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spack/var/spack/repos/builtin/packages/mpiblast/mpiBLAST-1.6.0-patch-110806
Audrey Thoma ad8c60239f mpiblast: new package (#5106)
2017-08-16 10:48:39 -05:00

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diff -rwu mpiblast-1.6.0/ncbi/corelib/ncbienv.c mpiblast-1.6.0-patched/ncbi/corelib/ncbienv.c
--- mpiblast-1.6.0/ncbi/corelib/ncbienv.c 2009-11-22 01:17:48.000000000 -0500
+++ mpiblast-1.6.0-patched/ncbi/corelib/ncbienv.c 2011-08-06 17:10:08.000000000 -0400
@@ -1932,7 +1932,7 @@
static char **targv = NULL;
-#if defined(WIN_MAC)
+#if defined(WIN_MAC) || defined(OS_UNIX_DARWIN)
static FSSpec apFileSpec;
static Str255 apName;
static Handle apParam;
@@ -2047,7 +2047,7 @@
}
}
#endif /* defined(OS_UNIX_DARWIN) */
-#endif /* defined(WIN_MAC) */
+#endif /* defined(WIN_MAC) || defined(OS_UNIX_DARWIN) */
#if defined(OS_MSWIN) || defined(OS_VMS)
diff -rwu mpiblast-1.6.0/ncbi/make/makedis.csh mpiblast-1.6.0-patched/ncbi/make/makedis.csh
--- mpiblast-1.6.0/ncbi/make/makedis.csh 2010-06-28 21:04:36.000000000 -0400
+++ mpiblast-1.6.0-patched/ncbi/make/makedis.csh 2011-08-06 17:06:42.000000000 -0400
@@ -1,6 +1,6 @@
#!/bin/csh -f
#
-# $Id: makedis.csh 148594 2008-12-30 15:11:36Z ucko $
+# $Id: makedis.csh 179886 2010-01-04 17:28:02Z ucko $
#
## PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
@@ -54,7 +54,7 @@
endif
ls -l $tar_file
- tar xvf $tar_file
+ tar xf $tar_file
else
# make sure that ncbi/build directory exists
if ( ! -d "ncbi/build" ) then
@@ -74,6 +74,7 @@
set HAVE_MAC=0
#we will try to build OpenGL version of vibrant
set HAVE_OGL=1
+set MPBL_HAVE_MAC=0
switch ($os)
case SunOS:
@@ -164,7 +165,7 @@
gcc -v
switch (`uname -m`)
case "ia64":
- if (-e `which ecc`) then
+ if (-e `which icc`) then
set platform=linux_ecc
else
set platform=linux
@@ -253,7 +254,11 @@
endif
endif
set HAVE_MOTIF=0
- set HAVE_MAC=1
+#MPIBLAST <<<
+# set HAVE_MAC=1
+ set MPBL_HAVE_MAC=1
+ set HAVE_MAC=0
+#MPIBLAST
breaksw
case NetBSD:
set platform=netbsd
@@ -319,6 +324,7 @@
goto BADPLATFORM
endif
+
set noglob
# take the file $NCBI_DOT_MK and convert it to be suitable for csh eval:
# (1) remove comments at the beginning of the lines
@@ -328,6 +334,7 @@
eval `sed -e 's/^ *#.*//g' -e 's/\$(\([a-zA-Z_]*\))/\${\1}/g' -e 's/ *= */=/g' -e 's/^\([^=]*\)=\(.*\)$/setenv \1 "\2";/' < $NCBI_DOT_MK`
unset noglob
+
# disable assert() unless ENABLE_ASSERT is set
if ("$?ENABLE_ASSERT" == 0) then
set NCBI_OPTFLAG="-DNDEBUG $NCBI_OPTFLAG"
@@ -441,13 +448,23 @@
set NET_VIB=(VIB=\"blastcl3 taxblast idfetch bl2seq asn2gb tbl2asn gene2xml $NONVIBWWWBLAST \")
endif
+# MPIBLAST <<<<<
+if ("$MPBL_HAVE_MAC" == 1) then
+set CMD='make $MFLG \
+ CFLAGS1=\"-I/Developer/Headers/FlatCarbon $NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE $PNG_INCLUDE\" \
+ LDFLAGS1=\"$NCBI_LDFLAGS1\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
+ SHELL=\"$NCBI_MAKE_SHELL\" LCL=\"$NCBI_DEFAULT_LCL\" \
+ RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $ALL_VIB all'
+else
set CMD='make $MFLG \
CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE $PNG_INCLUDE\" \
LDFLAGS1=\"$NCBI_LDFLAGS1\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
SHELL=\"$NCBI_MAKE_SHELL\" LCL=\"$NCBI_DEFAULT_LCL\" \
RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $ALL_VIB all'
+endif
eval echo $CMD
eval echo $CMD | sh
+# MPIBLAST >>>>>
set make_stat = $status
@@ -463,12 +480,18 @@
endif
# MPIBLAST <<<<<
-
+if ("$MPBL_HAVE_MAC" == 1) then
set CMD='make $MFLG -f makempiblast.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \
LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\"'
+else
+set CMD='make $MFLG -f makempiblast.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \
+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
+ LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\"'
+endif
eval echo $CMD
eval echo $CMD | sh
+if ($status != 0) exit $status
if( "$platform" == "bluegenel" || "$platform" == "bluegenep" ) then
exit 0
@@ -476,7 +499,7 @@
# MPIBLAST >>>>>
set CMD='make $MFLG -f makedemo.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \
- LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $DEMO_VIB'
eval echo $CMD
eval echo $CMD | sh
@@ -495,7 +518,7 @@
set CMD='make $MFLG -f makedemo.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \
- LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" \
THREAD_OBJ=$NCBI_THREAD_OBJ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
$DEMO_VIB $mtapps'
diff -rwu mpiblast-1.6.0/src/Makefile.am mpiblast-1.6.0-patched/src/Makefile.am
--- mpiblast-1.6.0/src/Makefile.am 2009-11-22 01:17:48.000000000 -0500
+++ mpiblast-1.6.0-patched/src/Makefile.am 2011-08-06 17:06:42.000000000 -0400
@@ -2,7 +2,7 @@
-D_LARGEFILE64_SOURCE -DMPIBLAST_PIO \
-I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/ $(MPE_INCS) \
-I@CONFIG_NCBIDIR@/corelib/
-AM_CXXFLAGS = -DMPICH_IGNORE_CXX_SEEK -DINSTALL_PREFIX="\"@prefix@\"" \
+AM_CXXFLAGS = -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX -DINSTALL_PREFIX="\"@prefix@\"" \
@COMPILE_FLAGS@ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE \
-I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/ $(MPE_INCS) \
-I@CONFIG_NCBIDIR@/corelib/
@@ -31,7 +31,7 @@
@CONFIG_NCBIDIR@/build/blast_hooks.o -lmyncbitool -lblastcompadj -lmyncbiobj \
-lmyncbi -L. -L@CONFIG_NCBIDIR@/lib/ $(MPE_LIBS) -lm @LINK_FLAGS@
mpiblast_DEPENDENCIES = @GETOPT_LONG_SYSTEM@
-mpiblast_CPPFLAGS = -DUSING_MPI -DMPICH_IGNORE_CXX_SEEK
+mpiblast_CPPFLAGS = -DUSING_MPI -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX
mpiformatdb_SOURCES = mpiformatdb.cpp mpiblast_config.cpp mpiblast_config.hpp \
file_util.cpp file_util.hpp mpiblast_util.cpp mpiblast_util.hpp \
diff -rwu mpiblast-1.6.0/src/pio_intercept.h mpiblast-1.6.0-patched/src/pio_intercept.h
--- mpiblast-1.6.0/src/pio_intercept.h 2009-11-22 01:17:48.000000000 -0500
+++ mpiblast-1.6.0-patched/src/pio_intercept.h 2011-08-06 17:06:42.000000000 -0400
@@ -60,7 +60,7 @@
#include <txalign.h>
/* marcros are duplicated in ncbi files to avoid header file conflict */
-#define CHECK_NULPTR(x) if(x==NULL) fprintf(stderr, "%s, line%d: cannot allocate enough memory\n", __FILE__, __LINE__);
+#define CHECK_NULPTR(x) if(x==NULL) { perror("Cannot allocate enough memory:"); exit(-1); }
#ifndef NO_MPI
typedef struct _output_record {
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