Siesta: only apply patch to <4.1 and fix Intel compiler (#6466)

* Siesta: add 3.2 and don't apply patch to 4.1

* siesta: fix bad optimization with Intel compiler

* siesta: Fix download URL

* siesta: build utilities too

* siesta: fix binary name collision

* siesta: Cleanup

var/spack/repos/builtin/packages/siesta/configure.patch

@@ -18,4 +18,36 @@
  else
    NETCDF_LIBS="";tw_netcdf_ok=no;if test ! -z "$with_netcdf"; then { { echo "$as_me:$LINENO: error: Could not find NetCDF library." >&5
  echo "$as_me: error: Could not find NetCDF library." >&2;}
-
+--- a/Util/TBTrans_rep/Makefile	2017-12-08 09:49:02.307877000 +0100
++++ b/Util/TBTrans_rep/Makefile	2017-12-08 09:49:44.385288000 +0100
+@@ -14,7 +14,7 @@
+ # Please see note about Linear-Algebra libraries below
+ #
+ 
+-default: what tbtrans 
++default: what tbtrans_rep 
+ 
+ VPATH:=$(shell pwd)/../../Src
+ OBJDIR=Obj
+@@ -91,16 +91,16 @@
+                           "ARCH_MAKE=../$(ARCH_MAKE)" \
+                           "INCFLAGS=$(LINALG_INCFLAGS)" "FFLAGS=$(FFLAGS:$(IPO_FLAG)=)" $(LINALG))
+ 
+-tbtrans: FPPFLAGS+=$(DEFS_PREFIX) -DTBTRANS
+-tbtrans: DEFS+=$(DEFS_PREFIX) -DTBTRANS
+-tbtrans: $(MPI_INTERFACE) $(FDF) $(TBTOBJS) $(SYSOBJ) $(LINALG)
+-	$(FC) $(FFLAGS) $(LDFLAGS) -o tbtrans \
++tbtrans_rep: FPPFLAGS+=$(DEFS_PREFIX) -DTBTRANS
++tbtrans_rep: DEFS+=$(DEFS_PREFIX) -DTBTRANS
++tbtrans_rep: $(MPI_INTERFACE) $(FDF) $(TBTOBJS) $(SYSOBJ) $(LINALG)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o tbtrans_rep \
+               $(TBTOBJS) $(MPI_INTERFACE)  \
+               $(FDF) $(LIBS) $(LINALG)  || echo "***Please see top of Makefile"
+ 
+ clean: 
+ 	@echo "==> Cleaning object, library, and executable files"
+-	rm -f tbtrans *.o *.a *.mod
++	rm -f tbtrans_rep *.o *.a *.mod
+ 	rm -rf ./fdf
+ 	rm -rf ./MPI
+ 	rm -rf ./Libs

var/spack/repos/builtin/packages/siesta/package.py

@@ -24,6 +24,7 @@
 ##############################################################################
 
 from spack import *
+import os
 
 
 class Siesta(Package):
@@ -31,11 +32,11 @@ class Siesta(Package):
        dynamics simulations of molecules and solids."""
 
     homepage = "https://departments.icmab.es/leem/siesta/"
-    url      = "https://launchpad.net/siesta/4.0/4.0.1/+download/siesta-4.0.1.tar.gz"
 
-    version('4.0.1', '5cb60ce068f2f6e84fa9184ffca94c08')
+    version('4.0.1', '5cb60ce068f2f6e84fa9184ffca94c08', url='https://launchpad.net/siesta/4.0/4.0.1/+download/siesta-4.0.1.tar.gz')
+    version('3.2-pl-5', '27a300c65eb2a25d107d910d26aaf81a', url='http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-3.2-pl-5.tgz')
 
-    patch('configure.patch')
+    patch('configure.patch', when='@:4.0')
 
     depends_on('mpi')
     depends_on('blas')
@@ -63,18 +64,24 @@ def configure(self, spec, prefix):
                           # Intel's mpiifort is not found
                           'MPIFC=%s' % spec['mpi'].mpifc
                           ]
-        with working_dir('Obj'):
+        for d in ['Obj', 'Obj_trans']:
-            sh('../Src/configure', *configure_args)
+            with working_dir(d, create=True):
-            sh('../Src/obj_setup.sh')
+                sh('../Src/configure', *configure_args)
-        with working_dir('Obj_trans', create=True):
+                if spec.satisfies('@:4.0%intel'):
-            sh('../Src/configure', *configure_args)
+                    with open('arch.make', 'a') as f:
-            sh('../Src/obj_setup.sh')
+                        f.write('\natom.o: atom.F\n')
+                        f.write('\t$(FC) -c $(FFLAGS) -O1')
+                        f.write('$(INCFLAGS) $(FPPFLAGS) $<')
+                sh('../Src/obj_setup.sh')
 
     def build(self, spec, prefix):
         with working_dir('Obj'):
             make(parallel=False)
         with working_dir('Obj_trans'):
             make('transiesta', parallel=False)
+        with working_dir('Util'):
+            sh = which('sh')
+            sh('build_all.sh')
 
     def install(self, spec, prefix):
         mkdir(prefix.bin)
@@ -82,3 +89,8 @@ def install(self, spec, prefix):
             install('siesta', prefix.bin)
         with working_dir('Obj_trans'):
             install('transiesta', prefix.bin)
+        for root, _, files in os.walk('Util'):
+            for fname in files:
+                fname = join_path(root, fname)
+                if os.access(fname, os.X_OK):
+                    install(fname, prefix.bin)