diff options
author | Pjotr Prins | 2017-08-14 07:43:07 +0000 |
---|---|---|
committer | Pjotr Prins | 2017-08-14 08:23:14 +0000 |
commit | ff1252fe3db1ba639fe148f45b0408a4f182da0d (patch) | |
tree | e11ee6858159b53b2570273f9ba3d1ac882232f7 | |
parent | 3763f477e17a74942e1bf545aa9493d39bf9448e (diff) | |
download | pangemma-ff1252fe3db1ba639fe148f45b0408a4f182da0d.tar.gz |
Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26
-rw-r--r-- | .travis.yml | 8 | ||||
-rw-r--r-- | INSTALL.md | 6 | ||||
-rw-r--r-- | Makefile | 22 | ||||
-rw-r--r-- | README.md | 52 | ||||
-rw-r--r-- | src/debug.h | 6 | ||||
-rw-r--r-- | src/gemma.cpp | 37 | ||||
-rw-r--r-- | src/main.cpp | 10 | ||||
-rw-r--r-- | src/mathfunc.cpp | 8 | ||||
-rw-r--r-- | src/mathfunc.h | 1 | ||||
-rw-r--r-- | src/param.h | 1 | ||||
-rw-r--r-- | test/data/issue26/mydata.bed | bin | 0 -> 10845153 bytes | |||
-rw-r--r-- | test/data/issue26/mydata.bim | 2000 | ||||
-rw-r--r-- | test/data/issue26/mydata.fam | 120 | ||||
-rw-r--r-- | test/data/issue26/mydata_kinship.sXX.txt | 120 | ||||
-rwxr-xr-x | test/dev_test_suite.sh | 19 |
15 files changed, 2357 insertions, 53 deletions
diff --git a/.travis.yml b/.travis.yml index 1eaffd8..bc033f9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -26,6 +26,8 @@ before_install: - sudo apt-get install -y libeigen3-dev - sudo apt-get install -y libgsl0-dev - sudo apt-get install -y liblapack-dev + # for the static release version we need the following + # - sudo apt-get install -y gfortran-dev - dpkg -l - eval "${MATRIX_EVAL}" - $CXX --version @@ -37,5 +39,9 @@ script: - time make check - make clean # build and test release version - - make CXX=$CXX FORCE_DYNAMIC=1 WITH_OPENBLAS=1 -j 4 check + - make CXX=$CXX FORCE_DYNAMIC=1 WITH_OPENBLAS=1 -j 4 - time make check + # build static release (fast-check only) + # - make clean + # - make CXX=$CXX TRAVIS_CI=1 -j 4 fast-check + # - ldd ./bin/gemma @@ -14,7 +14,7 @@ GEMMA runs on Linux and MAC OSX and the runtime has the following dependencies: * C++ tool chain >= 4.9 -* GNU Science library (GSL) 1.x (does not currently work with GSL >= 2). +* GNU Science library (GSL) 1.x (GEMMA does not currently work with GSL >= 2). * blas/openblas * lapack * [Eigen3 library](http://eigen.tuxfamily.org/dox/) @@ -67,6 +67,10 @@ work make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 FORCE_DYNAMIC=1 WITH_OPENBLAS=1 DEBUG=1 +another example overriding optimization and LIB flags (so as to link against gslv1) would be + + make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 WITH_OPENBLAS=1 DEBUG=1 FORCE_DYNAMIC=1 GCC_FLAGS="-O3" LIBS="$HOME/opt/gsl1/lib/libgsl.a $HOME/opt/gsl1/lib/libgslcblas.a -L$HOME/.guix-profile/lib -pthread -llapack -lblas -lz" + to run GEMMA tests time make check @@ -16,7 +16,9 @@ WITH_OPENBLAS = NO_INTEL_COMPAT = FORCE_32BIT = FORCE_DYNAMIC = +GCC_FLAGS = -O3 # extra flags -Wl,--allow-multiple-definition DIST_NAME = gemma-0.97.1 +TRAVIS_CI = # -------------------------------------------------------------------- # Edit below this line with caution @@ -36,11 +38,10 @@ else endif ifdef DEBUG - # development mode - CPPFLAGS = -g -O3 -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH) + CPPFLAGS = -g $(GCC_FLAGS) -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH) else - # release - CPPFLAGS = -DNDEBUG -O3 -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH) + # release mode + CPPFLAGS = -DNDEBUG $(GCC_FLAGS) -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH) endif ifdef SHOW_COMPILER_WARNINGS @@ -50,7 +51,9 @@ endif ifdef FORCE_DYNAMIC LIBS = -lgsl -lgslcblas -pthread -lz else - LIBS = -lgsl -lgslcblas -pthread -lz + ifndef TRAVIS_CI # Travis static compile we cheat a little + CPPFLAGS += -static + endif endif OUTPUT = $(BIN_DIR)/gemma @@ -65,8 +68,10 @@ LIBS_LNX_D_LAPACK = -llapack LIBS_LNX_D_BLAS = -lblas LIBS_LNX_D_OPENBLAS = -lopenblas LIBS_MAC_D_LAPACK = -framework Veclib +# LIBS_LNX_S_LAPACK = /usr/lib/libgsl.a /usr/lib/libgslcblas.a /usr/lib/lapack/liblapack.a -lz LIBS_LNX_S_LAPACK = /usr/lib/lapack/liblapack.a -lgfortran /usr/lib/atlas-base/libatlas.a /usr/lib/libblas/libblas.a -Wl,--allow-multiple-definition + SOURCES += $(SRC_DIR)/param.cpp $(SRC_DIR)/gemma.cpp $(SRC_DIR)/io.cpp $(SRC_DIR)/lm.cpp $(SRC_DIR)/lmm.cpp $(SRC_DIR)/vc.cpp $(SRC_DIR)/mvlmm.cpp $(SRC_DIR)/bslmm.cpp $(SRC_DIR)/prdt.cpp $(SRC_DIR)/mathfunc.cpp $(SRC_DIR)/gzstream.cpp $(SRC_DIR)/eigenlib.cpp $(SRC_DIR)/ldr.cpp $(SRC_DIR)/bslmmdap.cpp $(SRC_DIR)/logistic.cpp $(SRC_DIR)/varcov.cpp HDR += $(SRC_DIR)/param.h $(SRC_DIR)/gemma.h $(SRC_DIR)/io.h $(SRC_DIR)/lm.h $(SRC_DIR)/lmm.h $(SRC_DIR)/vc.h $(SRC_DIR)/mvlmm.h $(SRC_DIR)/bslmm.h $(SRC_DIR)/prdt.h $(SRC_DIR)/mathfunc.h $(SRC_DIR)/gzstream.h $(SRC_DIR)/eigenlib.h @@ -82,6 +87,8 @@ else LIBS += $(LIBS_LNX_D_BLAS) endif LIBS += $(LIBS_LNX_D_LAPACK) + else + LIBS += $(LIBS_LNX_S_LAPACK) endif endif SOURCES += $(SRC_DIR)/lapack.cpp @@ -97,11 +104,6 @@ ifdef NO_INTEL_COMPAT endif endif -ifdef FORCE_DYNAMIC -else - CPPFLAGS += -static -endif - # all OBJS = $(SOURCES:.cpp=.o) @@ -134,61 +134,37 @@ of this.* To install GEMMA you can -1. Download the precompiled binaries (64-bit Linux and Mac only). +1. Download the precompiled binaries (64-bit Linux and Mac only), see + [latest stable release][latest_release]. 2. Use existing package managers, see [INSTALL.md](INSTALL.md). -3. Compile the GEMMA executable from source. +3. Compile GEMMA from source, see [INSTALL.md](INSTALL.md). Compiling from source takes more work, but can boost performance of -the program, especially when using specialized C++ compilers and -numerical libraries. +GEMMA when using specialized C++ compilers and numerical libraries. Source code and [latest stable release][latest_release] are available from the Github repository. ### Precompiled binaries -1. Go to the [latest stable release](latest_release) and download the +1. Fetch the [latest stable release][latest_release] and download the file appropriate for your platform: `gemma.linux.gz` for Linux, or `gemma.macosx.gz` for Mac OS X. 2. Run `gunzip gemma.linux.gz` or `gunzip gemma.linux.gz` to -decompress the file. - -3. For convenience, the binaries we provide are linked to static -versions of the GSL, LAPACK and BLAS libraries. So you do not need to -install these libraries. - -4. Cince the program dynamically links to standard C++ and system -libraries, *you need to make sure that you have installed on your -system the same C++ compiler that was used to build the program.* For -example, `gemma.linux` was built using `gcc 4.8.5`, so you should have -`gcc 4.8.x`. If the libraries are installed somewhere non-standard, -you can tell where GEMMA can find the libraries by setting the -`LD_LIBRARY_PATH` environment variable. If you have the wrong version -of the C++ compiler, or if the libraries are in a place where GEMMA -cannot find them, then the program will complain about dynamic linking -errors. +unpack the file. -### Building from source - -*We provide a simple Makefile which will need to be customized; please -see the comments at the top of the Makefile. Explain why we -automatically generate a Makefile using programs such as CMake or -Autotools.* +3. Downloadable binaries are linked to static versions of the GSL, +LAPACK and BLAS libraries. There is no need to install these +libraries. -You will need a standard C/C++ compiler such as GNU gcc, as well as -[GSL](http://www.gnu.org/s/gsl) and -[LAPACK](http://www.netlib.org/lapack) libraries. You will need to -change the library paths in the Makefile accordingly. *Note that GEMMA -currently does not work with GSL 2.x. We recommend linking to the -latest version of GSL 1.x, which is GSL 1.16 as of this writing.* +### Building from source -*Revise this step:* You will need to download the -[Eigen C++ library](http://eigen.tuxfamily.org), and copy the `Eigen` -subdirectory into the `src` directory of the GEMMA repository. (It was -last tested using Eigen version 3.3.3.) +*Note that GEMMA currently does not work with GSL 2.x. We recommend +linking to the latest version of GSL 1.x, which is GSL 1.16 as of this +writing.* More information on source code, dependencies and installation can be found in [INSTALL.md](INSTALL.md). @@ -205,4 +181,4 @@ University of Michigan<br> Peter Carbonetto, Tim Flutre, Matthew Stephens, Pjotr Prins and others have also contributed to the development of this software. -[latest_release]: https://github.com/genetics-statistics/GEMMA/releases/tag/v0.96 "Most recent stable release" +[latest_release]: https://github.com/genetics-statistics/GEMMA/releases "Most recent stable releases" diff --git a/src/debug.h b/src/debug.h index fafebcf..3fbe9e0 100644 --- a/src/debug.h +++ b/src/debug.h @@ -7,10 +7,15 @@ // enforce works like assert but also when NDEBUG is set (i.e., it // always works). enforce_msg prints message instead of expr +#define ROUND(f) round(f * 10000.)/10000 #if defined NDEBUG #define debug_msg(msg) +#define assert_issue(is_issue, expr) #else #define debug_msg(msg) cout << "**** DEBUG: " << msg << endl; +#define assert_issue(is_issue, expr) \ + ((is_issue) ? enforce_msg(expr,"FAIL: ISSUE assert") : __ASSERT_VOID_CAST(0)) + #endif /* This prints an "Assertion failed" message and aborts. */ @@ -49,4 +54,5 @@ inline void __enforce_fail(const char *__assertion, const char *__file, : __enforce_fail(gsl_strerror(COMBINE(res, __LINE__)), __FILE__, \ __LINE__, __ASSERT_FUNCTION)) + #endif diff --git a/src/gemma.cpp b/src/gemma.cpp index a678b8c..3197043 100644 --- a/src/gemma.cpp +++ b/src/gemma.cpp @@ -697,6 +697,7 @@ void GEMMA::PrintHelp(size_t option) { cout << " -silence silent terminal display" << endl; cout << " -debug debug output" << endl; cout << " -nind [num] read up to num individuals" << endl; + cout << " -issue [num] enable tests relevant to issue tracker" << endl; cout << endl; } @@ -1347,6 +1348,16 @@ void GEMMA::Assign(int argc, char **argv, PARAM &cPar) { str.clear(); str.assign(argv[i]); cPar.ni_max = atoi(str.c_str()); // for testing purposes + enforce(cPar.ni_max > 0); + } else if (strcmp(argv[i], "-issue") == 0) { + if (argv[i + 1] == NULL || argv[i + 1][0] == '-') { + continue; + } + ++i; + str.clear(); + str.assign(argv[i]); + cPar.issue = atoi(str.c_str()); // for testing purposes + enforce(cPar.issue > 0); } else if (strcmp(argv[i], "-emp") == 0) { if (argv[i + 1] == NULL || argv[i + 1][0] == '-') { continue; @@ -2656,11 +2667,12 @@ return;} gsl_matrix *se_B = gsl_matrix_alloc(Y->size2, W->size2); gsl_matrix *G = gsl_matrix_alloc(Y->size1, Y->size1); gsl_matrix *U = gsl_matrix_alloc(Y->size1, Y->size1); - gsl_matrix *UtW = gsl_matrix_alloc(Y->size1, W->size2); - gsl_matrix *UtY = gsl_matrix_alloc(Y->size1, Y->size2); - gsl_vector *eval = gsl_vector_alloc(Y->size1); + gsl_matrix *UtW = gsl_matrix_calloc(Y->size1, W->size2); + gsl_matrix *UtY = gsl_matrix_calloc(Y->size1, Y->size2); + gsl_vector *eval = gsl_vector_calloc(Y->size1); gsl_vector *env = gsl_vector_alloc(Y->size1); gsl_vector *weight = gsl_vector_alloc(Y->size1); + assert_issue(cPar.issue == 26, UtY->data[0] == 0.0); // set covariates matrix W and phenotype matrix Y // an intercept should be included in W, @@ -2769,6 +2781,8 @@ return;} CalcUtX(U, W, UtW); CalcUtX(U, Y, UtY); + assert_issue(cPar.issue == 26, ROUND(UtY->data[0]) == -16.6143); + LMM cLmm; cLmm.CopyFromParam(cPar); @@ -2784,6 +2798,7 @@ return;} // calculate UtW and Uty CalcUtX(U, W, UtW); CalcUtX(U, Y, UtY); + assert_issue(cPar.issue == 26, ROUND(UtY->data[0]) == -16.6143); // calculate REMLE/MLE estimate and pve for univariate model if (cPar.n_ph == 1) { // one phenotype @@ -2791,24 +2806,40 @@ return;} gsl_vector_view se_beta = gsl_matrix_row(se_B, 0); gsl_vector_view UtY_col = gsl_matrix_column(UtY, 0); + assert_issue(cPar.issue == 26, ROUND(UtY->data[0]) == -16.6143); + CalcLambda('L', eval, UtW, &UtY_col.vector, cPar.l_min, cPar.l_max, cPar.n_region, cPar.l_mle_null, cPar.logl_mle_H0); + assert(!std::isnan(UtY->data[0])); + assert(!std::isnan(B->data[0])); + assert(!std::isnan(se_B->data[0])); + CalcLmmVgVeBeta(eval, UtW, &UtY_col.vector, cPar.l_mle_null, cPar.vg_mle_null, cPar.ve_mle_null, &beta.vector, &se_beta.vector); + assert(!std::isnan(UtY->data[0])); + assert(!std::isnan(B->data[0])); + assert(!std::isnan(se_B->data[0])); + cPar.beta_mle_null.clear(); cPar.se_beta_mle_null.clear(); for (size_t i = 0; i < B->size2; i++) { cPar.beta_mle_null.push_back(gsl_matrix_get(B, 0, i)); cPar.se_beta_mle_null.push_back(gsl_matrix_get(se_B, 0, i)); } + assert(!std::isnan(UtY->data[0])); + assert(!std::isnan(B->data[0])); + assert(!std::isnan(se_B->data[0])); + assert(!std::isnan(cPar.beta_mle_null.front())); + assert(!std::isnan(cPar.se_beta_mle_null.front())); CalcLambda('R', eval, UtW, &UtY_col.vector, cPar.l_min, cPar.l_max, cPar.n_region, cPar.l_remle_null, cPar.logl_remle_H0); CalcLmmVgVeBeta(eval, UtW, &UtY_col.vector, cPar.l_remle_null, cPar.vg_remle_null, cPar.ve_remle_null, &beta.vector, &se_beta.vector); + cPar.beta_remle_null.clear(); cPar.se_beta_remle_null.clear(); for (size_t i = 0; i < B->size2; i++) { diff --git a/src/main.cpp b/src/main.cpp index 833136c..e37b154 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -25,10 +25,20 @@ using namespace std; +void gemma_gsl_error_handler (const char * reason, + const char * file, + int line, int gsl_errno) { + cerr << "GSL ERROR: " << reason << " in " << file + << " at line " << line << " errno " << gsl_errno <<endl; + exit(22); +} + int main(int argc, char *argv[]) { GEMMA cGemma; PARAM cPar; + gsl_set_error_handler (&gemma_gsl_error_handler); + if (argc <= 1) { cGemma.PrintHeader(); return EXIT_SUCCESS; diff --git a/src/mathfunc.cpp b/src/mathfunc.cpp index 9e19bf1..9a4bb8b 100644 --- a/src/mathfunc.cpp +++ b/src/mathfunc.cpp @@ -187,6 +187,14 @@ double ScaleMatrix(gsl_matrix *G) { return d; } +double SumVector(const gsl_vector *v) { + double sum = 0; + for (int i = 0; i < v->size; i++ ) { + sum += gsl_vector_get(v, i); + } + return( sum ); +} + // Center the vector y. double CenterVector(gsl_vector *y) { double d = 0.0; diff --git a/src/mathfunc.h b/src/mathfunc.h index 29eafe4..b9f3c73 100644 --- a/src/mathfunc.h +++ b/src/mathfunc.h @@ -32,6 +32,7 @@ void CenterMatrix(gsl_matrix *G, const gsl_vector *w); void CenterMatrix(gsl_matrix *G, const gsl_matrix *W); void StandardizeMatrix(gsl_matrix *G); double ScaleMatrix(gsl_matrix *G); +double SumVector(const gsl_vector *v); double CenterVector(gsl_vector *y); void CenterVector(gsl_vector *y, const gsl_matrix *W); void StandardizeVector(gsl_vector *y); diff --git a/src/param.h b/src/param.h index 45d8c0f..f4d649f 100644 --- a/src/param.h +++ b/src/param.h @@ -114,6 +114,7 @@ public: // IO-related parameters. bool mode_silence; bool mode_debug = false; + uint issue; // enable tests for issue on github tracker int a_mode; // Analysis mode, 1/2/3/4 for Frequentist tests int k_mode; // Kinship read mode: 1: n by n matrix, 2: id/id/k_value; vector<size_t> p_column; // Which phenotype column needs analysis. diff --git a/test/data/issue26/mydata.bed b/test/data/issue26/mydata.bed Binary files differnew file mode 100644 index 0000000..bcfe4fe --- /dev/null +++ b/test/data/issue26/mydata.bed diff --git a/test/data/issue26/mydata.bim b/test/data/issue26/mydata.bim new file mode 100644 index 0000000..6597ab3 --- /dev/null +++ b/test/data/issue26/mydata.bim @@ -0,0 +1,2000 @@ +12 61823995 0 61823995 A T +1 282891830 0 282891830 T C +9 50466003 0 50466003 A G +16 76439488 0 76439488 G A +1 62197375 0 62197375 C T +1 105170181 0 105170181 C T +7 124862365 0 124862365 A C +10 20807211 0 20807211 G A +13 163532928 0 163532928 T C +5 95385873 0 95385873 G C +13 188878430 0 188878430 A G +5 90729355 0 90729355 T C +10 44711788 0 44711788 G C +13 80012907 0 80012907 T C +10 16939645 0 16939645 A G +11 21324076 0 21324076 C G +4 134225606 0 134225606 A G +3 54564266 0 54564266 G T +3 110081590 0 110081590 G A +10 13376877 0 13376877 C T +16 59909955 0 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-0.1522498322 0.05788929426 -0.1318577905 -0.1428769236 0.0590248186 0.07418906785 -0.1577959635 -0.1615338991 -0.08378397545 0.2457328434 -0.1236089604 -0.1334074576 -0.1236913548 -0.1419950539 -0.1465453505 -0.1328615751 -0.1400798285 -0.125899148 0.01073262585 0.01066130604 0.07172783775 0.2398701085 0.1499149813 0.01798923893 0.07229451458 0.01630707829 0.05717640422 0.1629847058 -0.01424529711 0.237465903 -0.1464322694 0.01097677067 0.004075278699 0.007221425588 -0.0354278431 -0.005251333288 0.3238045878 0.3606979959 0.2638715017 0.09286882372 0.1472971312 0.002977235382 1.180225756 diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh index 522cf3d..fb88e9d 100755 --- a/test/dev_test_suite.sh +++ b/test/dev_test_suite.sh @@ -2,8 +2,26 @@ gemma=../bin/gemma +# Test for https://github.com/genetics-statistics/GEMMA/issues/26 +# Always getting 'pve estimate =0.99xxx se(pve) =-nan' +testIssue26() { + outn=issue26 + rm -f output/$outn.* + $gemma -bfile data/issue26/mydata -k data/issue26/mydata_kinship.sXX.txt \ + -miss 1 -maf 0.01 -r2 1 -lmm \ + -debug -issue 26 \ + -o $outn + assertEquals 0 $? + outfn=output/$outn.assoc.txt + grep "total computation time" < output/$outn.log.txt + assertEquals 0 $? + assertEquals "2001" `wc -l < $outfn` + assertEquals "1582899231.18" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} + testCenteredRelatednessMatrixKLOCO1() { outn=mouse_hs1940_LOCO1 + rm -f output/$outn.* $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \ -a ../example/mouse_hs1940.anno.txt -snps ../example/mouse_hs1940_snps.txt -nind 400 -loco 1 -gk -debug -o $outn assertEquals 0 $? @@ -17,6 +35,7 @@ testCenteredRelatednessMatrixKLOCO1() { testUnivariateLinearMixedModelLOCO1() { outn=mouse_hs1940_CD8_LOCO1_lmm + rm -f output/$outn.* $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \ -n 1 \ -loco 1 \ |