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author | Kelly (KT) Thompson <kgt@lanl.gov> | 2016-03-30 08:28:53 -0600 |
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committer | Kelly (KT) Thompson <kgt@lanl.gov> | 2016-03-30 08:28:53 -0600 |
commit | f2051f04407bba6d603cfd473881242f1b3e6517 (patch) | |
tree | 6b928b99b236bbbb9a4317a76f4c7a41c46d7e46 | |
parent | 40cea0110f4ad33fcc0045c67b5379b0b92fd2fc (diff) | |
parent | 7f469eadff9dfd7b1ac3cb4ff8c0476ac9027031 (diff) | |
download | spack-f2051f04407bba6d603cfd473881242f1b3e6517.tar.gz spack-f2051f04407bba6d603cfd473881242f1b3e6517.tar.bz2 spack-f2051f04407bba6d603cfd473881242f1b3e6517.tar.xz spack-f2051f04407bba6d603cfd473881242f1b3e6517.zip |
Merge remote-tracking branch 'upstream/develop' into pkg-graphviz
17 files changed, 532 insertions, 231 deletions
diff --git a/lib/spack/env/cc b/lib/spack/env/cc index 4a3e6eddc9..2eb6f46afe 100755 --- a/lib/spack/env/cc +++ b/lib/spack/env/cc @@ -65,7 +65,7 @@ function die { } for param in $parameters; do - if [ -z "${!param}" ]; then + if [[ -z ${!param} ]]; then die "Spack compiler must be run from spack! Input $param was missing!" fi done @@ -78,12 +78,17 @@ done # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90] # # 'mode' is set to one of: +# cpp preprocess # cc compile +# as assemble # ld link # ccld compile & link -# cpp preprocessor # vcheck version check # +# Depending on the mode, we may or may not add extra rpaths. +# This variable controls whether they are added. +add_rpaths=true + command=$(basename "$0") case "$command" in cc|c89|c99|gcc|clang|icc|pgcc|xlc) @@ -107,13 +112,26 @@ case "$command" in ;; ld) mode=ld + + # Darwin's linker has a -r argument that merges object files + # together. It doesn't work with -rpath. + if [[ $OSTYPE = darwin* ]]; then + for arg in "$@"; do + if [ "$arg" = -r ]; then + add_rpaths=false + break + fi + done + fi ;; *) die "Unkown compiler: $command" ;; esac -# If any of the arguments below is present then the mode is vcheck. In vcheck mode nothing is added in terms of extra search paths or libraries +# If any of the arguments below is present then the mode is vcheck. In +# vcheck mode nothing is added in terms of extra search paths or +# libraries if [ -z "$mode" ]; then for arg in "$@"; do if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then @@ -124,13 +142,15 @@ if [ -z "$mode" ]; then fi # Finish setting up the mode. - if [ -z "$mode" ]; then mode=ccld for arg in "$@"; do if [ "$arg" = -E ]; then mode=cpp break + elif [ "$arg" = -S ]; then + mode=as + break elif [ "$arg" = -c ]; then mode=cc break @@ -146,168 +166,56 @@ fi # Check that at least one of the real commands was actually selected, # otherwise we don't know what to execute. -if [ -z "$command" ]; then +if [[ -z $command ]]; then die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs." fi -# Save original command for debug logging -input_command="$@" - if [ "$mode" == vcheck ] ; then exec ${command} "$@" fi -# -# Now do real parsing of the command line args, trying hard to keep -# non-rpath linker arguments in the proper order w.r.t. other command -# line arguments. This is important for things like groups. -# -includes=() -libraries=() -libs=() -rpaths=() -other_args=() - -while [ -n "$1" ]; do - case "$1" in - -I*) - arg="${1#-I}" - if [ -z "$arg" ]; then shift; arg="$1"; fi - includes+=("$arg") - ;; - -L*) - arg="${1#-L}" - if [ -z "$arg" ]; then shift; arg="$1"; fi - libraries+=("$arg") - ;; - -l*) - arg="${1#-l}" - if [ -z "$arg" ]; then shift; arg="$1"; fi - libs+=("$arg") - ;; - -Wl,*) - arg="${1#-Wl,}" - # TODO: Handle multiple -Wl, continuations of -Wl,-rpath - if [[ $arg == -rpath=* ]]; then - arg="${arg#-rpath=}" - for rpath in ${arg//,/ }; do - rpaths+=("$rpath") - done - elif [[ $arg == -rpath,* ]]; then - arg="${arg#-rpath,}" - for rpath in ${arg//,/ }; do - rpaths+=("$rpath") - done - elif [[ $arg == -rpath ]]; then - shift; arg="$1" - if [[ $arg != '-Wl,'* ]]; then - die "-Wl,-rpath was not followed by -Wl,*" - fi - arg="${arg#-Wl,}" - for rpath in ${arg//,/ }; do - rpaths+=("$rpath") - done - else - other_args+=("-Wl,$arg") - fi - ;; - -Xlinker) - shift; arg="$1"; - if [[ $arg = -rpath=* ]]; then - rpaths+=("${arg#-rpath=}") - elif [[ $arg = -rpath ]]; then - shift; arg="$1" - if [[ $arg != -Xlinker ]]; then - die "-Xlinker -rpath was not followed by -Xlinker <arg>" - fi - shift; arg="$1" - rpaths+=("$arg") - else - other_args+=("-Xlinker") - other_args+=("$arg") - fi - ;; - *) - other_args+=("$1") - ;; - esac - shift -done - -# Dump parsed values for unit testing if asked for -if [ -n "$SPACK_TEST_COMMAND" ]; then - IFS=$'\n' - case "$SPACK_TEST_COMMAND" in - dump-includes) echo "${includes[*]}";; - dump-libraries) echo "${libraries[*]}";; - dump-libs) echo "${libs[*]}";; - dump-rpaths) echo "${rpaths[*]}";; - dump-other-args) echo "${other_args[*]}";; - dump-all) - echo "INCLUDES:" - echo "${includes[*]}" - echo - echo "LIBRARIES:" - echo "${libraries[*]}" - echo - echo "LIBS:" - echo "${libs[*]}" - echo - echo "RPATHS:" - echo "${rpaths[*]}" - echo - echo "ARGS:" - echo "${other_args[*]}" - ;; - *) - echo "ERROR: Unknown test command" - exit 1 ;; - esac - exit -fi +# Save original command for debug logging +input_command="$@" +args=("$@") # Read spack dependencies from the path environment variable IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES" for dep in "${deps[@]}"; do - if [ -d "$dep/include" ]; then - includes+=("$dep/include") + # Prepend include directories + if [[ -d $dep/include ]]; then + if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then + args=("-I$dep/include" "${args[@]}") + fi fi - if [ -d "$dep/lib" ]; then - libraries+=("$dep/lib") - rpaths+=("$dep/lib") + # Prepend lib and RPATH directories + if [[ -d $dep/lib ]]; then + if [[ $mode = ccld ]]; then + $add_rpaths && args=("-Wl,-rpath,$dep/lib" "${args[@]}") + args=("-L$dep/lib" "${args[@]}") + elif [[ $mode = ld ]]; then + $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}") + args=("-L$dep/lib" "${args[@]}") + fi fi - if [ -d "$dep/lib64" ]; then - libraries+=("$dep/lib64") - rpaths+=("$dep/lib64") + # Prepend lib64 and RPATH directories + if [[ -d $dep/lib64 ]]; then + if [[ $mode = ccld ]]; then + $add_rpaths && args=("-Wl,-rpath,$dep/lib64" "${args[@]}") + args=("-L$dep/lib64" "${args[@]}") + elif [[ $mode = ld ]]; then + $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}") + args=("-L$dep/lib64" "${args[@]}") + fi fi done # Include all -L's and prefix/whatever dirs in rpath -for dir in "${libraries[@]}"; do - [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir") -done -rpaths+=("$SPACK_PREFIX/lib") -rpaths+=("$SPACK_PREFIX/lib64") - -# Put the arguments together -args=() -for dir in "${includes[@]}"; do args+=("-I$dir"); done -args+=("${other_args[@]}") -for dir in "${libraries[@]}"; do args+=("-L$dir"); done -for lib in "${libs[@]}"; do args+=("-l$lib"); done - -if [ "$mode" = ccld ]; then - for dir in "${rpaths[@]}"; do - args+=("-Wl,-rpath") - args+=("-Wl,$dir"); - done -elif [ "$mode" = ld ]; then - for dir in "${rpaths[@]}"; do - args+=("-rpath") - args+=("$dir"); - done +if [[ $mode = ccld ]]; then + $add_rpaths && args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}") +elif [[ $mode = ld ]]; then + $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}") fi # @@ -323,34 +231,37 @@ unset DYLD_LIBRARY_PATH # IFS=':' read -ra env_path <<< "$PATH" IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH" -spack_env_dirs+=(".") +spack_env_dirs+=("" ".") PATH="" for dir in "${env_path[@]}"; do remove="" for rm_dir in "${spack_env_dirs[@]}"; do - if [ "$dir" = "$rm_dir" ]; then remove=True; fi + if [[ $dir = $rm_dir ]]; then remove=True; fi done - if [ -z "$remove" ]; then - if [ -z "$PATH" ]; then - PATH="$dir" - else - PATH="$PATH:$dir" - fi + if [[ -z $remove ]]; then + PATH="${PATH:+$PATH:}$dir" fi done export PATH -full_command=("$command") -full_command+=("${args[@]}") +full_command=("$command" "${args[@]}") + +# In test command mode, write out full command for Spack tests. +if [[ $SPACK_TEST_COMMAND = dump-args ]]; then + echo "${full_command[@]}" + exit +elif [[ -n $SPACK_TEST_COMMAND ]]; then + die "ERROR: Unknown test command" +fi # # Write the input and output commands to debug logs if it's asked for. # -if [ "$SPACK_DEBUG" = "TRUE" ]; then +if [[ $SPACK_DEBUG = TRUE ]]; then input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log" output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log" - echo "$input_command" >> $input_log - echo "$mode ${full_command[@]}" >> $output_log + echo "[$mode] $command $input_command" >> $input_log + echo "[$mode] ${full_command[@]}" >> $output_log fi exec "${full_command[@]}" diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index 0d0a7db8a9..4ea87bea7e 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -289,8 +289,14 @@ class URLFetchStrategy(FetchStrategy): if not self.archive_file: raise NoArchiveFileError("Tried to reset URLFetchStrategy before fetching", "Failed on reset() for URL %s" % self.url) - if self.stage.source_path: - shutil.rmtree(self.stage.source_path, ignore_errors=True) + + # Remove everythigng but the archive from the stage + for filename in os.listdir(self.stage.path): + abspath = os.path.join(self.stage.path, filename) + if abspath != self.archive_file: + shutil.rmtree(abspath, ignore_errors=True) + + # Expand the archive again self.expand() def __repr__(self): diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py index f3f6d4a22e..0b1aeb2a8f 100644 --- a/lib/spack/spack/test/cc.py +++ b/lib/spack/spack/test/cc.py @@ -28,6 +28,8 @@ arguments correctly. """ import os import unittest +import tempfile +import shutil from llnl.util.filesystem import * import spack @@ -55,13 +57,40 @@ class CompilerTest(unittest.TestCase): self.ld = Executable(join_path(spack.build_env_path, "ld")) self.cpp = Executable(join_path(spack.build_env_path, "cpp")) - os.environ['SPACK_CC'] = "/bin/mycc" - os.environ['SPACK_PREFIX'] = "/usr" + self.realcc = "/bin/mycc" + self.prefix = "/spack-test-prefix" + + os.environ['SPACK_CC'] = self.realcc + os.environ['SPACK_PREFIX'] = self.prefix os.environ['SPACK_ENV_PATH']="test" os.environ['SPACK_DEBUG_LOG_DIR'] = "." os.environ['SPACK_COMPILER_SPEC'] = "gcc@4.4.7" os.environ['SPACK_SHORT_SPEC'] = "foo@1.2" + # Make some fake dependencies + self.tmp_deps = tempfile.mkdtemp() + self.dep1 = join_path(self.tmp_deps, 'dep1') + self.dep2 = join_path(self.tmp_deps, 'dep2') + self.dep3 = join_path(self.tmp_deps, 'dep3') + self.dep4 = join_path(self.tmp_deps, 'dep4') + + mkdirp(join_path(self.dep1, 'include')) + mkdirp(join_path(self.dep1, 'lib')) + + mkdirp(join_path(self.dep2, 'lib64')) + + mkdirp(join_path(self.dep3, 'include')) + mkdirp(join_path(self.dep3, 'lib64')) + + mkdirp(join_path(self.dep4, 'include')) + + if 'SPACK_DEPENDENCIES' in os.environ: + del os.environ['SPACK_DEPENDENCIES'] + + + def tearDown(self): + shutil.rmtree(self.tmp_deps, True) + def check_cc(self, command, args, expected): os.environ['SPACK_TEST_COMMAND'] = command @@ -92,6 +121,10 @@ class CompilerTest(unittest.TestCase): self.check_cpp('dump-mode', [], "cpp") + def test_as_mode(self): + self.check_cc('dump-mode', ['-S'], "as") + + def test_ccld_mode(self): self.check_cc('dump-mode', [], "ccld") self.check_cc('dump-mode', ['foo.c', '-o', 'foo'], "ccld") @@ -104,27 +137,85 @@ class CompilerTest(unittest.TestCase): self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ld") - def test_includes(self): - self.check_cc('dump-includes', test_command, - "\n".join(["/test/include", "/other/include"])) + def test_dep_rpath(self): + """Ensure RPATHs for root package are added.""" + self.check_cc('dump-args', test_command, + self.realcc + ' ' + + '-Wl,-rpath,' + self.prefix + '/lib ' + + '-Wl,-rpath,' + self.prefix + '/lib64 ' + + ' '.join(test_command)) + + + def test_dep_include(self): + """Ensure a single dependency include directory is added.""" + os.environ['SPACK_DEPENDENCIES'] = self.dep4 + self.check_cc('dump-args', test_command, + self.realcc + ' ' + + '-Wl,-rpath,' + self.prefix + '/lib ' + + '-Wl,-rpath,' + self.prefix + '/lib64 ' + + '-I' + self.dep4 + '/include ' + + ' '.join(test_command)) + + + def test_dep_lib(self): + """Ensure a single dependency RPATH is added.""" + os.environ['SPACK_DEPENDENCIES'] = self.dep2 + self.check_cc('dump-args', test_command, + self.realcc + ' ' + + '-Wl,-rpath,' + self.prefix + '/lib ' + + '-Wl,-rpath,' + self.prefix + '/lib64 ' + + '-L' + self.dep2 + '/lib64 ' + + '-Wl,-rpath,' + self.dep2 + '/lib64 ' + + ' '.join(test_command)) + + + def test_all_deps(self): + """Ensure includes and RPATHs for all deps are added. """ + os.environ['SPACK_DEPENDENCIES'] = ':'.join([ + self.dep1, self.dep2, self.dep3, self.dep4]) + + # This is probably more constrained than it needs to be; it + # checks order within prepended args and doesn't strictly have + # to. We could loosen that if it becomes necessary + self.check_cc('dump-args', test_command, + self.realcc + ' ' + + '-Wl,-rpath,' + self.prefix + '/lib ' + + '-Wl,-rpath,' + self.prefix + '/lib64 ' + + + '-I' + self.dep4 + '/include ' + + + '-L' + self.dep3 + '/lib64 ' + + '-Wl,-rpath,' + self.dep3 + '/lib64 ' + + '-I' + self.dep3 + '/include ' + + + '-L' + self.dep2 + '/lib64 ' + + '-Wl,-rpath,' + self.dep2 + '/lib64 ' + + + '-L' + self.dep1 + '/lib ' + + '-Wl,-rpath,' + self.dep1 + '/lib ' + + '-I' + self.dep1 + '/include ' + + + ' '.join(test_command)) - def test_libraries(self): - self.check_cc('dump-libraries', test_command, - "\n".join(["/test/lib", "/other/lib"])) + def test_ld_deps(self): + """Ensure no (extra) -I args or -Wl, are passed in ld mode.""" + os.environ['SPACK_DEPENDENCIES'] = ':'.join([ + self.dep1, self.dep2, self.dep3, self.dep4]) + self.check_ld('dump-args', test_command, + 'ld ' + + '-rpath ' + self.prefix + '/lib ' + + '-rpath ' + self.prefix + '/lib64 ' + - def test_libs(self): - self.check_cc('dump-libs', test_command, - "\n".join(["lib1", "lib2", "lib3", "lib4"])) + '-L' + self.dep3 + '/lib64 ' + + '-rpath ' + self.dep3 + '/lib64 ' + + '-L' + self.dep2 + '/lib64 ' + + '-rpath ' + self.dep2 + '/lib64 ' + - def test_rpaths(self): - self.check_cc('dump-rpaths', test_command, - "\n".join(["/first/rpath", "/second/rpath", "/third/rpath", "/fourth/rpath"])) + '-L' + self.dep1 + '/lib ' + + '-rpath ' + self.dep1 + '/lib ' + + ' '.join(test_command)) - def test_other_args(self): - self.check_cc('dump-other-args', test_command, - "\n".join(["arg1", "-Wl,--start-group", "arg2", "arg3", "arg4", - "-Wl,--end-group", "arg5", "arg6"])) diff --git a/var/spack/repos/builtin/packages/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py new file mode 100644 index 0000000000..7260fd74a1 --- /dev/null +++ b/var/spack/repos/builtin/packages/astyle/package.py @@ -0,0 +1,17 @@ +from spack import * +import os + +class Astyle(Package): + """A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java Source Code.""" + homepage = "http://astyle.sourceforge.net/" + url = "http://downloads.sourceforge.net/project/astyle/astyle/astyle%202.04/astyle_2.04_linux.tar.gz" + + version('2.04', '30b1193a758b0909d06e7ee8dd9627f6') + + def install(self, spec, prefix): + + with working_dir('src'): + make('-f', + join_path(self.stage.source_path,'build','clang','Makefile'), + parallel=False) + install(join_path(self.stage.source_path, 'src','bin','astyle'), self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index 82ce6fbb74..f889da21f2 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -2,6 +2,9 @@ from spack import * import spack import sys +import os +import sys + class Boost(Package): """Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ @@ -173,6 +176,16 @@ class Boost(Package): return threadingOpts def install(self, spec, prefix): + # On Darwin, Boost expects the Darwin libtool. However, one of the + # dependencies may have pulled in Spack's GNU libtool, and these two are + # not compatible. We thus create a symlink to Darwin's libtool and add + # it at the beginning of PATH. + if sys.platform == 'darwin': + newdir = os.path.abspath('darwin-libtool') + mkdirp(newdir) + force_symlink('/usr/bin/libtool', join_path(newdir, 'libtool')) + env['PATH'] = newdir + ':' + env['PATH'] + withLibs = list() for lib in Boost.all_libs: if "+{0}".format(lib) in spec: diff --git a/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 new file mode 100644 index 0000000000..444e292786 --- /dev/null +++ b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 @@ -0,0 +1,42 @@ +diff --git a/gcc/configure b/gcc/configure +index 9523773..52b0bf7 100755 +--- a/gcc/configure ++++ b/gcc/configure +@@ -24884,7 +24884,7 @@ if test "${gcc_cv_as_ix86_filds+set}" = set; then : + else + gcc_cv_as_ix86_filds=no + if test x$gcc_cv_as != x; then +- $as_echo 'filds mem; fists mem' > conftest.s ++ $as_echo 'filds (%ebp); fists (%ebp)' > conftest.s + if { ac_try='$gcc_cv_as $gcc_cv_as_flags -o conftest.o conftest.s >&5' + { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5 + (eval $ac_try) 2>&5 +@@ -24915,7 +24915,7 @@ if test "${gcc_cv_as_ix86_fildq+set}" = set; then : + else + gcc_cv_as_ix86_fildq=no + if test x$gcc_cv_as != x; then +- $as_echo 'fildq mem; fistpq mem' > conftest.s ++ $as_echo 'fildq (%ebp); fistpq (%ebp)' > conftest.s + if { ac_try='$gcc_cv_as $gcc_cv_as_flags -o conftest.o conftest.s >&5' + { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5 + (eval $ac_try) 2>&5 +diff --git a/gcc/configure.ac b/gcc/configure.ac +index 68b0ee8..bd53978 100644 +--- a/gcc/configure.ac ++++ b/gcc/configure.ac +@@ -3869,13 +3869,13 @@ foo: nop + + gcc_GAS_CHECK_FEATURE([filds and fists mnemonics], + gcc_cv_as_ix86_filds,,, +- [filds mem; fists mem],, ++ [filds (%ebp); fists (%ebp)],, + [AC_DEFINE(HAVE_AS_IX86_FILDS, 1, + [Define if your assembler uses filds and fists mnemonics.])]) + + gcc_GAS_CHECK_FEATURE([fildq and fistpq mnemonics], + gcc_cv_as_ix86_fildq,,, +- [fildq mem; fistpq mem],, ++ [fildq (%ebp); fistpq (%ebp)],, + [AC_DEFINE(HAVE_AS_IX86_FILDQ, 1, + [Define if your assembler uses fildq and fistq mnemonics.])]) + diff --git a/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 new file mode 100644 index 0000000000..b065997f45 --- /dev/null +++ b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 @@ -0,0 +1,28 @@ +From 82f81877458ea372176eabb5de36329431dce99b Mon Sep 17 00:00:00 2001 +From: Iain Sandoe <iain@codesourcery.com> +Date: Sat, 21 Dec 2013 00:30:18 +0000 +Subject: [PATCH] don't try to mark local symbols as no-dead-strip + +--- + gcc/config/darwin.c | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/gcc/config/darwin.c b/gcc/config/darwin.c +index 40804b8..0080299 100644 +--- a/gcc/config/darwin.c ++++ b/gcc/config/darwin.c +@@ -1259,6 +1259,11 @@ darwin_encode_section_info (tree decl, rtx rtl, int first ATTRIBUTE_UNUSED) + void + darwin_mark_decl_preserved (const char *name) + { ++ /* Actually we shouldn't mark any local symbol this way, but for now ++ this only happens with ObjC meta-data. */ ++ if (darwin_label_is_anonymous_local_objc_name (name)) ++ return; ++ + fprintf (asm_out_file, "\t.no_dead_strip "); + assemble_name (asm_out_file, name); + fputc ('\n', asm_out_file); +-- +2.2.1 + diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index f8958ee290..6043b62279 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -26,6 +26,8 @@ from spack import * from contextlib import closing from glob import glob +import sys +import os class Gcc(Package): """The GNU Compiler Collection includes front ends for C, C++, @@ -47,24 +49,33 @@ class Gcc(Package): version('4.6.4', 'b407a3d1480c11667f293bfb1f17d1a4') version('4.5.4', '27e459c2566b8209ab064570e1b378f7') - variant('gold', default=True, description="Build the gold linker plugin for ld-based LTO") + variant('binutils', default=sys.platform != 'darwin', + description="Build via binutils") + variant('gold', default=sys.platform != 'darwin', + description="Build the gold linker plugin for ld-based LTO") depends_on("mpfr") depends_on("gmp") depends_on("mpc", when='@4.5:') depends_on("isl", when='@5.0:') - depends_on("binutils~libiberty", when='~gold') - depends_on("binutils~libiberty+gold", when='+gold') + depends_on("binutils~libiberty", when='+binutils ~gold') + depends_on("binutils~libiberty+gold", when='+binutils +gold') + # TODO: integrate these libraries. #depends_on("ppl") #depends_on("cloog") + if sys.platform == 'darwin': + patch('darwin/gcc-4.9.patch1', when='@4.9.3') + patch('darwin/gcc-4.9.patch2', when='@4.9.3') def install(self, spec, prefix): # libjava/configure needs a minor fix to install into spack paths. - filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure', string=True) + filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure', + string=True) enabled_languages = set(('c', 'c++', 'fortran', 'java', 'objc')) - if spec.satisfies("@4.7.1:"): + + if spec.satisfies("@4.7.1:") and sys.platform != 'darwin': enabled_languages.add('go') # Generic options to compile GCC @@ -72,32 +83,40 @@ class Gcc(Package): "--libdir=%s/lib64" % prefix, "--disable-multilib", "--enable-languages=" + ','.join(enabled_languages), - "--with-mpc=%s" % spec['mpc'].prefix, - "--with-mpfr=%s" % spec['mpfr'].prefix, - "--with-gmp=%s" % spec['gmp'].prefix, + "--with-mpc=%s" % spec['mpc'].prefix, + "--with-mpfr=%s" % spec['mpfr'].prefix, + "--with-gmp=%s" % spec['gmp'].prefix, "--enable-lto", - "--with-gnu-ld", - "--with-gnu-as", "--with-quad"] # Binutils - static_bootstrap_flags = "-static-libstdc++ -static-libgcc" - binutils_options = ["--with-sysroot=/", - "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags), - "--with-boot-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags), - "--with-ld=%s/bin/ld" % spec['binutils'].prefix, - "--with-as=%s/bin/as" % spec['binutils'].prefix] - options.extend(binutils_options) + if spec.satisfies('+binutils'): + static_bootstrap_flags = "-static-libstdc++ -static-libgcc" + binutils_options = ["--with-sysroot=/", + "--with-stage1-ldflags=%s %s" % + (self.rpath_args, static_bootstrap_flags), + "--with-boot-ldflags=%s %s" % + (self.rpath_args, static_bootstrap_flags), + "--with-gnu-ld", + "--with-ld=%s/bin/ld" % spec['binutils'].prefix, + "--with-gnu-as", + "--with-as=%s/bin/as" % spec['binutils'].prefix] + options.extend(binutils_options) # Isl if 'isl' in spec: isl_options = ["--with-isl=%s" % spec['isl'].prefix] options.extend(isl_options) + if sys.platform == 'darwin' : + darwin_options = [ "--with-build-config=bootstrap-debug" ] + options.extend(darwin_options) + build_dir = join_path(self.stage.path, 'spack-build') configure = Executable( join_path(self.stage.source_path, 'configure') ) with working_dir(build_dir, create=True): # Rest of install is straightforward. configure(*options) - make() + if sys.platform == 'darwin' : make("bootstrap") + else: make() make("install") self.write_rpath_specs() @@ -114,7 +133,8 @@ class Gcc(Package): """Generate a spec file so the linker adds a rpath to the libs the compiler used to build the executable.""" if not self.spec_dir: - tty.warn("Could not install specs for %s." % self.spec.format('$_$@')) + tty.warn("Could not install specs for %s." % + self.spec.format('$_$@')) return gcc = Executable(join_path(self.prefix.bin, 'gcc')) @@ -124,5 +144,6 @@ class Gcc(Package): for line in lines: out.write(line + "\n") if line.startswith("*link:"): - out.write("-rpath %s/lib:%s/lib64 \\\n"% (self.prefix, self.prefix)) + out.write("-rpath %s/lib:%s/lib64 \\\n" % + (self.prefix, self.prefix)) set_install_permissions(specs_file) diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py new file mode 100644 index 0000000000..4f1f1ec2dd --- /dev/null +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -0,0 +1,69 @@ +from spack import * + +class Gdal(Package): + """ + GDAL is a translator library for raster and vector geospatial + data formats that is released under an X/MIT style Open Source + license by the Open Source Geospatial Foundation. As a library, + it presents a single raster abstract data model and vector + abstract data model to the calling application for all supported + formats. It also comes with a variety of useful command line + utilities for data translation and processing + """ + + homepage = "http://www.gdal.org/" + url = "http://download.osgeo.org/gdal/2.0.2/gdal-2.0.2.tar.gz" + list_url = "http://download.osgeo.org/gdal/" + list_depth = 2 + + version('2.0.2', '573865f3f59ba7b4f8f4cddf223b52a5') + + extends('python') + + variant('hdf5', default=False, description='Enable HDF5 support') + variant('hdf', default=False, description='Enable HDF4 support') + variant('openjpeg', default=False, description='Enable JPEG2000 support') + variant('geos', default=False, description='Enable GEOS support') + variant('kea', default=False, description='Enable KEA support') + variant('netcdf', default=False, description='Enable netcdf support') + + depends_on('swig') + depends_on("hdf5", when='+hdf5') + depends_on("hdf", when='+hdf') + depends_on("openjpeg", when='+openjpeg') + depends_on("geos", when='+geos') + depends_on("kealib", when='+kea') + depends_on("netcdf", when='+netcdf') + depends_on("libtiff") + depends_on("libpng") + depends_on("zlib") + depends_on("proj") + depends_on("py-numpy") + + parallel = False + + def install(self, spec, prefix): + args = [] + args.append("--prefix=%s" % prefix) + args.append("--with-liblzma=yes") + args.append("--with-zlib=%s" % spec['zlib'].prefix) + args.append("--with-python=%s" % spec['python'].prefix.bin + "/python") + args.append("--without-libtool") + + if '+geos' in spec: + args.append('--with-geos=yes') + if '+hdf' in spec: + args.append('--with-hdf4=%s' % spec['hdf'].prefix) + if '+hdf5' in spec: + args.append('--with-hdf5=%s' % spec['hdf5'].prefix) + if '+openjpeg' in spec: + args.append('--with-openjpeg=%s' % spec['openjpeg'].prefix) + if '+kea' in spec: + args.append('--with-kea=yes') + if '+netcdf' in spec: + args.append('--with-netcdf=%s' % spec['netcdf'].prefix) + + configure(*args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 0e99553293..4b915daa68 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -42,6 +42,9 @@ class Hypre(Package): if '~internal-superlu' in self.spec: configure_args.append("--without-superlu") + # MLI and FEI do not build without superlu on Linux + configure_args.append("--without-mli") + configure_args.append("--without-fei") # Hypre's source is staged under ./src so we'll have to manually # cd into it. diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py new file mode 100644 index 0000000000..475d21e1d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/kealib/package.py @@ -0,0 +1,35 @@ +from spack import * + +class Kealib(Package): + """An HDF5 Based Raster File Format + + KEALib provides an implementation of the GDAL data model. + The format supports raster attribute tables, image pyramids, + meta-data and in-built statistics while also handling very + large files and compression throughout. + + Based on the HDF5 standard, it also provides a base from which + other formats can be derived and is a good choice for long + term data archiving. An independent software library (libkea) + provides complete access to the KEA image format and a GDAL + driver allowing KEA images to be used from any GDAL supported software. + + Development work on this project has been funded by Landcare Research. + """ + homepage = "http://kealib.org/" + url = "https://bitbucket.org/chchrsc/kealib/get/kealib-1.4.5.tar.gz" + + version('1.4.5', '112e9c42d980b2d2987a3c15d0833a5d') + + depends_on("hdf5") + + def install(self, spec, prefix): + with working_dir('trunk', create=False): + cmake_args = [] + cmake_args.append("-DCMAKE_INSTALL_PREFIX=%s" % prefix) + cmake_args.append("-DHDF5_INCLUDE_DIR=%s" % spec['hdf5'].prefix.include) + cmake_args.append("-DHDF5_LIB_PATH=%s" % spec['hdf5'].prefix.lib) + cmake('.', *cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/mumps/Makefile.inc b/var/spack/repos/builtin/packages/mumps/Makefile.inc index 2e6a041878..22d8f5518a 100644 --- a/var/spack/repos/builtin/packages/mumps/Makefile.inc +++ b/var/spack/repos/builtin/packages/mumps/Makefile.inc @@ -8,12 +8,9 @@ IORDERINGSF = $(ISCOTCH) IORDERINGSC = $(IMETIS) $(IPORD) $(ISCOTCH) PLAT = -LIBEXT = .a -OUTC = -o +OUTC = -o OUTF = -o RM = /bin/rm -f -AR = ar vr -RANLIB = ranlib INCSEQ = -I$(topdir)/libseq LIBSEQ = -L$(topdir)/libseq -lmpiseq diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 5a254dfd00..26440ab7c8 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -1,6 +1,5 @@ from spack import * -import os - +import os, sys class Mumps(Package): """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver""" @@ -19,6 +18,7 @@ class Mumps(Package): variant('float', default=True, description='Activate the compilation of smumps') variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps') variant('idx64', default=False, description='Use int64_t/integer*8 as default index type') + variant('shared', default=True, description='Build shared libraries') depends_on('scotch + esmumps', when='~ptscotch+scotch') @@ -70,6 +70,9 @@ class Mumps(Package): makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings))) + # when building shared libs need -fPIC, otherwise + # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC + fpic = '-fPIC' if '+shared' in self.spec else '' # TODO: test this part, it needs a full blas, scalapack and # partitionning environment with 64bit integers if '+idx64' in self.spec: @@ -77,14 +80,14 @@ class Mumps(Package): # the fortran compilation flags most probably are # working only for intel and gnu compilers this is # perhaps something the compiler should provide - ['OPTF = -O -DALLOW_NON_INIT %s' % '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8', - 'OPTL = -O ', - 'OPTC = -O -DINTSIZE64']) + ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), + 'OPTL = %s -O ' % fpic, + 'OPTC = %s -O -DINTSIZE64' % fpic]) else: makefile_conf.extend( - ['OPTF = -O -DALLOW_NON_INIT', - 'OPTL = -O ', - 'OPTC = -O ']) + ['OPTF = %s -O -DALLOW_NON_INIT' % fpic, + 'OPTL = %s -O ' % fpic, + 'OPTC = %s -O ' % fpic]) if '+mpi' in self.spec: @@ -105,6 +108,27 @@ class Mumps(Package): # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER makefile_conf.append("CDEFS = -DAdd_") + if '+shared' in self.spec: + if sys.platform == 'darwin': + # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew) + makefile_conf.extend([ + 'LIBEXT=.dylib', + 'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib), + 'RANLIB=echo' + ]) + else: + makefile_conf.extend([ + 'LIBEXT=.so', + 'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, + 'RANLIB=echo' + ]) + else: + makefile_conf.extend([ + 'LIBEXT = .a', + 'AR = ar vr', + 'RANLIB = ranlib' + ]) + makefile_inc_template = join_path(os.path.dirname(self.module.__file__), 'Makefile.inc') @@ -121,7 +145,7 @@ class Mumps(Package): def install(self, spec, prefix): make_libs = [] - # the coice to compile ?examples is to have kind of a sanity + # the choice to compile ?examples is to have kind of a sanity # check on the libraries generated. if '+float' in spec: make_libs.append('sexamples') @@ -135,10 +159,24 @@ class Mumps(Package): self.write_makefile_inc() - # Build fails in parallel, at least on OS-X + # Build fails in parallel make(*make_libs, parallel=False) install_tree('lib', prefix.lib) install_tree('include', prefix.include) if '~mpi' in spec: - install('libseq/libmpiseq.a', prefix.lib) + lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' + lib_suffix = lib_dsuffix if '+shared' in spec else '.a' + install('libseq/libmpiseq%s' % lib_suffix, prefix.lib) + + # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI + # FIXME: use something like numdiff to compare blessed output with the current + with working_dir('examples'): + if '+float' in spec: + os.system('./ssimpletest < input_simpletest_real') + if '+complex' in spec: + os.system('./csimpletest < input_simpletest_real') + if '+double' in spec: + os.system('./dsimpletest < input_simpletest_real') + if '+complex' in spec: + os.system('./zsimpletest < input_simpletest_cmplx') diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py index a1a9ff90e5..19ca8ce287 100644 --- a/var/spack/repos/builtin/packages/muparser/package.py +++ b/var/spack/repos/builtin/packages/muparser/package.py @@ -14,5 +14,5 @@ class Muparser(Package): configure(*options) - make() + make(parallel=False) make("install") diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py new file mode 100644 index 0000000000..afec197d11 --- /dev/null +++ b/var/spack/repos/builtin/packages/openjpeg/package.py @@ -0,0 +1,26 @@ +from spack import * + +class Openjpeg(Package): + """ + OpenJPEG is an open-source JPEG 2000 codec written in C language. + It has been developed in order to promote the use of JPEG 2000, a + still-image compression standard from the Joint Photographic + Experts Group (JPEG). + Since April 2015, it is officially recognized by ISO/IEC and + ITU-T as a JPEG 2000 Reference Software. + """ + homepage = "https://github.com/uclouvain/openjpeg" + url = "https://github.com/uclouvain/openjpeg/archive/version.2.1.tar.gz" + + version('2.1' , '3e1c451c087f8462955426da38aa3b3d') + version('2.0.1', '105876ed43ff7dbb2f90b41b5a43cfa5') + version('2.0' , 'cdf266530fee8af87454f15feb619609') + version('1.5.2', '545f98923430369a6b046ef3632ef95c') + version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e') + + + def install(self, spec, prefix): + cmake('.', *std_cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/py-libxml2/package.py b/var/spack/repos/builtin/packages/py-libxml2/package.py deleted file mode 100644 index 59005428e4..0000000000 --- a/var/spack/repos/builtin/packages/py-libxml2/package.py +++ /dev/null @@ -1,15 +0,0 @@ -from spack import * - -class PyLibxml2(Package): - """A Python wrapper around libxml2.""" - homepage = "https://xmlsoft.org/python.html" - url = "ftp://xmlsoft.org/libxml2/python/libxml2-python-2.6.21.tar.gz" - - version('2.6.21', '229dd2b3d110a77defeeaa73af83f7f3') - - extends('python') - depends_on('libxml2') - depends_on('libxslt') - - def install(self, spec, prefix): - python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py new file mode 100644 index 0000000000..984b4196b1 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tuiview/package.py @@ -0,0 +1,19 @@ +from spack import * + +class PyTuiview(Package): + """ + TuiView is a lightweight raster GIS with powerful raster attribute + table manipulation abilities. + """ + homepage = "https://bitbucket.org/chchrsc/tuiview" + url = "https://bitbucket.org/chchrsc/tuiview/get/tuiview-1.1.7.tar.gz" + + version('1.1.7', '4b3b38a820cc239c8ab4a181ac5d4c30') + + extends("python") + depends_on("py-pyqt") + depends_on("py-numpy") + depends_on("gdal") + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) |