diff options
64 files changed, 814 insertions, 63 deletions
diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 0000000000..a1271a94fc --- /dev/null +++ b/.coveragerc @@ -0,0 +1,34 @@ +# -*- conf -*- +# .coveragerc to control coverage.py +[run] +branch = True +source = lib +omit = + lib/spack/spack/test/* + lib/spack/env/* + lib/spack/docs/* + lib/spack/external/* + +[report] +# Regexes for lines to exclude from consideration +exclude_lines = + # Have to re-enable the standard pragma + pragma: no cover + + # Don't complain about missing debug-only code: + def __repr__ + if self\.debug + + # Don't complain if tests don't hit defensive assertion code: + raise AssertionError + raise NotImplementedError + + # Don't complain if non-runnable code isn't run: + if 0: + if False: + if __name__ == .__main__.: + +ignore_errors = True + +[html] +directory = htmlcov diff --git a/.gitignore b/.gitignore index 4b97de5d50..643e5d9b03 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,5 @@ /share/spack/dotkit /share/spack/modules /TAGS +/htmlcov +.coverage diff --git a/.style.yapf b/.style.yapf new file mode 100644 index 0000000000..4741fb4f3b --- /dev/null +++ b/.style.yapf @@ -0,0 +1,3 @@ +[style] +based_on_style = pep8 +column_limit = 80 diff --git a/.travis.yml b/.travis.yml index 1bed6b0874..4ff4d5f483 100644 --- a/.travis.yml +++ b/.travis.yml @@ -6,20 +6,32 @@ python: # Use new Travis infrastructure (Docker can't sudo yet) sudo: false -# No need to install any deps. -install: true +# Install coveralls to obtain code coverage +install: + - "pip install coveralls" + - "pip install flake8" before_install: # Need this for the git tests to succeed. - git config --global user.email "spack@example.com" - git config --global user.name "Test User" + # Need this to be able to compute the list of changed files + - git fetch origin develop:develop script: - . share/spack/setup-env.sh - spack compilers - spack config get compilers - - spack test - spack install -v libdwarf + # Run unit tests with code coverage + - coverage run bin/spack test + # Checks if the file that have been changed are flake8 conformant + - CHANGED_PYTHON_FILES=`git diff develop... --name-only | perl -ne 'print if /\.py$/'` + - if [[ ${CHANGED_PYTHON_FILES} ]] ; then flake8 --format pylint --config flake8.ini ${CHANGED_PYTHON_FILES} ; fi + + +after_success: + - coveralls notifications: email: @@ -1,7 +1,8 @@  ============ -[](https://travis-ci.org/LLNL/spack) +[](https://travis-ci.org/LLNL/spack) +[](https://coveralls.io/github/LLNL/spack?branch=develop) Spack is a package management tool designed to support multiple versions and configurations of software on a wide variety of platforms diff --git a/flake8.ini b/flake8.ini new file mode 100644 index 0000000000..757c71705e --- /dev/null +++ b/flake8.ini @@ -0,0 +1,3 @@ +[flake8] +ignore = W391,F403 +max-line-length = 120
\ No newline at end of file diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 519c0da232..31c676d4f5 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -1831,6 +1831,42 @@ successfully find ``libdwarf.h`` and ``libdwarf.so``, without the packager having to provide ``--with-libdwarf=/path/to/libdwarf`` on the command line. +Compiler flags +~~~~~~~~~~~~~~ +In rare circumstances such as compiling and running small unit tests, a package +developer may need to know what are the appropriate compiler flags to enable +features like ``OpenMP``, ``c++11``, ``c++14`` and alike. To that end the +compiler classes in ``spack`` implement the following _properties_ : +``openmp_flag``, ``cxx11_flag``, ``cxx14_flag``, which can be accessed in a +package by ``self.compiler.cxx11_flag`` and alike. Note that the implementation +is such that if a given compiler version does not support this feature, an +error will be produced. Therefore package developers can also use these properties +to assert that a compiler supports the requested feature. This is handy when a +package supports additional variants like + +.. code-block:: python + + variant('openmp', default=True, description="Enable OpenMP support.") + + + +Message Parsing Interface (MPI) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +It is common for high performance computing software/packages to use ``MPI``. +As a result of conretization, a given package can be built using different +implementations of MPI such as ``Openmpi``, ``MPICH`` or ``IntelMPI``. +In some scenarios to configure a package one have to provide it with appropriate MPI +compiler wrappers such as ``mpicc``, ``mpic++``. +However different implementations of ``MPI`` may have different names for those +wrappers. In order to make package's ``install()`` method indifferent to the +choice ``MPI`` implementation, each package which implements ``MPI`` sets up +``self.spec.mpicc``, ``self.spec.mpicxx``, ``self.spec.mpifc`` and ``self.spec.mpif77`` +to point to ``C``, ``C++``, ``Fortran 90`` and ``Fortran 77`` ``MPI`` wrappers. +Package developers are advised to use these variables, for example ``self.spec['mpi'].mpicc`` +instead of hard-coding ``join_path(self.spec['mpi'].prefix.bin, 'mpicc')`` for +the reasons outlined above. + + Forking ``install()`` ~~~~~~~~~~~~~~~~~~~~~ diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py index d38c0b00b1..b53c17494c 100644 --- a/lib/spack/spack/compiler.py +++ b/lib/spack/spack/compiler.py @@ -94,9 +94,6 @@ class Compiler(object): # Names of generic arguments used by this compiler arg_rpath = '-Wl,-rpath,%s' - # argument used to get C++11 options - cxx11_flag = "-std=c++11" - def __init__(self, cspec, cc, cxx, f77, fc): def check(exe): @@ -117,6 +114,37 @@ class Compiler(object): def version(self): return self.spec.version + # This property should be overridden in the compiler subclass if + # OpenMP is supported by that compiler + @property + def openmp_flag(self): + # If it is not overridden, assume it is not supported and warn the user + tty.die("The compiler you have chosen does not currently support OpenMP.", + "If you think it should, please edit the compiler subclass and", + "submit a pull request or issue.") + + + # This property should be overridden in the compiler subclass if + # C++11 is supported by that compiler + @property + def cxx11_flag(self): + # If it is not overridden, assume it is not supported and warn the user + tty.die("The compiler you have chosen does not currently support C++11.", + "If you think it should, please edit the compiler subclass and", + "submit a pull request or issue.") + + + # This property should be overridden in the compiler subclass if + # C++14 is supported by that compiler + @property + def cxx14_flag(self): + # If it is not overridden, assume it is not supported and warn the user + tty.die("The compiler you have chosen does not currently support C++14.", + "If you think it should, please edit the compiler subclass and", + "submit a pull request or issue.") + + + # # Compiler classes have methods for querying the version of # specific compiler executables. This is used when discovering compilers. diff --git a/lib/spack/spack/compilers/clang.py b/lib/spack/spack/compilers/clang.py index e406d86a24..8c646905c7 100644 --- a/lib/spack/spack/compilers/clang.py +++ b/lib/spack/spack/compilers/clang.py @@ -26,6 +26,8 @@ import re import spack.compiler as cpr from spack.compiler import * from spack.util.executable import * +import llnl.util.tty as tty +from spack.version import ver class Clang(Compiler): # Subclasses use possible names of C compiler @@ -47,6 +49,29 @@ class Clang(Compiler): 'f77' : 'f77', 'fc' : 'f90' } + @property + def is_apple(self): + ver_string = str(self.version) + return ver_string.endswith('-apple') + + @property + def openmp_flag(self): + if self.is_apple: + tty.die("Clang from Apple does not support Openmp yet.") + else: + return "-fopenmp" + + @property + def cxx11_flag(self): + if self.is_apple: + # FIXME: figure out from which version Apple's clang supports c++11 + return "-std=c++11" + else: + if self.version < ver('3.3'): + tty.die("Only Clang 3.3 and above support c++11.") + else: + return "-std=c++11" + @classmethod def default_version(self, comp): """The '--version' option works for clang compilers. diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py index 64214db32d..91c498ac82 100644 --- a/lib/spack/spack/compilers/gcc.py +++ b/lib/spack/spack/compilers/gcc.py @@ -50,13 +50,24 @@ class Gcc(Compiler): 'fc' : 'gcc/gfortran' } @property + def openmp_flag(self): + return "-fopenmp" + + @property def cxx11_flag(self): if self.version < ver('4.3'): tty.die("Only gcc 4.3 and above support c++11.") elif self.version < ver('4.7'): - return "-std=gnu++0x" + return "-std=c++0x" + else: + return "-std=c++11" + + @property + def cxx14_flag(self): + if self.version < ver('4.8'): + tty.die("Only gcc 4.8 and above support c++14.") else: - return "-std=gnu++11" + return "-std=c++14" @classmethod def fc_version(cls, fc): diff --git a/lib/spack/spack/compilers/intel.py b/lib/spack/spack/compilers/intel.py index 69e9764790..9b1cf07c36 100644 --- a/lib/spack/spack/compilers/intel.py +++ b/lib/spack/spack/compilers/intel.py @@ -23,6 +23,8 @@ # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack.compiler import * +import llnl.util.tty as tty +from spack.version import ver class Intel(Compiler): # Subclasses use possible names of C compiler @@ -44,6 +46,13 @@ class Intel(Compiler): 'fc' : 'intel/ifort' } @property + def openmp_flag(self): + if self.version < ver('16.0'): + return "-openmp" + else: + return "-qopenmp" + + @property def cxx11_flag(self): if self.version < ver('11.1'): tty.die("Only intel 11.1 and above support c++11.") @@ -68,5 +77,3 @@ class Intel(Compiler): """ return get_compiler_version( comp, '--version', r'\((?:IFORT|ICC)\) ([^ ]+)') - - diff --git a/lib/spack/spack/compilers/nag.py b/lib/spack/spack/compilers/nag.py index 527a05a090..e9038c1039 100644 --- a/lib/spack/spack/compilers/nag.py +++ b/lib/spack/spack/compilers/nag.py @@ -1,4 +1,5 @@ from spack.compiler import * +import llnl.util.tty as tty class Nag(Compiler): # Subclasses use possible names of C compiler @@ -20,6 +21,16 @@ class Nag(Compiler): 'f77' : 'nag/nagfor', 'fc' : 'nag/nagfor' } + @property + def openmp_flag(self): + return "-openmp" + + @property + def cxx11_flag(self): + # NAG does not have a C++ compiler + # However, it can be mixed with a compiler that does support it + return "-std=c++11" + @classmethod def default_version(self, comp): """The '-V' option works for nag compilers. diff --git a/lib/spack/spack/compilers/pgi.py b/lib/spack/spack/compilers/pgi.py index c6a1078bd9..94c6b8365c 100644 --- a/lib/spack/spack/compilers/pgi.py +++ b/lib/spack/spack/compilers/pgi.py @@ -23,6 +23,7 @@ # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack.compiler import * +import llnl.util.tty as tty class Pgi(Compiler): # Subclasses use possible names of C compiler @@ -43,6 +44,15 @@ class Pgi(Compiler): 'f77' : 'pgi/pgfortran', 'fc' : 'pgi/pgfortran' } + @property + def openmp_flag(self): + return "-mp" + + @property + def cxx11_flag(self): + return "-std=c++11" + + @classmethod def default_version(cls, comp): """The '-V' option works for all the PGI compilers. @@ -54,4 +64,3 @@ class Pgi(Compiler): """ return get_compiler_version( comp, '-V', r'pg[^ ]* ([^ ]+) \d\d\d?-bit target') - diff --git a/lib/spack/spack/compilers/xl.py b/lib/spack/spack/compilers/xl.py index c1d55109a3..61a2e730dc 100644 --- a/lib/spack/spack/compilers/xl.py +++ b/lib/spack/spack/compilers/xl.py @@ -24,6 +24,8 @@ # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack.compiler import * +import llnl.util.tty as tty +from spack.version import ver class Xl(Compiler): # Subclasses use possible names of C compiler @@ -45,6 +47,10 @@ class Xl(Compiler): 'fc' : 'xl/xlf90' } @property + def openmp_flag(self): + return "-qsmp=omp" + + @property def cxx11_flag(self): if self.version < ver('13.1'): tty.die("Only xlC 13.1 and above have some c++11 support.") diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh index 764af68400..11a4c0a70c 100755 --- a/share/spack/setup-env.sh +++ b/share/spack/setup-env.sh @@ -1,4 +1,4 @@ -############################################################################## +##################################################################### # Copyright (c) 2013, Lawrence Livermore National Security, LLC. # Produced at the Lawrence Livermore National Laboratory. # @@ -84,7 +84,10 @@ function spack { if [ "$_sp_arg" = "-h" ]; then command spack cd -h else - cd $(spack location $_sp_arg "$@") + LOC="$(spack location $_sp_arg "$@")" + if [[ -d "$LOC" ]] ; then + cd "$LOC" + fi fi return ;; diff --git a/var/spack/repos/builtin/packages/LuaJIT/package.py b/var/spack/repos/builtin/packages/LuaJIT/package.py new file mode 100644 index 0000000000..7b2a269212 --- /dev/null +++ b/var/spack/repos/builtin/packages/LuaJIT/package.py @@ -0,0 +1,15 @@ +import os +from spack import * + +class Luajit(Package): + """Flast flexible JITed lua""" + homepage = "http://www.luajit.org" + url = "http://luajit.org/download/LuaJIT-2.0.4.tar.gz" + + version('2.0.4', 'dd9c38307f2223a504cbfb96e477eca0') + + def install(self, spec, prefix): + # Linking with the C++ compiler is a dirty hack to deal with the fact + # that unwinding symbols are not included by libc, this is necessary + # on some platforms for the final link stage to work + make("install", "PREFIX=" + prefix, "TARGET_LD=" + os.environ['CXX']) diff --git a/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch b/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch new file mode 100644 index 0000000000..8e21c72d92 --- /dev/null +++ b/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch @@ -0,0 +1,13 @@ +diff --git a/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp b/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp +index fc6fc28..14103d2 100644 +--- a/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp ++++ b/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp +@@ -27,7 +27,7 @@ using namespace std; + #include <ctime> + #include <cmath> + +-#include "adolc.h" ++#include <adolc/adolc.h> + + #ifdef _OPENMP + #include <omp.h> diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py new file mode 100644 index 0000000000..70933542ca --- /dev/null +++ b/var/spack/repos/builtin/packages/adol-c/package.py @@ -0,0 +1,80 @@ +from spack import * +import sys + +class AdolC(Package): + """A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading.""" + homepage = "https://projects.coin-or.org/ADOL-C" + url = "http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.6.1.tgz" + + version('head', svn='https://projects.coin-or.org/svn/ADOL-C/trunk/') + version('2.6.1', '1032b28427d6e399af4610e78c0f087b') + + variant('doc', default=True, description='Install documentation') + variant('openmp', default=False, description='Enable OpenMP support') + variant('sparse', default=False, description='Enable sparse drivers') + variant('tests', default=True, description='Build all included examples as a test case') + + patch('openmp_exam.patch') + + def install(self, spec, prefix): + make_args = ['--prefix=%s' % prefix] + + # --with-cflags=FLAGS use CFLAGS=FLAGS (default: -O3 -Wall -ansi) + # --with-cxxflags=FLAGS use CXXFLAGS=FLAGS (default: -O3 -Wall) + + if '+openmp' in spec: + if spec.satisfies('%gcc'): + make_args.extend([ + '--with-openmp-flag=-fopenmp' # FIXME: Is this required? -I <path to omp.h> -L <LLVM OpenMP library path> + ]) + else: + raise InstallError("OpenMP flags for compilers other than GCC are not implemented.") + + if '+sparse' in spec: + make_args.extend([ + '--enable-sparse' + ]) + + # We can simply use the bundled examples to check + # whether Adol-C works as expected + if '+tests' in spec: + make_args.extend([ + '--enable-docexa', # Documeted examples + '--enable-addexa' # Additional examples + ]) + if '+openmp' in spec: + make_args.extend([ + '--enable-parexa' # Parallel examples + ]) + + configure(*make_args) + make() + make("install") + + # Copy the config.h file, as some packages might require it + source_directory = self.stage.source_path + config_h = join_path(source_directory,'ADOL-C','src','config.h') + install(config_h, join_path(prefix.include,'adolc')) + + # Install documentation to {prefix}/share + if '+doc' in spec: + install_tree(join_path('ADOL-C','doc'), + join_path(prefix.share,'doc')) + + # Install examples to {prefix}/share + if '+tests' in spec: + install_tree(join_path('ADOL-C','examples'), + join_path(prefix.share,'examples')) + + # Run some examples that don't require user input + # TODO: Check that bundled examples produce the correct results + with working_dir(join_path(source_directory,'ADOL-C','examples')): + Executable('./tapeless_scalar')() + Executable('./tapeless_vector')() + + with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')): + Executable('./checkpointing/checkpointing')() + + if '+openmp' in spec: + with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')): + Executable('./checkpointing/checkpointing')() diff --git a/var/spack/repos/builtin/packages/antlr/package.py b/var/spack/repos/builtin/packages/antlr/package.py new file mode 100644 index 0000000000..c7c7e3e850 --- /dev/null +++ b/var/spack/repos/builtin/packages/antlr/package.py @@ -0,0 +1,47 @@ +from spack import * + +class Antlr(Package): + + homepage = "http://www.antlr.org" + url = "https://github.com/antlr/antlr/tarball/v2.7.7" + + # NOTE: This requires that a system Java be available. + # Spack does not yet know how to install Java compilers + + # Notes from http://nco.sourceforge.net/#bld + # The first steps to build (i.e., compile, for the most part) NCO from + # source code are to install the pre-requisites: ANTLR version 2.7.7 + # (like this one not version 3.x or 4.x!) (required for ncap2)... ANTLR + # binaries from major distributions are pre-built with the source patch + # necessary to allow NCO to link to ANTLR... The ANTLR source file + # CharScanner.hpp must include this line: #include <cstring> or else + # ncap2 will not compile (this tarball is already patched). + version('2.7.7', '914865e853fe8e1e61a9f23d045cb4ab', + # Patched version as described above + url='http://dust.ess.uci.edu/tmp/antlr-2.7.7.tar.gz') + # Unpatched version + # url='http://dust.ess.uci.edu/nco/antlr-2.7.7.tar.gz') + + variant('cxx', default=False, description='Enable ANTLR for C++') + variant('java', default=False, description='Enable ANTLR for Java') + variant('python', default=False, description='Enable ANTLR for Python') + variant('csharp', default=False, description='Enable ANTLR for Csharp') + + + def install(self, spec, prefix): + # Check for future enabling of variants + for v in ('+java', '+python', '+csharp'): + if v in spec: + raise Error('Illegal variant %s; for now, Spack only knows how to build antlr or antlr+cxx') + + config_args = [ + '--prefix=%s' % prefix, + '--%s-cxx' % ('enable' if '+cxx' in spec else 'disable'), + '--%s-java' % ('enable' if '+java' in spec else 'disable'), + '--%s-python' % ('enable' if '+python' in spec else 'disable'), + '--%s-csharp' % ('enable' if '+csharp' in spec else 'disable')] + + # which('autoreconf')('-iv') + configure(*config_args) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py index 6412e810a6..b5e29b8a27 100644 --- a/var/spack/repos/builtin/packages/autoconf/package.py +++ b/var/spack/repos/builtin/packages/autoconf/package.py @@ -8,6 +8,8 @@ class Autoconf(Package): version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b') version('2.62', '6c1f3b3734999035d77da5024aab4fbd') + depends_on("m4") + def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/bbcp/package.py b/var/spack/repos/builtin/packages/bbcp/package.py new file mode 100644 index 0000000000..e9baa5ccf4 --- /dev/null +++ b/var/spack/repos/builtin/packages/bbcp/package.py @@ -0,0 +1,17 @@ +from spack import * + +class Bbcp(Package): + """Securely and quickly copy data from source to target""" + homepage = "http://www.slac.stanford.edu/~abh/bbcp/" + + version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git', branch="master") + + def install(self, spec, prefix): + cd("src") + make() + # BBCP wants to build the executable in a directory whose name depends on the system type + makesname = Executable("../MakeSname") + bbcp_executable_path = "../bin/%s/bbcp" % makesname(output=str).rstrip("\n") + destination_path = "%s/bin/" % prefix + mkdirp(destination_path) + install(bbcp_executable_path, destination_path) diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index b8064093d2..158d722046 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -29,6 +29,7 @@ class Binutils(Package): configure_args = [ '--prefix=%s' % prefix, '--disable-dependency-tracking', + '--disable-werror', '--enable-interwork', '--enable-multilib', '--enable-shared', diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py index 7c526fb958..9a2ddcbf96 100644 --- a/var/spack/repos/builtin/packages/bison/package.py +++ b/var/spack/repos/builtin/packages/bison/package.py @@ -10,6 +10,8 @@ class Bison(Package): version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8') + depends_on("m4") + def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/cnmem/package.py b/var/spack/repos/builtin/packages/cnmem/package.py new file mode 100644 index 0000000000..0a83e8fc20 --- /dev/null +++ b/var/spack/repos/builtin/packages/cnmem/package.py @@ -0,0 +1,12 @@ +from spack import * + +class Cnmem(Package): + """CNMem mempool for CUDA devices""" + homepage = "https://github.com/NVIDIA/cnmem" + + version('git', git='https://github.com/NVIDIA/cnmem.git', branch="master") + + def install(self, spec, prefix): + cmake('.',*std_cmake_args) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py index bc83cb2b65..c2778e14da 100644 --- a/var/spack/repos/builtin/packages/cryptopp/package.py +++ b/var/spack/repos/builtin/packages/cryptopp/package.py @@ -13,6 +13,7 @@ class Cryptopp(Package): version('5.6.3', '3c5b70e2ec98b7a24988734446242d07') version('5.6.2', '7ed022585698df48e65ce9218f6c6a67') + version('5.6.1', '96cbeba0907562b077e26bcffb483828') def install(self, spec, prefix): make() diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 674fe3150a..df8330384d 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -12,6 +12,7 @@ class Dealii(Package): variant('mpi', default=True, description='Compile with MPI') variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)') variant('doc', default=False, description='Compile with documentation') + variant('gsl' , default=True, description='Compile with GSL') variant('hdf5', default=True, description='Compile with HDF5 (only with MPI)') variant('metis', default=True, description='Compile with Metis') variant('netcdf', default=True, description='Compile with Netcdf (only with MPI)') @@ -39,6 +40,8 @@ class Dealii(Package): depends_on ("mpi", when="+mpi") depends_on ("arpack-ng+mpi", when='+arpack+mpi') depends_on ("doxygen", when='+doc') + depends_on ("gsl", when='@8.5.0:+gsl') + depends_on ("gsl", when='@dev+gsl') depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why? depends_on ("metis@5:", when='+metis') depends_on ("netcdf+mpi", when="+netcdf+mpi") @@ -80,7 +83,6 @@ class Dealii(Package): (join_path(spec['lapack'].prefix.lib,'liblapack.%s' % dsuf), # FIXME don't hardcode names join_path(spec['blas'].prefix.lib,'libblas.%s' % dsuf)), # FIXME don't hardcode names '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix, - '-DP4EST_DIR=%s' % spec['p4est'].prefix, '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix, '-DTBB_DIR=%s' % spec['tbb'].prefix, '-DZLIB_DIR=%s' % spec['zlib'].prefix @@ -100,7 +102,7 @@ class Dealii(Package): ]) # Optional dependencies for which librariy names are the same as CMake variables - for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis'): + for library in ('gsl','hdf5','p4est','petsc','slepc','trilinos','metis'): if library in spec: options.extend([ '-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix), diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py index b065904912..e4795893e0 100644 --- a/var/spack/repos/builtin/packages/flex/package.py +++ b/var/spack/repos/builtin/packages/flex/package.py @@ -6,6 +6,7 @@ class Flex(Package): homepage = "http://flex.sourceforge.net/" url = "http://download.sourceforge.net/flex/flex-2.5.39.tar.gz" + version('2.6.0', '5724bcffed4ebe39e9b55a9be80859ec') version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 6043b62279..8f90757232 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -38,6 +38,7 @@ class Gcc(Package): list_url = 'http://open-source-box.org/gcc/' list_depth = 2 + version('6.1.0', '8fb6cb98b8459f5863328380fbf06bd1') version('5.3.0', 'c9616fd448f980259c31de613e575719') version('5.2.0', 'a51bcfeb3da7dd4c623e27207ed43467') version('4.9.3', '6f831b4d251872736e8e9cc09746f327') diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py index b346fe80c2..0e9e8fc099 100644 --- a/var/spack/repos/builtin/packages/gdb/package.py +++ b/var/spack/repos/builtin/packages/gdb/package.py @@ -34,6 +34,7 @@ class Gdb(Package): homepage = "https://www.gnu.org/software/gdb" url = "http://ftp.gnu.org/gnu/gdb/gdb-7.10.tar.gz" + version('7.11', 'f585059252836a981ea5db9a5f8ce97f') version('7.10.1', 'b93a2721393e5fa226375b42d567d90b') version('7.10', 'fa6827ad0fd2be1daa418abb11a54d86') version('7.9.1', 'f3b97de919a9dba84490b2e076ec4cb0') diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py index d00c301b4c..ecae89f1e8 100644 --- a/var/spack/repos/builtin/packages/glm/package.py +++ b/var/spack/repos/builtin/packages/glm/package.py @@ -11,6 +11,8 @@ class Glm(Package): url = "https://github.com/g-truc/glm/archive/0.9.7.1.tar.gz" version('0.9.7.1', '61af6639cdf652d1cdd7117190afced8') + + depends_on ("cmake") def install(self, spec, prefix): with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index 9d759303cb..5f659c56df 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -63,6 +63,11 @@ class Gmsh(Package): build_directory = join_path(self.stage.path, 'spack-build') source_directory = self.stage.source_path + options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) + + # Prevent GMsh from using its own strange directory structure on OSX + options.append('-DENABLE_OS_SPECIFIC_INSTALL=OFF') + if '+shared' in spec: options.extend(['-DENABLE_BUILD_SHARED:BOOL=ON', '-DENABLE_BUILD_DYNAMIC:BOOL=ON']) # Builds dynamic executable and installs shared library diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py index ab7205646e..a461a7482c 100644 --- a/var/spack/repos/builtin/packages/hwloc/package.py +++ b/var/spack/repos/builtin/packages/hwloc/package.py @@ -17,6 +17,7 @@ class Hwloc(Package): list_url = "http://www.open-mpi.org/software/hwloc/" list_depth = 3 + version('1.11.3', 'c1d36a9de6028eac1d18ea4782ef958f') version('1.11.2', 'e4ca55c2a5c5656da4a4e37c8fc51b23') version('1.11.1', 'feb4e416a1b25963ed565d8b42252fdc') version('1.9', '1f9f9155682fe8946a97c08896109508') diff --git a/var/spack/repos/builtin/packages/hydra/package.py b/var/spack/repos/builtin/packages/hydra/package.py new file mode 100644 index 0000000000..c1b8868276 --- /dev/null +++ b/var/spack/repos/builtin/packages/hydra/package.py @@ -0,0 +1,21 @@ +from spack import * + +class Hydra(Package): + """Hydra is a process management system for starting parallel jobs. + Hydra is designed to natively work with existing launcher daemons + (such as ssh, rsh, fork), as well as natively integrate with resource + management systems (such as slurm, pbs, sge).""" + + homepage = "http://www.mpich.org" + url = "http://www.mpich.org/static/downloads/3.2/hydra-3.2.tar.gz" + list_url = "http://www.mpich.org/static/downloads/" + list_depth = 2 + + version('3.2', '4d670916695bf7e3a869cc336a881b39') + + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/jpeg/package.py b/var/spack/repos/builtin/packages/jpeg/package.py index 87820467db..2f15e59ad4 100644 --- a/var/spack/repos/builtin/packages/jpeg/package.py +++ b/var/spack/repos/builtin/packages/jpeg/package.py @@ -1,14 +1,19 @@ from spack import * class Jpeg(Package): - """jpeg library""" + """libjpeg is a widely used free library with functions for handling the + JPEG image data format. It implements a JPEG codec (encoding and decoding) + alongside various utilities for handling JPEG data.""" + homepage = "http://www.ijg.org" - url = "http://www.ijg.org/files/jpegsrc.v9a.tar.gz" + url = "http://www.ijg.org/files/jpegsrc.v9b.tar.gz" + version('9b', '6a9996ce116ec5c52b4870dbcd6d3ddb') version('9a', '3353992aecaee1805ef4109aadd433e7') def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() + make("test") make("install") diff --git a/var/spack/repos/builtin/packages/kripke/package.py b/var/spack/repos/builtin/packages/kripke/package.py new file mode 100644 index 0000000000..7d067ea44d --- /dev/null +++ b/var/spack/repos/builtin/packages/kripke/package.py @@ -0,0 +1,32 @@ +from spack import * + +class Kripke(Package): + """Kripke is a simple, scalable, 3D Sn deterministic particle + transport proxy/mini app. + """ + homepage = "https://codesign.llnl.gov/kripke.php" + url = "https://codesign.llnl.gov/downloads/kripke-openmp-1.1.tar.gz" + + version('1.1', '7fe6f2b26ed983a6ce5495ab701f85bf') + + variant('mpi', default=True, description='Build with MPI.') + variant('openmp', default=True, description='Build with OpenMP enabled.') + + depends_on('mpi', when="+mpi") + + def install(self, spec, prefix): + with working_dir('build', create=True): + def enabled(variant): + return (1 if variant in spec else 0) + + cmake('-DCMAKE_INSTALL_PREFIX:PATH=.', + '-DENABLE_OPENMP=%d' % enabled('+openmp'), + '-DENABLE_MPI=%d' % enabled('+mpi'), + '..', + *std_cmake_args) + make() + + # Kripke does not provide install target, so we have to copy + # things into place. + mkdirp(prefix.bin) + install('kripke', prefix.bin) diff --git a/var/spack/repos/builtin/packages/libtermkey/package.py b/var/spack/repos/builtin/packages/libtermkey/package.py new file mode 100644 index 0000000000..7f25edaf76 --- /dev/null +++ b/var/spack/repos/builtin/packages/libtermkey/package.py @@ -0,0 +1,17 @@ +from spack import * + +class Libtermkey(Package): + """Easy keyboard entry processing for terminal programs""" + homepage = "http://www.leonerd.org.uk/code/libtermkey/" + url = "http://www.leonerd.org.uk/code/libtermkey/libtermkey-0.18.tar.gz" + + version('0.18' , '3be2e3e5a851a49cc5e8567ac108b520') + version('0.17' , '20edb99e0d95ec1690fe90e6a555ae6d') + version('0.16' , '7a24b675aaeb142d30db28e7554987d4') + version('0.15b', '27689756e6c86c56ae454f2ac259bc3d') + version('0.14' , 'e08ce30f440f9715c459060e0e048978') + + + def install(self, spec, prefix): + make() + make("install", "PREFIX=" + prefix) diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py index 82a54953b2..c804f5ab5d 100644 --- a/var/spack/repos/builtin/packages/libtool/package.py +++ b/var/spack/repos/builtin/packages/libtool/package.py @@ -8,6 +8,8 @@ class Libtool(Package): version('2.4.6' , 'addf44b646ddb4e3919805aa88fa7c5e') version('2.4.2' , 'd2f3b7d4627e69e13514a40e72a24d50') + depends_on('m4') + def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py new file mode 100644 index 0000000000..eace94d1a6 --- /dev/null +++ b/var/spack/repos/builtin/packages/libuv/package.py @@ -0,0 +1,21 @@ +from spack import * + +class Libuv(Package): + """Multi-platform library with a focus on asynchronous IO""" + homepage = "http://libuv.org" + url = "https://github.com/libuv/libuv/archive/v1.9.0.tar.gz" + + version('1.9.0', '14737f9c76123a19a290dabb7d1cd04c') + + depends_on('automake') + depends_on('autoconf') + depends_on('libtool') + + def install(self, spec, prefix): + bash = which("bash") + bash('autogen.sh') + configure('--prefix=%s' % prefix) + + make() + make("check") + make("install") diff --git a/var/spack/repos/builtin/packages/libvterm/package.py b/var/spack/repos/builtin/packages/libvterm/package.py new file mode 100644 index 0000000000..3212f6550d --- /dev/null +++ b/var/spack/repos/builtin/packages/libvterm/package.py @@ -0,0 +1,12 @@ +from spack import * + +class Libvterm(Package): + """An abstract library implementation of a terminal emulator""" + homepage = "http://www.leonerd.org.uk/code/libvterm/" + url = "http://www.leonerd.org.uk/code/libvterm/libvterm-0+bzr681.tar.gz" + + version('681', '7a4325a7350b7092245c04e8ee185ac3') + + def install(self, spec, prefix): + make() + make("install", "PREFIX=" + prefix) diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index b317ec6651..2179086fe5 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -43,6 +43,8 @@ class Mpich(Package): version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0') variant('verbs', default=False, description='Build support for OpenFabrics verbs.') + variant('pmi', default=True, description='Build with PMI support') + variant('hydra', default=True, description='Build the hydra process manager') provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') @@ -55,12 +57,15 @@ class Mpich(Package): spack_env.set('MPICH_FC', spack_fc) def setup_dependent_package(self, module, dep_spec): - """For dependencies, make mpicc's use spack wrapper.""" - # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers? - module.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') def install(self, spec, prefix): config_args = ["--prefix=" + prefix, + "--with-pmi=" + ("yes" if '+pmi' in spec else 'no'), + "--with-pm=" + ('hydra' if '+hydra' in spec else 'no'), "--enable-shared"] # Variants diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py index a3abb71285..b52233be4a 100644 --- a/var/spack/repos/builtin/packages/mrnet/package.py +++ b/var/spack/repos/builtin/packages/mrnet/package.py @@ -6,6 +6,7 @@ class Mrnet(Package): url = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_5.0.1.tar.gz" list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet" + version('5.0.1-2', git='https://github.com/dyninst/mrnet.git', commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9') version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd') version('4.1.0', '5a248298b395b329e2371bf25366115c') version('4.0.0', 'd00301c078cba57ef68613be32ceea2f') diff --git a/var/spack/repos/builtin/packages/msgpack-c/package.py b/var/spack/repos/builtin/packages/msgpack-c/package.py new file mode 100644 index 0000000000..a363bc89be --- /dev/null +++ b/var/spack/repos/builtin/packages/msgpack-c/package.py @@ -0,0 +1,14 @@ +from spack import * + +class MsgpackC(Package): + """A small, fast binary interchange format convertible to/from JSON""" + homepage = "http://www.msgpack.org" + url = "https://github.com/msgpack/msgpack-c/archive/cpp-1.4.1.tar.gz" + + version('1.4.1', 'e2fd3a7419b9bc49e5017fdbefab87e0') + + def install(self, spec, prefix): + cmake('.', *std_cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index 3e60b517db..c68a04d251 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -147,6 +147,12 @@ class Mvapich2(Package): spack_env.set('MPICH_F90', spack_fc) spack_env.set('MPICH_FC', spack_fc) + def setup_dependent_package(self, module, dep_spec): + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') + def install(self, spec, prefix): # we'll set different configure flags depending on our environment configure_args = [ diff --git a/var/spack/repos/builtin/packages/nco/package.py b/var/spack/repos/builtin/packages/nco/package.py new file mode 100644 index 0000000000..3a9aeaa656 --- /dev/null +++ b/var/spack/repos/builtin/packages/nco/package.py @@ -0,0 +1,30 @@ +from spack import * +import os + +class Nco(Package): + """The NCO toolkit manipulates and analyzes data stored in + netCDF-accessible formats""" + + homepage = "https://sourceforge.net/projects/nco" + url = "https://github.com/nco/nco/archive/4.5.5.tar.gz" + + version('4.5.5', '9f1f1cb149ad6407c5a03c20122223ce') + + # See "Compilation Requirements" at: + # http://nco.sourceforge.net/#bld + + depends_on('netcdf') + depends_on('antlr@2.7.7+cxx') # (required for ncap2) + depends_on('gsl') # (desirable for ncap2) + depends_on('udunits2') # (allows dimensional unit transformations) + # depends_on('opendap') # (enables network transparency), + + def install(self, spec, prefix): + opts = [ + '--prefix=%s' % prefix, + '--disable-openmp', # TODO: Make this a variant + '--disable-dap', # TODO: Make this a variant + '--disable-esmf'] + configure(*opts) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index b60a2c4e9a..4aad0f6f3c 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -12,15 +12,19 @@ class Netcdf(Package): version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e') version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae') - variant('mpi', default=True, description='Enables MPI parallelism') - variant('hdf4', default=False, description="Enable HDF4 support") + variant('mpi', default=True, description='Enables MPI parallelism') + variant('hdf4', default=False, description='Enable HDF4 support') - # Dependencies: - depends_on("curl") # required for DAP support + depends_on("m4") depends_on("hdf", when='+hdf4') - depends_on("hdf5+mpi~cxx", when='+mpi') # required for NetCDF-4 support - depends_on("hdf5~mpi", when='~mpi') # required for NetCDF-4 support - depends_on("zlib") # required for NetCDF-4 support + + # Required for DAP support + depends_on("curl") + + # Required for NetCDF-4 support + depends_on("zlib") + depends_on("hdf5+mpi", when='+mpi') + depends_on("hdf5~mpi", when='~mpi') def install(self, spec, prefix): # Environment variables @@ -48,7 +52,7 @@ class Netcdf(Package): # /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) + LDFLAGS.append( "-L%s" % spec['curl'].prefix.lib) if '+mpi' in spec: config_args.append('--enable-parallel4') diff --git a/var/spack/repos/builtin/packages/openblas/make.patch b/var/spack/repos/builtin/packages/openblas/make.patch new file mode 100644 index 0000000000..851214211a --- /dev/null +++ b/var/spack/repos/builtin/packages/openblas/make.patch @@ -0,0 +1,35 @@ +diff --git a/Makefile.system b/Makefile.system +index b89f60e..2dbdad0 100644 +--- a/Makefile.system ++++ b/Makefile.system +@@ -139,6 +139,10 @@ NO_PARALLEL_MAKE=0 + endif + GETARCH_FLAGS += -DNO_PARALLEL_MAKE=$(NO_PARALLEL_MAKE) + ++ifdef MAKE_NO_J ++GETARCH_FLAGS += -DMAKE_NO_J=$(MAKE_NO_J) ++endif ++ + ifdef MAKE_NB_JOBS + GETARCH_FLAGS += -DMAKE_NB_JOBS=$(MAKE_NB_JOBS) + endif +diff --git a/getarch.c b/getarch.c +index f9c49e6..dffad70 100644 +--- a/getarch.c ++++ b/getarch.c +@@ -1012,6 +1012,7 @@ int main(int argc, char *argv[]){ + #endif + #endif + ++#ifndef MAKE_NO_J + #ifdef MAKE_NB_JOBS + printf("MAKE += -j %d\n", MAKE_NB_JOBS); + #elif NO_PARALLEL_MAKE==1 +@@ -1021,6 +1022,7 @@ int main(int argc, char *argv[]){ + printf("MAKE += -j %d\n", get_num_cores()); + #endif + #endif ++#endif + + break; + diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index f5d656f659..99649da9ca 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -20,13 +20,15 @@ class Openblas(Package): provides('blas') provides('lapack') + patch('make.patch') def install(self, spec, prefix): # Openblas is picky about compilers. Configure fails with # FC=/abs/path/to/f77, whereas FC=f77 works fine. # To circumvent this, provide basename only: make_defs = ['CC=%s' % os.path.basename(spack_cc), - 'FC=%s' % os.path.basename(spack_f77)] + 'FC=%s' % os.path.basename(spack_f77), + 'MAKE_NO_J=1'] make_targets = ['libs', 'netlib'] diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 9a127f1812..d0dd2d657f 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -1,7 +1,5 @@ -import os - from spack import * - +import os class Openmpi(Package): """Open MPI is a project combining technologies and resources from @@ -28,6 +26,7 @@ class Openmpi(Package): patch('configure.patch', when="@1.10.0:1.10.1") variant('psm', default=False, description='Build support for the PSM library.') + variant('pmi', default=True, description='Build support for PMI-based launchers') variant('verbs', default=False, description='Build support for OpenFabrics verbs.') # TODO : variant support for other schedulers is missing @@ -38,6 +37,7 @@ class Openmpi(Package): depends_on('hwloc') + def url_for_version(self, version): return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) @@ -48,6 +48,12 @@ class Openmpi(Package): spack_env.set('OMPI_FC', spack_fc) spack_env.set('OMPI_F77', spack_f77) + def setup_dependent_package(self, module, dep_spec): + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') + def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix, @@ -62,6 +68,9 @@ class Openmpi(Package): if '+psm' in spec: config_args.append("--with-psm") + if '+pmi' in spec: + config_args.append("--with-pmi") #TODO: let user specify directory when possible + if '+verbs' in spec: # Up through version 1.6, this option was previously named --with-openib if spec.satisfies('@:1.6'): diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 9e3109bfed..d0c95731a2 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -15,10 +15,12 @@ class Openssl(Package): version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf') version('1.0.1r', '1abd905e079542ccae948af37e393d28') + version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1') version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a') version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5') version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d') version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa') + version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0') depends_on("zlib") parallel = False diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py index 017c4e3fbf..adf75babb9 100644 --- a/var/spack/repos/builtin/packages/p4est/package.py +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -7,6 +7,8 @@ class P4est(Package): version('1.1', '37ba7f4410958cfb38a2140339dbf64f') + variant('tests', default=True, description='Run small tests') + # build dependencies depends_on('automake') depends_on('autoconf') @@ -24,14 +26,20 @@ class P4est(Package): '--without-blas', 'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL', 'CFLAGS=-O2', - 'CC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # TODO: use ENV variables or MPI class wrappers - 'CXX=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), - 'FC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), - 'F77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'), + 'CC=%s' % self.spec['mpi'].mpicc, + 'CXX=%s' % self.spec['mpi'].mpicxx, + 'FC=%s' % self.spec['mpi'].mpifc, + 'F77=%s' % self.spec['mpi'].mpif77 ] configure('--prefix=%s' % prefix, *options) make() - make("check") + # Make tests optional as sometimes mpiexec can't be run with an error: + # mpiexec has detected an attempt to run as root. + # Running at root is *strongly* discouraged as any mistake (e.g., in + # defining TMPDIR) or bug can result in catastrophic damage to the OS + # file system, leaving your system in an unusable state. + if '+tests' in self.spec: + make("check") make("install") diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py index c254234b32..34766099da 100644 --- a/var/spack/repos/builtin/packages/paradiseo/package.py +++ b/var/spack/repos/builtin/packages/paradiseo/package.py @@ -20,15 +20,20 @@ class Paradiseo(Package): #variant('tests', default=False, description='Compile with build tests') #variant('doc', default=False, description='Compile with documentation') variant('debug', default=False, description='Builds a debug version of the libraries') + variant('openmp', default=False, description='Enable OpenMP support') + variant('gnuplot', default=False, description='Enable GnuPlot support') # Required dependencies depends_on ("cmake") - depends_on ("eigen") # Optional dependencies depends_on ("mpi", when="+mpi") depends_on ("doxygen", when='+doc') - + depends_on ("gnuplot", when='+gnuplot') + depends_on ("eigen", when='+edo') + depends_on ("boost~mpi", when='+edo~mpi') + depends_on ("boost+mpi", when='+edo+mpi') + # Patches patch('enable_eoserial.patch') patch('fix_osx_detection.patch') @@ -45,7 +50,9 @@ class Paradiseo(Package): '-DMPI:BOOL=%s' % ('TRUE' if '+mpi' in spec else 'FALSE'), '-DSMP:BOOL=%s' % ('TRUE' if '+smp' in spec else 'FALSE'), # Note: This requires a C++11 compatible compiler '-DEDO:BOOL=%s' % ('TRUE' if '+edo' in spec else 'FALSE'), - '-DENABLE_CMAKE_TESTING:BOOL=%s' % ('TRUE' if '+tests' in spec else 'FALSE') + '-DENABLE_CMAKE_TESTING:BOOL=%s' % ('TRUE' if '+tests' in spec else 'FALSE'), + '-DENABLE_OPENMP:BOOL=%s' % ('TRUE' if '+openmp' in spec else 'FALSE'), + '-DENABLE_GNUPLOT:BOOL=%s' % ('TRUE' if '+gnuplot' in spec else 'FALSE') ]) with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 93688fb777..1e1d6302f3 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -101,7 +101,7 @@ class Qt(Package): @property def common_config_args(self): - return [ + config_args = [ '-prefix', self.prefix, '-v', '-opensource', @@ -115,7 +115,16 @@ class Qt(Package): '-no-openvg', '-no-pch', # NIS is deprecated in more recent glibc - '-no-nis'] + '-no-nis' + ] + + if '+gtk' in self.spec: + config_args.append('-gtkstyle') + else: + config_args.append('-no-gtkstyle') + + return config_args + # Don't disable all the database drivers, but should # really get them into spack at some point. @@ -128,8 +137,7 @@ class Qt(Package): '-thread', '-shared', '-release', - '-fast' - ) + '-fast') @when('@4') def configure(self): diff --git a/var/spack/repos/builtin/packages/qthreads/ldflags.patch b/var/spack/repos/builtin/packages/qthreads/ldflags.patch new file mode 100644 index 0000000000..0c15eab386 --- /dev/null +++ b/var/spack/repos/builtin/packages/qthreads/ldflags.patch @@ -0,0 +1,11 @@ +--- a/configure ++++ b/configure +@@ -40456,7 +40456,7 @@ + hwloc_saved_LDFLAGS="$LDFLAGS" + if test "x$with_hwloc" != x; then + CPPFLAGS="-I$with_hwloc/include $CPPFLAGS" +- LDFLAGS="-L$with_hwloc/lib $CPPFLAGS" ++ LDFLAGS="-L$with_hwloc/lib $LDFLAGS" + fi + + diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py index dacdb71524..5da9340927 100644 --- a/var/spack/repos/builtin/packages/qthreads/package.py +++ b/var/spack/repos/builtin/packages/qthreads/package.py @@ -16,7 +16,12 @@ class Qthreads(Package): version('1.10', '5af8c8bbe88c2a6d45361643780d1671') + patch("ldflags.patch") + patch("restrict.patch") + patch("trap.patch") + def install(self, spec, prefix): - configure("--prefix=%s" % prefix) + configure("--prefix=%s" % prefix, + "--enable-guard-pages") make() make("install") diff --git a/var/spack/repos/builtin/packages/qthreads/restrict.patch b/var/spack/repos/builtin/packages/qthreads/restrict.patch new file mode 100644 index 0000000000..4c95714f6b --- /dev/null +++ b/var/spack/repos/builtin/packages/qthreads/restrict.patch @@ -0,0 +1,12 @@ +--- a/include/qthread/common.h.in ++++ b/include/qthread/common.h.in +@@ -84,7 +84,9 @@ + /* Define to the equivalent of the C99 'restrict' keyword, or to + nothing if this is not supported. Do not define if restrict is + supported directly. */ ++#ifndef restrict + #undef restrict ++#endif + /* Work around a bug in Sun C++: it does not support _Restrict or + __restrict__, even though the corresponding Sun C compiler ends up with + "#define restrict _Restrict" or "#define restrict __restrict__" in the diff --git a/var/spack/repos/builtin/packages/qthreads/trap.patch b/var/spack/repos/builtin/packages/qthreads/trap.patch new file mode 100644 index 0000000000..7aa94d82d5 --- /dev/null +++ b/var/spack/repos/builtin/packages/qthreads/trap.patch @@ -0,0 +1,11 @@ +--- a/include/qthread/qthread.hpp ++++ b/include/qthread/qthread.hpp +@@ -236,7 +236,7 @@ + return qthread_incr64((uint64_t *)operand, incr); + + default: +- *(int *)(0) = 0; ++ __builtin_trap(); + } + return T(0); // never hit - keep compiler happy + } diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py new file mode 100644 index 0000000000..f807ab71af --- /dev/null +++ b/var/spack/repos/builtin/packages/raja/package.py @@ -0,0 +1,12 @@ +from spack import * + +class Raja(Package): + """RAJA Parallel Framework.""" + homepage = "http://software.llnl.gov/RAJA/" + + version('git', git='https://github.com/LLNL/RAJA.git', branch="master") + + def install(self, spec, prefix): + cmake('.',*std_cmake_args) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/scons/package.py b/var/spack/repos/builtin/packages/scons/package.py new file mode 100644 index 0000000000..594aeced88 --- /dev/null +++ b/var/spack/repos/builtin/packages/scons/package.py @@ -0,0 +1,13 @@ +from spack import * + +class Scons(Package): + """SCons is a software construction tool""" + homepage = "http://scons.org" + url = "http://downloads.sourceforge.net/project/scons/scons/2.5.0/scons-2.5.0.tar.gz" + + version('2.5.0', '9e00fa0df8f5ca5c5f5975b40e0ed354') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py new file mode 100644 index 0000000000..a5c9057b99 --- /dev/null +++ b/var/spack/repos/builtin/packages/serf/package.py @@ -0,0 +1,51 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written 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 General Public License (as published by +# the Free Software Foundation) version 2.1 dated 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 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 Serf(Package): + """Apache Serf - a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library""" + homepage = 'https://serf.apache.org/' + url = 'https://archive.apache.org/dist/serf/serf-1.3.8.tar.bz2' + + version('1.3.8', '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446') + + depends_on('apr') + depends_on('apr-util') + depends_on('scons') + depends_on('expat') + depends_on('openssl') + + def install(self, spec, prefix): + scons = which("scons") + + options = ['PREFIX=%s' % prefix] + options.append('APR=%s' % spec['apr'].prefix) + options.append('APU=%s' % spec['apr-util'].prefix) + options.append('OPENSSL=%s' % spec['openssl'].prefix) + options.append('LINKFLAGS=-L%s/lib' % spec['expat'].prefix) + options.append('CPPFLAGS=-I%s/include' % spec['expat'].prefix) + + scons(*options) + scons('install') diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py index 5db1c3eb92..04cde94aad 100644 --- a/var/spack/repos/builtin/packages/subversion/package.py +++ b/var/spack/repos/builtin/packages/subversion/package.py @@ -37,6 +37,7 @@ class Subversion(Package): depends_on('apr-util') depends_on('zlib') depends_on('sqlite') + depends_on('serf') # Optional: We need swig if we want the Perl, Python or Ruby # bindings. @@ -54,6 +55,7 @@ class Subversion(Package): options.append('--with-apr-util=%s' % spec['apr-util'].prefix) options.append('--with-zlib=%s' % spec['zlib'].prefix) options.append('--with-sqlite=%s' % spec['sqlite'].prefix) + options.append('--with-serf=%s' % spec['serf'].prefix) #options.append('--with-swig=%s' % spec['swig'].prefix) configure(*options) diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index 5cf5e129b4..3420d9b90a 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -6,7 +6,9 @@ class SuperluDist(Package): homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz" - version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae') + version('5.0.0', '2b53baf1b0ddbd9fcf724992577f0670') + # default to version 4.3 since petsc and trilinos are not tested with 5.0. + version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae', preferred=True) version('4.2', 'ae9fafae161f775fbac6eba11e530a65') version('4.1', '4edee38cc29f687bd0c8eb361096a455') version('4.0', 'c0b98b611df227ae050bc1635c6940e0') diff --git a/var/spack/repos/builtin/packages/the_silver_searcher/package.py b/var/spack/repos/builtin/packages/the_silver_searcher/package.py index e4020b6766..30f06354bf 100644 --- a/var/spack/repos/builtin/packages/the_silver_searcher/package.py +++ b/var/spack/repos/builtin/packages/the_silver_searcher/package.py @@ -9,6 +9,7 @@ class TheSilverSearcher(Package): depends_on('pcre') depends_on('xz') + depends_on('pkg-config') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/unibilium/package.py b/var/spack/repos/builtin/packages/unibilium/package.py new file mode 100644 index 0000000000..ef5de56f79 --- /dev/null +++ b/var/spack/repos/builtin/packages/unibilium/package.py @@ -0,0 +1,12 @@ +from spack import * + +class Unibilium(Package): + """A terminfo parsing library""" + homepage = "https://github.com/mauke/unibilium" + url = "https://github.com/mauke/unibilium/archive/v1.2.0.tar.gz" + + version('1.2.0', '9b1c97839a880a373da6c097443b43c4') + + def install(self, spec, prefix): + make("PREFIX="+prefix) + make("install", "PREFIX="+prefix) diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py index e36fb936e0..bd02ddcd4b 100644 --- a/var/spack/repos/builtin/packages/xerces-c/package.py +++ b/var/spack/repos/builtin/packages/xerces-c/package.py @@ -1,19 +1,3 @@ -# FIXME: -# This is a template package file for Spack. We've conveniently -# put "FIXME" labels next to all the things you'll want to change. -# -# Once you've edited all the FIXME's, delete this whole message, -# save this file, and test out your package like this: -# -# spack install xerces-c -# -# You can always get back here to change things with: -# -# spack edit xerces-c -# -# See the spack documentation for more information on building -# packages. -# from spack import * class XercesC(Package): |