svn commit: r376238 - in head/biology/tinker: . files
Kurt Jaeger
pi at FreeBSD.org
Sun Jan 4 15:21:15 UTC 2015
Author: pi
Date: Sun Jan 4 15:21:12 2015
New Revision: 376238
URL: https://svnweb.freebsd.org/changeset/ports/376238
QAT: https://qat.redports.org/buildarchive/r376238/
Log:
biology/tinker: 6.2.6 -> 7.0.1
PR: 196376
Submitted by: Nikola Kolev <koue at chaosophia.net>
Modified:
head/biology/tinker/Makefile
head/biology/tinker/distinfo
head/biology/tinker/files/patch-bench__bench4.run
head/biology/tinker/files/patch-bench__bench5.run
head/biology/tinker/files/patch-make__Makefile
head/biology/tinker/pkg-plist
Modified: head/biology/tinker/Makefile
==============================================================================
--- head/biology/tinker/Makefile Sun Jan 4 15:05:06 2015 (r376237)
+++ head/biology/tinker/Makefile Sun Jan 4 15:21:12 2015 (r376238)
@@ -2,8 +2,7 @@
# $FreeBSD$
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)
Modified: head/biology/tinker/distinfo
==============================================================================
--- head/biology/tinker/distinfo Sun Jan 4 15:05:06 2015 (r376237)
+++ head/biology/tinker/distinfo Sun Jan 4 15:21:12 2015 (r376238)
@@ -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
Modified: head/biology/tinker/files/patch-bench__bench4.run
==============================================================================
--- head/biology/tinker/files/patch-bench__bench4.run Sun Jan 4 15:05:06 2015 (r376237)
+++ head/biology/tinker/files/patch-bench__bench4.run Sun Jan 4 15:21:12 2015 (r376238)
@@ -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
Modified: head/biology/tinker/files/patch-bench__bench5.run
==============================================================================
--- head/biology/tinker/files/patch-bench__bench5.run Sun Jan 4 15:05:06 2015 (r376237)
+++ head/biology/tinker/files/patch-bench__bench5.run Sun Jan 4 15:21:12 2015 (r376238)
@@ -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
Modified: head/biology/tinker/files/patch-make__Makefile
==============================================================================
--- head/biology/tinker/files/patch-make__Makefile Sun Jan 4 15:05:06 2015 (r376237)
+++ head/biology/tinker/files/patch-make__Makefile Sun Jan 4 15:21:12 2015 (r376238)
@@ -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
Modified: head/biology/tinker/pkg-plist
==============================================================================
--- head/biology/tinker/pkg-plist Sun Jan 4 15:05:06 2015 (r376237)
+++ head/biology/tinker/pkg-plist Sun Jan 4 15:21:12 2015 (r376238)
@@ -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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