[med-svn] [Git][med-team/bolt-lmm][master] 3 commits: Fix clean target

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / bolt-lmm


Commits:
6e30516b by Andreas Tille at 2024-01-27T21:03:54+01:00
Fix clean target

- - - - -
8d19580e by Andreas Tille at 2024-01-27T21:04:51+01:00
Remove patch simde.patch that is missing from debian/patches/series.

Changes-By: lintian-brush
Fixes: lintian: patch-file-present-but-not-mentioned-in-series
See-also: https://lintian.debian.org/tags/patch-file-present-but-not-mentioned-in-series.html

- - - - -
63ae03a4 by Andreas Tille at 2024-01-27T21:06:44+01:00
routine-update: Ready to upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/clean
- − debian/patches/simde.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+bolt-lmm (2.4.1+dfsg-2) unstable; urgency=medium
+
+  * Team upload.
+  * Fix clean target
+    Closes: #1043783, #1049735
+  Remove patch simde.patch that is missing from debian/patches/series.
+
+ -- Andreas Tille <tille at debian.org>  Sat, 27 Jan 2024 21:05:33 +0100
+
 bolt-lmm (2.4.1+dfsg-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/clean
=====================================
@@ -0,0 +1 @@
+example/examples.tar.xz


=====================================
debian/patches/simde.patch deleted
=====================================
@@ -1,86 +0,0 @@
---- a/src/MemoryUtils.hpp
-+++ b/src/MemoryUtils.hpp
-@@ -25,14 +25,17 @@
- 
- //#define ALIGNED_MALLOC(size) mkl_malloc(size, MEM_ALIGNMENT)
- //#define ALIGNED_MALLOC(size) _mm_malloc(size, MEM_ALIGNMENT)
-+
- void *ALIGNED_MALLOC(uint64 size);
- 
- #ifdef USE_MKL_MALLOC
- #include <mkl.h>
- #define ALIGNED_FREE mkl_free
--#else
--#include <xmmintrin.h>
-+#elif defined(__SSE__)
-+ #include <xmmintrin.h>
- #define ALIGNED_FREE _mm_free
-+#else
-+#define ALIGNED_FREE free
- #endif
- 
- #define ALIGNED_MALLOC_DOUBLES(numDoubles) (double *) ALIGNED_MALLOC((numDoubles)*sizeof(double))
---- a/src/SnpData.cpp
-+++ b/src/SnpData.cpp
-@@ -25,9 +25,8 @@
- #include <sstream>
- #include <map>
- 
--#ifdef USE_SSE
--#include <emmintrin.h> // SSE2 for packed doubles
--#endif
-+#define SIMDE_ENABLE_NATIVE_ALIASES
-+#include <simde/x86/sse2.h>
- 
- #include "Types.hpp"
- #include "SnpData.hpp"
-@@ -892,26 +891,12 @@
- 
-     uchar *ptr = genotypes + m * (Nstride>>2);
-     for (uint64 n4 = 0; n4 < Nstride; n4 += 4) {
--#ifdef USE_SSE // todo: add AVX instructions to do all at once?
--      __m128d x01 = _mm_load_pd(&work[*ptr][0]);
--      __m128d x23 = _mm_load_pd(&work[*ptr][2]);
--      __m128d mask01 = _mm_load_pd(&subMaskIndivs[n4]);
--      __m128d mask23 = _mm_load_pd(&subMaskIndivs[n4+2]);
--      _mm_store_pd(&out[n4], _mm_mul_pd(x01, mask01));
--      _mm_store_pd(&out[n4+2], _mm_mul_pd(x23, mask23));
--#else
--      // non-lookup approach
--      /*
--      uchar g = *ptr;
--      out[n4] = lookupBedCode[g&3] * subMaskIndivs[n4];
--      out[n4+1] = lookupBedCode[(g>>2)&3] * subMaskIndivs[n4+1];
--      out[n4+2] = lookupBedCode[(g>>4)&3] * subMaskIndivs[n4+2];
--      out[n4+3] = lookupBedCode[(g>>6)&3] * subMaskIndivs[n4+3];
--      */
--      memcpy(out + n4, work[*ptr], sizeof(work[0]));
--      for (int k = 0; k < 4; k++)
--	out[n4+k] *= subMaskIndivs[n4+k];
--#endif
-+      simde__m128d x01 = simde_mm_load_pd(&work[*ptr][0]);
-+      simde__m128d x23 = simde_mm_load_pd(&work[*ptr][2]);
-+      simde__m128d mask01 = simde_mm_load_pd(&subMaskIndivs[n4]);
-+      simde__m128d mask23 = simde_mm_load_pd(&subMaskIndivs[n4+2]);
-+      simde_mm_store_pd(&out[n4], simde_mm_mul_pd(x01, mask01));
-+      simde_mm_store_pd(&out[n4+2], simde_mm_mul_pd(x23, mask23));
-       ptr++;
-     }
-   }
---- a/src/MemoryUtils.cpp
-+++ b/src/MemoryUtils.cpp
-@@ -25,8 +25,11 @@
- void *ALIGNED_MALLOC(uint64 size) {
- #ifdef USE_MKL_MALLOC
-   void *p = mkl_malloc(size, MEM_ALIGNMENT);
--#else
-+#elif defined(__SSE__)
-   void *p = _mm_malloc(size, MEM_ALIGNMENT);
-+#else
-+#include <stdlib.h>
-+  void *p = aligned_alloc(MEM_ALIGNMENT, size);
- #endif
-   // TODO: change to assert() or dispense with altogether and change ALIGNED_MALLOC to macro?
-   if (p == NULL) {
-
-



View it on GitLab: https://salsa.debian.org/med-team/bolt-lmm/-/compare/f4a768572610b3e72a95326d3b0ee891bd2fbc7b...63ae03a4a8000f00e9d1bf2b820eee7dc4caa595

-- 
View it on GitLab: https://salsa.debian.org/med-team/bolt-lmm/-/compare/f4a768572610b3e72a95326d3b0ee891bd2fbc7b...63ae03a4a8000f00e9d1bf2b820eee7dc4caa595
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