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-rw-r--r--VERSION2
-rw-r--r--src/debug.cpp4
-rw-r--r--src/debug.h3
-rw-r--r--src/lapack.cpp2
-rw-r--r--src/lmm.cpp3
-rw-r--r--src/mvlmm.cpp6
-rw-r--r--src/param.cpp3
-rw-r--r--src/version.h6
-rw-r--r--test/performance/releases.org54
9 files changed, 72 insertions, 11 deletions
diff --git a/VERSION b/VERSION
index 4ab938a..f4df5d0 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.98-pre2
+0.98-beta1
diff --git a/src/debug.cpp b/src/debug.cpp
index 2f1f861..9f9f862 100644
--- a/src/debug.cpp
+++ b/src/debug.cpp
@@ -137,7 +137,7 @@ void enable_segfpe() {
if (!is_fpe_check_mode() || is_legacy_mode()) return;
#ifdef __GNUC__
#if defined(__x86_64__)
- debug_msg("enable segfpe hardware floating point error detection");
+ // debug_msg("enable segfpe hardware floating point error detection");
signal(SIGFPE, sighandler);
feenableexcept(FE_INVALID | FE_DIVBYZERO | FE_OVERFLOW | FE_UNDERFLOW);
#endif
@@ -148,7 +148,7 @@ void disable_segfpe() {
if (!is_fpe_check_mode() || is_legacy_mode()) return;
#ifdef __GNUC__
#if defined(__x86_64__)
- debug_msg("disable segfpe");
+ // debug_msg("disable segfpe");
fedisableexcept(FE_INVALID | FE_DIVBYZERO | FE_OVERFLOW | FE_UNDERFLOW);
#endif
#endif
diff --git a/src/debug.h b/src/debug.h
index e83c813..a665a37 100644
--- a/src/debug.h
+++ b/src/debug.h
@@ -115,6 +115,9 @@ inline void fail_msg(std::string msg) {
std::raise(SIGINT); // keep stack trace for gdb
}
+#define info_msg(msg) cerr << "**** INFO: " << msg << "." << endl;
+#define msg(msg) info_msg(msg);
+
#if defined NDEBUG
#define __SHOW_FUNC __func__
diff --git a/src/lapack.cpp b/src/lapack.cpp
index 125e5a0..79d49fd 100644
--- a/src/lapack.cpp
+++ b/src/lapack.cpp
@@ -319,7 +319,7 @@ void LUDecomp(gsl_matrix *LU, gsl_permutation *p, int *signum) {
void LUInvert(const gsl_matrix *LU, const gsl_permutation *p, gsl_matrix *ret_inverse) {
// debug_msg("entering");
auto det = LULndet(LU);
- assert(det != 1.0);
+ enforce_msg(det != 1.0,"LU determinant is zero -> LU is not invertable");
enforce_gsl(gsl_linalg_LU_invert(LU, p, ret_inverse));
}
diff --git a/src/lmm.cpp b/src/lmm.cpp
index d08c90e..80372ee 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -296,7 +296,8 @@ void CalcPab(const size_t n_cvt, const size_t e_mode, const gsl_vector *Hi_eval,
write(Hi_eval,"Hi_eval");
write(Uab,"Uab");
// write(ab,"ab");
- assert(!has_nan(Hi_eval));
+ if (is_check_mode())
+ assert(!has_nan(Hi_eval));
assert(!has_nan(Uab));
// assert(!has_nan(ab));
diff --git a/src/mvlmm.cpp b/src/mvlmm.cpp
index d877302..faea21e 100644
--- a/src/mvlmm.cpp
+++ b/src/mvlmm.cpp
@@ -321,12 +321,15 @@ double CalcQi(const gsl_vector *eval, const gsl_vector *D_l,
}
// xHiy=\sum_{k=1}^n x_k\otimes ((delta_k*Dl+I)^{-1}Ul^TVe^{-1/2}y.
+//
+// FIXME: mvlmm spends a massive amount of time here
void CalcXHiY(const gsl_vector *eval, const gsl_vector *D_l,
const gsl_matrix *X, const gsl_matrix *UltVehiY,
gsl_vector *xHiy) {
+ debug_msg("enter");
size_t n_size = eval->size, c_size = X->size1, d_size = D_l->size;
- gsl_vector_set_zero(xHiy);
+ // gsl_vector_set_zero(xHiy);
double x, delta, dl, y, d;
for (size_t i = 0; i < d_size; i++) {
@@ -342,6 +345,7 @@ void CalcXHiY(const gsl_vector *eval, const gsl_vector *D_l,
gsl_vector_set(xHiy, j * d_size + i, d);
}
}
+ // debug_msg("exit");
return;
}
diff --git a/src/param.cpp b/src/param.cpp
index 6537379..de0c257 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -1942,8 +1942,7 @@ void PARAM::CheckCvt() {
indicator_cvt.clear();
n_cvt = 1;
} else if (flag_ipt == 0) {
- cout << "no intercept term is found in the cvt file. "
- << "a column of 1s is added." << endl;
+ info_msg("no intercept term is found in the cvt file: a column of 1s is added");
for (vector<int>::size_type i = 0; i < indicator_idv.size(); ++i) {
if (indicator_idv[i] == 0 || indicator_cvt[i] == 0) {
continue;
diff --git a/src/version.h b/src/version.h
index 518a9f3..5afd64d 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1,5 +1,5 @@
// version.h generated by GEMMA scripts/gen_version_info.sh
-#define GEMMA_VERSION "0.98-pre2"
-#define GEMMA_DATE "2018-07-14"
+#define GEMMA_VERSION "0.98-beta1"
+#define GEMMA_DATE "2018-09-06"
#define GEMMA_YEAR "2018"
-#define GEMMA_PROFILE "/gnu/store/9ahrb1swr06kjm2gr2zg0fsyvps3xqgz-profile"
+#define GEMMA_PROFILE "/gnu/store/8h46wb8hi8n492i2vlbfcz4dm44xwlpc-profile"
diff --git a/test/performance/releases.org b/test/performance/releases.org
index b54a4cf..4497d2f 100644
--- a/test/performance/releases.org
+++ b/test/performance/releases.org
@@ -10,6 +10,60 @@ core Eigenlib version and 0.97 went multi-core with
openblas. Unfortunately I linked in lapack and an older BLAS which
slowed things down. In 0.98 openblas is mostly used and is faster.
+* GEMMA 0.98-beta1
+
+#+BEGIN_SRC bash
+ linux-vdso.so.1 (0x00007ffe475d2000)
+ libgsl.so.23 => /home/wrk/opt/gemma-dev-env/lib/libgsl.so.23 (0x00007f95a21e3000)
+ libopenblas.so.0 => /home/wrk/opt/gemma-dev-env/lib/libopenblas.so.0 (0x00007f959fc45000)
+ libz.so.1 => /home/wrk/opt/gemma-dev-env/lib/libz.so.1 (0x00007f959fa2a000)
+ libgfortran.so.3 => /home/wrk/opt/gemma-dev-env/lib/libgfortran.so.3 (0x00007f959f709000)
+ libquadmath.so.0 => /home/wrk/opt/gemma-dev-env/lib/libquadmath.so.0 (0x00007f959f4c8000)
+ libstdc++.so.6 => /home/wrk/opt/gemma-dev-env/lib/libstdc++.so.6 (0x00007f959f14d000)
+ libm.so.6 => /home/wrk/opt/gemma-dev-env/lib/libm.so.6 (0x00007f959ee01000)
+ libgcc_s.so.1 => /home/wrk/opt/gemma-dev-env/lib/libgcc_s.so.1 (0x00007f959ebea000)
+ libpthread.so.0 => /home/wrk/opt/gemma-dev-env/lib/libpthread.so.0 (0x00007f959e9cc000)
+ libc.so.6 => /home/wrk/opt/gemma-dev-env/lib/libc.so.6 (0x00007f959e61a000)
+#+END_SRC
+
+#+BEGIN_SRC bash
+time ./bin/gemma -g ~/tmp/mouse_hs1940/mouse_hs1940.geno.txt.gz -p ~/tmp/mouse_hs1940/mouse_hs1940.pheno.txt -a ~/tmp/mouse_hs1940/mouse_hs1940.anno.txt -gk -no-check
+GEMMA 0.98-beta1 (2018-09-06) by Xiang Zhou and team (C) 2012-2018
+Reading Files ...
+## number of total individuals = 1940
+## number of analyzed individuals = 1410
+## number of covariates = 1
+## number of phenotypes = 1
+## number of total SNPs/var = 12226
+## number of analyzed SNPs = 10768
+Calculating Relatedness Matrix ...
+================================================== 100%
+
+real 0m16.875s
+user 0m25.180s
+sys 0m1.740s
+#+END_SRC
+
+#+BEGIN_SRC bash
+lario:~/izip/git/opensource/genenetwork/gemma$ time bin/gemma -g ~/tmp/mouse_hs1940/mouse_hs1940.geno.txt.gz -p ~/tmp/mouse_hs1940/mouse_hs1940.pheno.txt -n 1 -a ~/tmp/mouse_hs1940/mouse_hs1940.anno.txt -k ./output/result.cXX.txt -lmm -no-check
+GEMMA 0.98-beta1 (2018-09-06) by Xiang Zhou and team (C) 2012-2018
+Reading Files ...
+## number of total individuals = 1940
+## number of analyzed individuals = 1410
+## number of covariates = 1
+## number of phenotypes = 1
+## number of total SNPs/var = 12226
+## number of analyzed SNPs = 10768
+Start Eigen-Decomposition...
+pve estimate =0.608801
+se(pve) =0.032774
+================================================== 100%
+
+real 0m13.255s
+user 0m18.272s
+sys 0m3.324s
+#+END_SRC
+
* GEMMA 0.98-pre
#+BEGIN_SRC bash
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-18 12:55:00 +0000