From a271bb206202fca8e73643633f2ea64e5d2ec01b Mon Sep 17 00:00:00 2001 From: Dariusz Murakowski Date: Thu, 13 Feb 2014 12:14:27 -0500 Subject: [PATCH] Extra output and tests for debugging. --- Makefile | 2 +- population.cpp | 5 +- test/importState.test.expected-out | 3 + test/runTests.sh | 19 +- test/verbose.test | 6 + test/verbose.test.expected-dat | 205 ++++++++++++ test/verbose.test.expected-err | 0 test/verbose.test.expected-out | 627 +++++++++++++++++++++++++++++++++++++ test/verbose.test.expected-sum | 2 + wf.cpp | 14 + 10 files changed, 874 insertions(+), 9 deletions(-) create mode 100755 test/verbose.test create mode 100644 test/verbose.test.expected-dat create mode 100644 test/verbose.test.expected-err create mode 100644 test/verbose.test.expected-out create mode 100644 test/verbose.test.expected-sum diff --git a/Makefile b/Makefile index 8e208f9..63367d5 100644 --- a/Makefile +++ b/Makefile @@ -12,7 +12,7 @@ LIBS = -lgsl -lgslcblas -lm # = `gsl-config --libs` ifeq ($(dbg),1) - DBGFLAG = -g + DBGFLAG = -g -DDEBUG else DBGFLAG = -O3 -combine endif diff --git a/population.cpp b/population.cpp index 7d0c7b3..560ff56 100644 --- a/population.cpp +++ b/population.cpp @@ -82,7 +82,10 @@ void Population::next_generation(const Hamiltonian &H, gsl_rng* r, bool useRelat std::cout << "survival probability " << ((useRelative) ? iter->first.survival(Eavg) : iter->first.survival()) << " number survived " << num_survive << " total number " - << iter->second << std::endl; + << iter->second ; //<< std::endl; + std::set ms = iter->first.mutated_sites; + for (std::set::iterator v = ms.begin(); v!=ms.end(); ++v) fprintf(stdout,"\t%d",*v); + fprintf(stdout,"\n"); } diff --git a/test/importState.test.expected-out b/test/importState.test.expected-out index 59a0962..7312035 100644 --- a/test/importState.test.expected-out +++ b/test/importState.test.expected-out @@ -1 +1,4 @@ seed = 66314 +1 30 57 60 74 78 90; +24 25 26 27 28 29 31 32 +30 diff --git a/test/runTests.sh b/test/runTests.sh index 9671752..b7676ed 100755 --- a/test/runTests.sh +++ b/test/runTests.sh @@ -12,26 +12,31 @@ checkTest () { ./$t 2>$t.err 1>$t.out - # stop as soon as a test fails + # report every failure + + retval=0 if ! cmp -s $t.out $t.expected-out; then - return 1 + echo "FAIL: $t.out" + retval=1 fi if ! cmp -s $t.err $t.expected-err; then - return 1 + echo "FAIL: $t.err" + retval=1 fi if ! cmp -s $t.sum $t.expected-sum; then - return 1 + echo "FAIL: $t.sum" + retval=1 fi if ! cmp -s $t.dat $t.expected-dat; then - return 1 + echo "FAIL: $t.dat" + retval=1 fi - # all tests succeeded - return 0 + return $retval } for t in *.test; do diff --git a/test/verbose.test b/test/verbose.test new file mode 100755 index 0000000..b0cffba --- /dev/null +++ b/test/verbose.test @@ -0,0 +1,6 @@ +#!/bin/bash + +WF=../wf + +${WF} -seed 66314 -r -v -n 100000 -g 3 -numruns 2 -i importState.test -s importState.test -o verbose.test + diff --git a/test/verbose.test.expected-dat 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57 60 74 78 90 93 +survival probability 0.000719616 number survived 0 total number 0 30 57 60 74 78 90 94 +survival probability 0.00585304 number survived 0 total number 0 30 57 60 74 78 90 95 +survival probability 0.00318602 number survived 0 total number 0 30 57 60 74 78 90 96 +survival probability 0.0128314 number survived 0 total number 0 30 57 60 74 78 90 97 +survival probability 0.060085 number survived 2 total number 2 30 57 60 74 78 90 98 +survival probability 0.997612 number survived 17 total number 17 30 57 60 74 90 +survival probability 0.999832 number survived 17 total number 17 30 57 60 78 90 +survival probability 0.996567 number survived 20 total number 20 30 57 74 78 90 +survival probability 0.998663 number survived 21 total number 21 30 60 74 78 90 +survival probability 1 number survived 16 total number 16 57 60 74 78 90 +checkpoint, total_deaths = 50176 +The total population size is 49824 +survival probability 0.00233974 number survived 0 total number 0 0 30 57 60 74 78 90 +survival probability 0.00715237 number survived 0 total number 0 1 30 57 60 74 78 90 +survival probability 0.000420122 number survived 0 total number 0 2 30 57 60 74 78 90 +survival probability 0.0198664 number survived 0 total number 0 3 12 30 57 60 74 78 90 +survival probability 0.0132351 number survived 0 total number 0 3 30 57 60 74 78 90 +survival probability 0.000207994 number survived 0 total number 0 4 30 57 60 74 78 90 +survival probability 0.00637779 number survived 0 total number 0 5 30 57 60 74 78 90 +survival probability 0.00300126 number survived 0 total number 0 6 30 57 60 74 78 90 +survival probability 0.000121983 number survived 0 total number 0 7 30 57 60 74 78 90 +survival probability 2.20715e-05 number survived 0 total number 0 8 30 57 60 74 78 90 +survival probability 0.0217135 number survived 0 total number 0 9 30 57 60 74 78 90 +survival probability 0.001345 number survived 0 total number 0 10 30 57 60 74 78 90 +survival probability 0.24091 number survived 1 total number 1 11 30 57 60 74 78 90 +survival probability 0.619081 number survived 8 total number 8 12 30 57 60 74 78 90 +survival probability 0.0643017 number survived 1 total number 1 13 30 57 60 74 78 90 +survival probability 0.25753 number survived 3 total number 3 14 30 57 60 74 78 90 +survival probability 0.000799028 number survived 0 total number 0 15 30 57 60 74 78 90 +survival probability 0.00769011 number survived 0 total number 0 16 30 57 60 74 78 90 +survival probability 0.00415483 number survived 0 total number 0 17 30 57 60 74 78 90 +survival probability 0.0412063 number survived 1 total number 1 18 30 57 60 74 78 90 +survival probability 0.0208123 number survived 0 total number 0 19 30 57 60 74 78 90 +survival probability 0.000212186 number survived 0 total number 0 20 30 57 60 62 74 78 90 +survival probability 0.000507922 number survived 0 total number 0 20 30 57 60 74 78 90 +survival probability 0.00146593 number survived 0 total number 0 21 30 57 60 74 78 90 +survival probability 0.00588442 number survived 1 total number 1 22 30 57 60 74 78 90 +survival probability 0.00199929 number survived 0 total number 0 23 30 57 60 74 78 90 +survival probability 0.98297 number survived 66 total number 66 24 30 57 60 74 78 90 +survival probability 0.116433 number survived 0 total number 0 25 30 57 60 74 78 81 90 +survival probability 0.98438 number survived 31 total number 31 25 30 57 60 74 78 90 +survival probability 0.877855 number survived 16 total number 16 26 30 57 60 74 78 90 +survival probability 0.850863 number survived 20 total number 20 27 30 57 60 74 78 90 +survival probability 0.864174 number survived 24 total number 24 28 30 57 60 74 78 90 +survival probability 0.997317 number survived 22 total number 22 29 30 57 60 74 78 90 +survival probability 0.930181 number survived 27 total number 27 30 31 57 60 74 78 90 +survival probability 0.999047 number survived 43 total number 43 30 32 57 60 74 78 90 +survival probability 0.000255733 number survived 0 total number 0 30 33 57 60 74 78 90 +survival probability 0.107552 number survived 1 total number 1 30 34 57 60 74 78 90 +survival probability 0.11404 number survived 2 total number 2 30 35 57 60 74 78 90 +survival probability 0.525526 number survived 11 total number 11 30 36 57 60 74 78 90 +survival probability 0.0356148 number survived 0 total number 0 30 37 57 60 74 78 90 +survival probability 0.0227783 number survived 2 total number 2 30 38 57 60 74 78 90 +survival probability 0.000650656 number survived 0 total number 0 30 39 57 60 74 78 90 +survival probability 0.122174 number survived 0 total number 0 30 40 57 60 74 78 90 +survival probability 0.000330423 number survived 0 total number 0 30 41 57 60 74 78 90 +survival probability 0.00142626 number survived 0 total number 0 30 42 57 60 74 78 90 +survival probability 7.73316e-05 number survived 0 total number 0 30 43 57 60 74 78 90 +survival probability 0.120552 number survived 0 total number 0 30 44 57 60 74 78 90 +survival probability 0.000471261 number survived 0 total number 0 30 45 57 60 74 78 90 +survival probability 0.000866158 number survived 0 total number 0 30 46 57 60 74 78 90 +survival probability 0.000140769 number survived 0 total number 0 30 47 57 60 74 78 90 +survival probability 0.000168652 number survived 0 total number 0 30 48 57 60 74 78 90 +survival probability 0.000116374 number survived 0 total number 0 30 49 57 60 74 78 90 +survival probability 0.00027318 number survived 0 total number 0 30 50 57 60 74 78 90 +survival probability 0.000154042 number survived 0 total number 0 30 51 57 60 74 78 90 +survival probability 0.000697793 number survived 0 total number 0 30 52 57 60 74 78 90 +survival probability 6.3903e-05 number survived 0 total number 0 30 53 57 60 74 78 90 +survival probability 0.000679102 number survived 0 total number 0 30 54 57 60 74 78 90 +survival probability 0.000493123 number survived 0 total number 0 30 55 57 60 74 78 90 +survival probability 0.112107 number survived 2 total number 2 30 56 57 60 74 78 90 +survival probability 0.00960649 number survived 0 total number 0 30 57 58 60 74 78 90 +survival probability 0.345142 number survived 5 total number 5 30 57 59 60 74 78 90 +survival probability 0.121508 number survived 1 total number 1 30 57 60 61 74 78 90 +survival probability 0.274451 number survived 8 total number 8 30 57 60 62 74 78 90 +survival probability 0.180643 number survived 2 total number 2 30 57 60 63 74 78 90 +survival probability 0.0133615 number survived 0 total number 0 30 57 60 64 74 78 90 +survival probability 0.00896365 number survived 0 total number 0 30 57 60 65 74 78 90 +survival probability 0.353864 number survived 4 total number 4 30 57 60 66 74 78 90 +survival probability 0.000149786 number survived 0 total number 0 30 57 60 67 74 78 90 +survival probability 0.0861939 number survived 0 total number 0 30 57 60 68 74 78 90 +survival probability 0.175688 number survived 0 total number 0 30 57 60 69 74 78 90 +survival probability 0.196844 number survived 4 total number 4 30 57 60 70 74 78 90 +survival probability 0.11124 number survived 0 total number 0 30 57 60 71 74 78 90 +survival probability 0.000764383 number survived 0 total number 0 30 57 60 72 74 78 90 +survival probability 0.0150105 number survived 1 total number 1 30 57 60 73 74 78 90 +survival probability 0.0003264 number survived 0 total number 0 30 57 60 74 75 78 90 +survival probability 0.367872 number survived 2 total number 2 30 57 60 74 76 78 90 +survival probability 0.000209046 number survived 0 total number 0 30 57 60 74 77 78 90 +survival probability 0.999924 number survived 56 total number 56 30 57 60 74 78 +survival probability 2.07e-05 number survived 0 total number 0 30 57 60 74 78 79 90 +survival probability 4.59324e-06 number survived 0 total number 0 30 57 60 74 78 80 90 +survival probability 0.00322161 number survived 0 total number 0 30 57 60 74 78 81 90 +survival probability 0.00968319 number survived 0 total number 0 30 57 60 74 78 82 90 +survival probability 0.00468566 number survived 0 total number 0 30 57 60 74 78 83 90 +survival probability 0.00743931 number survived 0 total number 0 30 57 60 74 78 84 90 +survival probability 0.00347156 number survived 0 total number 0 30 57 60 74 78 85 90 +survival probability 0.0137208 number survived 0 total number 0 30 57 60 74 78 86 90 +survival probability 0.0169232 number survived 1 total number 1 30 57 60 74 78 87 90 +survival probability 0.0029116 number survived 0 total number 0 30 57 60 74 78 88 90 +survival probability 0.00886135 number survived 0 total number 0 30 57 60 74 78 89 90 +survival probability 0.493035 number survived 48586 total number 48586 30 57 60 74 78 90 +survival probability 0.428268 number survived 11 total number 11 30 57 60 74 78 90 91 +survival probability 0.240265 number survived 0 total number 0 30 57 60 74 78 90 92 +survival probability 0.00152583 number survived 0 total number 0 30 57 60 74 78 90 93 +survival probability 0.000706293 number survived 0 total number 0 30 57 60 74 78 90 94 +survival probability 0.00574522 number survived 0 total number 0 30 57 60 74 78 90 95 +survival probability 0.00312718 number survived 0 total number 0 30 57 60 74 78 90 96 +survival probability 0.0125967 number survived 0 total number 0 30 57 60 74 78 90 97 +survival probability 0.0590376 number survived 0 total number 0 30 57 60 74 78 90 98 +survival probability 0.997567 number survived 40 total number 40 30 57 60 74 90 +survival probability 0.999829 number survived 41 total number 41 30 57 60 78 90 +survival probability 0.996502 number survived 45 total number 45 30 57 74 78 90 +survival probability 0.998638 number survived 54 total number 54 30 60 74 78 90 +survival probability 1 number survived 36 total number 36 57 60 74 78 90 +checkpoint, total_deaths = 50821 +The total population size is 49179 diff --git a/test/verbose.test.expected-sum b/test/verbose.test.expected-sum new file mode 100644 index 0000000..1fc5d79 --- /dev/null +++ b/test/verbose.test.expected-sum @@ -0,0 +1,2 @@ +3 103 29 30 57 60 74 78 90 +3 129 24 30 57 60 74 78 90 diff --git a/wf.cpp b/wf.cpp index bc23b18..7570931 100644 --- a/wf.cpp +++ b/wf.cpp @@ -53,6 +53,7 @@ void run(RunParameters &r, unsigned seed) { if (r.useTwoSite && supout == NULL) { perror("File error"); exit(1); } if (r.importState) importState(r); // .st + fflush(stdout); if(r.useTwoSite) { @@ -176,18 +177,23 @@ void importState(RunParameters &r) { // Import initial state of the population while (fscanf(input,"%le",&frac)==1) { + + std::cout << frac; // XXX r.initFrac.push_back(frac); std::set tempSet; while (fscanf(input,"%c",&o)==1) { + + std::cout << o; // XXX if (o=='\n' || o==';') break; else { fscanf(input,"%u",&site); + std::cout << site; // XXX tempSet.insert(site); } @@ -199,23 +205,31 @@ void importState(RunParameters &r) { if (o==';') break; } + + std::cout << "\n"; // XXX // Import targeted epitope while (fscanf(input,"%u",&site)==1) { + + std::cout << site; // XXX r.eWT.push_back(site); fscanf(input,"%c",&o); + std::cout << o; // XXX if (o=='\n') break; } while (fscanf(input,"%u",&site)==1) { + + std::cout << site; // XXX r.eMut.push_back(site); fscanf(input,"%c",&o); + std::cout << o; // XXX if (o=='\n') break; } -- 2.7.4