siesta.py.patch

--- siesta.py.ake	2017-03-26 14:20:45.916387226 +0800
+++ siesta.py	2017-03-27 18:21:40.186696130 +0800
@@ -124,7 +124,7 @@

             # ScaLAPACK (and BLACS)
             self.cfg.update('configopts', '--with-scalapack="%s"' % scalapack)
-            self.cfg.update('configopts', '--with-blacs="$%s"' % blacs)
+            self.cfg.update('configopts', '--with-blacs="%s"' % blacs)

             # NetCDF-Fortran
             if netcdff_loc:
@@ -132,6 +132,21 @@

             super(EB_Siesta, self).configure_step(cmd_prefix='../Src/')

+            # make sure suffixes are after include
+            suffixes = ".f .f90 .F .F90 .c .o .a"
+            regex_subSUFFIXES = [
+                (r"^(\.SUFFIXES:\s*.+)$", ""),
+                (r"^(include.*)$", r"\1\n.SUFFIXES: %s" % suffixes)
+                ]
+
+            apply_regex_substitutions(os.path.join(start_dir, 'Util', 'Sockets', 'Makefile'),
+                                      regex_subSUFFIXES)
+            apply_regex_substitutions(os.path.join(start_dir, 'Util', 'SiestaSubroutine', 'SimpleTest', 'Src', 'Makefile'),
+                                      regex_subSUFFIXES)
+
+            if self.version == "4.0-b1" or self.version == "4.0-b2":
+                apply_regex_substitutions(os.path.join(obj_dir, 'Makefile'), [(r"\$\(CFLAGS\)\-c", "$(CFLAGS) -c")])
+
         else: # there's no configure on newer versions

             if self.toolchain.comp_family() in [toolchain.INTELCOMP]:
@@ -160,7 +175,7 @@

             if netcdff_loc:
                 regex_subs.extend([
-                    (r"^(COMP_LIBS\s*=.*)$", r"\1\nNETCDF_LIBS = -lnetcdff"),
+                    (r"^(WXML\s*=.*)$", r"\1\nNETCDF_LIBS = -lnetcdff"),
                     (r"^(LIBS\s*=.*)$", r"\1 $(NETCDF_LIBS)"),
                     (r"^(FPPFLAGS\s*=.*)$", r"\1 -DCDF"),
                 ])
@@ -184,7 +199,7 @@
             adjust_permissions('./clean_all.sh', stat.S_IXUSR, recursive=False, relative=True)
             run_cmd('./clean_all.sh', log_all=True, simple=True, log_output=True)

-            if LooseVersion(self.version) >= LooseVersion("4.0"):
+            if LooseVersion(self.version) >= LooseVersion("4.1"):
                 regex_subs_TS = [
                     (r"^default:.*$", r""),
                     (r"^EXE\s*=.*$", r""),
@@ -194,12 +209,22 @@

                 apply_regex_substitutions(os.path.join(self.cfg['start_dir'], 'Util', 'TS', 'tshs2tshs', 'Makefile'), regex_subs_TS)

+                regex_subs_UtilFPP = [(r"^(CPP\s*=\s*)\$\(FC\)(.*)$", r"\1 cpp \2")]
+                apply_regex_substitutions(os.path.join(self.cfg['start_dir'], 'Src', 'fdict', 'Makefile'), regex_subs_UtilFPP)
+
             regex_subs_UtilLDFLAGS = [
                 (r'(\$\(FC\)\s*-o\s)', r'$(FC) %s %s -o ' % (os.environ['FCFLAGS'], os.environ['LDFLAGS'])),
             ]
             apply_regex_substitutions(os.path.join(self.cfg['start_dir'], 'Util', 'Optimizer', 'Makefile'), regex_subs_UtilLDFLAGS)
             apply_regex_substitutions(os.path.join(self.cfg['start_dir'], 'Util', 'JobList', 'Src', 'Makefile'), regex_subs_UtilLDFLAGS)

+            regex_subs_UtilFFT = [
+                (r"^(FFTW_ROOT.*=\s*).*$", r"\1%s" % os.path.split(os.environ['FFTW_LIB_DIR'])[0]),
+                (r"^(FFTW_LIBS.*=\s*).*$", r"\1%s" % os.environ['LIBFFT']),
+                ]
+
+            apply_regex_substitutions(os.path.join(self.cfg['start_dir'], 'Util', 'STM', 'ol-stm', 'Src',  'Makefile'), regex_subs_UtilFFT)
+
             run_cmd('./build_all.sh', log_all=True, simple=True, log_output=True)

             # Now move all the built utils to the temp installdir