[med-svn] [Git][med-team/plink1-9][upstream] New upstream version 1.90~b6.6-181012
Dylan Aïssi
gitlab at salsa.debian.org
Thu Nov 1 06:37:57 GMT 2018
Dylan Aïssi pushed to branch upstream at Debian Med / plink1.9
Commits:
868d9efd by Dylan Aïssi at 2018-11-01T06:30:14Z
New upstream version 1.90~b6.6-181012
- - - - -
9 changed files:
- Makefile
- Makefile.std
- plink.c
- plink_common.h
- plink_family.c
- plink_matrix.c
- plink_matrix.h
- plink_rserve.c
- toy.ped
Changes:
=====================================
Makefile
=====================================
@@ -31,7 +31,7 @@ CC ?= gcc
CXX ?= g++
CFLAGS ?= -Wall -O2
CXXFLAGS ?= -Wall -O2
-BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lcblas -latlas
+BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lblas -lcblas -latlas
LDFLAGS ?= -lm -lpthread -ldl
ZLIB ?= ../zlib-1.2.11/libz.so.1.2.11
=====================================
Makefile.std
=====================================
@@ -31,7 +31,7 @@ CC ?= gcc
CXX ?= g++
CFLAGS ?= -Wall -O2
CXXFLAGS ?= -Wall -O2
-BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lcblas -latlas
+BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lblas -lcblas -latlas
LDFLAGS ?= -lm -lpthread -ldl
ZLIB ?= ../zlib-1.2.11/libz.so.1.2.11
=====================================
plink.c
=====================================
@@ -93,7 +93,7 @@
static const char ver_str[] =
#ifdef STABLE_BUILD
- "PLINK v1.90b6.5"
+ "PLINK v1.90b6.6"
#else
"PLINK v1.90p"
#endif
@@ -105,7 +105,7 @@ static const char ver_str[] =
#else
" 32-bit"
#endif
- " (13 Sep 2018)";
+ " (12 Oct 2018)";
static const char ver_str2[] =
// include leading space if day < 10, so character length stays the same
""
=====================================
plink_common.h
=====================================
@@ -27,6 +27,9 @@
#include <string.h>
#include <math.h>
#include <stdint.h>
+#ifndef __STDC_FORMAT_MACROS
+# define __STDC_FORMAT_MACROS 1
+#endif
#include <inttypes.h>
// avoid compiler warning
@@ -59,7 +62,13 @@
// needed for MEMORYSTATUSEX
#ifndef _WIN64
#define WINVER 0x0500
+ #else
+ #define __LP64__
#endif
+ #ifndef WIN32_LEAN_AND_MEAN
+ #define WIN32_LEAN_AND_MEAN
+ #endif
+ #include <windows.h>
#else // Unix
#include <sys/stat.h>
#endif
@@ -77,12 +86,13 @@
#endif
#ifdef _WIN32
- #define PRId64 "I64d"
- #define PRIu64 "I64u"
#define fseeko fseeko64
#define ftello ftello64
- #include <windows.h>
#include <process.h>
+# undef PRId64
+# undef PRIu64
+# define PRId64 "I64d"
+# define PRIu64 "I64u"
#define pthread_t HANDLE
#define THREAD_RET_TYPE unsigned __stdcall
#define THREAD_RETURN return 0
@@ -96,8 +106,10 @@
#define getc_unlocked getc
#define putc_unlocked putc
#endif
- #define uint64_t unsigned long long
- #define int64_t long long
+ #if __cplusplus < 201103L
+ #define uint64_t unsigned long long
+ #define int64_t long long
+ #endif
#else
#include <pthread.h>
#define THREAD_RET_TYPE void*
@@ -144,6 +156,27 @@
#ifdef __cplusplus
#include <algorithm>
+# ifdef _WIN32
+// Windows C++11 <algorithm> resets these values :(
+# undef PRIu64
+# undef PRId64
+# define PRIu64 "I64u"
+# define PRId64 "I64d"
+# undef PRIuPTR
+# undef PRIdPTR
+# ifdef __LP64__
+# define PRIuPTR PRIu64
+# define PRIdPTR PRId64
+# else
+# if __cplusplus < 201103L
+# define PRIuPTR "lu"
+# define PRIdPTR "ld"
+# else
+# define PRIuPTR "u"
+# define PRIdPTR "d"
+# endif
+# endif
+# endif
#define HEADER_INLINE inline
#else
#define HEADER_INLINE static inline
@@ -206,12 +239,12 @@
#define ZEROLU 0LU
#define ONELU 1LU
- #ifndef PRIuPTR
- #define PRIuPTR "lu"
- #endif
- #ifndef PRIdPTR
- #define PRIdPTR "ld"
- #endif
+# if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8) && (__cplusplus < 201103L)
+# undef PRIuPTR
+# undef PRIdPTR
+# define PRIuPTR "lu"
+# define PRIdPTR "ld"
+# endif
#define PRIxPTR2 "08lx"
// todo: update code so this still works when reduced to 4
=====================================
plink_family.c
=====================================
@@ -1749,6 +1749,7 @@ int32_t tdt_poo(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* o
// entry bit 16 & 24: hhh?
// entry bit 17: paternal A1 transmitted?
// entry bit 25: maternal A1 transmitted?
+ // bugfix (10 Oct 2018): missed a few chrX possibilities
const uint32_t poo_table[] =
{0, 0, 0, 0,
0, 0, 0, 0,
@@ -1758,10 +1759,10 @@ int32_t tdt_poo(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* o
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
- 0x2000200, 0, 0x200, 0,
+ 0x2000200, 0, 0x200, 0x200,
0, 0, 0, 0,
0x2020202, 0, 0x1010202, 0x202,
- 0, 0, 0x2000200, 0x200,
+ 0x2000200, 0, 0x2000200, 0x200,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0x20002, 2};
=====================================
plink_matrix.c
=====================================
@@ -20,9 +20,9 @@
#include "plink_matrix.h"
#ifndef NOLAPACK
-#ifndef __APPLE__
+# ifndef __APPLE__
void xerbla_(void) {} // fix static linking error
-#endif
+# endif
#endif
static inline double SQR(const double a) {
@@ -286,7 +286,7 @@ int32_t invert_matrix(int32_t dim, double* matrix, MATRIX_INVERT_BUF1_TYPE* dbl_
}
return 0;
}
-#else
+#else // !NOLAPACK
int32_t invert_matrix(__CLPK_integer dim, double* matrix, MATRIX_INVERT_BUF1_TYPE* int_1d_buf, double* dbl_2d_buf) {
// dgetrf_/dgetri_ is more efficient than dpotrf_/dpotri_ on OS X.
__CLPK_integer lwork = dim * dim;
@@ -321,7 +321,7 @@ int32_t invert_matrix_checked(__CLPK_integer dim, double* matrix, MATRIX_INVERT_
dgetri_(&dim, matrix, &dim, int_1d_buf, dbl_2d_buf, &lwork, &info);
return 0;
}
-#endif
+#endif // !NOLAPACK
void col_major_matrix_multiply(__CLPK_integer row1_ct, __CLPK_integer col2_ct, __CLPK_integer common_ct, double* inmatrix1, double* inmatrix2, double* outmatrix) {
#ifdef NOLAPACK
@@ -345,15 +345,15 @@ void col_major_matrix_multiply(__CLPK_integer row1_ct, __CLPK_integer col2_ct, _
}
}
#else
-#ifdef _WIN32
+# ifndef USE_CBLAS_XGEMM
char blas_char = 'N';
double dyy = 1;
double dzz = 0;
dgemm_(&blas_char, &blas_char, &row1_ct, &col2_ct, &common_ct, &dyy, inmatrix1, &row1_ct, inmatrix2, &common_ct, &dzz, outmatrix, &row1_ct);
-#else
+# else
cblas_dgemm(CblasColMajor, CblasNoTrans, CblasNoTrans, row1_ct, col2_ct, common_ct, 1.0, inmatrix1, row1_ct, inmatrix2, common_ct, 0.0, outmatrix, row1_ct);
-#endif // _WIN32
-#endif // NOLAPACK
+# endif // USE_CBLAS_XGEMM
+#endif // !NOLAPACK
}
void col_major_fmatrix_multiply(__CLPK_integer row1_ct, __CLPK_integer col2_ct, __CLPK_integer common_ct, float* inmatrix1, float* inmatrix2, float* outmatrix) {
@@ -378,15 +378,15 @@ void col_major_fmatrix_multiply(__CLPK_integer row1_ct, __CLPK_integer col2_ct,
}
}
#else
-#ifdef _WIN32
+# ifndef USE_CBLAS_XGEMM
char blas_char = 'N';
float fyy = 1;
float fzz = 0;
sgemm_(&blas_char, &blas_char, &row1_ct, &col2_ct, &common_ct, &fyy, inmatrix1, &row1_ct, inmatrix2, &common_ct, &fzz, outmatrix, &row1_ct);
-#else
+# else
cblas_sgemm(CblasColMajor, CblasNoTrans, CblasNoTrans, row1_ct, col2_ct, common_ct, 1.0, inmatrix1, row1_ct, inmatrix2, common_ct, 0.0, outmatrix, row1_ct);
-#endif // _WIN32
-#endif // NOLAPACK
+# endif // USE_CBLAS_XGEMM
+#endif // !NOLAPACK
}
// Todo: replace these with cache-oblivious, or at least -friendlier,
=====================================
plink_matrix.h
=====================================
@@ -19,66 +19,118 @@
// Wrappers for frequent LAPACK calls (sometimes with no-LAPACK fallbacks).
-// May want to make this comprehensive to make linking with Intel MKL practical
-// in the future.
-
-// todo: allow this to take advantage of 64-bit integer LAPACK. As of this
-// writing, it's available on Amazon EC2 64-bit Linux instances, but I can't
-// find it for Windows. (And even if OS X vecLib adds it soon, we can't use it
-// there anytime soon because static linking is not an option.)
-
-#ifdef __APPLE__
-#include <Accelerate/Accelerate.h>
-#endif
+// (Update, 11 Oct 2018: Backported PLINK 2.0's MKL support.)
#ifdef NOLAPACK
-#define MATRIX_INVERT_BUF1_TYPE double
-#define MATRIX_INVERT_BUF1_ELEM_ALLOC (2 * sizeof(double))
-#define MATRIX_INVERT_BUF1_CHECKED_ALLOC (2 * sizeof(double))
-#define __CLPK_integer int
+# define MATRIX_INVERT_BUF1_TYPE double
+# define MATRIX_INVERT_BUF1_ELEM_ALLOC (2 * sizeof(double))
+# define MATRIX_INVERT_BUF1_CHECKED_ALLOC (2 * sizeof(double))
+# define __CLPK_integer int
-#else // not NOLAPACK
+#else // !NOLAPACK
-#ifndef __APPLE__
+# ifdef __APPLE__
+# include <Accelerate/Accelerate.h>
+# define USE_CBLAS_XGEMM
+# endif
-#ifdef __cplusplus
+# ifndef __APPLE__
+
+# ifdef __cplusplus
extern "C" {
-#endif
+# endif
+
typedef double __CLPK_doublereal;
-#ifdef _WIN32
-#define HAVE_LAPACK_CONFIG_H
-#define LAPACK_COMPLEX_STRUCTURE
-#include "lapack/lapacke/include/lapacke.h"
+# if defined(__LP64__) || defined(_WIN32)
typedef int32_t __CLPK_integer;
+# else
+ typedef long int __CLPK_integer;
+# endif
+
+# ifdef _WIN32
+ // openblas is easy enough to set up on Windows nowadays.
+ // not worth the trouble of ripping out vector extensions, etc. just so we
+ // can compile with Visual Studio and gain access to MKL.
+ // (todo: upgrade from 0.2.19 to a later version, build setup will probably
+ // need to change a bit)
+# define HAVE_LAPACK_CONFIG_H
+# define LAPACK_COMPLEX_STRUCTURE
+# include "lapacke.h"
+
+ __CLPK_doublereal ddot_(__CLPK_integer* n, __CLPK_doublereal* dx,
+ __CLPK_integer* incx, __CLPK_doublereal* dy,
+ __CLPK_integer* incy);
void dger_(int* m, int* n, double* alpha, double* x, int* incx, double* y,
int* incy, double* a, int* lda);
- void dgemm_(char* transa, char* transb, int* m, int* n, int* k,
- double* alpha, double* a, int* lda, double* b, int* ldb,
- double* beta, double* c, int* ldc);
+ void dgemm_(char* transa, char* transb, __CLPK_integer* m, __CLPK_integer* n,
+ __CLPK_integer* k, double* alpha, double* a, __CLPK_integer* lda,
+ double* b, __CLPK_integer* ldb, double* beta, double* c,
+ __CLPK_integer* ldc);
void dsymv_(char* uplo, int* n, double* alpha, double* a, int* lda,
double* x, int* incx, double* beta, double* y, int* incy);
- double ddot_(int* n, double* dx, int* incx, double* dy, int* incy);
-
void dgetrf_(__CLPK_integer* m, __CLPK_integer* n,
__CLPK_doublereal* a, __CLPK_integer* lda,
__CLPK_integer* ipiv, __CLPK_integer* info);
- void sgemm_(char* transa, char* transb, int* m, int* n, int* k,
- float* alpha, float* a, int* lda, float* b, int* ldb,
- float* beta, float* c, int* ldc);
+ void sgemm_(char* transa, char* transb, __CLPK_integer* m, __CLPK_integer* n,
+ __CLPK_integer* k, float* alpha, float* a, __CLPK_integer* lda,
+ float* b, __CLPK_integer* ldb, float* beta, float* c,
+ __CLPK_integer* ldc);
+
+# else // Linux
+# ifdef USE_MKL
+# ifndef __LP64__
+# error "32-bit Linux build does not support Intel MKL."
+# endif
+# define USE_CBLAS_XGEMM
+ // sizeof(MKL_INT) should be 4.
+# define MKL_LP64
+# ifdef DYNAMIC_MKL
+# include <mkl_service.h>
+# include <mkl_cblas.h>
+# include <mkl_lapack.h>
+# else
+# include "mkl_service.h"
+# include "mkl_cblas.h"
+# include "mkl_lapack.h"
+# endif
+# else
+# ifdef USE_CBLAS_XGEMM
+# include <cblas.h>
+# else
+ // ARGH
+ // cmake on Ubuntu 14 seems to require use of cblas_f77.h instead of cblas.h.
+ // Conversely, cblas_f77.h does not seem to be available on the Scientific
+ // Linux ATLAS/LAPACK install, and right now that's my only option for
+ // producing 32-bit static builds...
+ // So. Default include is cblas.h. To play well with cmake + Ubuntu 14 and
+ // 16 simultaneously, there is a CBLAS_F77_ON_OLD_GCC mode which picks
+ // cblas_f77.h on Ubuntu 14 and cblas.h on 16.
+# ifdef FORCE_CBLAS_F77
+# include <cblas_f77.h>
+# elif !defined(CBLAS_F77_ON_OLD_GCC)
+# include <cblas.h>
+# else
+# if (__GNUC__ <= 4)
+# include <cblas_f77.h>
+# else
+# if __has_include(<cblas.h>)
+# include <cblas.h>
+# else
+# include <cblas_f77.h>
+# endif
+# endif
+# endif
+ __CLPK_doublereal ddot_(__CLPK_integer* n, __CLPK_doublereal* dx,
+ __CLPK_integer* incx, __CLPK_doublereal* dy,
+ __CLPK_integer* incy);
+# endif
-#else // not _WIN32
-#include <cblas.h>
-#ifdef __LP64__
- typedef int32_t __CLPK_integer;
-#else
- typedef long int __CLPK_integer;
-#endif
int dgetrf_(__CLPK_integer* m, __CLPK_integer* n,
__CLPK_doublereal* a, __CLPK_integer* lda,
__CLPK_integer* ipiv, __CLPK_integer* info);
@@ -118,27 +170,46 @@ extern "C" {
__CLPK_doublereal* vt, __CLPK_integer* ldvt,
__CLPK_doublereal* work, __CLPK_integer* lwork,
__CLPK_integer* iwork, __CLPK_integer* info);
-#endif
+
+# ifndef USE_CBLAS_XGEMM
+ void dgemm_(char* transa, char* transb, __CLPK_integer* m, __CLPK_integer* n,
+ __CLPK_integer* k, double* alpha, double* a, __CLPK_integer* lda,
+ double* b, __CLPK_integer* ldb, double* beta, double* c,
+ __CLPK_integer* ldc);
+
+ void dsymv_(char* uplo, int* n, double* alpha, double* a, int* lda,
+ double* x, int* incx, double* beta, double* y, int* incy);
+
+ void sgemm_(char* transa, char* transb, __CLPK_integer* m, __CLPK_integer* n,
+ __CLPK_integer* k, float* alpha, float* a, __CLPK_integer* lda,
+ float* b, __CLPK_integer* ldb, float* beta, float* c,
+ __CLPK_integer* ldc);
+# endif
+
+# endif // !USE_MKL
+# endif
+
void xerbla_(void);
-#ifdef __cplusplus
-}
-#endif // __cplusplus
-#endif // __APPLE__
+# ifdef __cplusplus
+} // extern "C"
+# endif
+
+# endif // !__APPLE__
-#define MATRIX_INVERT_BUF1_TYPE __CLPK_integer
-#define MATRIX_INVERT_BUF1_ELEM_ALLOC sizeof(__CLPK_integer)
+# define MATRIX_INVERT_BUF1_TYPE __CLPK_integer
+# define MATRIX_INVERT_BUF1_ELEM_ALLOC sizeof(__CLPK_integer)
// invert_matrix_checked() usually requires a larger buffer
-#define MATRIX_INVERT_BUF1_CHECKED_ALLOC (2 * sizeof(__CLPK_integer))
+# define MATRIX_INVERT_BUF1_CHECKED_ALLOC (2 * sizeof(__CLPK_integer))
-#endif // NOLAPACK
+#endif // !NOLAPACK
#define MATRIX_SINGULAR_RCOND 1e-14
#ifdef NOLAPACK
int32_t invert_matrix(int32_t dim, double* matrix, MATRIX_INVERT_BUF1_TYPE* dbl_1d_buf, double* dbl_2d_buf);
-#define invert_matrix_checked invert_matrix
+# define invert_matrix_checked invert_matrix
#else
int32_t invert_matrix(__CLPK_integer dim, double* matrix, MATRIX_INVERT_BUF1_TYPE* int_1d_buf, double* dbl_2d_buf);
=====================================
plink_rserve.c
=====================================
@@ -20,14 +20,14 @@
// gcc instead of g++.
#if defined __cplusplus && !defined _WIN32
-#include "plink_common.h"
-#include "plink_cluster.h"
-
#define MAIN
#define SOCK_ERRORS
#include "sisocks.h"
#include "Rconnection.h"
+#include "plink_common.h"
+#include "plink_cluster.h"
+
#define RPLUGIN_BLOCK_SIZE 100
int32_t rserve_call(char* rplugin_fname, char* rplugin_host_or_socket, int32_t rplugin_port, uint32_t rplugin_debug, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, char** marker_allele_ptrs, uint32_t* marker_pos, uint32_t plink_maxsnp, Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t* pheno_nm, uint32_t pheno_nm_ct, uintptr_t* pheno_c, double* pheno_d, uint32_t cluster_ct, uint32_t* cluster_map, uint32_t* cluster_starts, uintptr_t covar_ct, double* covar_d, char* outname, char* outname_end) {
=====================================
toy.ped
=====================================
@@ -1,2 +1,2 @@
-1 1000000000 0 0 1 1 0 0 1 1
-1 1000000001 0 0 1 2 1 1 1 2
+1 1000000000 0 0 1 1 0 0 A A
+1 1000000001 0 0 1 2 C C A G
View it on GitLab: https://salsa.debian.org/med-team/plink1-9/commit/868d9efd315a33e16f52340ecbcb18e579f731e7
--
View it on GitLab: https://salsa.debian.org/med-team/plink1-9/commit/868d9efd315a33e16f52340ecbcb18e579f731e7
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