Merge remote-tracking branch 'upstream/develop' into efischer/160311-StagedPackage

var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch

@@ -0,0 +1,22 @@
+# HG changeset patch
+# User Sean Farley <sean@mcs.anl.gov>
+# Date 1332269671 18000
+#      Tue Mar 20 13:54:31 2012 -0500
+# Node ID b95c0c2e1d8bf8e3273f7d45e856f0c0127d998e
+# Parent  88049269953c67c3fdcc4309bf901508a875f0dc
+cmake: add gklib headers to install into include
+
+diff -r 88049269953c -r b95c0c2e1d8b libmetis/CMakeLists.txt
+Index: libmetis/CMakeLists.txt
+===================================================================
+--- a/libmetis/CMakeLists.txt Tue Mar 20 13:54:29 2012 -0500
++++ b/libmetis/CMakeLists.txt Tue Mar 20 13:54:31 2012 -0500
+@@ -12,6 +12,8 @@ endif()
+ if(METIS_INSTALL)
+   install(TARGETS metis
+     LIBRARY DESTINATION lib
+     RUNTIME DESTINATION lib
+     ARCHIVE DESTINATION lib)
++  install(FILES gklib_defs.h DESTINATION include)
++  install(FILES gklib_rename.h DESTINATION include)
+ endif()

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

@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-
+import glob
 
 class Metis(Package):
     """
@@ -49,6 +49,8 @@ class Metis(Package):
 
     depends_on('gdb', when='+gdb')
 
+    patch('install_gklib_defs_rename.patch')
+
     def install(self, spec, prefix):
 
         options = []
@@ -81,3 +83,10 @@ def install(self, spec, prefix):
             cmake(source_directory, *options)
             make()
             make("install")
+
+            # install GKlib headers, which will be needed for ParMETIS
+            GKlib_dist = join_path(prefix.include,'GKlib')
+            mkdirp(GKlib_dist)
+            fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
+            for f in fs:
+                install(f, GKlib_dist)

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

@@ -43,6 +43,13 @@ def install(self, spec, prefix):
             "--enable-dap"
         ]
 
+        # Make sure Netcdf links against Spack's curl
+        # Otherwise it may pick up system's curl, which could lead to link errors:
+        # /usr/lib/x86_64-linux-gnu/libcurl.so: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0'
+        LIBS.append("-lcurl")
+        CPPFLAGS.append("-I%s" % spec['curl'].prefix.include)
+        LDFLAGS.append ("-L%s" % spec['curl'].prefix.lib)
+
         if '+mpi' in spec:
             config_args.append('--enable-parallel4')
 

var/spack/repos/builtin/packages/netlib-blas/package.py

@@ -1,46 +0,0 @@
-from spack import *
-import os
-
-
-class NetlibBlas(Package):
-    """Netlib reference BLAS"""
-    homepage = "http://www.netlib.org/lapack/"
-    url      = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
-
-    version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
-
-    variant('fpic', default=False, description="Build with -fpic compiler option")
-
-    # virtual dependency
-    provides('blas')
-
-    # Doesn't always build correctly in parallel
-    parallel = False
-
-    def patch(self):
-        os.symlink('make.inc.example', 'make.inc')
-
-        mf = FileFilter('make.inc')
-        mf.filter('^FORTRAN.*', 'FORTRAN = f90')
-        mf.filter('^LOADER.*',  'LOADER = f90')
-        mf.filter('^CC =.*',  'CC = cc')
-
-        if '+fpic' in self.spec:
-            mf.filter('^OPTS.*=.*',  'OPTS = -O2 -frecursive -fpic')
-            mf.filter('^CFLAGS =.*',  'CFLAGS = -O3 -fpic')
-
-
-    def install(self, spec, prefix):
-        make('blaslib')
-
-        # Tests that blas builds correctly
-        make('blas_testing')
-
-        # No install provided
-        mkdirp(prefix.lib)
-        install('librefblas.a', prefix.lib)
-
-        # Blas virtual package should provide blas.a and libblas.a
-        with working_dir(prefix.lib):
-            symlink('librefblas.a', 'blas.a')
-            symlink('librefblas.a', 'libblas.a')

var/spack/repos/builtin/packages/netlib-lapack/package.py

@@ -1,13 +1,12 @@
 from spack import *
 
+
 class NetlibLapack(Package):
     """
-    LAPACK version 3.X is a comprehensive FORTRAN library that does
+    LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix
-    linear algebra operations including matrix inversions, least
+    inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value
-    squared solutions to linear sets of equations, eigenvector
+    decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the
-    analysis, singular value decomposition, etc. It is a very
+    scientific community.
-    comprehensive and reputable package that has found extensive
-    use in the scientific community.
     """
     homepage = "http://www.netlib.org/lapack/"
     url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
@@ -19,41 +18,34 @@ class NetlibLapack(Package):
     version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
     version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
 
-    variant('shared', default=False, description="Build shared library version")
+    variant('debug', default=False, description='Activates the Debug build type')
-    variant('fpic', default=False, description="Build with -fpic compiler option")
+    variant('shared', default=True, description="Build shared library version")
+    variant('external-blas', default=False, description='Build lapack with an external blas')
+
+    variant('lapacke', default=True, description='Activates the build of the LAPACKE C interface')
 
     # virtual dependency
+    provides('blas', when='~external-blas')
     provides('lapack')
 
-    # blas is a virtual dependency.
-    depends_on('blas')
     depends_on('cmake')
-
+    depends_on('blas', when='+external-blas')
-    # Doesn't always build correctly in parallel
-    parallel = False
-
-    @when('^netlib-blas')
-    def get_blas_libs(self):
-        blas = self.spec['netlib-blas']
-        return [join_path(blas.prefix.lib, 'blas.a')]
-
-    @when('^atlas')
-    def get_blas_libs(self):
-        blas = self.spec['atlas']
-        return [join_path(blas.prefix.lib, l)
-                for l in ('libf77blas.a', 'libatlas.a')]
 
     def install(self, spec, prefix):
-        blas_libs = ";".join(self.get_blas_libs())
+        cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
-        cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
+                      '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+                      '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
+        if '+external-blas' in spec:
+            # TODO : the mechanism to specify the library should be more general,
+            # TODO : but this allows to have an hook to an external blas
+            cmake_args.extend([
+                '-DUSE_OPTIMIZED_BLAS:BOOL=ON',
+                '-DBLAS_LIBRARIES:PATH=%s' % join_path(spec['blas'].prefix.lib, 'libblas.a')
+            ])
 
-        if '+shared' in spec:
+        cmake_args.extend(std_cmake_args)
-            cmake_args.append('-DBUILD_SHARED_LIBS=ON')
-        if '+fpic' in spec:
-            cmake_args.append('-DCMAKE_POSITION_INDEPENDENT_CODE=ON')
 
-        cmake_args += std_cmake_args
+        with working_dir('spack-build', create=True):
-
+            cmake('..', *cmake_args)
-        cmake(*cmake_args)
             make()
             make("install")

var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch

@@ -1,13 +1,71 @@
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index ca945dd..1bf94e9 100644
+index ca945dd..aff8b5f 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
+@@ -23,7 +23,7 @@ else()
+   set(ParMETIS_LIBRARY_TYPE STATIC)
+ endif()
+ 
+-include(${GKLIB_PATH}/GKlibSystem.cmake)
++include_directories(${GKLIB_PATH})
+ 
+ # List of paths that the compiler will search for header files.
+ # i.e., the -I equivalent
 @@ -33,7 +33,7 @@ include_directories(${GKLIB_PATH})
  include_directories(${METIS_PATH}/include)
  
  # List of directories that cmake will look for CMakeLists.txt
 -add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
-+#add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
++find_library(METIS_LIBRARY metis PATHS ${METIS_PATH}/lib)
  add_subdirectory(include)
  add_subdirectory(libparmetis)
  add_subdirectory(programs)
+diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt
+index 9cfc8a7..e0c4de7 100644
+--- a/libparmetis/CMakeLists.txt
++++ b/libparmetis/CMakeLists.txt
+@@ -5,7 +5,10 @@ file(GLOB parmetis_sources *.c)
+ # Create libparmetis
+ add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources})
+ # Link with metis and MPI libraries.
+-target_link_libraries(parmetis metis ${MPI_LIBRARIES})
++target_link_libraries(parmetis ${METIS_LIBRARY} ${MPI_LIBRARIES})
++if(UNIX)
++  target_link_libraries(parmetis m)
++endif()
+ set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}")
+ 
+ install(TARGETS parmetis
+diff --git a/libparmetis/parmetislib.h b/libparmetis/parmetislib.h
+index c1daeeb..07511f6 100644
+--- a/libparmetis/parmetislib.h
++++ b/libparmetis/parmetislib.h
+@@ -20,13 +20,12 @@
+ 
+ #include <parmetis.h>
+ 
+-#include "../metis/libmetis/gklib_defs.h"
++#include <gklib_defs.h>
+ 
+-#include <mpi.h> 
++#include <mpi.h>
+ 
+ #include <rename.h>
+ #include <defs.h>
+ #include <struct.h>
+ #include <macros.h>
+ #include <proto.h>
+-
+diff --git a/programs/parmetisbin.h b/programs/parmetisbin.h
+index e26cd2d..d156480 100644
+--- a/programs/parmetisbin.h
++++ b/programs/parmetisbin.h
+@@ -19,7 +19,7 @@
+ #include <GKlib.h>
+ #include <parmetis.h>
+ 
+-#include "../metis/libmetis/gklib_defs.h"
++#include <gklib_defs.h>
+ #include "../libparmetis/rename.h"
+ #include "../libparmetis/defs.h"
+ #include "../libparmetis/struct.h"

var/spack/repos/builtin/packages/parmetis/link-to-lm.patch

@@ -1,14 +0,0 @@
-diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt
-index 9cfc8a7..dfc0125 100644
---- a/libparmetis/CMakeLists.txt
-+++ b/libparmetis/CMakeLists.txt
-@@ -5,7 +5,7 @@ file(GLOB parmetis_sources *.c)
- # Create libparmetis
- add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources})
- # Link with metis and MPI libraries.
--target_link_libraries(parmetis metis ${MPI_LIBRARIES})
-+target_link_libraries(parmetis metis ${MPI_LIBRARIES} "-lm")
- set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}")
-
- install(TARGETS parmetis
-

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

@@ -52,8 +52,6 @@ class Parmetis(Package):
     # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
     patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
-    patch('link-to-lm.patch')
-
     depends_on('gdb', when='+gdb')
 
     def install(self, spec, prefix):
@@ -66,7 +64,7 @@ def install(self, spec, prefix):
 
         # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
         # FIXME : they use a non-standard name
-        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), # still need headers from METIS source, and they are not installed with METIS. shame...
+        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=spec['metis'].prefix.include),
                         '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
                         '-DCMAKE_C_COMPILER:STRING=mpicc',
                         '-DCMAKE_CXX_COMPILER:STRING=mpicxx'])