Attachment 151110 Details for Bug 196376 – tinker 7.0.1 patch

[patch] tinker 7.0.1 patch

tinker-7.0.1.patch (text/plain), 10.02 KB, created by Nikola Kolev on 2014-12-30 09:38:03 UTC

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Creator: Nikola Kolev

Created: 2014-12-30 09:38:03 UTC

Size: 10.02 KB

patch

obsolete

>diff -rupN tinker.orig/Makefile tinker/Makefile
>--- tinker.orig/Makefile	2014-12-29 10:22:50.000000000 +0200
>+++ tinker/Makefile	2014-12-29 10:20:59.000000000 +0200
>@@ -1,9 +1,8 @@
> # Created by: Glenn Johnson
>-# $FreeBSD: head/biology/tinker/Makefile 367888 2014-09-10 20:50:31Z gerald $
>+# $FreeBSD$
> 
> PORTNAME=	tinker
>-PORTVERSION=	6.2.6
>-PORTREVISION=	6
>+PORTVERSION=	7.0.1
> CATEGORIES=	biology
> MASTER_SITES=	http://dasher.wustl.edu/tinker/downloads/
> 
>@@ -27,9 +26,11 @@ INSTALL_WRKSRC=	${WRKSRC}/source
> USES=		fortran
> MAKE_ENV=	HAVE_G2C=yes
> MAKEFILE=	${WRKSRC}/make/Makefile
>-ALL_TARGET=	all listing
>+ALL_TARGET=	all
> INSTALL_TARGET=	rename
> 
>+MAKE_JOBS_UNSAFE=yes
>+
> SUB_FILES=	pkg-message
> 
> .include <bsd.port.options.mk>
>@@ -49,10 +50,9 @@ pre-build:
> 
> post-install:
> 	${MKDIR} ${STAGEDIR}${DATADIR}
>-	(cd ${INSTALL_WRKSRC} && ${INSTALL_DATA} tinker.txt ${STAGEDIR}${DATADIR})
> 	${MKDIR} ${STAGEDIR}${DATADIR}/bench
> 	(cd ${WRKSRC}/bench && ${INSTALL_DATA} \
>-		0README *.dyn0 *.log *.key *.run *.xyz results* \
>+		0README *.log *.key *.run *.xyz results* \
> 		${STAGEDIR}${DATADIR}/bench)
> 	${MKDIR} ${STAGEDIR}${DATADIR}/params
> 	(cd ${WRKSRC}/params && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/params)
>diff -rupN tinker.orig/distinfo tinker/distinfo
>--- tinker.orig/distinfo	2014-12-29 10:22:50.000000000 +0200
>+++ tinker/distinfo	2014-12-29 10:20:59.000000000 +0200
>@@ -1,2 +1,2 @@
>-SHA256 (tinker-6.2.6.tar.gz) = a6eb5cb31b7e93a1f2d323ca73e45f16291763a3e0faa3615a3219e6f9814277
>-SIZE (tinker-6.2.6.tar.gz) = 20181780
>+SHA256 (tinker-7.0.1.tar.gz) = 5c68c097e2843a497224ee58833fb0a816a99529426be612f4dcc5eebd797b1c
>+SIZE (tinker-7.0.1.tar.gz) = 28384106
>diff -rupN tinker.orig/files/patch-bench__bench4.run tinker/files/patch-bench__bench4.run
>--- tinker.orig/files/patch-bench__bench4.run	2014-12-29 10:22:50.000000000 +0200
>+++ tinker/files/patch-bench__bench4.run	2014-12-29 10:20:59.000000000 +0200
>@@ -1,7 +1,5 @@
>---- bench/bench4.run.orig	Tue Jul 24 14:02:20 2001
>-+++ bench/bench4.run	Wed Sep  5 14:02:17 2001
>-@@ -1,3 +1,3 @@
>- cp bench4.dyn0 bench4.dyn
>+--- bench/bench4.run.orig	2014-12-16 05:17:53.000000000 +0200
>++++ bench/bench4.run	2014-12-28 18:56:02.000000000 +0200
>+@@ -1 +1 @@
> -time ../bin/dynamic bench4 1000 1.0 10.0 2 298.0
> +time dynamic bench4 1000 1.0 10.0 2 298.0
>- rm bench4.dyn
>diff -rupN tinker.orig/files/patch-bench__bench5.run tinker/files/patch-bench__bench5.run
>--- tinker.orig/files/patch-bench__bench5.run	2014-12-29 10:22:50.000000000 +0200
>+++ tinker/files/patch-bench__bench5.run	2014-12-29 10:20:59.000000000 +0200
>@@ -1,7 +1,5 @@
>---- bench/bench5.run.orig	2010-08-25 00:58:15.000000000 +0400
>-+++ bench/bench5.run	2011-01-26 23:35:18.000000000 +0300
>-@@ -1,3 +1,3 @@
>- cp bench5.dyn0 bench5.dyn
>+--- bench/bench5.run.orig	2014-12-16 05:17:53.000000000 +0200
>++++ bench/bench5.run	2014-12-28 18:58:45.000000000 +0200
>+@@ -1 +1 @@
> -time ../bin/dynamic bench5 1000 1.0 10.0 2 298.0
> +time dynamic bench5 1000 1.0 10.0 2 298.0
>- rm bench5.dyn
>diff -rupN tinker.orig/files/patch-make__Makefile tinker/files/patch-make__Makefile
>--- tinker.orig/files/patch-make__Makefile	2014-12-29 10:22:50.000000000 +0200
>+++ tinker/files/patch-make__Makefile	2014-12-30 10:32:27.000000000 +0200
>@@ -1,10 +1,10 @@
>---- make/Makefile.orig	2013-07-14 11:23:53.000000000 +0900
>-+++ make/Makefile	2014-03-14 16:59:17.000000000 +0900
>-@@ -30,9 +30,9 @@
>+--- make/Makefile.orig	2014-12-16 05:18:02.000000000 +0200
>++++ make/Makefile	2014-12-30 10:29:50.000000000 +0200
>+@@ -33,9 +33,9 @@
>+ ##  BINDIR       Hard Copies of TINKER Executables
>  ##  LINKDIR      Linked Copies of TINKER Executables
>- ##
>  
>--TINKERDIR = /Users/ponder/tinker
>+-TINKERDIR = $(HOME)/tinker
> -BINDIR = $(TINKERDIR)/bin
> -LINKDIR = /usr/local/bin
> +TINKERDIR = ${WRKDIR}
>@@ -13,68 +13,83 @@
>  
>  ####################################################################
>  ##  Known Machine Types; Uncomment One of the Following Sections  ##
>-@@ -40,6 +40,20 @@
>- ####################################################################
>+@@ -46,26 +46,26 @@ LINKDIR = /usr/local/bin
>+ ##  CPU Type: Intel x86 Compatible
>+ ##  Compiler: GNU gfortran
>  
>- ##
>-+##  Machine:  IntelPC / FreeBSD
>-+##  CPU Type: Intel, AMD, Cyrix
>-+##  Oper Sys: FreeBSD 4.2
>-+##  Compiler: f77 , aka g77
>-+##
>-+
>+-#F77 = gfortran
>+-#LIBS =
>+-#F77FLAGS = -c
>+-#OPTFLAGS = -O3 -ffast-math
>+-#LIBFLAGS = -crusv
>+-#RANLIB = ranlib -c
>+-#LINKFLAGS = $(OPTFLAGS) -static-libgcc
> +F77 = ${FC}
>-+LIBS = 
>++LIBS =
> +F77FLAGS = -c ${FFLAGS}
>-+LINKFLAGS = ${LDFLAGS}
> +OPTFLAGS = 
> +LIBFLAGS = -rcuv
>-+
>-+##
>- ##  Machine:  Generic Linux
>++RANLIB = ranlib
>++LINKFLAGS = ${LDFLAGS}
>+ 
>+ ##  Machine:  Generic Linux or Macintosh
>  ##  CPU Type: Intel x86 Compatible
>- ##  Oper Sys: Fedora Core
>-@@ -104,12 +118,12 @@
>+ ##  Compiler: GNU gfortran
>  ##  Parallel: OpenMP
>- ##
>  
>--F77 = /opt/intel/bin/ifort
>--LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_omp -lfftw3
>--F77FLAGS = -c -axSSSE3 -assume cc_omp
>--OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp
>+-F77 = gfortran
>+-LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_threads -lfftw3
>+-F77FLAGS = -c
>+-OPTFLAGS = -O3 -ffast-math -fopenmp
> -LIBFLAGS = -crusv
>--LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4
>-+#F77 = /opt/intel/bin/ifort
>-+#LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_omp -lfftw3
>-+#F77FLAGS = -c -axSSSE3 -assume cc_omp
>-+#OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp
>+-RANLIB = ranlib -c
>+-LINKFLAGS = $(OPTFLAGS) -static-libgcc
>++#F77 = gfortran
>++#LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_threads -lfftw3
>++#F77FLAGS = -c
>++#OPTFLAGS = -O3 -ffast-math -fopenmp
> +#LIBFLAGS = -crusv
>-+#LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4
>++#RANLIB = ranlib -c
>++#LINKFLAGS = $(OPTFLAGS) -static-libgcc
>+ 
>+ ##  Machine:  Generic Linux
>+ ##  CPU Type: Intel x86 Compatible (also AMD)
>+@@ -106,7 +106,7 @@ LINKFLAGS = $(OPTFLAGS) -static-libgcc
>+ #LIBFLAGS = -crusv
>+ #RANLIB = ranlib -c
>+ #LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.6 \
>+-             -Wl,-stack_size,0x10000000
>++#             -Wl,-stack_size,0x10000000
>  
>- ##
>  ##  Machine:  Macintosh
>-@@ -597,14 +611,13 @@
>+ ##  CPU Type: Intel Xeon
>+@@ -710,93 +710,88 @@ EXEFILES = alchemy.x \
>             xyzpdb.x \
>             xyzsybyl.x
>  
> -%.o: %.f
> -	${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ 
>-+.SUFFIXES: .x
>- 
>+-
> -%.o: %.c
> -	${CC} ${CFLAGS} ${INCLUDEDIR} ${OPTFLAGS} $<
>-+.f.o:
>-+	${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ 
>++.SUFFIXES: .x
>  
> -%.x: %.o libtinker.a
> -	${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@
>++.f.o:
>++	${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ 
>+ 
>+-all:
>+-	${EXEFILES}
> +.o.x: libtinker.a
> +	${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS}
>  
>- all:	${EXEFILES}
>+-install:
>+-	rename
>++all:	${EXEFILES}
>  
>-@@ -612,74 +625,74 @@
>- 	rm -f *.o *.a *.x
>+ clean:
>+ 	rm -f *.o *.mod *.a *.x
>  
>  listing:
> -	cat *.i *.f *.c > tinker.txt
>@@ -211,7 +226,7 @@
>  	rm -f $(LINKDIR)/anneal
>  	rm -f $(LINKDIR)/archive
>  	rm -f $(LINKDIR)/bar
>-@@ -742,7 +755,7 @@
>+@@ -859,7 +854,7 @@ remove_links:
>  
>  create_links:
>  	ln -s $(BINDIR)/alchemy    $(LINKDIR)/alchemy
>diff -rupN tinker.orig/pkg-plist tinker/pkg-plist
>--- tinker.orig/pkg-plist	2014-12-29 10:22:50.000000000 +0200
>+++ tinker/pkg-plist	2014-12-29 10:20:59.000000000 +0200
>@@ -162,8 +162,10 @@ bin/xyzsybyl
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.pdb
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.seq
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.xyz
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.key
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.xyz
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin2.key
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin2.xyz
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin3.key
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin3.xyz
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.int
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.key
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.xyz
>@@ -398,6 +400,8 @@ bin/xyzsybyl
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4f.xyz
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4p.key
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4p.xyz
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4pbox.key
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4pbox.xyz
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip5p.key
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip5p.xyz
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/trpcage.key
>@@ -451,14 +455,13 @@ bin/xyzsybyl
> %%DATADIR%%/bench/bench2.run
> %%DATADIR%%/bench/bench2.xyz
> %%DATADIR%%/bench/bench3.key
>+%%DATADIR%%/bench/bench3.log
> %%DATADIR%%/bench/bench3.run
> %%DATADIR%%/bench/bench3.xyz
>-%%DATADIR%%/bench/bench4.dyn0
> %%DATADIR%%/bench/bench4.key
> %%DATADIR%%/bench/bench4.log
> %%DATADIR%%/bench/bench4.run
> %%DATADIR%%/bench/bench4.xyz
>-%%DATADIR%%/bench/bench5.dyn0
> %%DATADIR%%/bench/bench5.key
> %%DATADIR%%/bench/bench5.log
> %%DATADIR%%/bench/bench5.run
>@@ -471,6 +474,14 @@ bin/xyzsybyl
> %%DATADIR%%/bench/bench7.log
> %%DATADIR%%/bench/bench7.run
> %%DATADIR%%/bench/bench7.xyz
>+%%DATADIR%%/bench/bench8.key
>+%%DATADIR%%/bench/bench8.log
>+%%DATADIR%%/bench/bench8.run
>+%%DATADIR%%/bench/bench8.xyz
>+%%DATADIR%%/bench/bench9.key
>+%%DATADIR%%/bench/bench9.log
>+%%DATADIR%%/bench/bench9.run
>+%%DATADIR%%/bench/bench9.xyz
> %%DATADIR%%/bench/results-2.3
> %%DATADIR%%/bench/results-2.4
> %%DATADIR%%/bench/results-2.9
>@@ -489,6 +500,8 @@ bin/xyzsybyl
> %%DATADIR%%/bench/results-5.1
> %%DATADIR%%/bench/results-6.0
> %%DATADIR%%/bench/results-6.2
>+%%DATADIR%%/bench/results-6.3
>+%%DATADIR%%/bench/results-7.0
> %%DATADIR%%/params/0README
> %%DATADIR%%/params/amber94.prm
> %%DATADIR%%/params/amber96.prm
>@@ -516,7 +529,8 @@ bin/xyzsybyl
> %%DATADIR%%/params/smoothaa.prm
> %%DATADIR%%/params/smoothua.prm
> %%DATADIR%%/params/tiny.prm
>-%%DATADIR%%/params/water.prm
>+%%DATADIR%%/params/water03.prm
>+%%DATADIR%%/params/water14.prm
> %%DATADIR%%/test/0README
> %%DATADIR%%/test/anion.dat
> %%DATADIR%%/test/anion.dyn0
>@@ -593,6 +607,11 @@ bin/xyzsybyl
> %%DATADIR%%/test/ifabp.log
> %%DATADIR%%/test/ifabp.run
> %%DATADIR%%/test/ifabp.xyz
>+%%DATADIR%%/test/nitrogen.arc
>+%%DATADIR%%/test/nitrogen.key
>+%%DATADIR%%/test/nitrogen.log
>+%%DATADIR%%/test/nitrogen.run
>+%%DATADIR%%/test/nitrogen.xyz
> %%DATADIR%%/test/salt.cell
> %%DATADIR%%/test/salt.key
> %%DATADIR%%/test/salt.log
>@@ -606,4 +625,3 @@ bin/xyzsybyl
> %%DATADIR%%/test/water.pot
> %%DATADIR%%/test/water.run
> %%DATADIR%%/test/water.xyz
>-%%DATADIR%%/tinker.txt

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Attachments on bug 196376: 151110