_suffix_array.hpp:262

I don't get this error when using the random data supplied in this package. Are there some limitations regarding what symbols/encodings/characters can be used? E.g. at the start I see

Alphabet: {sigma=200, l=8, A=[ ,  , !, ", #, $, %, &, ', (, ), *, +, ,, -, ., /, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, :, ;, <, =, >, ?, @, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, [, \, ], ^, _, `, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z, {, |, }, ~, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ]}  

Does this mean that only these characters can be used?

I was under the assumption that psac would produce the suffix array as output file. Is this true because I only see output similar to the following?

Alphabet: [
, , ,, ., A, C, D, F, I, O, S, T, V, W, Y, a, b, c, d, e, f, g, h, i, k, l, m, n, o, p, r, s, t, u, v, w, x, y]
Detecting sigma=38 => l=6, k=10
TIMER 1.520e-01 1.520e-01 1.520e-01 1 initial-bucketing
TIMER 1.400e-02 1.400e-02 1.400e-02 2 arr-tupelize
TIMER 3.070e-01 3.070e-01 3.070e-01 2 shift-buckets
TIMER 5.300e-02 5.300e-02 5.300e-02 3 isa2sa_samplesort
TIMER 7.300e-02 7.300e-02 7.300e-02 2 ISA-to-SA
iteration 10: unfinished buckets = 0, unfinished elements = 0
TIMER 1.102e+00 1.102e+00 1.102e+00 2 rebucket
TIMER 5.000e-03 5.000e-03 5.000e-03 2 arr-untupelize
TIMER 7.300e-02 7.300e-02 7.300e-02 2 SA-to-ISA
TIMER 1.699e+00 1.699e+00 1.699e+00 1 construct-msgs
TIMER 1.000e-03 1.000e-03 1.000e-03 1 fix-isa
PSAC time: 2.477e+00 ms

Thank for your sharing,when I follow the Compiling,
I do make ,it's result is ：
#include <mxx/file.hpp>
^~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [src/CMakeFiles/benchmark_sac.dir/build.make:82: src/CMakeFiles/benchmark_sac.dir/benchmark.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:362: src/CMakeFiles/benchmark_sac.dir/all] Error 2
make: *** [Makefile:171: all] Error 2

I go to the /ext/mxx, it's empty,why is this? could you help me ? thank you very much