xsdk: fix @develop build (#21749)

- petsc4py: update @develop build from petsc repo
- omega-h: develop branch is now main branch

5 files changed, 47 insertions, 20 deletions

diff --git a/var/spack/repos/builtin/packages/omega-h/package.py b/var/spack/repos/builtin/packages/omega-h/package.py
index 74d9787a12..e562f3836e 100644
--- a/var/spack/repos/builtin/packages/omega-h/package.py
+++ b/var/spack/repos/builtin/packages/omega-h/package.py
@@ -17,7 +17,7 @@ class OmegaH(CMakePackage):
 
     maintainers = ['ibaned']
 
-    version('develop', branch='master')
+    version('main', branch='main')
     version('9.32.5', sha256='963a203e9117024cd48d829d82b8543cd9133477fdc15386113b594fdc3246d8')
     version('9.29.0', sha256='b41964b018909ffe9cea91c23a0509b259bfbcf56874fcdf6bd9f6a179938014')
     version('9.27.0', sha256='aa51f83508cbd14a41ae953bda7da98a6ad2979465c76e5b3a3d9a7a651cb34a')
diff --git a/var/spack/repos/builtin/packages/py-petsc4py/ldshared-dev.patch b/var/spack/repos/builtin/packages/py-petsc4py/ldshared-dev.patch
new file mode 100644
index 0000000000..46a403d1ff
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-petsc4py/ldshared-dev.patch
@@ -0,0 +1,13 @@
+diff --git a/src/binding/petsc4py/conf/baseconf.py b/src/binding/petsc4py/conf/baseconf.py
+index 8a2466a5bd..73c08b923a 100644
+--- a/src/binding/petsc4py/conf/baseconf.py
++++ b/src/binding/petsc4py/conf/baseconf.py
+@@ -211,7 +211,7 @@ class PetscConfig:
+         ldshared = getenv('LDSHARED', ldshared)
+         ldflags = getenv('LDFLAGS', cflags + ' ' + (ldflags or ''))
+         ldcmd = split_quoted(ld) + split_quoted(ldflags)
+-        ldshared = [flg for flg in split_quoted(ldshared) if flg not in ldcmd]
++        ldshared = [flg for flg in split_quoted(ldshared) if flg not in ldcmd and (flg.find('/lib/spack/env')<0)]
+         ldshared = str.join(' ', ldshared)
+         #
+         def get_flags(cmd):
diff --git a/var/spack/repos/builtin/packages/py-petsc4py/package.py b/var/spack/repos/builtin/packages/py-petsc4py/package.py
index f158071bb0..ba25eebf12 100644
--- a/var/spack/repos/builtin/packages/py-petsc4py/package.py
+++ b/var/spack/repos/builtin/packages/py-petsc4py/package.py
@@ -12,7 +12,7 @@ class PyPetsc4py(PythonPackage):
 
     homepage = "https://gitlab.com/petsc/petsc4py"
     pypi = "petsc4py/petsc4py-3.14.0.tar.gz"
-    git      = "https://gitlab.com/petsc/petsc4py.git"
+    git      = "https://gitlab.com/petsc/petsc.git"
 
     maintainers = ['dalcinl', 'balay']
 
@@ -32,7 +32,8 @@ class PyPetsc4py(PythonPackage):
 
     variant('mpi', default=True,  description='Activates MPI support')
 
-    patch('ldshared.patch')
+    patch('ldshared.patch', when='@:99')
+    patch('ldshared-dev.patch', when='@develop')
 
     depends_on('py-cython', type='build', when='@develop')
     depends_on('python@2.6:2.8,3.3:', type=('build', 'run'))
@@ -54,3 +55,11 @@ class PyPetsc4py(PythonPackage):
     depends_on('petsc@3.8:3.8.99', when='@3.8:3.8.99')
     depends_on('petsc@3.7:3.7.99', when='@3.7:3.7.99')
     depends_on('petsc@3.6:3.6.99', when='@3.6:3.6.99')
+
+    @property
+    def build_directory(self):
+        import os
+        if self.spec.satisfies('@develop'):
+            return os.path.join(self.stage.source_path, 'src', 'binding', 'petsc4py')
+        else:
+            return self.stage.source_path
diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py
index ee57d79c60..b5c3b5e31f 100644
--- a/var/spack/repos/builtin/packages/slepc/package.py
+++ b/var/spack/repos/builtin/packages/slepc/package.py
@@ -54,7 +54,7 @@ class Slepc(Package):
     depends_on('python@2.6:2.8,3.4:', type='build', when='@3.11:')
 
     # Cannot mix release and development versions of SLEPc and PETSc:
-    depends_on('petsc@develop', when='@develop')
+    depends_on('petsc@develop', when='@master')
     depends_on('petsc@3.14:3.14.99', when='@3.14:3.14.99')
     depends_on('petsc@3.13:3.13.99', when='@3.13:3.13.99')
     depends_on('petsc@3.12:3.12.99', when='@3.12:3.12.99')
diff --git a/var/spack/repos/builtin/packages/xsdk/package.py b/var/spack/repos/builtin/packages/xsdk/package.py
index 2d0931c47d..bd0103cff2 100644
--- a/var/spack/repos/builtin/packages/xsdk/package.py
+++ b/var/spack/repos/builtin/packages/xsdk/package.py
@@ -32,6 +32,7 @@ class Xsdk(BundlePackage):
     variant('omega-h', default=True, description='Enable omega-h package build')
     variant('strumpack', default=True, description='Enable strumpack package build')
     variant('dealii', default=True, description='Enable dealii package build')
+    variant('alquimia', default=True, description='Enable alquimia package build')
     variant('phist', default=True, description='Enable phist package build')
     variant('ginkgo', default=True, description='Enable ginkgo package build')
     variant('libensemble', default=True, description='Enable py-libensemble package build')
@@ -61,7 +62,7 @@ class Xsdk(BundlePackage):
     depends_on('superlu-dist@5.2.2', when='@0.3.0')
     depends_on('superlu-dist@xsdk-0.2.0', when='@xsdk-0.2.0')
 
-    depends_on('trilinos@develop+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse+tpetra+nox+ifpack2+zoltan2+amesos2~exodus+dtk+intrepid2+shards gotype=int',
+    depends_on('trilinos@develop+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse+tpetra+nox+ifpack2+zoltan2+amesos2~exodus~dtk+intrepid2+shards+stratimikos gotype=int cxxstd=14',
                when='@develop +trilinos')
     depends_on('trilinos@13.0.1+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse+tpetra+nox+ifpack2+zoltan2+amesos2~exodus~dtk+intrepid2+shards gotype=int',
                when='@0.6.0 +trilinos')
@@ -74,6 +75,7 @@ class Xsdk(BundlePackage):
     depends_on('trilinos@xsdk-0.2.0+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse~tpetra~ifpack2~zoltan2~amesos2~exodus',
                when='@xsdk-0.2.0 +trilinos')
 
+    depends_on('datatransferkit@master', when='@develop +trilinos +datatransferkit')
     depends_on('datatransferkit@3.1-rc2', when='@0.6.0 +trilinos +datatransferkit')
 
     depends_on('petsc +trilinos', when='+trilinos')
@@ -94,7 +96,7 @@ class Xsdk(BundlePackage):
 
     depends_on('dealii +trilinos~adol-c', when='+trilinos +dealii')
     depends_on('dealii ~trilinos', when='~trilinos +dealii')
-    depends_on('dealii@develop~assimp~python~doc~gmsh+petsc+slepc+mpi~int64+hdf5~netcdf+metis~sundials~ginkgo~symengine', when='@develop +dealii')
+    depends_on('dealii@master~assimp~python~doc~gmsh+petsc+slepc+mpi~int64+hdf5~netcdf+metis~sundials~ginkgo~symengine~nanoflann', when='@develop +dealii')
     depends_on('dealii@9.2.0~assimp~python~doc~gmsh+petsc+slepc+mpi~int64+hdf5~netcdf+metis~sundials~ginkgo~symengine', when='@0.6.0 +dealii')
     depends_on('dealii@9.1.1~assimp~python~doc~gmsh+petsc+slepc+mpi~int64+hdf5~netcdf+metis~sundials~ginkgo~symengine', when='@0.5.0 +dealii')
     depends_on('dealii@9.0.1~assimp~python~doc~gmsh+petsc~slepc+mpi~int64+hdf5~netcdf+metis~ginkgo~symengine', when='@0.4.0 +dealii')
@@ -106,12 +108,12 @@ class Xsdk(BundlePackage):
     depends_on('pflotran@xsdk-0.3.0', when='@0.3.0')
     depends_on('pflotran@xsdk-0.2.0', when='@xsdk-0.2.0')
 
-    depends_on('alquimia@develop', when='@develop')
-    depends_on('alquimia@xsdk-0.6.0', when='@0.6.0')
-    depends_on('alquimia@xsdk-0.5.0', when='@0.5.0')
-    depends_on('alquimia@xsdk-0.4.0', when='@0.4.0')
-    depends_on('alquimia@xsdk-0.3.0', when='@0.3.0')
-    depends_on('alquimia@xsdk-0.2.0', when='@xsdk-0.2.0')
+    depends_on('alquimia@develop', when='@develop +alquimia')
+    depends_on('alquimia@xsdk-0.6.0', when='@0.6.0 +alquimia')
+    depends_on('alquimia@xsdk-0.5.0', when='@0.5.0 +alquimia ')
+    depends_on('alquimia@xsdk-0.4.0', when='@0.4.0 +alquimia')
+    depends_on('alquimia@xsdk-0.3.0', when='@0.3.0 +alquimia')
+    depends_on('alquimia@xsdk-0.2.0', when='@xsdk-0.2.0 +alquimia')
 
     depends_on('sundials +cuda', when='+cuda @0.6.0:')
     depends_on('sundials +trilinos', when='+trilinos @0.6.0:')
@@ -141,25 +143,25 @@ class Xsdk(BundlePackage):
     depends_on('amrex@18.10.1', when='@0.4.0 %intel')
     depends_on('amrex@18.10.1', when='@0.4.0 %gcc')
 
-    depends_on('slepc@develop', when='@develop')
+    depends_on('slepc@master', when='@develop')
     depends_on('slepc@3.14.0', when='@0.6.0')
     depends_on('slepc@3.12.0', when='@0.5.0')
     depends_on('slepc@3.10.1', when='@0.4.0')
 
     depends_on('omega-h +trilinos', when='+trilinos +omega-h')
     depends_on('omega-h ~trilinos', when='~trilinos +omega-h')
-    depends_on('omega-h@develop', when='@develop +omega-h')
+    depends_on('omega-h@main', when='@develop +omega-h')
     depends_on('omega-h@9.32.5', when='@0.6.0 +omega-h')
     depends_on('omega-h@9.29.0', when='@0.5.0 +omega-h')
     depends_on('omega-h@9.19.1', when='@0.4.0 +omega-h')
 
-    depends_on('strumpack ~cuda', when='~cuda @0.6.0:')
-    depends_on('strumpack@master', when='@develop +strumpack')
+    depends_on('strumpack ~cuda', when='~cuda @0.6.0: +strumpack')
+    depends_on('strumpack@master~slate', when='@develop +strumpack')
     depends_on('strumpack@5.0.0~slate', when='@0.6.0 +strumpack')
     depends_on('strumpack@3.3.0~slate', when='@0.5.0 +strumpack')
     depends_on('strumpack@3.1.1~slate', when='@0.4.0 +strumpack')
 
-    depends_on('pumi@develop', when='@develop')
+    depends_on('pumi@master', when='@develop')
     depends_on('pumi@2.2.5', when='@0.6.0')
     depends_on('pumi@2.2.1', when='@0.5.0')
     depends_on('pumi@2.2.0', when='@0.4.0')
@@ -182,7 +184,7 @@ class Xsdk(BundlePackage):
 
     depends_on('phist kernel_lib=tpetra', when='+trilinos +phist')
     depends_on('phist kernel_lib=petsc', when='~trilinos +phist')
-    depends_on('phist@develop ~fortran ~scamac ~host', when='@develop +phist')
+    depends_on('phist@develop ~fortran ~scamac ~openmp ~host ~int64', when='@develop +phist')
     depends_on('phist@1.9.3 ~fortran ~scamac ~openmp ~host ~int64', when='@0.6.0 +phist')
     depends_on('phist@1.8.0 ~fortran ~scamac ~openmp ~host ~int64', when='@0.5.0 +phist')
     depends_on('phist@1.7.5 ~fortran ~scamac ~openmp ~host ~int64', when='@0.4.0 +phist')
@@ -195,6 +197,7 @@ class Xsdk(BundlePackage):
     depends_on('ginkgo@1.1.0 ~openmp+cuda', when='@0.5.0 +cuda +ginkgo')
 
     depends_on('py-libensemble@develop+petsc4py', type='run', when='@develop +libensemble')
+    depends_on('py-petsc4py@develop', type='run', when='@develop +libensemble')
     depends_on('py-libensemble@0.7.1+petsc4py', type='run', when='@0.6.0 +libensemble')
     depends_on('py-petsc4py@3.14.0', type='run', when='@0.6.0 +libensemble')
     depends_on('py-libensemble@0.5.2+petsc4py', type='run', when='@0.5.0 +libensemble')
@@ -214,8 +217,10 @@ class Xsdk(BundlePackage):
     depends_on('heffte@develop+fftw', when='@develop +heffte')
     depends_on('heffte@2.0.0+fftw', when='@0.6.0 +heffte')
 
-    depends_on('slate@2020.10.00 ~cuda', when='~cuda +slate %gcc@6.0:')
-    depends_on('slate@2020.10.00 +cuda', when='+cuda +slate %gcc@6.0:')
+    depends_on('slate@master ~cuda', when='@develop ~cuda +slate %gcc@6.0:')
+    depends_on('slate@master +cuda', when='@develop +cuda +slate %gcc@6.0:')
+    depends_on('slate@2020.10.00 ~cuda', when='@0.6.0 ~cuda +slate %gcc@6.0:')
+    depends_on('slate@2020.10.00 +cuda', when='@0.6.0 +cuda +slate %gcc@6.0:')
 
     # xSDKTrilinos depends on the version of Trilinos built with
     # +tpetra which is turned off for faster xSDK