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Merge branch 'develop' of https://github.com/LLNL/spack into bugfix/compiler_find

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Forgot to pull branch changes before
This commit is contained in:
Mario Melara
2016-06-20 10:59:28 -07:00
parent 88888f5ba0 f74d4b0660
commit 6fb7b0fcf7
44 changed files with 1619 additions and 343 deletions
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4
lib/spack/env/cc vendored
View File

@@ -324,8 +324,8 @@ fi
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-$SPACK_SHORT_SPEC.out.log"
echo "[$mode] $command $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[@]}"

76
lib/spack/llnl/util/filesystem.py
View File

@@ -22,28 +22,28 @@
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
__all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree',
'expand_user', 'working_dir', 'touch', 'touchp', 'mkdirp',
'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
'set_executable', 'copy_mode', 'unset_executable_mode',
'remove_dead_links', 'remove_linked_tree', 'find_library_path',
'fix_darwin_install_name']
import os
import glob
import sys
import re
import shutil
import stat
import errno
import getpass
from contextlib import contextmanager, closing
from tempfile import NamedTemporaryFile
import subprocess
import llnl.util.tty as tty
from spack.util.compression import ALLOWED_ARCHIVE_TYPES
__all__ = ['set_install_permissions', 'install', 'install_tree',
'traverse_tree',
'expand_user', 'working_dir', 'touch', 'touchp', 'mkdirp',
'force_remove', 'join_path', 'ancestor', 'can_access',
'filter_file',
'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
'set_executable', 'copy_mode', 'unset_executable_mode',
'remove_dead_links', 'remove_linked_tree', 'find_library_path',
'fix_darwin_install_name', 'to_link_flags']
def filter_file(regex, repl, *filenames, **kwargs):
"""Like sed, but uses python regular expressions.
@@ -69,6 +69,7 @@ def filter_file(regex, repl, *filenames, **kwargs):
# Allow strings to use \1, \2, etc. for replacement, like sed
if not callable(repl):
unescaped = repl.replace(r'\\', '\\')
def replace_groups_with_groupid(m):
def groupid_to_group(x):
return m.group(int(x.group(1)))
@@ -157,9 +158,12 @@ def set_install_permissions(path):
def copy_mode(src, dest):
src_mode = os.stat(src).st_mode
dest_mode = os.stat(dest).st_mode
if src_mode & stat.S_IXUSR: dest_mode |= stat.S_IXUSR
if src_mode & stat.S_IXGRP: dest_mode |= stat.S_IXGRP
if src_mode & stat.S_IXOTH: dest_mode |= stat.S_IXOTH
if src_mode & stat.S_IXUSR:
dest_mode |= stat.S_IXUSR
if src_mode & stat.S_IXGRP:
dest_mode |= stat.S_IXGRP
if src_mode & stat.S_IXOTH:
dest_mode |= stat.S_IXOTH
os.chmod(dest, dest_mode)
@@ -224,9 +228,10 @@ def force_remove(*paths):
for path in paths:
try:
os.remove(path)
except OSError, e:
except OSError:
pass
@contextmanager
def working_dir(dirname, **kwargs):
if kwargs.get('create', False):
@@ -240,7 +245,7 @@ def working_dir(dirname, **kwargs):
def touch(path):
"""Creates an empty file at the specified path."""
with open(path, 'a') as file:
with open(path, 'a'):
os.utime(path, None)
@@ -253,7 +258,7 @@ def touchp(path):
def force_symlink(src, dest):
try:
os.symlink(src, dest)
except OSError as e:
except OSError:
os.remove(dest)
os.symlink(src, dest)
@@ -275,7 +280,7 @@ def ancestor(dir, n=1):
def can_access(file_name):
"""True if we have read/write access to the file."""
return os.access(file_name, os.R_OK|os.W_OK)
return os.access(file_name, os.R_OK | os.W_OK)
def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
@@ -343,13 +348,14 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
# Treat as a directory
if os.path.isdir(source_child) and (
follow_links or not os.path.islink(source_child)):
follow_links or not os.path.islink(source_child)):
# When follow_nonexisting isn't set, don't descend into dirs
# in source that do not exist in dest
if follow_nonexisting or os.path.exists(dest_child):
tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs)
for t in tuples: yield t
tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs) # NOQA: ignore=E501
for t in tuples:
yield t
# Treat as a file.
elif not ignore(os.path.join(rel_path, f)):
@@ -379,6 +385,7 @@ def remove_dead_links(root):
if not os.path.exists(real_path):
os.unlink(path)
def remove_linked_tree(path):
"""
Removes a directory and its contents. If the directory is a
@@ -402,28 +409,41 @@ def fix_darwin_install_name(path):
Fix install name of dynamic libraries on Darwin to have full path.
There are two parts of this task:
(i) use install_name('-id',...) to change install name of a single lib;
(ii) use install_name('-change',...) to change the cross linking between libs.
The function assumes that all libraries are in one folder and currently won't
follow subfolders.
(ii) use install_name('-change',...) to change the cross linking between
libs. The function assumes that all libraries are in one folder and
currently won't follow subfolders.
Args:
path: directory in which .dylib files are alocated
"""
libs = glob.glob(join_path(path,"*.dylib"))
libs = glob.glob(join_path(path, "*.dylib"))
for lib in libs:
# fix install name first:
subprocess.Popen(["install_name_tool", "-id",lib,lib], stdout=subprocess.PIPE).communicate()[0]
long_deps = subprocess.Popen(["otool", "-L",lib], stdout=subprocess.PIPE).communicate()[0].split('\n')
subprocess.Popen(["install_name_tool", "-id", lib, lib], stdout=subprocess.PIPE).communicate()[0] # NOQA: ignore=E501
long_deps = subprocess.Popen(["otool", "-L", lib], stdout=subprocess.PIPE).communicate()[0].split('\n') # NOQA: ignore=E501
deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]]
# fix all dependencies:
for dep in deps:
for loc in libs:
if dep == os.path.basename(loc):
subprocess.Popen(["install_name_tool", "-change",dep,loc,lib], stdout=subprocess.PIPE).communicate()[0]
subprocess.Popen(["install_name_tool", "-change", dep, loc, lib], stdout=subprocess.PIPE).communicate()[0] # NOQA: ignore=E501
break
def to_link_flags(library):
"""Transforms a path to a <library> into linking flags -L<dir> -l<name>.
Return:
A string of linking flags.
"""
dir = os.path.dirname(library)
# Asume libXYZ.suffix
name = os.path.basename(library)[3:].split(".")[0]
res = '-L%s -l%s' % (dir, name)
return res
def find_library_path(libname, *paths):
"""Searches for a file called <libname> in each path.

8
lib/spack/spack/hooks/sbang.py
View File

@@ -24,7 +24,6 @@
##############################################################################
import os
from llnl.util.filesystem import *
import llnl.util.tty as tty
import spack
@@ -34,6 +33,7 @@
# here, as it is the shortest I could find on a modern OS.
shebang_limit = 127
def shebang_too_long(path):
"""Detects whether a file has a shebang line that is too long."""
with open(path, 'r') as script:
@@ -57,16 +57,10 @@ def filter_shebang(path):
if original.startswith(new_sbang_line):
return
backup = path + ".shebang.bak"
os.rename(path, backup)
with open(path, 'w') as new_file:
new_file.write(new_sbang_line)
new_file.write(original)
copy_mode(backup, path)
unset_executable_mode(backup)
tty.warn("Patched overly long shebang in %s" % path)

67
lib/spack/spack/test/cmd/test_compiler_cmd.py
View File

@@ -1,8 +1,16 @@
import os
import shutil
from tempfile import mkdtemp
from llnl.util.filesystem import set_executable, mkdirp
import spack.spec
import spack.cmd.compiler
import spack.compilers
from spack.version import Version
from spack.test.mock_packages_test import *
test_version = '4.5-spacktest'
class MockArgs(object):
def __init__(self, add_paths=[], scope=None, compiler_spec=None, all=None):
@@ -12,23 +20,62 @@ def __init__(self, add_paths=[], scope=None, compiler_spec=None, all=None):
self.all = all
def make_mock_compiler():
"""Make a directory containing a fake, but detectable compiler."""
mock_compiler_dir = mkdtemp()
bin_dir = os.path.join(mock_compiler_dir, 'bin')
mkdirp(bin_dir)
gcc_path = os.path.join(bin_dir, 'gcc')
gxx_path = os.path.join(bin_dir, 'g++')
gfortran_path = os.path.join(bin_dir, 'gfortran')
with open(gcc_path, 'w') as f:
f.write("""\
#!/bin/sh
for arg in "$@"; do
if [ "$arg" = -dumpversion ]; then
echo '%s'
fi
done
""" % test_version)
# Create some mock compilers in the temporary directory
set_executable(gcc_path)
shutil.copy(gcc_path, gxx_path)
shutil.copy(gcc_path, gfortran_path)
return mock_compiler_dir
class CompilerCmdTest(MockPackagesTest):
""" Test compiler commands for add and remove """
def test_compiler_remove(self):
args = MockArgs(all=True, compiler_spec='gcc@4.5.0')
spack.cmd.compiler.compiler_remove(args)
compilers = spack.compilers.all_compilers()
self.assertTrue(spack.spec.CompilerSpec("gcc@4.5.0") not in compilers)
def test_compiler_add(self):
# Probably not a good a assumption but might try finding local
# compilers
# installed in /usr
compilers = spack.compilers.all_compilers()
s = set(compilers)
args = MockArgs(add_paths=["/usr"])
spack.cmd.compiler.compiler_find(args)
new_compilers = spack.compilers.all_compilers()
new_compiler = [x for x in new_compilers if x not in s]
self.assertTrue(new_compiler)
# compilers available by default.
old_compilers = set(spack.compilers.all_compilers())
# add our new compiler and find again.
compiler_dir = make_mock_compiler()
try:
args = MockArgs(add_paths=[compiler_dir])
spack.cmd.compiler.compiler_find(args)
# ensure new compiler is in there
new_compilers = set(spack.compilers.all_compilers())
new_compiler = new_compilers - old_compilers
self.assertTrue(new_compiler)
self.assertTrue(new_compiler.pop().version == Version(test_version))
finally:
shutil.rmtree(compiler_dir, ignore_errors=True)