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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)
|
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