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387 lines
14 KiB
387 lines
14 KiB
diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure
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--- amber11.orig/AmberTools/src/configure 2011-04-14 15:30:55.000000000 +0300
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+++ amber11/AmberTools/src/configure 2011-06-04 12:26:45.000000000 +0300
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@@ -293,7 +293,8 @@
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echo "Your AMBERHOME environment variable is not set! It should be set to"
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echo "$ambhome NOT doing so may cause errors when you compile. Continue"
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echo "anyway? (yes or no)"
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- read answer
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+ #read answer
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+ answer='yes'
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if [ "$answer" = 'yes' -o "$answer" = 'Yes' -o "$answer" = 'YES' -o "$answer" = 'y' -o "$answer" = 'Y' ]; then
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echo ""
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echo "Continuing anyway... Setting AMBERHOME to $ambhome temporarily"
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@@ -356,11 +357,11 @@
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mpi_flag=
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lex=flex
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flibs_mkl=
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-lapack=install
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-blas=install
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+lapack=skip
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+blas=skip
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f2c=skip
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-ucpp=install
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-cpp="\$(BINDIR)/ucpp -l"
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+ucpp=skip
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+cpp="\$(EPREFIX)/usr/bin/ucpp -l"
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#-----------------------------------
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# skip building of sleap?
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@@ -1655,24 +1656,24 @@
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#--------------------------------------------------------------------------
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# Configure fftw-3.2.2:
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#--------------------------------------------------------------------------
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- if [ "$mdgx" = 'yes' ]; then
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- mdgxflag="--prefix=$AMBERHOME --disable-fortran"
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- echo
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- echo "Configuring fftw-3.2.2 (may be time-consuming)..."
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- echo
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- cd fftw-3.2.2 && \
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- env CC="$cc" CFLAGS="$cflags $cnooptflags" \
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- ./configure $mdgxflag > ../fftw3_config.log 2>&1
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- ncerror=$?
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- if [ $ncerror -gt 0 ]; then
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- echo " Error: FFTW configure returned $ncerror"
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- echo " FFTW configure failed! Check the fftw3_config.log file."
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- exit 1
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- else
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- echo " fftw-3.2.2 configure succeeded."
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- fi
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- cd ..
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- fi
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+ #if [ "$mdgx" = 'yes' ]; then
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+ # mdgxflag="--prefix=$AMBERHOME --disable-fortran"
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+ # echo
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+ # echo "Configuring fftw-3.2.2 (may be time-consuming)..."
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+ # echo
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+ # cd fftw-3.2.2 && \
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+ # env CC="$cc" CFLAGS="$cflags $cnooptflags" \
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+ # ./configure $mdgxflag > ../fftw3_config.log 2>&1
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+ # ncerror=$?
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+ # if [ $ncerror -gt 0 ]; then
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+ # echo " Error: FFTW configure returned $ncerror"
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+ # echo " FFTW configure failed! Check the fftw3_config.log file."
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+ # exit 1
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+ # else
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+ # echo " fftw-3.2.2 configure succeeded."
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+ # fi
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+ # cd ..
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+ #fi
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#--------------------------------------------------------------------------
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# Configure python
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@@ -1792,27 +1793,27 @@
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echo
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echo "Configuring fftw-2.1.5 (may be time-consuming)..."
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echo
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- cd fftw-2.1.5
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- if [ "$mpi" = 'yes' ]; then
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- ./configure $rismflag --enable-mpi \
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- CC="$cc" CFLAGS="$cflags $coptflags" \
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- F77="$fc" FFLAGS="$fflags $foptflags" \
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- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
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- else
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- ./configure $rismflag \
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- CC="$cc" CFLAGS="$cflags $coptflags" \
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- F77="$fc" FFLAGS="$fflags $foptflags" \
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- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
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- fi
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- ncerror=$?
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- if [ $ncerror -gt 0 ]; then
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- echo " Error: fftw configure returned $ncerror"
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- echo " fftw configure failed! Check the fftw2_config.log file."
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- exit 1
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- else
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- echo " fftw-2.1.5 configure succeeded."
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- fi
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- cd ..
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+ # cd fftw-2.1.5
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+ # if [ "$mpi" = 'yes' ]; then
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+ # ./configure $rismflag --enable-mpi \
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+ # CC="$cc" CFLAGS="$cflags $coptflags" \
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+ # F77="$fc" FFLAGS="$fflags $foptflags" \
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+ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
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+ # else
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+ # ./configure $rismflag \
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+ # CC="$cc" CFLAGS="$cflags $coptflags" \
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+ # F77="$fc" FFLAGS="$fflags $foptflags" \
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+ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
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+ # fi
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+ # ncerror=$?
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+ # if [ $ncerror -gt 0 ]; then
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+ # echo " Error: fftw configure returned $ncerror"
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+ # echo " fftw configure failed! Check the fftw2_config.log file."
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+ # exit 1
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+ # else
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+ # echo " fftw-2.1.5 configure succeeded."
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+ # fi
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+ # cd ..
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flibs_fftw2="-ldrfftw -ldfftw"
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if [ "$mpi" = 'yes' ]; then
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flibs_fftw2="-ldrfftw_mpi -ldfftw_mpi $flibs_fftw2"
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diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at
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--- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at 2011-04-14 15:30:16.000000000 +0300
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+++ amber11/AmberTools/src/cpptraj/src/Makefile_at 2011-05-20 00:45:48.000000000 +0300
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@@ -65,8 +65,8 @@
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-/bin/rm FindDepend.o
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-/bin/rm findDepend
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-cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS)
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- $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB)
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+cpptraj$(SFX): $(OBJECTS)
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+ $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -lgomp
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$(NETCDFLIB): ../../netcdf_config.log
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cd ../../netcdf/src && $(MAKE) install
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diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile
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--- amber11.orig/AmberTools/src/Makefile 2011-04-14 15:30:12.000000000 +0300
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+++ amber11/AmberTools/src/Makefile 2011-05-19 23:36:36.000000000 +0300
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@@ -8,15 +8,15 @@
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install: $(INSTALLTYPE)
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-serial: configured_serial $(NETCDFLIB) $(PYINSTALL) $(MTKPP)
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+serial: configured_serial
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@echo "Starting installation of ${AMBERTOOLS} serial at `date`".
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# utility routines and libraries:
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- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
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+# (cd ucpp-1.3 && $(MAKE) $(UCPP) )
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(cd byacc && $(MAKE) install )
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- (cd arpack && $(MAKE) install );
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- (cd lapack && $(MAKE) $(LAPACK) )
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- (cd blas && $(MAKE) $(BLAS) )
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- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
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+# (cd arpack && $(MAKE) install );
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+# (cd lapack && $(MAKE) $(LAPACK) )
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+# (cd blas && $(MAKE) $(BLAS) )
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+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
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(cd etc && $(MAKE) install )
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(cd chamber && $(MAKE) install )
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(cd pbsa && $(MAKE) install )
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@@ -32,7 +32,7 @@
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(cd cpptraj && $(MAKE) $(CPPTRAJ))
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# miscellaneous:
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- (cd reduce && $(MAKE) install )
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+# (cd reduce && $(MAKE) install )
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# leap and gleap:
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(cd leap && $(MAKE) install )
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@@ -42,7 +42,7 @@
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(cd rism && $(MAKE) install )
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# nab:
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- (cd cifparse && $(MAKE) install )
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+# (cd cifparse && $(MAKE) install )
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(cd sff && $(MAKE) install )
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(cd pbsa && $(MAKE) libinstall )
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(cd nab && $(MAKE) install )
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@@ -63,19 +63,19 @@
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@echo "Installation of ${AMBERTOOLS} serial is complete at `date`."
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@echo ""
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-nabonly: $(NETCDFLIB)
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+nabonly:
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# utility routines and libraries:
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- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
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+# (cd ucpp-1.3 && $(MAKE) $(UCPP) )
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(cd byacc && $(MAKE) install )
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- (cd arpack && $(MAKE) install );
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- (cd lapack && $(MAKE) $(LAPACK) )
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- (cd blas && $(MAKE) $(BLAS) )
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- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
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+# (cd arpack && $(MAKE) install );
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+# (cd lapack && $(MAKE) $(LAPACK) )
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+# (cd blas && $(MAKE) $(BLAS) )
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+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
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(cd pbsa && $(MAKE) libinstall )
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(cd rism && $(MAKE) install )
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# nab:
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- (cd cifparse && $(MAKE) install )
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+# (cd cifparse && $(MAKE) install )
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(cd sff && $(MAKE) install )
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(cd nab && $(MAKE) install )
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(cd nss && $(MAKE) install )
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diff -urN amber11.orig/AmberTools/src/mdgx/Makefile amber11/AmberTools/src/mdgx/Makefile
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--- amber11.orig/AmberTools/src/mdgx/Makefile 2011-04-14 15:30:17.000000000 +0300
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+++ amber11/AmberTools/src/mdgx/Makefile 2011-05-20 12:44:38.000000000 +0300
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@@ -109,7 +109,7 @@
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FFTW_LIBS = $(LIBDIR)/libfftw3.a
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-mdgx$(SFX) : $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB)
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+mdgx$(SFX) : $(MDGX_OBJS)
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$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
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-o $@ $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) $(LM)
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diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile
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--- amber11.orig/AmberTools/src/pbsa/Makefile 2011-04-14 15:30:19.000000000 +0300
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+++ amber11/AmberTools/src/pbsa/Makefile 2011-05-19 22:27:40.000000000 +0300
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@@ -148,7 +148,7 @@
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)
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#---------------------------------------------------------------------------
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-pbsa$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial
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+pbsa$(SFX): $(OBJ) syslib configured_serial
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$(FC) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \
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../lib/nxtsec.o ../lib/random.o \
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$(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
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@@ -158,7 +158,7 @@
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../lib/nxtsec.o ../lib/random.o \
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$(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
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-simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
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+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
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$(FC) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \
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libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) \
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$(LDFLAGS) $(AMBERLDFLAGS)
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@@ -194,15 +194,15 @@
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sfflib:
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cd ../sff && $(MAKE) install
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-netlib:
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- cd ../lapack && $(MAKE) $(LAPACK)
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- cd ../blas && $(MAKE) $(BLAS)
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- cd ../arpack && $(MAKE) install
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-
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-c9x-complex:
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- @if test $(C9XCOMPLEX) != "skip"; then \
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- cd ../c9x-complex && $(MAKE) libmc.a; \
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- fi
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+#netlib:
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+# cd ../lapack && $(MAKE) $(LAPACK)
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+# cd ../blas && $(MAKE) $(BLAS)
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+# cd ../arpack && $(MAKE) install
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+
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+#c9x-complex:
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+# @if test $(C9XCOMPLEX) != "skip"; then \
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+# cd ../c9x-complex && $(MAKE) libmc.a; \
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+# fi
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%.LIBPBSA.o: %.f
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$(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$<
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diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile
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--- amber11.orig/AmberTools/src/ptraj/Makefile 2011-04-14 15:30:19.000000000 +0300
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+++ amber11/AmberTools/src/ptraj/Makefile 2011-05-19 23:38:36.000000000 +0300
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@@ -57,25 +57,25 @@
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pubfft.o: pubfft.f
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$(FC) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $<
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-rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS)
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+rdparm$(SFX): libs $(OBJECTS)
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$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
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-o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
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-ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS)
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+ptraj$(SFX): libs $(OBJECTS)
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$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
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-o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
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-ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS)
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+ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS)
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$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
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-o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM)
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libs:
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cd pdb && $(MAKE)
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- cd ../arpack && $(MAKE)
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+# cd ../arpack && $(MAKE)
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-netlib:
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- cd ../lapack && $(MAKE) $(LAPACK)
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- cd ../blas && $(MAKE) $(BLAS)
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+#netlib:
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+# cd ../lapack && $(MAKE) $(LAPACK)
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+# cd ../blas && $(MAKE) $(BLAS)
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clean:
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cd pdb && $(MAKE) clean
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diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h
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--- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2011-04-14 15:30:19.000000000 +0300
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+++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-05-19 22:30:43.000000000 +0300
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@@ -4,7 +4,7 @@
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# include "../../include/pnetcdf.h"
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# define nc_strerror ncmpi_strerror
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# else
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-# include "../../include/netcdf.h"
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+# include <netcdf.h>
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# endif
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#endif
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diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h
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--- amber11.orig/AmberTools/src/ptraj/ptraj.h 2011-04-14 15:30:19.000000000 +0300
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+++ amber11/AmberTools/src/ptraj/ptraj.h 2011-06-04 13:25:01.000000000 +0300
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@@ -94,7 +94,7 @@
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#define nc_strerror ncmpi_strerror
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#include "../../include/pnetcdf.h"
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#else
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-#include "../../include/netcdf.h"
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+#include <netcdf.h>
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#endif
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#endif
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diff -urN amber11.orig/AmberTools/src/rism/Makefile amber11/AmberTools/src/rism/Makefile
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--- amber11.orig/AmberTools/src/rism/Makefile 2011-04-14 15:30:19.000000000 +0300
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+++ amber11/AmberTools/src/rism/Makefile 2011-05-20 01:07:26.000000000 +0300
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@@ -49,7 +49,7 @@
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mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o \
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fce_c.o erfcfun.o safemem.o blend.o timer_c.o
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-librism: $(LIBOBJ) $(FLIBS_FFTW2)
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+librism: $(LIBOBJ)
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$(AR) $(LIBDIR)/$@.a $(LIBOBJ)
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$(RANLIB) $(LIBDIR)/$@.a
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diff -urN amber11.orig/AmberTools/src/sff/AmberNetcdf.c amber11/AmberTools/src/sff/AmberNetcdf.c
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--- amber11.orig/AmberTools/src/sff/AmberNetcdf.c 2011-04-14 15:30:19.000000000 +0300
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+++ amber11/AmberTools/src/sff/AmberNetcdf.c 2011-05-20 10:49:06.000000000 +0300
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@@ -27,7 +27,7 @@
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#endif
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#ifdef BINTRAJ
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-#include "../../include/netcdf.h"
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+#include <netcdf.h>
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#define NCFRAME "frame"
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#define NCSPATIAL "spatial"
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diff -urN amber11.orig/AmberTools/src/sff/Makefile amber11/AmberTools/src/sff/Makefile
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--- amber11.orig/AmberTools/src/sff/Makefile 2011-04-14 15:30:19.000000000 +0300
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+++ amber11/AmberTools/src/sff/Makefile 2011-05-20 09:53:27.000000000 +0300
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@@ -1,7 +1,7 @@
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include ../config.h
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.c.o:
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- $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@ $<
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+ $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFLIB) -o $@ $<
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OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
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prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \
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diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile
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--- amber11.orig/AmberTools/src/sqm/Makefile 2011-04-14 15:30:20.000000000 +0300
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+++ amber11/AmberTools/src/sqm/Makefile 2011-05-19 22:31:49.000000000 +0300
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@@ -77,7 +77,7 @@
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install: sqm$(SFX)
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mv sqm$(SFX) $(BINDIR)
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-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
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+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
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$(FC) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \
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$(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS)
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@@ -94,10 +94,10 @@
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sys:
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cd ../lib; $(MAKE) sys.a
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-netlib:
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- cd ../lapack; $(MAKE) $(LAPACK)
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- cd ../blas; $(MAKE) $(BLAS)
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- cd ../arpack && $(MAKE) install
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+#netlib:
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+# cd ../lapack; $(MAKE) $(LAPACK)
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+# cd ../blas; $(MAKE) $(BLAS)
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+# cd ../arpack && $(MAKE) install
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|
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clean:
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/bin/rm -f *.o _*.f *.mod *.d sqm$(SFX)
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