Repository: spack/spack

Issue:
ADIOS package doesn't declare NetCDF dependency
The ADIOS package expects NetCDF to be installed, but doesn't declare it as dependency.



Discussion:
Are you working on a PR for this?

No, I'm not.

will update that in a sec (is `netcdf` enough or do we need `netcdf-cxx`, `netcdf-cxx4` and `netcdf-fortran` as dependencies, too?).

will also update to ADIOS' `1.10.0` release

@ax3l: thanks!  Welcome to Spack!

thanks, looking forward to your SC16 tutorial!


Resolving patch:
diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py
--- a/var/spack/repos/builtin/packages/adios/package.py
+++ b/var/spack/repos/builtin/packages/adios/package.py
@@ -1,4 +1,27 @@
-import os
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 
 from spack import *
 
@@ -12,30 +35,94 @@ class Adios(Package):
     """
 
     homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
-    url = "https://github.com/ornladios/ADIOS/archive/v1.9.0.tar.gz"
+    url      = "https://github.com/ornladios/ADIOS/archive/v1.10.0.tar.gz"
 
+    version('1.10.0', 'eff450a4c0130479417cfd63186957f3')
     version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
 
+    variant('shared', default=True,
+            description='Builds a shared version of the library')
+
+    variant('fortran', default=False,
+            description='Enable Fortran bindings support')
+
+    variant('mpi', default=True, description='Enable MPI support')
+    variant('infiniband', default=False, description='Enable infiniband support')
+
+    variant('zlib', default=True, description='Enable szip transform support')
+    variant('szip', default=False, description='Enable szip transform support')
+    variant('hdf5', default=False, description='Enable HDF5 transport support')
+    variant('netcdf', default=False, description='Enable NetCDF transport support')
+
     # Lots of setting up here for this package
     # module swap PrgEnv-intel PrgEnv-$COMP
     # module load cray-netcdf/4.3.3.1
     # module load cray-hdf5/1.8.14
     # module load python/2.7.10
-    depends_on('hdf5')
-    depends_on('mxml')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('python', type='build')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('mxml@2.9:')
+    # optional transformations
+    depends_on('zlib', when='+zlib')
+    depends_on('szip', when='+szip')
+    # optional transports
+    depends_on('hdf5', when='+hdf5')
+    depends_on('netcdf', when='+netcdf')
+
+    def validate(self, spec):
+        """
+        Checks if incompatible variants have been activated at the same time
+        :param spec: spec of the package
+        :raises RuntimeError: in case of inconsistencies
+        """
+        if '+fortran' in spec and not self.compiler.fc:
+            msg = 'cannot build a fortran variant without a fortran compiler'
+            raise RuntimeError(msg)
 
     def install(self, spec, prefix):
-        configure_args = ["--prefix=%s" % prefix,
-                          "--with-mxml=%s" % spec['mxml'].prefix,
-                          "--with-hdf5=%s" % spec['hdf5'].prefix,
-                          "--with-netcdf=%s" % os.environ["NETCDF_DIR"],
-                          "--with-infiniband=no",
-                          "MPICC=cc", "MPICXX=CC", "MPIFC=ftn",
-                          "CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK"]
-
-        if spec.satisfies('%gcc'):
-            configure_args.extend(["CC=gcc", "CXX=g++", "FC=gfortran"])
-
-        configure(*configure_args)
+        self.validate(spec)
+        # Handle compilation after spec validation
+        extra_args = []
+
+        # required, otherwise building its python bindings on ADIOS will fail
+        extra_args.append("CFLAGS=-fPIC")
+
+        # always build external MXML, even in ADIOS 1.10.0+
+        extra_args.append('--with-mxml=%s' % spec['mxml'].prefix)
+
+        if '+shared' in spec:
+            extra_args.append('--enable-shared')
+
+        if '+mpi' in spec:
+            extra_args.append('--with-mpi')
+        if '+infiniband' in spec:
+            extra_args.append('--with-infiniband')
+        else:
+            extra_args.append('--with-infiniband=no')
+
+        if '+fortran' in spec:
+            extra_args.append('--enable-fortran')
+        else:
+            extra_args.append('--disable-fortran')
+
+        if '+zlib' in spec:
+            extra_args.append('--with-zlib=%s' % spec['zlib'].prefix)
+        if '+szip' in spec:
+            extra_args.append('--with-szip=%s' % spec['szip'].prefix)
+        if '+hdf5' in spec:
+            extra_args.append('--with-hdf5=%s' % spec['hdf5'].prefix)
+        if '+netcdf' in spec:
+            extra_args.append('--with-netcdf=%s' % spec['netcdf'].prefix)
+
+        sh = which('sh')
+        sh('./autogen.sh')
+
+        configure("--prefix=%s" % prefix,
+                  *extra_args)
         make()
         make("install")


Test patch: