From: "Alexey Shvetsov" <alexxy@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/
Date: Mon, 7 Mar 2011 01:49:08 +0000 (UTC) [thread overview]
Message-ID: <bdbd22b46c3db66d057fbc4e3cbb8f9ea95349ea.alexxy@gentoo> (raw)
commit: bdbd22b46c3db66d057fbc4e3cbb8f9ea95349ea
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 7 00:50:20 2011 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Mar 7 00:50:20 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bdbd22b4
More updates and fixes
(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key F82F92E6)
---
sci-chemistry/ambertools/ambertools-1.4.ebuild | 24 +-
sci-chemistry/ambertools/files/1.4-Makefile.patch | 30 --
.../ambertools/files/1.4-configure-fftw.patch | 86 ------
sci-chemistry/ambertools/files/1.4-configure.patch | 27 --
.../ambertools/files/ambertools-1.4-gentoo.patch | 289 ++++++++++++++++++++
5 files changed, 301 insertions(+), 155 deletions(-)
diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index 2ba836c..d5fb35b 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -15,12 +15,13 @@ SRC_URI="AmberTools-${PV}.tar.bz2"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="mpi openmp lapack X"
+IUSE="mpi openmp X"
RESTRICT="fetch"
RDEPEND="
virtual/cblas
virtual/lapack
+ sci-libs/arpack
sci-libs/cifparse-obj
sci-chemistry/mopac7
sci-libs/netcdf
@@ -51,34 +52,33 @@ pkg_setup() {
}
src_prepare() {
- epatch "${FILESDIR}/${PV}-configure.patch"
- epatch "${FILESDIR}/${PV}-configure-fftw.patch"
- epatch "${FILESDIR}/${PV}-Makefile.patch"
+ epatch "${FILESDIR}/${P}-gentoo.patch"
cd AmberTools/src
- rm -r byacc c9x-complex cifparse netcdf reduce ucpp-1.3 || die
+ rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die
}
src_configure() {
cd AmberTools/src
- sed -e "s:\\\\\$(LIBDIR)/arpack.a:/usr/$(get_libdir)/libarpack.a:g" \
- -e "s:\\\\\$(LIBDIR)/lapack.a:/usr/$(get_libdir)/libclapack.a:g" \
- -e "s:\\\\\$(LIBDIR)/blas.a:/usr/$(get_libdir)/libcblas.a:g" \
+ sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+ -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
+ -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+ -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+ -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
-e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \
-e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \
-e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \
-e "s:fc=g77:fc=${FORTRANC}:g" \
- -e "s:NETCDFLIB=\$netcdflib:NETCDFLIB=/usr/$(get_libdir)/libnetcdf.a:g" \
+ -e "s:NETCDFLIB=\$netcdflib:NETCDFLIB=$(pkg-config netcdf --libs):g" \
-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
-e "s:-O3::g" \
-i configure
-# -e "s:\\\\\$(LIBDIR)/f2c.a:/usr/$(get_libdir)/libf2c.a:g" \
local myconf
use X || myconf="${myconf} -noX11"
- for x in mpi openmp lapack; do
- use ${x} && myconf="${myconf/lapack/scalapack} -${x}"
+ for x in mpi openmp; do
+ use ${x} && myconf="${myconf} -${x}"
done
./configure \
diff --git a/sci-chemistry/ambertools/files/1.4-Makefile.patch b/sci-chemistry/ambertools/files/1.4-Makefile.patch
deleted file mode 100644
index 7a893e6..0000000
--- a/sci-chemistry/ambertools/files/1.4-Makefile.patch
+++ /dev/null
@@ -1,30 +0,0 @@
---- amber11/AmberTools/src/Makefile.orig 2011-03-07 00:08:41.000000000 +0300
-+++ amber11/AmberTools/src/Makefile 2011-03-07 00:10:01.000000000 +0300
-@@ -11,12 +11,12 @@
- serial: configured_serial $(NETCDFLIB)
- @echo "Starting installation of ${AMBERTOOLS} serial at `date`".
- # utility routines and libraries:
-- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
-- (cd byacc && $(MAKE) install )
-- (cd arpack && $(MAKE) install );
-- (cd lapack && $(MAKE) $(LAPACK) )
-- (cd blas && $(MAKE) $(BLAS) )
-- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
-+# (cd ucpp-1.3 && $(MAKE) $(UCPP) )
-+# (cd byacc && $(MAKE) install )
-+# (cd arpack && $(MAKE) install );
-+# (cd lapack && $(MAKE) $(LAPACK) )
-+# (cd blas && $(MAKE) $(BLAS) )
-+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
- (cd etc && $(MAKE) install )
- (cd chamber && $(MAKE) install )
- (cd pbsa && $(MAKE) install )
-@@ -30,7 +30,7 @@
- (cd ptraj && $(MAKE) install )
-
- # miscellaneous:
-- (cd reduce && $(MAKE) install )
-+# (cd reduce && $(MAKE) install )
-
- # leap and gleap:
- (cd leap && $(MAKE) install )
diff --git a/sci-chemistry/ambertools/files/1.4-configure-fftw.patch b/sci-chemistry/ambertools/files/1.4-configure-fftw.patch
deleted file mode 100644
index b91f0fc..0000000
--- a/sci-chemistry/ambertools/files/1.4-configure-fftw.patch
+++ /dev/null
@@ -1,86 +0,0 @@
---- amber11/AmberTools/src/configure.orig 2011-03-07 00:28:56.000000000 +0300
-+++ amber11/AmberTools/src/configure 2011-03-07 00:30:55.000000000 +0300
-@@ -1241,24 +1241,24 @@
- #--------------------------------------------------------------------------
- # Configure fftw-3.2.2:
- #--------------------------------------------------------------------------
-- if [ "$mdgx" = 'yes' ]; then
-- mdgxflag="--prefix=$AMBERHOME --disable-fortran"
-- echo
-- echo "Configuring fftw-3.2.2; (may be time-consuming)"
-- echo
-- cd fftw-3.2.2 && \
-- env CC="$cc" CFLAGS="$cflags" ./configure $mdgxflag \
-- > ../fftw3_config.log 2>&1
-- ncerror=$?
-- if [ $ncerror -gt 0 ]; then
-- echo " Error: fftw configure returned $ncerror"
-- echo " fftw configure failed! Check the fftw3_config.log file."
-- exit 1
-- else
-- echo " fftw-3.2.2 configure succeeded."
-- fi
-- cd ..
-- fi
-+ #if [ "$mdgx" = 'yes' ]; then
-+ # mdgxflag="--prefix=$AMBERHOME --disable-fortran"
-+ # echo
-+ # echo "Configuring fftw-3.2.2; (may be time-consuming)"
-+ # echo
-+ # cd fftw-3.2.2 && \
-+ # env CC="$cc" CFLAGS="$cflags" ./configure $mdgxflag \
-+ # > ../fftw3_config.log 2>&1
-+ # ncerror=$?
-+ # if [ $ncerror -gt 0 ]; then
-+ # echo " Error: fftw configure returned $ncerror"
-+ # echo " fftw configure failed! Check the fftw3_config.log file."
-+ # exit 1
-+ # else
-+ # echo " fftw-3.2.2 configure succeeded."
-+ # fi
-+ # cd ..
-+ #fi
-
- #--------------------------------------------------------------------------
- # Set up MPI 3D-RISM in NAB and SANDER
-@@ -1307,23 +1307,23 @@
- echo
- echo "Configuring fftw-2.1.5; (may be time-consuming)"
- echo
-- cd fftw-2.1.5
-- if [ "$mpi" = 'yes' ]; then
-- ./configure $rismflag --enable-mpi CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
-- > ../fftw2_config.log 2>&1
-- else
-- ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
-- > ../fftw2_config.log 2>&1
-- fi
-- ncerror=$?
-- if [ $ncerror -gt 0 ]; then
-- echo " Error: fftw configure returned $ncerror"
-- echo " fftw configure failed! Check the fftw2_config.log file."
-- exit 1
-- else
-- echo " fftw-2.1.5 configure succeeded."
-- fi
-- cd ..
-+ # cd fftw-2.1.5
-+ # if [ "$mpi" = 'yes' ]; then
-+ # ./configure $rismflag --enable-mpi CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
-+ # > ../fftw2_config.log 2>&1
-+ # else
-+ # ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
-+ # > ../fftw2_config.log 2>&1
-+ # fi
-+ # ncerror=$?
-+ # if [ $ncerror -gt 0 ]; then
-+ # echo " Error: fftw configure returned $ncerror"
-+ # echo " fftw configure failed! Check the fftw2_config.log file."
-+ # exit 1
-+ # else
-+ # echo " fftw-2.1.5 configure succeeded."
-+ # fi
-+ # cd ..
- flibs_fftw2="\$(LIBDIR)/libdrfftw.a \$(LIBDIR)/libdfftw.a"
- if [ "$mpi" = 'yes' ]; then
- flibs_fftw2="\$(LIBDIR)/libdrfftw_mpi.a \$(LIBDIR)/libdfftw_mpi.a $flibs_fftw2"
diff --git a/sci-chemistry/ambertools/files/1.4-configure.patch b/sci-chemistry/ambertools/files/1.4-configure.patch
deleted file mode 100644
index ce5377e..0000000
--- a/sci-chemistry/ambertools/files/1.4-configure.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- amber11/AmberTools/src/configure.orig 2011-03-07 00:05:24.000000000 +0300
-+++ amber11/AmberTools/src/configure 2011-03-07 00:07:59.000000000 +0300
-@@ -288,11 +288,11 @@
- mpi_flag=
- lex=flex
- flibs_mkl=
--lapack=install
--blas=install
-+lapack=skip
-+blas=skip
- f2c=skip
--ucpp=install
--cpp="\$(BINDIR)/ucpp -l"
-+ucpp=skip
-+cpp="\$(EPREFIX)/usr/bin/ucpp -l"
-
- #-----------------------------------
- # skip building of sleap?
-@@ -1451,7 +1451,7 @@
- LDFLAGS=$ldflags \$(AMBERBUILDFLAGS)
-
- LEX= $lex
--YACC= \$(BINDIR)/yacc
-+YACC= \$(EPREFIX)/usr/bin/yacc
- AR= ar rv
- M4= $m4
- RANLIB=$ranlib
diff --git a/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch
new file mode 100644
index 0000000..c067928
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch
@@ -0,0 +1,289 @@
+diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure
+--- amber11.orig/AmberTools/src/configure 2010-04-23 18:17:17.000000000 +0400
++++ amber11/AmberTools/src/configure 2011-03-07 03:39:14.000000000 +0300
+@@ -288,11 +288,11 @@
+ mpi_flag=
+ lex=flex
+ flibs_mkl=
+-lapack=install
+-blas=install
++lapack=skip
++blas=skip
+ f2c=skip
+-ucpp=install
+-cpp="\$(BINDIR)/ucpp -l"
++ucpp=skip
++cpp="\$(EPREFIX)/usr/bin/ucpp -l"
+
+ #-----------------------------------
+ # skip building of sleap?
+@@ -1241,24 +1241,24 @@
+ #--------------------------------------------------------------------------
+ # Configure fftw-3.2.2:
+ #--------------------------------------------------------------------------
+- if [ "$mdgx" = 'yes' ]; then
+- mdgxflag="--prefix=$AMBERHOME --disable-fortran"
+- echo
+- echo "Configuring fftw-3.2.2; (may be time-consuming)"
+- echo
+- cd fftw-3.2.2 && \
+- env CC="$cc" CFLAGS="$cflags" ./configure $mdgxflag \
+- > ../fftw3_config.log 2>&1
+- ncerror=$?
+- if [ $ncerror -gt 0 ]; then
+- echo " Error: fftw configure returned $ncerror"
+- echo " fftw configure failed! Check the fftw3_config.log file."
+- exit 1
+- else
+- echo " fftw-3.2.2 configure succeeded."
+- fi
+- cd ..
+- fi
++ #if [ "$mdgx" = 'yes' ]; then
++ # mdgxflag="--prefix=$AMBERHOME --disable-fortran"
++ # echo
++ # echo "Configuring fftw-3.2.2; (may be time-consuming)"
++ # echo
++ # cd fftw-3.2.2 && \
++ # env CC="$cc" CFLAGS="$cflags" ./configure $mdgxflag \
++ # > ../fftw3_config.log 2>&1
++ # ncerror=$?
++ # if [ $ncerror -gt 0 ]; then
++ # echo " Error: fftw configure returned $ncerror"
++ # echo " fftw configure failed! Check the fftw3_config.log file."
++ # exit 1
++ # else
++ # echo " fftw-3.2.2 configure succeeded."
++ # fi
++ # cd ..
++ #fi
+
+ #--------------------------------------------------------------------------
+ # Set up MPI 3D-RISM in NAB and SANDER
+@@ -1307,23 +1307,23 @@
+ echo
+ echo "Configuring fftw-2.1.5; (may be time-consuming)"
+ echo
+- cd fftw-2.1.5
+- if [ "$mpi" = 'yes' ]; then
+- ./configure $rismflag --enable-mpi CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
+- > ../fftw2_config.log 2>&1
+- else
+- ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
+- > ../fftw2_config.log 2>&1
+- fi
+- ncerror=$?
+- if [ $ncerror -gt 0 ]; then
+- echo " Error: fftw configure returned $ncerror"
+- echo " fftw configure failed! Check the fftw2_config.log file."
+- exit 1
+- else
+- echo " fftw-2.1.5 configure succeeded."
+- fi
+- cd ..
++ # cd fftw-2.1.5
++ # if [ "$mpi" = 'yes' ]; then
++ # ./configure $rismflag --enable-mpi CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
++ # > ../fftw2_config.log 2>&1
++ # else
++ # ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
++ # > ../fftw2_config.log 2>&1
++ # fi
++ # ncerror=$?
++ # if [ $ncerror -gt 0 ]; then
++ # echo " Error: fftw configure returned $ncerror"
++ # echo " fftw configure failed! Check the fftw2_config.log file."
++ # exit 1
++ # else
++ # echo " fftw-2.1.5 configure succeeded."
++ # fi
++ # cd ..
+ flibs_fftw2="\$(LIBDIR)/libdrfftw.a \$(LIBDIR)/libdfftw.a"
+ if [ "$mpi" = 'yes' ]; then
+ flibs_fftw2="\$(LIBDIR)/libdrfftw_mpi.a \$(LIBDIR)/libdfftw_mpi.a $flibs_fftw2"
+diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile
+--- amber11.orig/AmberTools/src/Makefile 2010-04-14 17:36:31.000000000 +0400
++++ amber11/AmberTools/src/Makefile 2011-03-07 03:39:38.000000000 +0300
+@@ -8,15 +8,15 @@
+
+ install: serial
+
+-serial: configured_serial $(NETCDFLIB)
++serial: configured_serial
+ @echo "Starting installation of ${AMBERTOOLS} serial at `date`".
+ # utility routines and libraries:
+- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
++# (cd ucpp-1.3 && $(MAKE) $(UCPP) )
+ (cd byacc && $(MAKE) install )
+- (cd arpack && $(MAKE) install );
+- (cd lapack && $(MAKE) $(LAPACK) )
+- (cd blas && $(MAKE) $(BLAS) )
+- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
++# (cd arpack && $(MAKE) install );
++# (cd lapack && $(MAKE) $(LAPACK) )
++# (cd blas && $(MAKE) $(BLAS) )
++# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+ (cd etc && $(MAKE) install )
+ (cd chamber && $(MAKE) install )
+ (cd pbsa && $(MAKE) install )
+@@ -30,14 +30,14 @@
+ (cd ptraj && $(MAKE) install )
+
+ # miscellaneous:
+- (cd reduce && $(MAKE) install )
++# (cd reduce && $(MAKE) install )
+
+ # leap and gleap:
+ (cd leap && $(MAKE) install )
+ (cd gleap && $(MAKE) install )
+
+ # nab:
+- (cd cifparse && $(MAKE) install )
++# (cd cifparse && $(MAKE) install )
+ (cd nab && $(MAKE) install )
+ (cd nss && $(MAKE) install )
+
+@@ -50,15 +50,15 @@
+
+ nabonly: $(NETCDFLIB)
+ # utility routines and libraries:
+- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
++# (cd ucpp-1.3 && $(MAKE) $(UCPP) )
+ (cd byacc && $(MAKE) install )
+- (cd arpack && $(MAKE) install );
+- (cd lapack && $(MAKE) $(LAPACK) )
+- (cd blas && $(MAKE) $(BLAS) )
+- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
++# (cd arpack && $(MAKE) install );
++# (cd lapack && $(MAKE) $(LAPACK) )
++# (cd blas && $(MAKE) $(BLAS) )
++# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+
+ # nab:
+- (cd cifparse && $(MAKE) install )
++# (cd cifparse && $(MAKE) install )
+ (cd nab && $(MAKE) install )
+ (cd nss && $(MAKE) install )
+
+diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile
+--- amber11.orig/AmberTools/src/pbsa/Makefile 2010-04-14 17:26:17.000000000 +0400
++++ amber11/AmberTools/src/pbsa/Makefile 2011-03-07 03:39:15.000000000 +0300
+@@ -47,10 +47,10 @@
+ $(LIBDIR)/libpbsa.a $(LIBDIR)/libFpbsa.a
+
+ #---------------------------------------------------------------------------
+-pbsa$(SFX): $(OBJ) syslib netlib c9x-complex
++pbsa$(SFX): $(OBJ) syslib
+ $(FC) -o pbsa$(SFX) $(OBJ) ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS)
+
+-simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
++simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
+ $(FC) -o simplepbsa$(SFX) simplepbsa.o gopt.o libpbsa.a \
+ $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS)
+ /bin/mv simplepbsa$(SFX) $(BINDIR)
+@@ -76,15 +76,15 @@
+ sfflib:
+ cd ../sff && $(MAKE) install
+
+-netlib:
+- cd ../lapack && $(MAKE) $(LAPACK)
+- cd ../blas && $(MAKE) $(BLAS)
+- cd ../arpack && $(MAKE) install
+-
+-c9x-complex:
+- @if test $(C9XCOMPLEX) != "skip"; then \
+- cd ../c9x-complex && $(MAKE) libmc.a; \
+- fi
++#netlib:
++# cd ../lapack && $(MAKE) $(LAPACK)
++# cd ../blas && $(MAKE) $(BLAS)
++# cd ../arpack && $(MAKE) install
++
++#c9x-complex:
++# @if test $(C9XCOMPLEX) != "skip"; then \
++# cd ../c9x-complex && $(MAKE) libmc.a; \
++# fi
+
+ %.LIBPBSA.o: %.f
+ $(FPP) -DLIBPBSA $< > _$<
+diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile
+--- amber11.orig/AmberTools/src/ptraj/Makefile 2010-03-31 07:05:16.000000000 +0400
++++ amber11/AmberTools/src/ptraj/Makefile 2011-03-07 03:39:16.000000000 +0300
+@@ -60,20 +60,20 @@
+ rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS)
+ $(CC) $(LDFLAGS) -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+
+-ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS)
++ptraj$(SFX): libs $(NETCDFLIB) $(OBJECTS)
+ $(CC) $(LDFLAGS) -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+
+-ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS)
++ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS)
+ $(CC) $(LDFLAGS) -o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM)
+ #
+
+ libs:
+ cd pdb && $(MAKE)
+- cd ../arpack && $(MAKE)
++# cd ../arpack && $(MAKE)
+
+-netlib:
+- cd ../lapack; $(MAKE) $(LAPACK)
+- cd ../blas; $(MAKE) $(BLAS)
++#netlib:
++# cd ../lapack; $(MAKE) $(LAPACK)
++# cd ../blas; $(MAKE) $(BLAS)
+
+ clean:
+ cd pdb; $(MAKE) clean
+diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h
+--- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2010-03-31 07:05:16.000000000 +0400
++++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-03-07 03:39:17.000000000 +0300
+@@ -4,7 +4,7 @@
+ # include "../pnetcdf/include/pnetcdf.h"
+ # define nc_strerror ncmpi_strerror
+ # else
+-# include "../netcdf/include/netcdf.h"
++# include <netcdf.h>
+ # endif
+ #endif
+
+diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h
+--- amber11.orig/AmberTools/src/ptraj/ptraj.h 2010-03-31 07:05:16.000000000 +0400
++++ amber11/AmberTools/src/ptraj/ptraj.h 2011-03-07 03:39:17.000000000 +0300
+@@ -94,7 +94,7 @@
+ #define nc_strerror ncmpi_strerror
+ #include "../pnetcdf/include/pnetcdf.h"
+ #else
+-#include "../netcdf/include/netcdf.h"
++#include <netcdf.h>
+ #endif
+ #endif
+
+diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile
+--- amber11.orig/AmberTools/src/sqm/Makefile 2010-04-14 16:13:28.000000000 +0400
++++ amber11/AmberTools/src/sqm/Makefile 2011-03-07 03:39:17.000000000 +0300
+@@ -77,7 +77,7 @@
+ install: sqm$(SFX)
+ mv sqm$(SFX) $(BINDIR)
+
+-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
++sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
+ $(FC) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) $(FLIBSF) ../lib/sys.a $(LDFLAGS)
+
+ #-----------LIBS
+@@ -93,10 +93,10 @@
+ sys:
+ cd ../lib; $(MAKE) sys.a
+
+-netlib:
+- cd ../lapack; $(MAKE) $(LAPACK)
+- cd ../blas; $(MAKE) $(BLAS)
+- cd ../arpack && $(MAKE) install
++#netlib:
++# cd ../lapack; $(MAKE) $(LAPACK)
++# cd ../blas; $(MAKE) $(BLAS)
++# cd ../arpack && $(MAKE) install
+
+ clean:
+ /bin/rm -f *.o _*.f *.mod *.d sqm$(SFX)
next reply other threads:[~2011-03-07 1:49 UTC|newest]
Thread overview: 18+ messages / expand[flat|nested] mbox.gz Atom feed top
2011-03-07 1:49 Alexey Shvetsov [this message]
-- strict thread matches above, loose matches on Subject: below --
2020-09-26 16:21 [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/ Aisha Tammy
2016-02-19 12:56 Justin Lecher
2016-02-19 12:56 Justin Lecher
2015-10-28 9:07 Justin Lecher
2014-11-11 15:48 Justin Lecher
2012-10-21 12:52 Reinis Danne
2012-10-20 16:41 Reinis Danne
2012-08-28 16:53 Reinis Danne
2012-03-03 22:11 Reinis Danne
2012-03-03 21:06 Reinis Danne
2011-10-26 20:06 Reinis Danne
2011-10-25 22:40 Reinis Danne
2011-07-28 13:08 Alexey Shvetsov
2011-06-25 17:21 Justin Lecher
2011-06-05 0:21 Reinis Danne
2011-03-08 13:40 Alexey Shvetsov
2011-03-06 21:40 Alexey Shvetsov
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