pjotrp
6 years ago
2 changed files with 129 additions and 18 deletions
@ -1,13 +1,126 @@ |
|||
diff --git a/Makefile.std b/Makefile.std
|
|||
index 95b0940..630188a 100644
|
|||
index 95b0940..30206be 100644
|
|||
--- a/Makefile.std
|
|||
+++ b/Makefile.std
|
|||
@@ -22,7 +22,7 @@ endif
|
|||
CFLAGS=-Wall -O2 |
|||
BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas |
|||
LINKFLAGS=-lm -lpthread |
|||
@@ -1,62 +1,22 @@
|
|||
# General-purpose Makefile for PLINK 1.90 |
|||
# |
|||
-# Compilation options:
|
|||
-# Do not link to LAPACK NO_LAPACK
|
|||
|
|||
-# Leave blank after "=" to disable; put "= 1" to enable
|
|||
-# (when enabled, "#define NOLAPACK" must be uncommented in plink_common.h)
|
|||
-NO_LAPACK =
|
|||
-
|
|||
-
|
|||
-# should autodetect system
|
|||
-SYS = UNIX
|
|||
-ifdef SystemRoot
|
|||
- SYS = WIN
|
|||
-else
|
|||
- UNAME := $(shell uname)
|
|||
- ifeq ($(UNAME), Darwin)
|
|||
- SYS = MAC
|
|||
- endif
|
|||
-endif
|
|||
-
|
|||
-CFLAGS=-Wall -O2
|
|||
-BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
|
|||
-LINKFLAGS=-lm -lpthread
|
|||
-ZLIB=zlib-1.2.8/libz.so.1.2.8
|
|||
-
|
|||
-ifeq ($(SYS), MAC)
|
|||
- GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300)
|
|||
- ifeq "$(GCC_GTEQ_43)" "1"
|
|||
- CFLAGS=-Wall -O2 -flax-vector-conversions
|
|||
- endif
|
|||
- BLASFLAGS=-framework Accelerate
|
|||
- LINKFLAGS=
|
|||
- ZLIB=zlib-1.2.8/libz.1.2.8.dylib
|
|||
-endif
|
|||
-
|
|||
-ifeq ($(SYS), WIN)
|
|||
-# Note that, unlike the Linux and Mac build processes, this STATICALLY links
|
|||
-# LAPACK, since we have not gotten around to trying dynamically-linked LAPACK
|
|||
-# on Windows.
|
|||
-# If you don't already have LAPACK built, you'll probably want to turn on
|
|||
-# NO_LAPACK.
|
|||
- BLASFLAGS=-L. lapack/liblapack.a -L. lapack/librefblas.a
|
|||
- LINKFLAGS=-lm -static-libgcc
|
|||
- ZLIB=zlib-1.2.8/libz.a
|
|||
-endif
|
|||
-
|
|||
-ifdef NO_LAPACK
|
|||
- BLASFLAGS=
|
|||
-endif
|
|||
+# CFLAGS=-Wall -O2
|
|||
+# BLASFLAGS=-lblas -llapack -latlas
|
|||
+LINKFLAGS=-lm -lpthread -lopenblas -llapack -latlas -lstdc++
|
|||
+ZLIB=-lz
|
|||
|
|||
ifeq ($(SYS), MAC) |
|||
GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300) |
|||
SRC = plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c |
|||
|
|||
+OBJ = plink.o plink_assoc.o plink_calc.o plink_cluster.o plink_cnv.o plink_common.o plink_data.o plink_dosage.o plink_family.o plink_filter.o plink_glm.o plink_help.o plink_homozyg.o plink_lasso.o plink_ld.o plink_matrix.o plink_misc.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o
|
|||
+
|
|||
# In the likely event that you are concurrently using PLINK 1.07, we suggest |
|||
# either renaming that binary to "plink1" or this one to "plink2". |
|||
|
|||
-plink: $(SRC)
|
|||
- g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
|
|||
+# plink: $(SRC)
|
|||
+# g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
|
|||
|
|||
-plinkw: $(SRC)
|
|||
+plink: $(SRC)
|
|||
g++ $(CFLAGS) $(SRC) -c |
|||
- gfortran -O2 $(OBJ) -o plink -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
|
|||
+ gfortran $(OBJ) -o plink2 $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
|
|||
+ # gfortran $^ -o plink2 -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
|
|||
diff --git a/dose2plink.c b/dose2plink.c
|
|||
index dc1f33a..ca2d31c 100644
|
|||
--- a/dose2plink.c
|
|||
+++ b/dose2plink.c
|
|||
@@ -96,7 +96,7 @@
|
|||
#endif |
|||
#endif |
|||
|
|||
-#include "zlib-1.2.8/zlib.h"
|
|||
+#include "zlib.h"
|
|||
|
|||
#ifdef __APPLE__ |
|||
#include <sys/sysctl.h> |
|||
diff --git a/pigz.c b/pigz.c
|
|||
index 6605925..3f4ca54 100644
|
|||
--- a/pigz.c
|
|||
+++ b/pigz.c
|
|||
@@ -303,7 +303,7 @@
|
|||
#include <stdio.h> |
|||
#include <stdlib.h> |
|||
#include <windows.h> |
|||
-#include "zlib-1.2.8/zlib.h"
|
|||
+#include "zlib.h"
|
|||
|
|||
void pigz_init(uint32_t setprocs) { |
|||
return; |
|||
@@ -383,7 +383,7 @@ void parallel_compress(char* out_fname, uint32_t do_append, uint32_t(* emitn)(ui
|
|||
# include <sys/pstat.h> |
|||
#endif |
|||
|
|||
-#include "zlib-1.2.8/zlib.h" /* deflateInit2(), deflateReset(), deflate(), */
|
|||
+#include "zlib.h" /* deflateInit2(), deflateReset(), deflate(), */
|
|||
/* deflateEnd(), deflateSetDictionary(), crc32(), |
|||
inflateBackInit(), inflateBack(), inflateBackEnd(), |
|||
Z_DEFAULT_COMPRESSION, Z_DEFAULT_STRATEGY, |
|||
diff --git a/plink_common.h b/plink_common.h
|
|||
index 5dd77e8..4da9371 100644
|
|||
--- a/plink_common.h
|
|||
+++ b/plink_common.h
|
|||
@@ -139,7 +139,7 @@
|
|||
|
|||
#endif // __LP64__ |
|||
|
|||
-#include "zlib-1.2.8/zlib.h"
|
|||
+#include "zlib.h"
|
|||
#include "SFMT.h" |
|||
|
|||
// 64MB of non-workspace memory guaranteed for now |
|||
Write
Preview
Loading…
Cancel
Save
Reference in new issue