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-rw-r--r--README.md1
-rw-r--r--src/debug.cpp75
-rw-r--r--src/debug.h2
-rw-r--r--src/gemma.cpp3
4 files changed, 58 insertions, 23 deletions
diff --git a/README.md b/README.md
index 2b5a812..31837fa 100644
--- a/README.md
+++ b/README.md
@@ -141,6 +141,7 @@ GEMMA has a wide range of debugging options which can be viewed with
-silence silent terminal display
-debug debug output
-debug-data debug data output
+ -debug-dump -debug-data, but store the data to files (grep write() calls for messages/names)
-nind [num] read up to num individuals
-issue [num] enable tests relevant to issue tracker
-legacy run gemma in legacy mode
diff --git a/src/debug.cpp b/src/debug.cpp
index 8ef8797..0aa4bfc 100644
--- a/src/debug.cpp
+++ b/src/debug.cpp
@@ -41,7 +41,9 @@
static bool debug_mode = false;
static bool debug_data_mode = false;
-static bool debug_check = false; // check data/algorithms
+static string debug_dump_path;
+static bool debug_dump_mode = false; // Dump all the pieces of data to files
+static bool debug_check = false; // check data/algorithms
static bool debug_fpe_check = true; // check floating point errors (intel hardware)
static bool debug_strict = false; // fail on error, more rigorous checks
static bool debug_quiet = false;
@@ -50,6 +52,7 @@ static bool debug_legacy = false; // legacy mode
void debug_set_debug_mode(bool setting) { debug_mode = setting; }
void debug_set_debug_data_mode(bool setting) { debug_data_mode = setting; }
+void debug_set_debug_dump_mode(bool setting, char *path) { debug_dump_mode = setting; debug_dump_path = path;}
void debug_set_check_mode(bool setting) {debug_check = setting; }
void debug_set_no_check_mode(bool setting) {debug_check = !setting; }
void debug_set_no_fpe_check_mode(bool setting) {debug_fpe_check = !setting; }
@@ -60,6 +63,7 @@ void debug_set_legacy_mode(bool setting) { debug_legacy = setting; }
bool is_debug_mode() { return debug_mode; };
bool is_debug_data_mode() { return debug_data_mode; };
+bool is_debug_dump_mode() { return debug_dump_mode; };
bool is_no_check_mode() { return !debug_check; };
bool is_check_mode() { return debug_check; };
bool is_fpe_check_mode() { return debug_fpe_check; };
@@ -157,29 +161,43 @@ void disable_segfpe() {
}
void write(const char *s, const char *msg) {
- if (!is_debug_data_mode()) return;
- cout << s << ": " << msg << endl;
+ if (!is_debug_data_mode() && !is_debug_dump_mode()) return;
+ ofstream out(debug_dump_path + "debug-dump-" + msg + ".txt");
+ (is_debug_dump_mode() ? out : cout)
+ << s << ": " << msg << endl;
}
void write(const double d, const char *msg) {
- if (!is_debug_data_mode()) return;
- cout << std::setprecision(6) << d << ": " << msg << endl;
+ if (!is_debug_data_mode() && !is_debug_dump_mode()) return;
+ ofstream out(debug_dump_path + "debug-dump-" + msg + ".txt");
+ (is_debug_dump_mode() ? out : cout)
+ << std::setprecision(6) << d << ": " << msg << endl;
}
void write(const gsl_vector *v, const char *msg) {
- if (!is_debug_data_mode()) return;
- if (msg) cout << "// " << msg << endl;
- cout << "// vector size: " << v->size << endl;
- cout << "double " << msg << "[] = {";
+ if (!is_debug_data_mode() && !is_debug_dump_mode()) return;
+ ofstream out(debug_dump_path + "debug-dump-" + msg + ".txt");
+ if (is_debug_data_mode()) {
+ if (msg)
+ cout << "// " << msg << endl;
+ cout << "// vector size: " << v->size << endl;
+ cout << "double " << msg << "[] = {";
+ }
for (size_t i=0; i < v->size; i++) {
- cout << gsl_vector_get(v,i) << ",";
+ (is_debug_dump_mode() ? out : cout)
+ << gsl_vector_get(v,i)
+ << (is_debug_dump_mode() ? "\t" : ",");
}
- cout << "}" << endl;
+ if (is_debug_dump_mode())
+ out << endl;
+ else
+ cout << "}" << endl;
}
void write(const gsl_matrix *m, const char *msg) {
- if (!is_debug_data_mode()) return;
- if (msg) cout << "// " << msg << endl;
+ if (!is_debug_data_mode() && !is_debug_dump_mode()) return;
+ if (msg && is_debug_data_mode())
+ cout << "// " << msg << endl;
// Matrices are stored in row-major order, meaning that each row of
// elements forms a contiguous block in memory. This is the standard
// “C-language ordering” of two-dimensional arrays. The number of
@@ -187,18 +205,29 @@ void write(const gsl_matrix *m, const char *msg) {
auto rows = m->size1; // see https://www.gnu.org/software/gsl/manual/html_node/Matrices.html#Matrices
auto cols = m->size2;
auto tda = m->tda;
+ ofstream out(debug_dump_path + "debug-dump-" + msg + ".txt");
- cout << "// matrix size: " << cols << " cols, " << rows << " rows," << tda << " tda" << endl;
- cout << "double " << msg << "[] = {";
- for (size_t row=0; row < rows; row++) {
- for (size_t col=0; col < cols; col++) {
- // cout << "(" << i << "," << j << ")";
- cout << gsl_matrix_safe_get(m,row,col);
- cout << ",";
- }
- cout << "// row " << row << endl;
+ if (is_debug_data_mode()) {
+ cout << "// matrix size: " << cols << " cols, " << rows << " rows," << tda << " tda" << endl;
+ cout << "double " << msg << "[] = {";
+ }
+ for (size_t row = 0; row < rows; row++) {
+ for (size_t col = 0; col < cols; col++) {
+ // cout << "(" << i << "," << j << ")";
+ (is_debug_dump_mode() ? out : cout)
+ << gsl_matrix_safe_get(m, row, col);
+ if (is_debug_dump_mode())
+ out << "\t";
+ else
+ cout << ",";
+ }
+ if (is_debug_dump_mode())
+ out << endl;
+ else
+ cout << "// row " << row << endl;
}
- cout << "}" << endl;
+ if (is_debug_data_mode())
+ cout << "}" << endl;
}
/*
diff --git a/src/debug.h b/src/debug.h
index ff22756..0489a81 100644
--- a/src/debug.h
+++ b/src/debug.h
@@ -33,6 +33,7 @@ void gemma_gsl_error_handler (const char * reason,
void debug_set_debug_mode(bool setting);
void debug_set_debug_data_mode(bool setting);
+void debug_set_debug_dump_mode(bool setting, char *path);
void debug_set_check_mode(bool setting);
void debug_set_no_check_mode(bool setting);
void debug_set_no_fpe_check_mode(bool setting);
@@ -43,6 +44,7 @@ void debug_set_legacy_mode(bool setting);
bool is_debug_mode();
bool is_debug_data_mode();
+bool is_debug_dump_mode();
bool is_no_check_mode();
bool is_check_mode();
bool is_fpe_check_mode();
diff --git a/src/gemma.cpp b/src/gemma.cpp
index b3ca4c5..c73c174 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -1601,6 +1601,9 @@ void GEMMA::Assign(int argc, char **argv, PARAM &cPar) {
// cPar.mode_debug = true;
debug_set_debug_data_mode(true);
debug_set_debug_mode(true);
+ } else if (strcmp(argv[i], "-debug-dump") == 0) {
+ debug_set_debug_dump_mode(true, (char *)cPar.path_out.c_str());
+ debug_set_debug_mode(true);
} else if (strcmp(argv[i], "-debug") == 0) {
// cPar.mode_debug = true;
debug_set_debug_mode(true);
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-18 18:34:34 +0000