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-rw-r--r--var/spack/repos/builtin.mock/packages/multimethod/package.py10
-rw-r--r--var/spack/repos/builtin/packages/adios/package.py (renamed from var/spack/packages/adios/package.py)23
-rw-r--r--var/spack/repos/builtin/packages/autoconf/package.py28
-rw-r--r--var/spack/repos/builtin/packages/automake/package.py20
-rw-r--r--var/spack/repos/builtin/packages/curl/package.py2
-rw-r--r--var/spack/repos/builtin/packages/eigen/package.py10
-rw-r--r--var/spack/repos/builtin/packages/emacs/package.py35
-rw-r--r--var/spack/repos/builtin/packages/fenics/package.py3
-rw-r--r--var/spack/repos/builtin/packages/fenics/petsc-3.7.patch394
-rw-r--r--var/spack/repos/builtin/packages/fenics/petsc-version-detection.patch39
-rw-r--r--var/spack/repos/builtin/packages/foam-extend/package.py235
-rw-r--r--var/spack/repos/builtin/packages/giflib/package.py41
-rw-r--r--var/spack/repos/builtin/packages/glib/g_date_strftime.patch34
-rw-r--r--var/spack/repos/builtin/packages/glib/package.py8
-rw-r--r--var/spack/repos/builtin/packages/hdf5/package.py29
-rw-r--r--var/spack/repos/builtin/packages/julia/package.py33
-rw-r--r--var/spack/repos/builtin/packages/libtool/package.py24
-rw-r--r--var/spack/repos/builtin/packages/libxpm/package.py44
-rw-r--r--var/spack/repos/builtin/packages/mpich/package.py5
-rw-r--r--var/spack/repos/builtin/packages/mvapich2/package.py5
-rw-r--r--var/spack/repos/builtin/packages/mxml/package.py (renamed from var/spack/packages/mxml/package.py)15
-rw-r--r--var/spack/repos/builtin/packages/netcdf-fortran/package.py2
-rw-r--r--var/spack/repos/builtin/packages/openmpi/package.py5
-rw-r--r--var/spack/repos/builtin/packages/parmgridgen/package.py71
-rw-r--r--var/spack/repos/builtin/packages/py-protobuf/package.py50
-rw-r--r--var/spack/repos/builtin/packages/scotch/package.py12
-rw-r--r--var/spack/repos/builtin/packages/swiftsim/package.py79
27 files changed, 1169 insertions, 87 deletions
diff --git a/var/spack/repos/builtin.mock/packages/multimethod/package.py b/var/spack/repos/builtin.mock/packages/multimethod/package.py
index 649afa5945..ca991632dd 100644
--- a/var/spack/repos/builtin.mock/packages/multimethod/package.py
+++ b/var/spack/repos/builtin.mock/packages/multimethod/package.py
@@ -106,17 +106,11 @@ class Multimethod(Package):
#
# Make sure we can switch methods on different target
#
-# for platform_name in ['cray_xc', 'darwin', 'linux']:
-# file_path = join_path(spack.platform_path, platform_name)
-# platform_mod = imp.load_source('spack.platforms', file_path + '.py')
-# cls = getattr(platform_mod, mod_to_class(platform_name))
-
-# platform = cls()
- platform = spack.architecture.sys_type()
+ platform = spack.architecture.platform()
targets = platform.targets.values()
if len(targets) > 1:
targets = targets[:-1]
-
+
for target in targets:
@when('target='+target.name)
def different_by_target(self):
diff --git a/var/spack/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py
index 260dcbe851..9e0452ba6f 100644
--- a/var/spack/packages/adios/package.py
+++ b/var/spack/repos/builtin/packages/adios/package.py
@@ -1,15 +1,18 @@
import os
from spack import *
+
+
class Adios(Package):
- """The Adaptable IO System (ADIOS) provides a simple,
- flexible way for scientists to describe the
- data in their code that may need to be written,
- read, or processed outside of the running simulation
"""
-
+ The Adaptable IO System (ADIOS) provides a simple,
+ flexible way for scientists to describe the
+ data in their code that may need to be written,
+ read, or processed outside of the running simulation
+ """
+
homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
- url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
+ url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76')
@@ -22,13 +25,13 @@ class Adios(Package):
depends_on('mxml')
def install(self, spec, prefix):
- configure_args = ["--prefix=%s" % prefix,
- "--with-mxml=%s" % spec['mxml'].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"]
+ "MPICC=cc", "MPICXX=CC", "MPIFC=ftn",
+ "CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK"]
if spec.satisfies('%gcc'):
configure_args.extend(["CC=gcc", "CXX=g++", "FC=gfortran"])
diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py
index d920855a2f..770ceed48b 100644
--- a/var/spack/repos/builtin/packages/autoconf/package.py
+++ b/var/spack/repos/builtin/packages/autoconf/package.py
@@ -24,18 +24,36 @@
##############################################################################
from spack import *
+
class Autoconf(Package):
- """Autoconf -- system configuration part of autotools"""
- homepage = "https://www.gnu.org/software/autoconf/"
- url = "http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz"
+ """
+ Autoconf -- system configuration part of autotools
+ """
+ homepage = 'https://www.gnu.org/software/autoconf/'
+ url = 'http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz'
version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
- depends_on("m4")
+ depends_on('m4')
+
+ def _make_executable(self, name):
+ return Executable(join_path(self.prefix.bin, name))
+
+ def setup_dependent_package(self, module, dependent_spec):
+ # Autoconf is very likely to be a build dependency,
+ # so we add the tools it provides to the dependent module
+ executables = ['autoconf',
+ 'autoheader',
+ 'autom4te',
+ 'autoreconf',
+ 'autoscan',
+ 'autoupdate',
+ 'ifnames']
+ for name in executables:
+ setattr(module, name, self._make_executable(name))
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
-
make()
make("install")
diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py
index 331b364496..78b0a5b34f 100644
--- a/var/spack/repos/builtin/packages/automake/package.py
+++ b/var/spack/repos/builtin/packages/automake/package.py
@@ -24,10 +24,13 @@
##############################################################################
from spack import *
+
class Automake(Package):
- """Automake -- make file builder part of autotools"""
- homepage = "http://www.gnu.org/software/automake/"
- url = "http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz"
+ """
+ Automake -- make file builder part of autotools
+ """
+ homepage = 'http://www.gnu.org/software/automake/'
+ url = 'http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz'
version('1.15', '716946a105ca228ab545fc37a70df3a3')
version('1.14.1', 'd052a3e884631b9c7892f2efce542d75')
@@ -35,8 +38,17 @@ class Automake(Package):
depends_on('autoconf')
+ def _make_executable(self, name):
+ return Executable(join_path(self.prefix.bin, name))
+
+ def setup_dependent_package(self, module, dependent_spec):
+ # Automake is very likely to be a build dependency,
+ # so we add the tools it provides to the dependent module
+ executables = ['aclocal', 'automake']
+ for name in executables:
+ setattr(module, name, self._make_executable(name))
+
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
-
make()
make("install")
diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py
index e3de6ee5a1..79570205fa 100644
--- a/var/spack/repos/builtin/packages/curl/package.py
+++ b/var/spack/repos/builtin/packages/curl/package.py
@@ -24,6 +24,7 @@
##############################################################################
from spack import *
+
class Curl(Package):
"""cURL is an open source command line tool and library for
transferring data with URL syntax"""
@@ -31,6 +32,7 @@ class Curl(Package):
homepage = "http://curl.haxx.se"
url = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2"
+ version('7.49.1', '6bb1f7af5b58b30e4e6414b8c1abccab')
version('7.47.1', '9ea3123449439bbd960cd25cf98796fb')
version('7.46.0', '9979f989a2a9930d10f1b3deeabc2148')
version('7.45.0', '62c1a352b28558f25ba6209214beadc8')
diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py
index e20fcffdd7..9ff4107619 100644
--- a/var/spack/repos/builtin/packages/eigen/package.py
+++ b/var/spack/repos/builtin/packages/eigen/package.py
@@ -28,7 +28,9 @@ from spack import *
class Eigen(Package):
"""
- Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms
+ Eigen is a C++ template library for linear algebra
+
+ Matrices, vectors, numerical solvers, and related algorithms
"""
homepage = 'http://eigen.tuxfamily.org/'
@@ -42,16 +44,16 @@ class Eigen(Package):
variant('scotch', default=True, description='Enables scotch backend')
variant('fftw', default=True, description='Enables FFTW backend')
variant('suitesparse', default=True, description='Enables SuiteSparse support')
+ variant('mpfr', default=True, description='Enables support for multi-precisions floating points via mpfr')
# TODO : dependency on googlehash, superlu, adolc missing
-
depends_on('cmake')
depends_on('metis@5:', when='+metis')
depends_on('scotch', when='+scotch')
depends_on('fftw', when='+fftw')
depends_on('suite-sparse', when='+suitesparse')
- depends_on('mpfr@2.3.0:') # Eigen 3.2.7 requires at least 2.3.0
- depends_on('gmp')
+ depends_on('mpfr@2.3.0:', when="+mpfr")
+ depends_on('gmp', when="+mpfr")
def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py
index 4b05864a1e..a9ebd6d42f 100644
--- a/var/spack/repos/builtin/packages/emacs/package.py
+++ b/var/spack/repos/builtin/packages/emacs/package.py
@@ -23,23 +23,44 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
+import llnl.util.tty as tty
+
class Emacs(Package):
"""The Emacs programmable text editor."""
+
homepage = "https://www.gnu.org/software/emacs"
url = "http://ftp.gnu.org/gnu/emacs/emacs-24.5.tar.gz"
version('24.5', 'd74b597503a68105e61b5b9f6d065b44')
+ variant('X', default=True, description="Enable a X toolkit (GTK+)")
+ variant('gtkplus', default=False, description="Enable a GTK+ as X toolkit (this variant is ignored if ~X)")
+
depends_on('ncurses')
- # Emacs also depends on:
- # GTK or other widget library
- # libtiff, png, etc.
- # For now, we assume the system provides all that stuff.
- # For Ubuntu 14.04 LTS:
- # sudo apt-get install libgtk-3-dev libxpm-dev libtiff5-dev libjpeg8-dev libgif-dev libpng12-dev
+ depends_on('libtiff', when='+X')
+ depends_on('libpng', when='+X')
+ depends_on('libxpm', when='+X')
+ depends_on('giflib', when='+X')
+ depends_on('gtkplus', when='+X+gtkplus')
def install(self, spec, prefix):
- configure('--prefix=%s' % prefix)
+ args = []
+ if '+X' in spec:
+ if '+gtkplus' in spec:
+ toolkit = 'gtk{0}'.format(spec['gtkplus'].version.up_to(1))
+ else:
+ toolkit = 'no'
+ args = [
+ '--with-x',
+ '--with-x-toolkit={0}'.format(toolkit)
+ ]
+ else:
+ args = ['--without-x']
+ if '+gtkplus' in spec:
+ tty.warn('The variant +gtkplus is ignored if ~X is selected.')
+
+ configure('--prefix={0}'.format(prefix), *args)
+
make()
make("install")
diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py
index 0845237656..465ab651be 100644
--- a/var/spack/repos/builtin/packages/fenics/package.py
+++ b/var/spack/repos/builtin/packages/fenics/package.py
@@ -57,6 +57,9 @@ class Fenics(Package):
# variant('slepc4py', default=True, description='Uses SLEPc4py')
# variant('pastix', default=True, description='Compile with Pastix')
+ patch('petsc-3.7.patch', when='^petsc@3.7:')
+ patch('petsc-version-detection.patch', when='@:1.6.1')
+
extends('python')
depends_on('py-numpy')
diff --git a/var/spack/repos/builtin/packages/fenics/petsc-3.7.patch b/var/spack/repos/builtin/packages/fenics/petsc-3.7.patch
new file mode 100644
index 0000000000..c1ba5c4da6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fenics/petsc-3.7.patch
@@ -0,0 +1,394 @@
+diff -Naur dolfin-1.6.0/dolfin/common/SubSystemsManager.cpp dolfin-1.6.0.new/dolfin/common/SubSystemsManager.cpp
+--- dolfin-1.6.0/dolfin/common/SubSystemsManager.cpp 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/common/SubSystemsManager.cpp 2016-06-26 23:42:56.391929550 +0200
+@@ -179,7 +179,7 @@
+ PetscInitialized(&is_initialized);
+ if (is_initialized)
+ {
+- PetscOptionsInsert(&argc, &argv, PETSC_NULL);
++ PetscOptionsInsert(NULL, &argc, &argv, PETSC_NULL);
+ }
+ else
+ {
+@@ -187,12 +187,12 @@
+ PetscInitializeNoArguments();
+
+ // Set options to avoid common failures with some 3rd party solvers
+- PetscOptionsSetValue("-mat_mumps_icntl_7", "0");
+- PetscOptionsSetValue("-mat_superlu_dist_colperm", "MMD_AT_PLUS_A");
++ PetscOptionsSetValue(NULL, "-mat_mumps_icntl_7", "0");
++ PetscOptionsSetValue(NULL, "-mat_superlu_dist_colperm", "MMD_AT_PLUS_A");
+
+ // Pass command line arguments to PETSc (will overwrite any
+ // default above)
+- PetscOptionsInsert(&argc, &argv, PETSC_NULL);
++ PetscOptionsInsert(NULL, &argc, &argv, PETSC_NULL);
+ }
+
+ // Set PETSc
+diff -Naur dolfin-1.6.0/dolfin/la/PETScKrylovSolver.cpp dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.cpp
+--- dolfin-1.6.0/dolfin/la/PETScKrylovSolver.cpp 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.cpp 2016-06-26 23:33:02.418351380 +0200
+@@ -564,6 +564,11 @@
+ return solve(x, b);
+ }
+ //-----------------------------------------------------------------------------
++PetscErrorCode PETScKrylovSolver::ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *vf)
++{
++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, static_cast<PetscViewerAndFormat *>(vf));
++}
++//-----------------------------------------------------------------------------
+ void PETScKrylovSolver::set_petsc_ksp_options()
+ {
+ PetscErrorCode ierr;
+@@ -585,7 +590,8 @@
+ const bool monitor_convergence = parameters["monitor_convergence"];
+ if (monitor_convergence)
+ {
+- ierr = KSPMonitorSet(_ksp, KSPMonitorTrueResidualNorm, 0, 0);
++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_vf);
++ ierr = KSPMonitorSet(_ksp, ksp_monitor_norm, _vf, 0);
+ if (ierr != 0) petsc_error(ierr, __FILE__, "KSPMonitorSet");
+ }
+
+diff -Naur dolfin-1.6.0/dolfin/la/PETScKrylovSolver.h dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.h
+--- dolfin-1.6.0/dolfin/la/PETScKrylovSolver.h 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.h 2016-06-26 23:19:40.767042975 +0200
+@@ -179,6 +179,12 @@
+ // PETSc solver pointer
+ KSP _ksp;
+
++ // viewer for monitoring
++ PetscViewerAndFormat* _vf;
++
++ // monitoring function
++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx);
++
+ // DOLFIN-defined PETScUserPreconditioner
+ PETScUserPreconditioner* pc_dolfin;
+
+diff -Naur dolfin-1.6.0/dolfin/la/PETScLUSolver.cpp dolfin-1.6.0.new/dolfin/la/PETScLUSolver.cpp
+--- dolfin-1.6.0/dolfin/la/PETScLUSolver.cpp 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/la/PETScLUSolver.cpp 2016-06-26 23:13:36.903732301 +0200
+@@ -246,14 +246,14 @@
+ if (parameters["num_threads"].is_set())
+ {
+ // Use number of threads specified for LU solver
+- ierr = PetscOptionsSetValue("-mat_pastix_threadnbr",
++ ierr = PetscOptionsSetValue(NULL, "-mat_pastix_threadnbr",
+ parameters["num_threads"].value_str().c_str());
+ if (ierr != 0) petsc_error(ierr, __FILE__, "PetscOptionsSetValue");
+ }
+ else
+ {
+ // Use global number of threads
+- ierr = PetscOptionsSetValue("-mat_pastix_threadnbr",
++ ierr = PetscOptionsSetValue(NULL, "-mat_pastix_threadnbr",
+ dolfin::parameters["num_threads"].value_str().c_str());
+ if (ierr != 0) petsc_error(ierr, __FILE__, "PetscOptionsSetValue");
+ }
+diff -Naur dolfin-1.6.0/dolfin/la/PETScOptions.cpp dolfin-1.6.0.new/dolfin/la/PETScOptions.cpp
+--- dolfin-1.6.0/dolfin/la/PETScOptions.cpp 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/la/PETScOptions.cpp 2016-06-26 23:37:58.613121118 +0200
+@@ -54,7 +54,7 @@
+ {
+ SubSystemsManager::init_petsc();
+ PetscErrorCode ierr;
+- ierr = PetscOptionsClearValue(option.c_str());
++ ierr = PetscOptionsClearValue(NULL, option.c_str());
+ if (ierr != 0)
+ {
+ dolfin_error("PETScOptions.cpp",
+diff -Naur dolfin-1.6.0/dolfin/la/PETScOptions.h dolfin-1.6.0.new/dolfin/la/PETScOptions.h
+--- dolfin-1.6.0/dolfin/la/PETScOptions.h 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/la/PETScOptions.h 2016-06-26 23:37:54.352023709 +0200
+@@ -65,7 +65,7 @@
+
+ PetscErrorCode ierr;
+ std::string _option = "-" + option;
+- ierr = PetscOptionsSetValue(_option.c_str(),
++ ierr = PetscOptionsSetValue(NULL, _option.c_str(),
+ boost::lexical_cast<std::string>(value).c_str());
+ if (ierr != 0)
+ {
+diff -Naur dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.cpp dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.cpp
+--- dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.cpp 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.cpp 2016-06-26 23:35:25.930631132 +0200
+@@ -99,6 +99,19 @@
+ solve(_matA->size(0));
+ }
+ //-----------------------------------------------------------------------------
++PetscErrorCode SLEPcEigenSolver::eps_monitor(EPS eps, PetscInt its, PetscInt nconv, PetscScalar* eigr,
++ PetscScalar* eigi, PetscReal* errest,
++ PetscInt nest, void *vf)
++{
++ EPSMonitorAll(eps, its, nconv, eigr, eigi, errest, nest,
++ static_cast<PetscViewerAndFormat *>(vf));
++}
++//-----------------------------------------------------------------------------
++PetscErrorCode SLEPcEigenSolver::ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *vf)
++{
++ KSPMonitorDefault(ksp, n, rnorm, static_cast<PetscViewerAndFormat *>(vf));
++}
++//-----------------------------------------------------------------------------
+ void SLEPcEigenSolver::solve(std::size_t n)
+ {
+ dolfin_assert(_matA);
+@@ -139,10 +152,11 @@
+ {
+ KSP ksp;
+ ST st;
+- EPSMonitorSet(_eps, EPSMonitorAll, NULL, NULL);
++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_vf);
++ EPSMonitorSet(_eps, eps_monitor, _vf, NULL);
+ EPSGetST(_eps, &st);
+ STGetKSP(st, &ksp);
+- KSPMonitorSet(ksp, KSPMonitorDefault, NULL, NULL);
++ KSPMonitorSet(ksp, ksp_monitor, _vf, NULL);
+ EPSView(_eps, PETSC_VIEWER_STDOUT_SELF);
+ }
+
+diff -Naur dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.h dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.h
+--- dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.h 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.h 2016-06-26 23:36:08.784610612 +0200
+@@ -231,6 +231,11 @@
+ // SLEPc solver pointer
+ EPS _eps;
+
++ PetscViewerAndFormat* _vf;
++ static PetscErrorCode eps_monitor(EPS eps, int its, int nconv, PetscScalar *eigr,
++ PetscScalar *eigi, PetscReal* errest,
++ int nest, void *mctx);
++ static PetscErrorCode ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *vf);
+ };
+
+ }
+diff -Naur dolfin-1.6.0/dolfin/nls/PETScSNESSolver.cpp dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.cpp
+--- dolfin-1.6.0/dolfin/nls/PETScSNESSolver.cpp 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.cpp 2016-06-26 23:19:40.166029256 +0200
+@@ -195,6 +195,15 @@
+ return this->solve(nonlinear_problem, x);
+ }
+ //-----------------------------------------------------------------------------
++PetscErrorCode
++PETScSNESSolver::snes_monitor(SNES snes, PetscInt its,
++ PetscReal fgnorm, void *vf)
++{
++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf);
++ SNESMonitorDefault(snes, its, fgnorm, _vf);
++ return(0);
++}
++//-----------------------------------------------------------------------------
+ void
+ PETScSNESSolver::init(NonlinearProblem& nonlinear_problem,
+ GenericVector& x)
+@@ -237,9 +246,11 @@
+ }
+
+ // Set some options from the parameters
+- if (report)
+- SNESMonitorSet(_snes, SNESMonitorDefault, PETSC_NULL, PETSC_NULL);
+-
++ if (report) {
++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_snes_ctx.vf);
++ SNESMonitorSet(_snes, PETScSNESSolver::snes_monitor, _snes_ctx.vf, PETSC_NULL);
++ }
++
+ // Set the bounds, if any
+ set_bounds(x);
+
+@@ -293,8 +304,8 @@
+ SNESGetLineSearch(_snes, &linesearch);
+ #endif
+
+- if (report)
+- SNESLineSearchSetMonitor(linesearch, PETSC_TRUE);
++ // if (report)
++ // SNESLineSearchSetMonitor(linesearch, PETSC_TRUE);
+ const std::string line_search_type = std::string(parameters["line_search"]);
+ SNESLineSearchSetType(linesearch, line_search_type.c_str());
+
+@@ -466,6 +477,24 @@
+ }
+ #endif
+ //-----------------------------------------------------------------------------
++PetscErrorCode
++PETScSNESSolver::ksp_monitor(KSP ksp, PetscInt n,
++ PetscReal rnorm, void *vf)
++{
++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf);
++ KSPMonitorDefault(ksp, n, rnorm, _vf);
++ return(0);
++}
++//-----------------------------------------------------------------------------
++PetscErrorCode
++PETScSNESSolver::ksp_monitor_norm(KSP ksp, PetscInt n,
++ PetscReal rnorm, void *vf)
++{
++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf);
++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf);
++ return(0);
++}
++//-----------------------------------------------------------------------------
+ void PETScSNESSolver::set_linear_solver_parameters()
+ {
+ KSP ksp;
+@@ -482,7 +511,7 @@
+ PetscObjectGetComm((PetscObject)_snes, &comm);
+
+ if (parameters["report"])
+- KSPMonitorSet(ksp, KSPMonitorDefault, PETSC_NULL, PETSC_NULL);
++ KSPMonitorSet(ksp, PETScSNESSolver::ksp_monitor, _snes_ctx.vf, PETSC_NULL);
+
+ const std::string linear_solver = parameters["linear_solver"];
+ const std::string preconditioner = parameters["preconditioner"];
+@@ -518,7 +547,7 @@
+ KSPSetInitialGuessNonzero(ksp, PETSC_FALSE);
+
+ if (krylov_parameters["monitor_convergence"])
+- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0);
++ KSPMonitorSet(ksp, PETScSNESSolver::ksp_monitor_norm, _snes_ctx.vf, 0);
+
+ // Set tolerances
+ const int max_iters = krylov_parameters["maximum_iterations"];
+diff -Naur dolfin-1.6.0/dolfin/nls/PETScSNESSolver.h dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.h
+--- dolfin-1.6.0/dolfin/nls/PETScSNESSolver.h 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.h 2016-06-26 22:31:21.554129282 +0200
+@@ -24,6 +24,7 @@
+
+ #include <map>
+ #include <petscsnes.h>
++#include <petscviewer.h>
+ #include <memory>
+ #include <dolfin/nls/NewtonSolver.h>
+ #include <dolfin/parameter/Parameters.h>
+@@ -124,8 +125,15 @@
+ Vec f_tmp;
+ const PETScVector* xl;
+ const PETScVector* xu;
++ PetscViewerAndFormat* vf;
+ };
+
++
++ // monitoring functions
++ static PetscErrorCode snes_monitor(SNES snes, PetscInt its, PetscReal fgnorm, void* ctx);
++ static PetscErrorCode ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx);
++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx);
++
+ // PETSc solver pointer
+ SNES _snes;
+
+diff -Naur dolfin-1.6.0/dolfin/nls/PETScTAOSolver.cpp dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.cpp
+--- dolfin-1.6.0/dolfin/nls/PETScTAOSolver.cpp 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.cpp 2016-06-27 19:14:47.367885081 +0200
+@@ -186,6 +186,15 @@
+ init(optimisation_problem, x.down_cast<PETScVector>(), lb, ub);
+ }
+ //-----------------------------------------------------------------------------
++PetscErrorCode
++PETScTAOSolver::ksp_monitor_norm(KSP ksp, PetscInt n,
++ PetscReal rnorm, void * vf)
++{
++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf);
++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf);
++ return(0);
++}
++//-----------------------------------------------------------------------------
+ void PETScTAOSolver::init(OptimisationProblem& optimisation_problem,
+ PETScVector& x,
+ const PETScVector& lb,
+@@ -365,9 +374,7 @@
+ set_tao(parameters["method"]);
+
+ // Set tolerances
+- TaoSetTolerances(_tao, parameters["function_absolute_tol"],
+- parameters["function_relative_tol"],
+- parameters["gradient_absolute_tol"],
++ TaoSetTolerances(_tao, parameters["gradient_absolute_tol"],
+ parameters["gradient_relative_tol"],
+ parameters["gradient_t_tol"]);
+
+@@ -490,8 +497,10 @@
+ KSPSetInitialGuessNonzero(ksp, PETSC_FALSE);
+
+ // KSP monitor
+- if (krylov_parameters["monitor_convergence"])
+- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0);
++ if (krylov_parameters["monitor_convergence"]) {
++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &vf);
++ KSPMonitorSet(ksp, ksp_monitor_norm, vf, 0);
++ }
+
+ // Get integer tolerances (to take care of casting to PetscInt)
+ const int max_iter = krylov_parameters["maximum_iterations"];
+diff -Naur dolfin-1.6.0/dolfin/nls/PETScTAOSolver.h dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.h
+--- dolfin-1.6.0/dolfin/nls/PETScTAOSolver.h 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.h 2016-06-27 19:08:00.634361160 +0200
+@@ -146,6 +146,10 @@
+ // TAO pointer
+ Tao _tao;
+
++ // monitoring functions
++ PetscViewerAndFormat* vf;
++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx);
++
+ // Update parameters when tao/ksp/pc_types are explictly given
+ void update_parameters(const std::string tao_type,
+ const std::string ksp_type,
+diff -Naur dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.cpp dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.cpp
+--- dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.cpp 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.cpp 2016-06-27 19:17:10.390216576 +0200
+@@ -313,9 +313,7 @@
+ dolfin_assert(_tao);
+
+ // Set tolerances
+- TaoSetTolerances(_tao, parameters["function_absolute_tol"],
+- parameters["function_relative_tol"],
+- parameters["gradient_absolute_tol"],
++ TaoSetTolerances(_tao, parameters["gradient_absolute_tol"],
+ parameters["gradient_relative_tol"],
+ parameters["gradient_t_tol"]);
+
+@@ -340,6 +338,15 @@
+ set_solver(method);
+ }
+ //-----------------------------------------------------------------------------
++PetscErrorCode
++TAOLinearBoundSolver::ksp_monitor_norm(KSP ksp, PetscInt n,
++ PetscReal rnorm, void * vf)
++{
++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf);
++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf);
++ return(0);
++}
++//-----------------------------------------------------------------------------
+ void TAOLinearBoundSolver::set_ksp_options()
+ {
+ dolfin_assert(_tao);
+@@ -360,8 +367,10 @@
+ else
+ KSPSetInitialGuessNonzero(ksp, PETSC_FALSE);
+
+- if (krylov_parameters["monitor_convergence"])
+- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0);
++ if (krylov_parameters["monitor_convergence"]) {
++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &vf);
++ KSPMonitorSet(ksp, ksp_monitor_norm, vf, 0);
++ }
+
+ // Set tolerances
+ const int max_ksp_it = krylov_parameters["maximum_iterations"];
+diff -Naur dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.h dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.h
+--- dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.h 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.h 2016-06-27 19:08:09.157561005 +0200
+@@ -174,6 +174,10 @@
+ // Tao solver pointer
+ Tao _tao;
+
++ // monitoring functions
++ PetscViewerAndFormat* vf;
++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx);
++
+ // Petsc preconditioner
+ std::shared_ptr<PETScPreconditioner> preconditioner;
+
diff --git a/var/spack/repos/builtin/packages/fenics/petsc-version-detection.patch b/var/spack/repos/builtin/packages/fenics/petsc-version-detection.patch
new file mode 100644
index 0000000000..1429cd7bc6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fenics/petsc-version-detection.patch
@@ -0,0 +1,39 @@
+--- dolfin-1.6.0.orig/cmake/modules/FindPETSc.cmake 2015-07-28 17:05:55.000000000 +0200
++++ dolfin-1.6.0/cmake/modules/FindPETSc.cmake 2016-06-27 17:16:02.484402705 +0200
+@@ -207,13 +207,7 @@
+
+ endif()
+
+-# Build PETSc test program
+-if (DOLFIN_SKIP_BUILD_TESTS)
+- set(PETSC_TEST_RUNS TRUE)
+- set(PETSC_VERSION "UNKNOWN")
+- set(PETSC_VERSION_OK TRUE)
+-elseif (FOUND_PETSC_CONF)
+-
++if (FOUND_PETSC_CONF)
+ # Set flags for building test program
+ set(CMAKE_REQUIRED_INCLUDES ${PETSC_INCLUDE_DIRS})
+ set(CMAKE_REQUIRED_LIBRARIES ${PETSC_LIBRARIES})
+@@ -271,7 +265,10 @@
+ set(PETSC_VERSION_OK TRUE)
+ endif()
+ mark_as_advanced(PETSC_VERSION_OK)
++endif()
+
++ # Build PETSc test program
++if (NOT DOLFIN_SKIP_BUILD_TESTS AND FOUND_PETSC_CONF)
+ # Run PETSc test program
+ set(PETSC_TEST_LIB_CPP
+ "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/petsc_test_lib.cpp")
+@@ -359,7 +356,9 @@
+ else()
+ message(STATUS "PETSc configured without Cusp support")
+ endif()
+-
++else()
++ set(PETSC_TEST_RUNS TRUE)
++
+ endif()
+
+ # Check sizeof(PetscInt)
diff --git a/var/spack/repos/builtin/packages/foam-extend/package.py b/var/spack/repos/builtin/packages/foam-extend/package.py
new file mode 100644
index 0000000000..4479fc9bee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/foam-extend/package.py
@@ -0,0 +1,235 @@
+from spack import *
+from spack.environment import *
+
+import multiprocessing
+import os
+
+
+class FoamExtend(Package):
+ """The foam-extend project is a fork of the OpenFOAM open source library
+ for Computational Fluid Dynamics (CFD)."""
+
+ homepage = "http://www.extend-project.de/"
+
+ version('3.2', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.2')
+ version('3.1', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.1')
+ version('3.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.0')
+
+ variant('paraview', default=False, description='Enable ParaFOAM')
+ variant('scotch', default=True, description='Activate Scotch as a possible decomposition library')
+ variant('ptscotch', default=True, description='Activate PT-Scotch as a possible decomposition library')
+ variant('metis', default=True, description='Activate Metis as a possible decomposition library')
+ variant('parmetis', default=True, description='Activate Parmetis as a possible decomposition library')
+ variant('parmgridgen', default=True, description='Activate Parmgridgen support')
+ variant('source', default=True, description='Installs also the source folder')
+
+ supported_compilers = {'clang': 'Clang', 'gcc': 'Gcc', 'intel': 'Icc'}
+
+ depends_on('mpi')
+ depends_on('python')
+ depends_on('flex@:2.5.99')
+ depends_on('zlib')
+
+ depends_on('scotch ~ metis', when='~ptscotch+scotch')
+ depends_on('scotch ~ metis + mpi', when='+ptscotch')
+ depends_on('metis@5:', when='+metis')
+ depends_on('parmetis', when='+parmetis')
+ depends_on('parmgridgen', when='+parmgridgen')
+
+ depends_on('paraview', when='+paraview')
+
+ def set_arch(self):
+ (sysname, nodename, release, version, machine) = os.uname()
+
+ if self.compiler.name not in self.supported_compilers:
+ raise RuntimeError('{0} is not a supported compiler \
+ to compile OpenFOAM'.format(self.compiler.name))
+
+ foam_compiler = self.supported_compilers[self.compiler.name]
+ if sysname == 'Linux':
+ arch = 'linux'
+ if foam_compiler == 'Clang':
+ raise RuntimeError('OS, compiler combination not\
+ supported ({0} {1})'.format(sysname, foam_compiler))
+ elif sysname == 'Darwin':
+ if machine == 'x86_64':
+ arch = 'darwinIntel'
+ if foam_compiler == 'Icc':
+ raise RuntimeError('OS, compiler combination not\
+ supported ({0} {1})'.format(sysname, foam_compiler))
+ else:
+ raise RuntimeError('{0} {1} is not a \
+ supported architecture'.format(sysname, machine))
+
+ return (arch, foam_compiler)
+
+ def get_openfoam_environment(self):
+ return EnvironmentModifications.from_sourcing_files(
+ join_path(self.stage.source_path,
+ 'etc/bashrc'))
+
+ def patch(self):
+ # change names to match the package and not the one patch in
+ # the Third-Party of foam-extend
+ if '+parmgridgen' in self.spec:
+ filter_file(r'-lMGridGen',
+ r'-lmgrid',
+ 'src/dbns/Make/options')
+
+ filter_file(
+ r'-lMGridGen',
+ r'-lmgrid',
+ 'src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options') # NOQA: ignore=501
+
+ # Get the wmake arch and compiler
+ (arch, foam_compiler) = self.set_arch()
+
+ prefs_dict = {
+ 'compilerInstall': 'System',
+ 'WM_COMPILER': foam_compiler,
+ 'WM_ARCH_OPTION': '64',
+ 'WM_PRECISION_OPTION': 'DP',
+ 'WM_COMPILE_OPTION': 'SPACKOpt',
+ 'WM_MPLIB': 'SPACK',
+
+ 'CMAKE_DIR': self.spec['cmake'].prefix,
+ 'CMAKE_BIN_DIR': self.spec['cmake'].prefix.bin,
+ 'PYTHON_DIR': self.spec['python'].prefix,
+ 'PYTHON_BIN_DIR': self.spec['python'].prefix.bin,
+
+ 'FLEX_SYSTEM': 1,
+ 'FLEX_DIR': self.spec['flex'].prefix,
+
+ 'BISON_SYSTEM': 1,
+ 'BISON_DIR': self.spec['flex'].prefix,
+
+ 'ZLIB_SYSTEM': 1,
+ 'ZLIB_DIR': self.spec['zlib'].prefix,
+ }
+
+ if '+scotch' in self.spec or '+ptscotch' in self.spec:
+ prefs_dict['SCOTCH_SYSTEM'] = 1
+ prefs_dict['SCOTCH_DIR'] = self.spec['scotch'].prefix
+ prefs_dict['SCOTCH_BIN_DIR'] = self.spec['scotch'].prefix.bin
+ prefs_dict['SCOTCH_LIB_DIR'] = self.spec['scotch'].prefix.lib
+ prefs_dict['SCOTCH_INCLUDE_DIR'] = \
+ self.spec['scotch'].prefix.include
+
+ if '+metis' in self.spec:
+ prefs_dict['METIS_SYSTEM'] = 1
+ prefs_dict['METIS_DIR'] = self.spec['metis'].prefix
+ prefs_dict['METIS_BIN_DIR'] = self.spec['metis'].prefix.bin
+ prefs_dict['METIS_LIB_DIR'] = self.spec['metis'].prefix.lib
+ prefs_dict['METIS_INCLUDE_DIR'] = self.spec['metis'].prefix.include
+
+ if '+parmetis' in self.spec:
+ prefs_dict['PARMETIS_SYSTEM'] = 1
+ prefs_dict['PARMETIS_DIR'] = self.spec['parmetis'].prefix
+ prefs_dict['PARMETIS_BIN_DIR'] = self.spec['parmetis'].prefix.bin
+ prefs_dict['PARMETIS_LIB_DIR'] = self.spec['parmetis'].prefix.lib
+ prefs_dict['PARMETIS_INCLUDE_DIR'] = \
+ self.spec['parmetis'].prefix.include
+
+ if '+parmgridgen' in self.spec:
+ prefs_dict['PARMGRIDGEN_SYSTEM'] = 1
+ prefs_dict['PARMGRIDGEN_DIR'] = self.spec['parmgridgen'].prefix
+ prefs_dict['PARMGRIDGEN_BIN_DIR'] = \
+ self.spec['parmgridgen'].prefix.bin
+ prefs_dict['PARMGRIDGEN_LIB_DIR'] = \
+ self.spec['parmgridgen'].prefix.lib
+ prefs_dict['PARMGRIDGEN_INCLUDE_DIR'] = \
+ self.spec['parmgridgen'].prefix.include
+
+ if '+paraview' in self.spec:
+ prefs_dict['PARAVIEW_SYSTEM'] = 1
+ prefs_dict['PARAVIEW_DIR'] = self.spec['paraview'].prefix,
+ prefs_dict['PARAVIEW_BIN_DIR'] = self.spec['paraview'].prefix.bin,
+ prefs_dict['QT_SYSTEM'] = 1
+ prefs_dict['QT_DIR'] = self.spec['qt'].prefix,
+ prefs_dict['QT_BIN_DIR'] = self.spec['qt'].prefix.bin,
+
+ # write the prefs files to define the configuration needed,
+ # only the prefs.sh is used by this script but both are
+ # installed for end users
+ with working_dir('.'):
+ with open("etc/prefs.sh", "w") as fh:
+ for key in sorted(prefs_dict):
+ fh.write('export {0}={1}\n'.format(key, prefs_dict[key]))
+
+ with open("etc/prefs.csh", "w") as fh:
+ for key in sorted(prefs_dict):
+ fh.write('setenv {0}={1}\n'.format(key, prefs_dict[key]))
+
+ # Defining a different mpi and optimisation file to be able to
+ # make wmake get spack info with minimum modifications on
+ # configurations scripts
+ mpi_info = [
+ 'PFLAGS = -DOMPI_SKIP_MPICXX -DMPICH_IGNORE_CXX_SEEK',
+ 'PINC = -I{0}'.format(self.spec['mpi'].prefix.include),
+ 'PLIBS = -L{0} -lmpi'.format(self.spec['mpi'].prefix.lib)
+ ]
+
+ arch_path = ''.join([arch, prefs_dict['WM_ARCH_OPTION'],
+ foam_compiler])
+ option_path = ''.join([arch_path,
+ prefs_dict['WM_PRECISION_OPTION'],
+ prefs_dict['WM_COMPILE_OPTION']])
+ rule_path = join_path("wmake", "rules", arch_path)
+ build_path = join_path(self.stage.source_path, 'lib', option_path)
+ install_path = \
+ join_path(self.prefix,
+ 'foam-extend-{0}'.format(self.version.up_to(2)),
+ option_path)
+
+ rpaths_foam = ' '.join([
+ '{0}{1}'.format(self.compiler.cxx_rpath_arg,
+ install_path),
+ '{0}{1}'.format(self.compiler.cxx_rpath_arg,
+ build_path)
+ ])
+
+ compiler_flags = {
+ 'DBUG': rpaths_foam,
+ 'OPT': '-O3',
+ }
+
+ with working_dir(rule_path):
+ with open('mplibSPACK', "w") as fh:
+ fh.write('\n'.join(mpi_info))
+
+ for comp in ['c', 'c++']:
+ with open('{0}SPACKOpt'.format(comp), "w") as fh:
+ for key, val in compiler_flags.iteritems():
+ fh.write('{0}{1} = {2}\n'.format(comp, key, val))
+
+ def setup_environment(self, spack_env, run_env):
+ with working_dir(self.stage.path):
+ spack_env.set('FOAM_INST_DIR', os.path.abspath('.'))
+
+ (arch, foam_compiler) = self.set_arch()
+
+ run_env.set('FOAM_INST_DIR', self.prefix)
+
+ def install(self, spec, prefix):
+ env_openfoam = self.get_openfoam_environment()
+ env_openfoam.apply_modifications()
+
+ if self.parallel:
+ os.environ['WM_NCOMPPROCS'] = str(self.make_jobs) \
+ if self.make_jobs else str(multiprocessing.cpu_count())
+
+ allwmake = Executable('./Allwmake')
+ allwmake()
+
+ install_path = \
+ join_path(self.prefix,
+ 'foam-extend-{0}'.format(self.version.up_to(2)))
+
+ if '+source' in spec:
+ install_tree('src', join_path(install_path, 'src'))
+
+ install_tree('lib', join_path(install_path, 'lib'))
+ install_tree('bin', join_path(install_path, 'bin'))
+ install_tree('applications', join_path(install_path, 'applications'))
+ install_tree('etc', join_path(install_path, 'etc'))
+ install_tree('wmake', join_path(install_path, 'wmake'))
diff --git a/var/spack/repos/builtin/packages/giflib/package.py b/var/spack/repos/builtin/packages/giflib/package.py
new file mode 100644
index 0000000000..7082384b9b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/giflib/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# 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 *
+
+
+class Giflib(Package):
+ """The GIFLIB project maintains the giflib service library, which has
+ been pulling images out of GIFs since 1989."""
+
+ homepage = "http://giflib.sourceforge.net/"
+ url = "https://downloads.sourceforge.net/project/giflib/giflib-5.1.4.tar.bz2"
+
+ version('5.1.4', '2c171ced93c0e83bb09e6ccad8e3ba2b')
+
+ def install(self, spec, prefix):
+ configure('--prefix=%s' % prefix)
+
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/glib/g_date_strftime.patch b/var/spack/repos/builtin/packages/glib/g_date_strftime.patch
new file mode 100644
index 0000000000..532c743277
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glib/g_date_strftime.patch
@@ -0,0 +1,34 @@
+From 00148329967adb196138372771052a3f606a6ea3 Mon Sep 17 00:00:00 2001
+From: coypu <coypu@sdf.org>
+Date: Wed, 2 Mar 2016 19:43:10 +0200
+Subject: [PATCH 2/2] gdate: Suppress string format literal warning
+
+Newer versions of GCC emit an error here, but we know it's safe.
+https://bugzilla.gnome.org/761550
+---
+ glib/gdate.c | 5 +++++
+ 1 file changed, 5 insertions(+)
+
+diff --git a/glib/gdate.c b/glib/gdate.c
+index 4aece02..92c34d2 100644
+--- a/glib/gdate.c
++++ b/glib/gdate.c
+@@ -2439,6 +2439,9 @@ win32_strftime_helper (const GDate *d,
+ *
+ * Returns: number of characters written to the buffer, or 0 the buffer was too small
+ */
++#pragma GCC diagnostic push
++#pragma GCC diagnostic ignored "-Wformat-nonliteral"
++
+ gsize
+ g_date_strftime (gchar *s,
+ gsize slen,
+@@ -2549,3 +2552,5 @@ g_date_strftime (gchar *s,
+ return retval;
+ #endif
+ }
++
++#pragma GCC diagnostic pop
+--
+2.7.1
+
diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index b146ea63d8..342a61a6a1 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -25,20 +25,24 @@
from spack import *
import sys
+
class Glib(Package):
"""The GLib package contains a low-level libraries useful for
providing data structure handling for C, portability wrappers
and interfaces for such runtime functionality as an event loop,
threads, dynamic loading and an object system."""
homepage = "https://developer.gnome.org/glib/"
- url = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz"
+ url = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz"
version('2.42.1', '89c4119e50e767d3532158605ee9121a')
depends_on("libffi")
depends_on("zlib")
depends_on("pkg-config")
- depends_on('gettext', sys.platform=='darwin')
+ depends_on('gettext', sys.platform == 'darwin')
+
+ # The following patch is needed for gcc-6.1
+ patch('g_date_strftime.patch')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index e46f432be5..51a5823aa5 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -70,7 +70,8 @@ class Hdf5(Package):
raise RuntimeError(msg)
if '+threadsafe' in spec and ('+cxx' in spec or '+fortran' in spec):
- raise RuntimeError("cannot use variant +threadsafe with either +cxx or +fortran")
+ msg = 'cannot use variant +threadsafe with either +cxx or +fortran'
+ raise RuntimeError(msg)
def install(self, spec, prefix):
self.validate(spec)
@@ -164,7 +165,7 @@ int main(int argc, char **argv) {
"""
expected = """\
HDF5 version {version} {version}
-""".format(version=str(spec.version))
+""".format(version=str(spec.version.up_to(3)))
with open("check.c", 'w') as f:
f.write(source)
if '+mpi' in spec:
@@ -185,24 +186,30 @@ HDF5 version {version} {version}
if not success:
print "Produced output does not match expected output."
print "Expected output:"
- print '-'*80
+ print '-' * 80
print expected
- print '-'*80
+ print '-' * 80
print "Produced output:"
- print '-'*80
+ print '-' * 80
print output
- print '-'*80
+ print '-' * 80
raise RuntimeError("HDF5 install check failed")
shutil.rmtree(checkdir)
def url_for_version(self, version):
- v = str(version)
+ base_url = "http://www.hdfgroup.org/ftp/HDF5/releases"
if version == Version("1.2.2"):
- return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + v + ".tar.gz"
+ return "{0}/hdf5-{1}.tar.gz".format(base_url, version)
+ elif version < Version("1.6.6"):
+ return "{0}/hdf5-{1}/hdf5-{2}.tar.gz".format(
+ base_url, version.up_to(2), version)
elif version < Version("1.7"):
- return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + version.up_to(2) + "/hdf5-" + v + ".tar.gz"
+ return "{0}/hdf5-{1}/hdf5-{2}/src/hdf5-{2}.tar.gz".format(
+ base_url, version.up_to(2), version)
elif version < Version("1.10"):
- return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + v + "/src/hdf5-" + v + ".tar.gz"
+ return "{0}/hdf5-{1}/src/hdf5-{1}.tar.gz".format(
+ base_url, version)
else:
- return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + version.up_to(2) + "/hdf5-" + v + "/src/hdf5-" + v + ".tar.gz"
+ return "{0}/hdf5-{1}/hdf5-{2}/src/hdf5-{2}.tar.gz".format(
+ base_url, version.up_to(2), version)
diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index 69b52130e9..99d138dcff 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -22,8 +22,9 @@
# 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 *
-import os
+
class Julia(Package):
"""The Julia Language: A fresh approach to technical computing"""
@@ -32,10 +33,14 @@ class Julia(Package):
version('master',
git='https://github.com/JuliaLang/julia.git', branch='master')
+ version('release-0.4',
+ git='https://github.com/JuliaLang/julia.git', branch='release-0.4')
+ version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d', preferred=True)
version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac')
- patch('gc.patch')
+ patch('gc.patch', when='@0.4:0.4.5')
+ patch('gc.patch', when='@release-0.4')
patch('openblas.patch', when='@0.4:0.4.5')
# Build-time dependencies:
@@ -92,25 +97,21 @@ class Julia(Package):
depends_on("mpi")
def install(self, spec, prefix):
- if '@master' in spec:
- # Julia needs to know the offset from a specific commit
- git = which('git')
- git('fetch', '--unshallow')
-
# Explicitly setting CC, CXX, or FC breaks building libuv, one
# of Julia's dependencies. This might be a Darwin-specific
# problem. Given how Spack sets up compilers, Julia should
# still use Spack's compilers, even if we don't specify them
# explicitly.
- options = [#"CC=cc",
- #"CXX=c++",
- #"FC=fc",
- #"USE_SYSTEM_ARPACK=1",
- #"USE_SYSTEM_FFTW=1",
- #"USE_SYSTEM_GMP=1",
- #"USE_SYSTEM_MPFR=1",
- #TODO "USE_SYSTEM_PCRE=1",
- "prefix=%s" % prefix]
+ options = [
+ # "CC=cc",
+ # "CXX=c++",
+ # "FC=fc",
+ # "USE_SYSTEM_ARPACK=1",
+ # "USE_SYSTEM_FFTW=1",
+ # "USE_SYSTEM_GMP=1",
+ # "USE_SYSTEM_MPFR=1",
+ # "USE_SYSTEM_PCRE=1",
+ "prefix=%s" % prefix]
with open('Make.user', 'w') as f:
f.write('\n'.join(options) + '\n')
make()
diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py
index 90e7b3b643..0e410a5061 100644
--- a/var/spack/repos/builtin/packages/libtool/package.py
+++ b/var/spack/repos/builtin/packages/libtool/package.py
@@ -24,18 +24,30 @@
##############################################################################
from spack import *
+
class Libtool(Package):
- """libtool -- library building part of autotools"""
- homepage = "https://www.gnu.org/software/libtool/"
- url = "http://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz"
+ """
+ libtool -- library building part of autotools
+ """
+ homepage = 'https://www.gnu.org/software/libtool/'
+ url = 'http://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz'
- version('2.4.6' , 'addf44b646ddb4e3919805aa88fa7c5e')
- version('2.4.2' , 'd2f3b7d4627e69e13514a40e72a24d50')
+ version('2.4.6', 'addf44b646ddb4e3919805aa88fa7c5e')
+ version('2.4.2', 'd2f3b7d4627e69e13514a40e72a24d50')
depends_on('m4')
+ def _make_executable(self, name):
+ return Executable(join_path(self.prefix.bin, name))
+
+ def setup_dependent_package(self, module, dependent_spec):
+ # Automake is very likely to be a build dependency,
+ # so we add the tools it provides to the dependent module
+ executables = ['libtoolize', 'libtool']
+ for name in executables:
+ setattr(module, name, self._make_executable(name))
+
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
-
make()
make("install")
diff --git a/var/spack/repos/builtin/packages/libxpm/package.py b/var/spack/repos/builtin/packages/libxpm/package.py
new file mode 100644
index 0000000000..10ca8158c2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libxpm/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# 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 *
+
+
+class Libxpm(Package):
+ """Xpm file format library"""
+
+ homepage = "https://www.x.org/"
+ url = "https://www.x.org/archive//individual/lib/libXpm-3.5.11.tar.gz"
+
+ version('3.5.11', '7c67c878ee048206b070bc0b24154f04')
+ version('3.5.10', 'a70507638d74541bf30a771f1e5938bb')
+ version('3.5.9', 'd6d4b0f76248a6b346eb42dfcdaa72a6')
+ version('3.5.8', '2d81d6633e67ac5562e2fbee126b2897')
+ version('3.5.7', '7bbc8f112f7143ed6961a58ce4e14558')
+
+ def install(self, spec, prefix):
+ configure('--prefix=%s' % prefix)
+
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index ea1844aea0..90670ee517 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -50,6 +50,11 @@ class Mpich(Package):
provides('mpi@:1.3', when='@1:')
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+ spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
+ spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
+ spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+ spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
+
spack_env.set('MPICH_CC', spack_cc)
spack_env.set('MPICH_CXX', spack_cxx)
spack_env.set('MPICH_F77', spack_f77)
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index 34bace10d6..da386445bb 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -191,6 +191,11 @@ class Mvapich2(Package):
run_env.set('SLURM_MPI_TYPE', 'pmi2')
def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+ spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
+ spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx'))
+ spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+ spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
+
spack_env.set('MPICH_CC', spack_cc)
spack_env.set('MPICH_CXX', spack_cxx)
spack_env.set('MPICH_F77', spack_f77)
diff --git a/var/spack/packages/mxml/package.py b/var/spack/repos/builtin/packages/mxml/package.py
index f79251d312..254a5f1595 100644
--- a/var/spack/packages/mxml/package.py
+++ b/var/spack/repos/builtin/packages/mxml/package.py
@@ -1,14 +1,15 @@
-import os
from spack import *
+
class Mxml(Package):
- """Mini-XML is a small XML library that you can use to read and write XML
- and XML-like data files in your application without requiring large
- non-standard libraries
+ """
+ Mini-XML is a small XML library that you can use to read and write XML
+ and XML-like data files in your application without requiring large
+ non-standard libraries
"""
homepage = "http://www.msweet.org"
- url = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz"
+ url = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz"
version('2.9', 'e21cad0f7aacd18f942aa0568a8dee19')
version('2.8', 'd85ee6d30de053581242c4a86e79a5d2')
@@ -16,11 +17,11 @@ class Mxml(Package):
version('2.6', '68977789ae64985dddbd1a1a1652642e')
version('2.5', 'f706377fba630b39fa02fd63642b17e5')
- # module swap PrgEnv-intel PrgEnv-$COMP (Can use whatever compiler you want to use)
+ # module swap PrgEnv-intel PrgEnv-$COMP
+ # (Can use whatever compiler you want to use)
# Case statement to change CC and CXX flags
def install(self, spec, prefix):
configure('--prefix=%s' % prefix, "--disable-shared", 'CFLAGS=-static')
make()
make("install")
-
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index 3d1951ceee..e52ff1af87 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -24,12 +24,14 @@
##############################################################################
from spack import *
+
class NetcdfFortran(Package):
"""Fortran interface for NetCDF4"""
homepage = "http://www.unidata.ucar.edu/software/netcdf"
url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz"
+ version('4.4.4', 'e855c789cd72e1b8bc1354366bf6ac72')
version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e')
depends_on('netcdf')
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 588d862d96..15c8eefe96 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -109,6 +109,11 @@ class Openmpi(Package):
return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) # NOQA: ignore=E501
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+ spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
+ spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
+ spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+ spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
+
spack_env.set('OMPI_CC', spack_cc)
spack_env.set('OMPI_CXX', spack_cxx)
spack_env.set('OMPI_FC', spack_fc)
diff --git a/var/spack/repos/builtin/packages/parmgridgen/package.py b/var/spack/repos/builtin/packages/parmgridgen/package.py
new file mode 100644
index 0000000000..02be777c36
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parmgridgen/package.py
@@ -0,0 +1,71 @@
+##############################################################################
+# 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 *
+
+
+class Parmgridgen(Package):
+ """MGRIDGEN is a serial library written entirely in ANSI C that implements
+ (serial) algorithms for obtaining a sequence of successive coarse grids
+ that are well-suited for geometric multigrid methods.
+ ParMGridGen is the parallel version of MGridGen
+ """
+
+ homepage = "http://www-users.cs.umn.edu/~moulitsa/software.html"
+ url = "http://www-users.cs.umn.edu/~moulitsa/download/ParMGridGen-1.0.tar.gz"
+
+ version('1.0', '2872fa95b7fb91d6bd525490eed62038')
+
+ depends_on('mpi')
+
+ def install(self, spec, prefix):
+ make_opts = [
+ 'make=make',
+ 'COPTIONS=-fPIC',
+ 'LDOPTIONS=-fPIC',
+ 'CC={0}'.format(self.compiler.cc),
+ 'PARCC={0}'.format(spec['mpi'].mpicc),
+ 'LD={0}'.format(self.compiler.cc),
+ 'PARLD={0}'.format(spec['mpi'].mpicc),
+ 'LIBDIR=-L../..',
+ 'PARLIBS=-L../../ -lparmgrid -lmgrid -lm',
+ 'LIBS=-L../../ -lmgrid -lm',
+ 'parallel'
+ ]
+
+ make(*make_opts, parallel=False)
+
+ mkdirp(prefix.include, prefix.lib, prefix.bin)
+
+ install("mgridgen.h", prefix.include)
+ install("parmgridgen.h", prefix.include)
+
+ install("MGridGen/IMlib/libIMlib.a",
+ join_path(prefix.lib, 'libIMlib.a'))
+ install("libmgrid.a", prefix.lib)
+ install("libparmgrid.a", prefix.lib)
+
+ install("mgridgen", prefix.bin)
+ install("parmgridgen", prefix.bin)
diff --git a/var/spack/repos/builtin/packages/py-protobuf/package.py b/var/spack/repos/builtin/packages/py-protobuf/package.py
new file mode 100644
index 0000000000..da3a65c22e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-protobuf/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# 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 *
+
+
+class PyProtobuf(Package):
+ """Protocol buffers are Google's language-neutral, platform-neutral,
+ extensible mechanism for serializing structured data - think XML, but
+ smaller, faster, and simpler. You define how you want your data to be
+ structured once, then you can use special generated source code to easily
+ write and read your structured data to and from a variety of data streams
+ and using a variety of languages."""
+
+ homepage = 'https://developers.google.com/protocol-buffers/'
+ url = 'https://pypi.python.org/packages/source/p/protobuf/protobuf-3.0.0b2.tar.gz'
+
+ version('3.0.0b2', 'f0d3bd2394345a9af4a277cd0302ae83')
+ version('2.6.1', '6bf843912193f70073db7f22e2ea55e2')
+ version('2.5.0', '338813f3629d59e9579fed9035ecd457')
+ version('2.4.1', '72f5141d20ab1bcae6b1e00acfb1068a')
+ version('2.3.0', 'bb020c962f252fe81bfda8fb433bafdd')
+
+ extends('python')
+
+ depends_on('py-setuptools')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py
index 3c2b4993ac..2f6e42c439 100644
--- a/var/spack/repos/builtin/packages/scotch/package.py
+++ b/var/spack/repos/builtin/packages/scotch/package.py
@@ -171,15 +171,13 @@ class Scotch(Package):
target == 'ptscotch'))
make(target, parallel=can_make_parallel)
- # todo change this to take into account darwin systems
- lib_ext = '.so' if '+shared' in self.spec else '.a'
+ lib_ext = dso_suffix if '+shared' in self.spec else 'a'
# It seams easier to remove metis wrappers from the folder that will be
# installed than to tweak the Makefiles
if '+metis' not in self.spec:
with working_dir('lib'):
- lib_ext = '.so' if '+shared' in self.spec else '.a'
- force_remove('libscotchmetis{0}'.format(lib_ext))
- force_remove('libptscotchparmetis{0}'.format(lib_ext))
+ force_remove('libscotchmetis.{0}'.format(lib_ext))
+ force_remove('libptscotchparmetis.{0}'.format(lib_ext))
with working_dir('include'):
force_remove('metis.h')
@@ -187,8 +185,8 @@ class Scotch(Package):
if '~esmumps' in self.spec and self.spec.version < Version('6.0.0'):
with working_dir('lib'):
- force_remove('libesmumps{0}'.format(lib_ext))
- force_remove('libptesmumps{0}'.format(lib_ext))
+ force_remove('libesmumps.{0}'.format(lib_ext))
+ force_remove('libptesmumps.{0}'.format(lib_ext))
with working_dir('include'):
force_remove('esmumps.h')
diff --git a/var/spack/repos/builtin/packages/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py
new file mode 100644
index 0000000000..e4607d9146
--- /dev/null
+++ b/var/spack/repos/builtin/packages/swiftsim/package.py
@@ -0,0 +1,79 @@
+##############################################################################
+# 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 *
+
+import spack.environment
+import llnl.util.tty as tty
+
+# Needed to be able to download from the Durham gitlab repository
+tty.warn('Setting "GIT_SSL_NO_VERIFY=1"')
+tty.warn('This is needed to clone SWIFT repository')
+gitlab_env = spack.environment.EnvironmentModifications()
+gitlab_env.set('GIT_SSL_NO_VERIFY', 1)
+gitlab_env.apply_modifications()
+
+
+class Swiftsim(Package):
+ """
+ SPH With Inter-dependent Fine-grained Tasking (SWIFT) provides
+ astrophysicists with a state of the art framework to perform
+ particle based simulations.
+ """
+
+ homepage = 'http://icc.dur.ac.uk/swift/'
+ url = 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0'
+
+ version('0.3.0', git='https://gitlab.cosma.dur.ac.uk/swift/swiftsim.git', tag='v0.3.0')
+
+ variant('mpi', default=True, description='Enable distributed memory parallelism')
+
+ # Build dependencies
+ depends_on('autoconf')
+ depends_on('automake')
+ depends_on('libtool')
+ depends_on('m4')
+ # link-time / run-time dependencies
+ depends_on('mpi', when='+mpi')
+ depends_on('metis')
+ depends_on('hdf5~mpi', when='~mpi')
+ depends_on('hdf5+mpi', when='+mpi')
+
+ def install(self, spec, prefix):
+ # Generate configure from configure.ac
+ # and Makefile.am
+ libtoolize()
+ aclocal()
+ autoconf()
+ autogen = Executable('./autogen.sh')
+ autogen()
+
+ # Configure and install
+ options = ['--prefix=%s' % prefix,
+ '--enable-mpi' if '+mpi' in spec else '--disable-mpi',
+ '--enable-optimization']
+ configure(*options)
+ make()
+ make("install")