diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/checkpoint.h | 8 | ||||
| -rw-r--r-- | src/debug.cpp | 2 | ||||
| -rw-r--r-- | src/gemma.cpp | 13 | ||||
| -rw-r--r-- | src/gemma_io.cpp | 2 | ||||
| -rw-r--r-- | src/guile/examples.scm | 6 | ||||
| -rw-r--r-- | src/guile_api.cpp | 44 | ||||
| -rw-r--r-- | src/guile_api.h | 14 | ||||
| -rw-r--r-- | src/lmm.cpp | 3 | ||||
| -rw-r--r-- | src/main.cpp | 4 | ||||
| -rw-r--r-- | src/version.h | 5 |
10 files changed, 93 insertions, 8 deletions
diff --git a/src/checkpoint.h b/src/checkpoint.h index c2457d9..ae46361 100644 --- a/src/checkpoint.h +++ b/src/checkpoint.h @@ -26,6 +26,14 @@ using namespace std; extern string checkpoint_name; +/* + Checkpoint functions display a message in debug mode when + reached. If the (unique) msg (tag) is equal to the global + checkpoint_name the program will stop. The idea is that we can + stop computation at any checkpoint. Later we can write the code to + restart at a checkpoint. + */ + void checkpoint_run(string msg, string filename, string srcfilename, int line, string funcname); #define checkpoint(msg, fname) \ diff --git a/src/debug.cpp b/src/debug.cpp index 0aa4bfc..b26e173 100644 --- a/src/debug.cpp +++ b/src/debug.cpp @@ -139,6 +139,7 @@ inline int fedisableexcept(unsigned int excepts) #endif +/* void enable_segfpe() { if (!is_fpe_check_mode() || is_legacy_mode()) return; #ifdef __GNUC__ @@ -159,6 +160,7 @@ void disable_segfpe() { #endif #endif } +*/ void write(const char *s, const char *msg) { if (!is_debug_data_mode() && !is_debug_dump_mode()) return; diff --git a/src/gemma.cpp b/src/gemma.cpp index 6c2b3f4..5804bde 100644 --- a/src/gemma.cpp +++ b/src/gemma.cpp @@ -62,6 +62,7 @@ extern "C" { #include "vc.h" #include "debug.h" #include "version.h" +#include <guile_api.h> using namespace std; @@ -81,10 +82,12 @@ void gemma_gsl_error_handler (const char * reason, #include <openblas_config.h> #endif +using namespace gemmaguile; + void GEMMA::PrintHeader(void) { cout << - "GEMMA forked executable --- part of PanGEMMA " << version << " (" << date << ") by Xiang Zhou, Pjotr Prins and team (C) 2012-" << year << endl; + "Pangemma --- GEMMA 0.98.5 compatible executable " << version << " (" << date << ") with guile " << global_guile_version() << " by Xiang Zhou, Pjotr Prins and team (C) 2012-" << year << endl ; return; } @@ -1653,7 +1656,7 @@ void GEMMA::BatchRun(PARAM &cPar) { clock_t time_begin, time_start; time_begin = clock(); - if (is_check_mode()) enable_segfpe(); // fast NaN checking by default + // if (is_check_mode()) enable_segfpe(); // fast NaN checking by default // Read Files. cout << "Reading Files ... " << endl; @@ -1943,7 +1946,7 @@ void GEMMA::BatchRun(PARAM &cPar) { VARCOV cVarcov; cVarcov.CopyFromParam(cPar); - if (is_check_mode()) disable_segfpe(); // disable fast NaN checking for now + // if (is_check_mode()) disable_segfpe(); // disable fast NaN checking for now if (!cPar.file_bfile.empty()) { cVarcov.AnalyzePlink(); @@ -2058,7 +2061,7 @@ void GEMMA::BatchRun(PARAM &cPar) { VARCOV cVarcov; cVarcov.CopyFromParam(cPar); - if (is_check_mode()) disable_segfpe(); // fast NaN checking for now + // if (is_check_mode()) disable_segfpe(); // fast NaN checking for now if (!cPar.file_bfile.empty()) { cVarcov.AnalyzePlink(); @@ -3169,7 +3172,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) { outfile << "##" << endl; outfile << "## GEMMA Version = " << version << " (" << date << ")" << endl; - outfile << "## Build profile = " << GEMMA_PROFILE << endl ; + // outfile << "## Build profile = " << GEMMA_PROFILE << endl ; #ifdef __GNUC__ outfile << "## GCC version = " << __GNUC__ << "." << __GNUC_MINOR__ << "." << __GNUC_PATCHLEVEL__ << endl; #endif diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp index f5a79a2..76f8a35 100644 --- a/src/gemma_io.cpp +++ b/src/gemma_io.cpp @@ -1431,6 +1431,7 @@ bool BimbamKin(const string file_geno, const set<string> ksnps, auto infilen = file_geno.c_str(); igzstream infile(infilen, igzstream::in); enforce_msg(infilen, "error reading genotype file"); + checkpoint("read-geno-file",file_geno); size_t n_miss; double geno_mean, geno_var; @@ -1758,6 +1759,7 @@ bool ReadFile_geno(const string file_geno, vector<int> &indicator_idv, cout << "error reading genotype file:" << file_geno << endl; return false; } + checkpoint("read-geno-file",file_geno); string line; char *ch_ptr; diff --git a/src/guile/examples.scm b/src/guile/examples.scm new file mode 100644 index 0000000..8855a34 --- /dev/null +++ b/src/guile/examples.scm @@ -0,0 +1,6 @@ +(define-module (example) + #:use-module (srfi srfi-4) + #:export (make-floats)) + +(define (make-floats) + #f64( 1.0 2.2 3.3 4.0)) diff --git a/src/guile_api.cpp b/src/guile_api.cpp new file mode 100644 index 0000000..e3ef482 --- /dev/null +++ b/src/guile_api.cpp @@ -0,0 +1,44 @@ +#include <guile_api.h> + +namespace gemmaguile { + + void global_start_guile() { + scm_init_guile(); + } + + string global_guile_version() { + SCM version_scm = scm_version(); + char* c_str = scm_to_utf8_string(version_scm); + string version_str(c_str); + free(c_str); // Must free the allocated memory + + return version_str; + } + + SCM make_floats() + { + return scm_call_0(scm_c_public_ref("example", "make-floats")); + } + + void use_floats() + { + SCM vec = make_floats(); + + scm_t_array_handle handle; + size_t len; + ssize_t inc; + const SCM *elt; + + const double *ny = scm_f64vector_elements (vec,&handle,&len,&inc); + for (size_t i = 0; i < len; i++) { + printf("elem %zu = %f\n", i, ny[i]); + } + scm_array_handle_release (&handle); + } + + void start_test() { + scm_c_primitive_load("src/guile/examples.scm"); + use_floats(); + } + +} diff --git a/src/guile_api.h b/src/guile_api.h new file mode 100644 index 0000000..b413342 --- /dev/null +++ b/src/guile_api.h @@ -0,0 +1,14 @@ +#pragma once + +#include <string> +#include <libguile.h> + +using namespace std; + +namespace gemmaguile { + + void global_start_guile(); + string global_guile_version(); + void start_test(); + +}; diff --git a/src/lmm.cpp b/src/lmm.cpp index 85e92fe..ccf880a 100644 --- a/src/lmm.cpp +++ b/src/lmm.cpp @@ -44,6 +44,7 @@ #include "gzstream.h" #include "gemma.h" #include "gemma_io.h" +#include "checkpoint.h" #include "fastblas.h" #include "lapack.h" #include "lmm.h" @@ -1663,6 +1664,7 @@ void LMM::AnalyzeBimbam(const gsl_matrix *U, const gsl_vector *eval, const set<string> gwasnps) { debug_msg(file_geno); auto infilen = file_geno.c_str(); + checkpoint("start-read-geno-file",file_geno); igzstream infile(infilen, igzstream::in); enforce_msg(infile, "error reading genotype file"); @@ -2291,6 +2293,7 @@ void LMM::AnalyzeBimbamGXE(const gsl_matrix *U, const gsl_vector *eval, cout << "error reading genotype file:" << file_geno << endl; return; } + checkpoint("start-read-geno-file",file_geno); clock_t time_start = clock(); diff --git a/src/main.cpp b/src/main.cpp index deadc63..ee6d597 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -22,6 +22,7 @@ #include <sstream> #include <sys/stat.h> #include <sys/types.h> +#include <guile_api.h> using namespace std; @@ -31,6 +32,9 @@ int main(int argc, char *argv[]) { gsl_set_error_handler (&gemma_gsl_error_handler); + gemmaguile::global_start_guile(); + gemmaguile::start_test(); + if (argc <= 1) { cGemma.PrintHeader(); cGemma.PrintHelp(0); diff --git a/src/version.h b/src/version.h index 3382003..02d4c09 100644 --- a/src/version.h +++ b/src/version.h @@ -1,5 +1,4 @@ // version.h generated by GEMMA scripts/gen_version_info.sh -#define GEMMA_VERSION "0.0.1" -#define GEMMA_DATE "2025-01-04" +#define GEMMA_VERSION "1.0.0" +#define GEMMA_DATE "2025-11-22" #define GEMMA_YEAR "2025" -#define GEMMA_PROFILE "/gnu/store/ln160n2kzn791jwgv36yrxlxygjwl9hh-profile" |