| 1 |
alexxy 11/07/28 13:19:06 |
| 2 |
|
| 3 |
Added: ambertools-1.5-gentoo.patch |
| 4 |
Log: |
| 5 |
[sci-chemistry/ambertools] Initial import to tree |
| 6 |
|
| 7 |
(Portage version: 2.2.0_alpha47/cvs/Linux x86_64) |
| 8 |
|
| 9 |
Revision Changes Path |
| 10 |
1.1 sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch |
| 11 |
|
| 12 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch?rev=1.1&view=markup |
| 13 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch?rev=1.1&content-type=text/plain |
| 14 |
|
| 15 |
Index: ambertools-1.5-gentoo.patch |
| 16 |
=================================================================== |
| 17 |
diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure |
| 18 |
--- amber11.orig/AmberTools/src/configure 2011-04-14 15:30:55.000000000 +0300 |
| 19 |
+++ amber11/AmberTools/src/configure 2011-06-04 12:26:45.000000000 +0300 |
| 20 |
@@ -293,7 +293,8 @@ |
| 21 |
echo "Your AMBERHOME environment variable is not set! It should be set to" |
| 22 |
echo "$ambhome NOT doing so may cause errors when you compile. Continue" |
| 23 |
echo "anyway? (yes or no)" |
| 24 |
- read answer |
| 25 |
+ #read answer |
| 26 |
+ answer='yes' |
| 27 |
if [ "$answer" = 'yes' -o "$answer" = 'Yes' -o "$answer" = 'YES' -o "$answer" = 'y' -o "$answer" = 'Y' ]; then |
| 28 |
echo "" |
| 29 |
echo "Continuing anyway... Setting AMBERHOME to $ambhome temporarily" |
| 30 |
@@ -356,11 +357,11 @@ |
| 31 |
mpi_flag= |
| 32 |
lex=flex |
| 33 |
flibs_mkl= |
| 34 |
-lapack=install |
| 35 |
-blas=install |
| 36 |
+lapack=skip |
| 37 |
+blas=skip |
| 38 |
f2c=skip |
| 39 |
-ucpp=install |
| 40 |
-cpp="\$(BINDIR)/ucpp -l" |
| 41 |
+ucpp=skip |
| 42 |
+cpp="\$(EPREFIX)/usr/bin/ucpp -l" |
| 43 |
|
| 44 |
#----------------------------------- |
| 45 |
# skip building of sleap? |
| 46 |
@@ -1655,24 +1656,24 @@ |
| 47 |
#-------------------------------------------------------------------------- |
| 48 |
# Configure fftw-3.2.2: |
| 49 |
#-------------------------------------------------------------------------- |
| 50 |
- if [ "$mdgx" = 'yes' ]; then |
| 51 |
- mdgxflag="--prefix=$AMBERHOME --disable-fortran" |
| 52 |
- echo |
| 53 |
- echo "Configuring fftw-3.2.2 (may be time-consuming)..." |
| 54 |
- echo |
| 55 |
- cd fftw-3.2.2 && \ |
| 56 |
- env CC="$cc" CFLAGS="$cflags $cnooptflags" \ |
| 57 |
- ./configure $mdgxflag > ../fftw3_config.log 2>&1 |
| 58 |
- ncerror=$? |
| 59 |
- if [ $ncerror -gt 0 ]; then |
| 60 |
- echo " Error: FFTW configure returned $ncerror" |
| 61 |
- echo " FFTW configure failed! Check the fftw3_config.log file." |
| 62 |
- exit 1 |
| 63 |
- else |
| 64 |
- echo " fftw-3.2.2 configure succeeded." |
| 65 |
- fi |
| 66 |
- cd .. |
| 67 |
- fi |
| 68 |
+ #if [ "$mdgx" = 'yes' ]; then |
| 69 |
+ # mdgxflag="--prefix=$AMBERHOME --disable-fortran" |
| 70 |
+ # echo |
| 71 |
+ # echo "Configuring fftw-3.2.2 (may be time-consuming)..." |
| 72 |
+ # echo |
| 73 |
+ # cd fftw-3.2.2 && \ |
| 74 |
+ # env CC="$cc" CFLAGS="$cflags $cnooptflags" \ |
| 75 |
+ # ./configure $mdgxflag > ../fftw3_config.log 2>&1 |
| 76 |
+ # ncerror=$? |
| 77 |
+ # if [ $ncerror -gt 0 ]; then |
| 78 |
+ # echo " Error: FFTW configure returned $ncerror" |
| 79 |
+ # echo " FFTW configure failed! Check the fftw3_config.log file." |
| 80 |
+ # exit 1 |
| 81 |
+ # else |
| 82 |
+ # echo " fftw-3.2.2 configure succeeded." |
| 83 |
+ # fi |
| 84 |
+ # cd .. |
| 85 |
+ #fi |
| 86 |
|
| 87 |
#-------------------------------------------------------------------------- |
| 88 |
# Configure python |
| 89 |
@@ -1792,27 +1793,27 @@ |
| 90 |
echo |
| 91 |
echo "Configuring fftw-2.1.5 (may be time-consuming)..." |
| 92 |
echo |
| 93 |
- cd fftw-2.1.5 |
| 94 |
- if [ "$mpi" = 'yes' ]; then |
| 95 |
- ./configure $rismflag --enable-mpi \ |
| 96 |
- CC="$cc" CFLAGS="$cflags $coptflags" \ |
| 97 |
- F77="$fc" FFLAGS="$fflags $foptflags" \ |
| 98 |
- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 |
| 99 |
- else |
| 100 |
- ./configure $rismflag \ |
| 101 |
- CC="$cc" CFLAGS="$cflags $coptflags" \ |
| 102 |
- F77="$fc" FFLAGS="$fflags $foptflags" \ |
| 103 |
- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 |
| 104 |
- fi |
| 105 |
- ncerror=$? |
| 106 |
- if [ $ncerror -gt 0 ]; then |
| 107 |
- echo " Error: fftw configure returned $ncerror" |
| 108 |
- echo " fftw configure failed! Check the fftw2_config.log file." |
| 109 |
- exit 1 |
| 110 |
- else |
| 111 |
- echo " fftw-2.1.5 configure succeeded." |
| 112 |
- fi |
| 113 |
- cd .. |
| 114 |
+ # cd fftw-2.1.5 |
| 115 |
+ # if [ "$mpi" = 'yes' ]; then |
| 116 |
+ # ./configure $rismflag --enable-mpi \ |
| 117 |
+ # CC="$cc" CFLAGS="$cflags $coptflags" \ |
| 118 |
+ # F77="$fc" FFLAGS="$fflags $foptflags" \ |
| 119 |
+ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 |
| 120 |
+ # else |
| 121 |
+ # ./configure $rismflag \ |
| 122 |
+ # CC="$cc" CFLAGS="$cflags $coptflags" \ |
| 123 |
+ # F77="$fc" FFLAGS="$fflags $foptflags" \ |
| 124 |
+ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 |
| 125 |
+ # fi |
| 126 |
+ # ncerror=$? |
| 127 |
+ # if [ $ncerror -gt 0 ]; then |
| 128 |
+ # echo " Error: fftw configure returned $ncerror" |
| 129 |
+ # echo " fftw configure failed! Check the fftw2_config.log file." |
| 130 |
+ # exit 1 |
| 131 |
+ # else |
| 132 |
+ # echo " fftw-2.1.5 configure succeeded." |
| 133 |
+ # fi |
| 134 |
+ # cd .. |
| 135 |
flibs_fftw2="-ldrfftw -ldfftw" |
| 136 |
if [ "$mpi" = 'yes' ]; then |
| 137 |
flibs_fftw2="-ldrfftw_mpi -ldfftw_mpi $flibs_fftw2" |
| 138 |
diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at |
| 139 |
--- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at 2011-04-14 15:30:16.000000000 +0300 |
| 140 |
+++ amber11/AmberTools/src/cpptraj/src/Makefile_at 2011-05-20 00:45:48.000000000 +0300 |
| 141 |
@@ -65,8 +65,8 @@ |
| 142 |
-/bin/rm FindDepend.o |
| 143 |
-/bin/rm findDepend |
| 144 |
|
| 145 |
-cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS) |
| 146 |
- $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) |
| 147 |
+cpptraj$(SFX): $(OBJECTS) |
| 148 |
+ $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -lgomp |
| 149 |
|
| 150 |
$(NETCDFLIB): ../../netcdf_config.log |
| 151 |
cd ../../netcdf/src && $(MAKE) install |
| 152 |
diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile |
| 153 |
--- amber11.orig/AmberTools/src/Makefile 2011-04-14 15:30:12.000000000 +0300 |
| 154 |
+++ amber11/AmberTools/src/Makefile 2011-05-19 23:36:36.000000000 +0300 |
| 155 |
@@ -8,15 +8,15 @@ |
| 156 |
|
| 157 |
install: $(INSTALLTYPE) |
| 158 |
|
| 159 |
-serial: configured_serial $(NETCDFLIB) $(PYINSTALL) $(MTKPP) |
| 160 |
+serial: configured_serial |
| 161 |
@echo "Starting installation of ${AMBERTOOLS} serial at `date`". |
| 162 |
# utility routines and libraries: |
| 163 |
- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
| 164 |
+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
| 165 |
(cd byacc && $(MAKE) install ) |
| 166 |
- (cd arpack && $(MAKE) install ); |
| 167 |
- (cd lapack && $(MAKE) $(LAPACK) ) |
| 168 |
- (cd blas && $(MAKE) $(BLAS) ) |
| 169 |
- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
| 170 |
+# (cd arpack && $(MAKE) install ); |
| 171 |
+# (cd lapack && $(MAKE) $(LAPACK) ) |
| 172 |
+# (cd blas && $(MAKE) $(BLAS) ) |
| 173 |
+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
| 174 |
(cd etc && $(MAKE) install ) |
| 175 |
(cd chamber && $(MAKE) install ) |
| 176 |
(cd pbsa && $(MAKE) install ) |
| 177 |
@@ -32,7 +32,7 @@ |
| 178 |
(cd cpptraj && $(MAKE) $(CPPTRAJ)) |
| 179 |
|
| 180 |
# miscellaneous: |
| 181 |
- (cd reduce && $(MAKE) install ) |
| 182 |
+# (cd reduce && $(MAKE) install ) |
| 183 |
|
| 184 |
# leap and gleap: |
| 185 |
(cd leap && $(MAKE) install ) |
| 186 |
@@ -42,7 +42,7 @@ |
| 187 |
(cd rism && $(MAKE) install ) |
| 188 |
|
| 189 |
# nab: |
| 190 |
- (cd cifparse && $(MAKE) install ) |
| 191 |
+# (cd cifparse && $(MAKE) install ) |
| 192 |
(cd sff && $(MAKE) install ) |
| 193 |
(cd pbsa && $(MAKE) libinstall ) |
| 194 |
(cd nab && $(MAKE) install ) |
| 195 |
@@ -63,19 +63,19 @@ |
| 196 |
@echo "Installation of ${AMBERTOOLS} serial is complete at `date`." |
| 197 |
@echo "" |
| 198 |
|
| 199 |
-nabonly: $(NETCDFLIB) |
| 200 |
+nabonly: |
| 201 |
# utility routines and libraries: |
| 202 |
- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
| 203 |
+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) |
| 204 |
(cd byacc && $(MAKE) install ) |
| 205 |
- (cd arpack && $(MAKE) install ); |
| 206 |
- (cd lapack && $(MAKE) $(LAPACK) ) |
| 207 |
- (cd blas && $(MAKE) $(BLAS) ) |
| 208 |
- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
| 209 |
+# (cd arpack && $(MAKE) install ); |
| 210 |
+# (cd lapack && $(MAKE) $(LAPACK) ) |
| 211 |
+# (cd blas && $(MAKE) $(BLAS) ) |
| 212 |
+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) |
| 213 |
(cd pbsa && $(MAKE) libinstall ) |
| 214 |
(cd rism && $(MAKE) install ) |
| 215 |
|
| 216 |
# nab: |
| 217 |
- (cd cifparse && $(MAKE) install ) |
| 218 |
+# (cd cifparse && $(MAKE) install ) |
| 219 |
(cd sff && $(MAKE) install ) |
| 220 |
(cd nab && $(MAKE) install ) |
| 221 |
(cd nss && $(MAKE) install ) |
| 222 |
diff -urN amber11.orig/AmberTools/src/mdgx/Makefile amber11/AmberTools/src/mdgx/Makefile |
| 223 |
--- amber11.orig/AmberTools/src/mdgx/Makefile 2011-04-14 15:30:17.000000000 +0300 |
| 224 |
+++ amber11/AmberTools/src/mdgx/Makefile 2011-05-20 12:44:38.000000000 +0300 |
| 225 |
@@ -109,7 +109,7 @@ |
| 226 |
|
| 227 |
FFTW_LIBS = $(LIBDIR)/libfftw3.a |
| 228 |
|
| 229 |
-mdgx$(SFX) : $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) |
| 230 |
+mdgx$(SFX) : $(MDGX_OBJS) |
| 231 |
$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \ |
| 232 |
-o $@ $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) $(LM) |
| 233 |
|
| 234 |
diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile |
| 235 |
--- amber11.orig/AmberTools/src/pbsa/Makefile 2011-04-14 15:30:19.000000000 +0300 |
| 236 |
+++ amber11/AmberTools/src/pbsa/Makefile 2011-05-19 22:27:40.000000000 +0300 |
| 237 |
@@ -148,7 +148,7 @@ |
| 238 |
) |
| 239 |
|
| 240 |
#--------------------------------------------------------------------------- |
| 241 |
-pbsa$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial |
| 242 |
+pbsa$(SFX): $(OBJ) syslib configured_serial |
| 243 |
$(FC) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \ |
| 244 |
../lib/nxtsec.o ../lib/random.o \ |
| 245 |
$(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) |
| 246 |
@@ -158,7 +158,7 @@ |
| 247 |
../lib/nxtsec.o ../lib/random.o \ |
| 248 |
$(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) |
| 249 |
|
| 250 |
-simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex |
| 251 |
+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib |
| 252 |
$(FC) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \ |
| 253 |
libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) \ |
| 254 |
$(LDFLAGS) $(AMBERLDFLAGS) |
| 255 |
@@ -194,15 +194,15 @@ |
| 256 |
sfflib: |
| 257 |
cd ../sff && $(MAKE) install |
| 258 |
|
| 259 |
-netlib: |
| 260 |
- cd ../lapack && $(MAKE) $(LAPACK) |
| 261 |
- cd ../blas && $(MAKE) $(BLAS) |
| 262 |
- cd ../arpack && $(MAKE) install |
| 263 |
- |
| 264 |
-c9x-complex: |
| 265 |
- @if test $(C9XCOMPLEX) != "skip"; then \ |
| 266 |
- cd ../c9x-complex && $(MAKE) libmc.a; \ |
| 267 |
- fi |
| 268 |
+#netlib: |
| 269 |
+# cd ../lapack && $(MAKE) $(LAPACK) |
| 270 |
+# cd ../blas && $(MAKE) $(BLAS) |
| 271 |
+# cd ../arpack && $(MAKE) install |
| 272 |
+ |
| 273 |
+#c9x-complex: |
| 274 |
+# @if test $(C9XCOMPLEX) != "skip"; then \ |
| 275 |
+# cd ../c9x-complex && $(MAKE) libmc.a; \ |
| 276 |
+# fi |
| 277 |
|
| 278 |
%.LIBPBSA.o: %.f |
| 279 |
$(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$< |
| 280 |
diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile |
| 281 |
--- amber11.orig/AmberTools/src/ptraj/Makefile 2011-04-14 15:30:19.000000000 +0300 |
| 282 |
+++ amber11/AmberTools/src/ptraj/Makefile 2011-05-19 23:38:36.000000000 +0300 |
| 283 |
@@ -57,25 +57,25 @@ |
| 284 |
pubfft.o: pubfft.f |
| 285 |
$(FC) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $< |
| 286 |
|
| 287 |
-rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS) |
| 288 |
+rdparm$(SFX): libs $(OBJECTS) |
| 289 |
$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ |
| 290 |
-o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) |
| 291 |
|
| 292 |
-ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS) |
| 293 |
+ptraj$(SFX): libs $(OBJECTS) |
| 294 |
$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ |
| 295 |
-o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) |
| 296 |
|
| 297 |
-ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS) |
| 298 |
+ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS) |
| 299 |
$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ |
| 300 |
-o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM) |
| 301 |
|
| 302 |
libs: |
| 303 |
cd pdb && $(MAKE) |
| 304 |
- cd ../arpack && $(MAKE) |
| 305 |
+# cd ../arpack && $(MAKE) |
| 306 |
|
| 307 |
-netlib: |
| 308 |
- cd ../lapack && $(MAKE) $(LAPACK) |
| 309 |
- cd ../blas && $(MAKE) $(BLAS) |
| 310 |
+#netlib: |
| 311 |
+# cd ../lapack && $(MAKE) $(LAPACK) |
| 312 |
+# cd ../blas && $(MAKE) $(BLAS) |
| 313 |
|
| 314 |
clean: |
| 315 |
cd pdb && $(MAKE) clean |
| 316 |
diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h |
| 317 |
--- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2011-04-14 15:30:19.000000000 +0300 |
| 318 |
+++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-05-19 22:30:43.000000000 +0300 |
| 319 |
@@ -4,7 +4,7 @@ |
| 320 |
# include "../../include/pnetcdf.h" |
| 321 |
# define nc_strerror ncmpi_strerror |
| 322 |
# else |
| 323 |
-# include "../../include/netcdf.h" |
| 324 |
+# include <netcdf.h> |
| 325 |
# endif |
| 326 |
#endif |
| 327 |
|
| 328 |
diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h |
| 329 |
--- amber11.orig/AmberTools/src/ptraj/ptraj.h 2011-04-14 15:30:19.000000000 +0300 |
| 330 |
+++ amber11/AmberTools/src/ptraj/ptraj.h 2011-06-04 13:25:01.000000000 +0300 |
| 331 |
@@ -94,7 +94,7 @@ |
| 332 |
#define nc_strerror ncmpi_strerror |
| 333 |
#include "../../include/pnetcdf.h" |
| 334 |
#else |
| 335 |
-#include "../../include/netcdf.h" |
| 336 |
+#include <netcdf.h> |
| 337 |
#endif |
| 338 |
#endif |
| 339 |
|
| 340 |
diff -urN amber11.orig/AmberTools/src/rism/Makefile amber11/AmberTools/src/rism/Makefile |
| 341 |
--- amber11.orig/AmberTools/src/rism/Makefile 2011-04-14 15:30:19.000000000 +0300 |
| 342 |
+++ amber11/AmberTools/src/rism/Makefile 2011-05-20 01:07:26.000000000 +0300 |
| 343 |
@@ -49,7 +49,7 @@ |
| 344 |
mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o \ |
| 345 |
fce_c.o erfcfun.o safemem.o blend.o timer_c.o |
| 346 |
|
| 347 |
-librism: $(LIBOBJ) $(FLIBS_FFTW2) |
| 348 |
+librism: $(LIBOBJ) |
| 349 |
$(AR) $(LIBDIR)/$@.a $(LIBOBJ) |
| 350 |
$(RANLIB) $(LIBDIR)/$@.a |
| 351 |
|
| 352 |
diff -urN amber11.orig/AmberTools/src/sff/AmberNetcdf.c amber11/AmberTools/src/sff/AmberNetcdf.c |
| 353 |
--- amber11.orig/AmberTools/src/sff/AmberNetcdf.c 2011-04-14 15:30:19.000000000 +0300 |
| 354 |
+++ amber11/AmberTools/src/sff/AmberNetcdf.c 2011-05-20 10:49:06.000000000 +0300 |
| 355 |
@@ -27,7 +27,7 @@ |
| 356 |
#endif |
| 357 |
|
| 358 |
#ifdef BINTRAJ |
| 359 |
-#include "../../include/netcdf.h" |
| 360 |
+#include <netcdf.h> |
| 361 |
|
| 362 |
#define NCFRAME "frame" |
| 363 |
#define NCSPATIAL "spatial" |
| 364 |
diff -urN amber11.orig/AmberTools/src/sff/Makefile amber11/AmberTools/src/sff/Makefile |
| 365 |
--- amber11.orig/AmberTools/src/sff/Makefile 2011-04-14 15:30:19.000000000 +0300 |
| 366 |
+++ amber11/AmberTools/src/sff/Makefile 2011-05-20 09:53:27.000000000 +0300 |
| 367 |
@@ -1,7 +1,7 @@ |
| 368 |
include ../config.h |
| 369 |
|
| 370 |
.c.o: |
| 371 |
- $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@ $< |
| 372 |
+ $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFLIB) -o $@ $< |
| 373 |
|
| 374 |
OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \ |
| 375 |
prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \ |
| 376 |
diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile |
| 377 |
--- amber11.orig/AmberTools/src/sqm/Makefile 2011-04-14 15:30:20.000000000 +0300 |
| 378 |
+++ amber11/AmberTools/src/sqm/Makefile 2011-05-19 22:31:49.000000000 +0300 |
| 379 |
@@ -77,7 +77,7 @@ |
| 380 |
install: sqm$(SFX) |
| 381 |
mv sqm$(SFX) $(BINDIR) |
| 382 |
|
| 383 |
-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys |
| 384 |
+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys |
| 385 |
$(FC) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \ |
| 386 |
$(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS) |
| 387 |
|
| 388 |
@@ -94,10 +94,10 @@ |
| 389 |
sys: |
| 390 |
cd ../lib; $(MAKE) sys.a |
| 391 |
|
| 392 |
-netlib: |
| 393 |
- cd ../lapack; $(MAKE) $(LAPACK) |
| 394 |
- cd ../blas; $(MAKE) $(BLAS) |
| 395 |
- cd ../arpack && $(MAKE) install |
| 396 |
+#netlib: |
| 397 |
+# cd ../lapack; $(MAKE) $(LAPACK) |
| 398 |
+# cd ../blas; $(MAKE) $(BLAS) |
| 399 |
+# cd ../arpack && $(MAKE) install |
| 400 |
|
| 401 |
clean: |
| 402 |
/bin/rm -f *.o _*.f *.mod *.d sqm$(SFX) |
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