Fixed BLAS and Lapack installations

5 files changed, 236 insertions, 17 deletions

diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 3b34e04740..8eff642938 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -40,7 +40,6 @@ from tempfile import NamedTemporaryFile
 import llnl.util.tty as tty
 from spack.util.compression import ALLOWED_ARCHIVE_TYPES
 
-
 def filter_file(regex, repl, *filenames, **kwargs):
     """Like sed, but uses python regular expressions.
 
diff --git a/lib/spack/llnl/util/filesystem.py.save b/lib/spack/llnl/util/filesystem.py.save
new file mode 100644
index 0000000000..e69de29bb2
--- /dev/null
+++ b/lib/spack/llnl/util/filesystem.py.save
diff --git a/lib/spack/llnl/util/filesystem.py.save.1 b/lib/spack/llnl/util/filesystem.py.save.1
new file mode 100644
index 0000000000..82cfe965b2
--- /dev/null
+++ b/lib/spack/llnl/util/filesystem.py.save.1
@@ -0,0 +1,229 @@
+##############################################################################
+# 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://scalability-llnl.github.io/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
+##############################################################################
+__all__ = ['set_install_permissions', 'install', 'expand_user', 'working_dir',
+           'touch', 'touchp', 'mkdirp', 'force_remove', 'join_path', 'ancestor',
+           'can_access', 'filter_file', 'change_sed_delimiter', 'is_exe']
+
+import os
+import sys
+import re
+import shutil
+import stat
+import errno
+import getpass
+from contextlib import contextmanager, closing
+from tempfile import NamedTemporaryFile
+
+import llnl.util.tty as tty
+from spack.util.compression import ALLOWED_ARCHIVE_TYPES
+
+def filter_file(regex, repl, *filenames, **kwargs):
+    """Like sed, but uses python regular expressions.
+
+       Filters every line of file through regex and replaces the file
+       with a filtered version.  Preserves mode of filtered files.
+
+       As with re.sub, ``repl`` can be either a string or a callable.
+       If it is a callable, it is passed the match object and should
+       return a suitable replacement string.  If it is a string, it
+       can contain ``\1``, ``\2``, etc. to represent back-substitution
+       as sed would allow.
+
+       Keyword Options:
+         string[=False]         If True, treat regex as a plain string.
+         backup[=True]          Make a backup files suffixed with ~
+         ignore_absent[=False]  Ignore any files that don't exist.
+    """
+    string = kwargs.get('string', False)
+    backup = kwargs.get('backup', True)
+    ignore_absent = kwargs.get('ignore_absent', False)
+
+    # 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)))
+            return re.sub(r'\\([1-9])', groupid_to_group, unescaped)
+        repl = replace_groups_with_groupid
+
+    if string:
+        regex = re.escape(regex)
+
+    for filename in filenames:
+        backup = filename + "~"
+
+        if ignore_absent and not os.path.exists(filename):
+            continue
+
+        shutil.copy(filename, backup)
+        try:
+            with closing(open(backup)) as infile:
+                with closing(open(filename, 'w')) as outfile:
+                    for line in infile:
+                        foo = re.sub(regex, repl, line)
+                        outfile.write(foo)
+        except:
+            # clean up the original file on failure.
+            shutil.move(backup, filename)
+            raise
+
+        finally:
+            if not backup:
+                shutil.rmtree(backup, ignore_errors=True)
+
+
+def change_sed_delimiter(old_delim, new_delim, *filenames):
+    """Find all sed search/replace commands and change the delimiter.
+       e.g., if the file contains seds that look like 's///', you can
+       call change_sed_delimeter('/', '@', file) to change the
+       delimiter to '@'.
+
+       NOTE that this routine will fail if the delimiter is ' or ".
+       Handling those is left for future work.
+    """
+    assert(len(old_delim) == 1)
+    assert(len(new_delim) == 1)
+
+    # TODO: handle these cases one day?
+    assert(old_delim != '"')
+    assert(old_delim != "'")
+    assert(new_delim != '"')
+    assert(new_delim != "'")
+
+    whole_lines = "^s@([^@]*)@(.*)@[gIp]$"
+    whole_lines = whole_lines.replace('@', old_delim)
+
+    single_quoted = r"'s@((?:\\'|[^@'])*)@((?:\\'|[^'])*)@[gIp]?'"
+    single_quoted = single_quoted.replace('@', old_delim)
+
+    double_quoted = r'"s@((?:\\"|[^@"])*)@((?:\\"|[^"])*)@[gIp]?"'
+    double_quoted = double_quoted.replace('@', old_delim)
+
+    repl = r's@\1@\2@g'
+    repl = repl.replace('@', new_delim)
+
+    for f in filenames:
+        filter_file(whole_lines, repl, f)
+        filter_file(single_quoted, "'%s'" % repl, f)
+        filter_file(double_quoted, '"%s"' % repl, f)
+
+
+def set_install_permissions(path):
+    """Set appropriate permissions on the installed file."""
+    if os.path.isdir(path):
+        os.chmod(path, 0755)
+    else:
+        os.chmod(path, 0644)
+
+
+def install(src, dest):
+    """Manually install a file to a particular location."""
+    tty.info("Installing %s to %s" % (src, dest))
+    shutil.copy(src, dest)
+    set_install_permissions(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
+    os.chmod(dest, dest_mode)
+
+
+def is_exe(path):
+    """True if path is an executable file."""
+    return os.path.isfile(path) and os.access(path, os.X_OK)
+
+
+def expand_user(path):
+    """Find instances of '%u' in a path and replace with the current user's
+       username."""
+    username = getpass.getuser()
+    if not username and '%u' in path:
+        tty.die("Couldn't get username to complete path '%s'" % path)
+
+    return path.replace('%u', username)
+
+
+def mkdirp(*paths):
+    """Creates a directory, as well as parent directories if needed."""
+    for path in paths:
+        if not os.path.exists(path):
+            os.makedirs(path)
+        elif not os.path.isdir(path):
+            raise OSError(errno.EEXIST, "File alredy exists", path)
+
+
+def force_remove(*paths):
+    """Remove files without printing errors.  Like rm -f, does NOT
+       remove directories."""
+    for path in paths:
+        try:
+            os.remove(path)
+        except OSError, e:
+            pass
+
+@contextmanager
+def working_dir(dirname, **kwargs):
+    if kwargs.get('create', False):
+        mkdirp(dirname)
+
+    orig_dir = os.getcwd()
+    os.chdir(dirname)
+    yield
+    os.chdir(orig_dir)
+
+
+def touch(path):
+    """Creates an empty file at the specified path."""
+    with closing(open(path, 'a')) as file:
+        os.utime(path, None)
+
+
+def touchp(path):
+    """Like touch, but creates any parent directories needed for the file."""
+    mkdirp(os.path.dirname(path))
+    touch(path)
+
+
+def join_path(prefix, *args):
+    path = str(prefix)
+    for elt in args:
+        path = os.path.join(path, str(elt))
+    return path
+
+
+def ancestor(dir, n=1):
+    """Get the nth ancestor of a directory."""
+    parent = os.path.abspath(dir)
+    for i in range(n):
+        parent = os.path.dirname(parent)
+    return parent
+
+
+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)
diff --git a/var/spack/packages/blas/package.py b/var/spack/packages/blas/package.py
index 7bab63bcd9..0cf495d0c1 100644
--- a/var/spack/packages/blas/package.py
+++ b/var/spack/packages/blas/package.py
@@ -12,10 +12,6 @@ class Blas(Package):
 
     def install(self, spec, prefix):    
         make()
-        mv = which('mv') # Create a shell wrapper for the mv command.
-        mkdir = which('mkdir') # Create a shell wrapper for the mkdir command.
-        pwd = os.getcwd() # Retrieve the current working dir.
-        mkdir('%s' % prefix.lib) # Create the lib dir inside the install dir.
-        mv('%s/blas_LINUX.a' % pwd, '%s/libblas.a' % pwd) # Rename the generated lib file to libblas.a
-        mv('%s/libblas.a' % pwd, '%s/libblas.a' % prefix.lib) # Move the library file to the install dir.
+        mkdirp('%s' % prefix.lib) # Create the lib dir inside the install dir.
+        move('./blas_LINUX.a', '%s/libblas.a' % prefix.lib) # Rename the generated lib file to libblas.a
         
diff --git a/var/spack/packages/lapack/package.py b/var/spack/packages/lapack/package.py
index f2dab5ecb6..de90acd742 100644
--- a/var/spack/packages/lapack/package.py
+++ b/var/spack/packages/lapack/package.py
@@ -12,20 +12,15 @@ class Lapack(Package):
 
     depends_on('blas')
 
-    def install(self, spec, prefix):
-        mv = which('mv') # Create a shell wrapper for the mv command.
-        mkdir = which('mkdir') # Create a shell wrapper for the mkdir command.
-        pwd = os.getcwd() # Retrieve the current working dir.
-
+    def install(self, spec, prefix):     
         # Lapack and BLAS testing fails for some reason, but the library is 
-        # built and ready to go at this point. The testing stuff is going to be 
-        # switched off for now.
+        # built and ready to go after make() is called. The testing stuff is 
+        # going to be switched off for now.
         filter_file('blas_testing lapack_testing ', ' ', 'Makefile', string=True)
-
-        mv('%s/make.inc.example' % pwd, '%s/make.inc' % pwd)
+        move('./make.inc.example', './make.inc')
         filter_file('../../librefblas.a', '%s/libblas.a' % spec['blas'].prefix.lib, 'make.inc', string=True) # Specify the BLAS lib to use.
 
         make()
         mkdir('%s' % prefix.lib) # Create the lib dir inside the install dir.
-        mv('%s/liblapack.a' % pwd, '%s/liblapack.a' % prefix.lib) # Move the library file to the install dir.
+        move('./liblapack.a', '%s/liblapack.a' % prefix.lib) # Move the library file to the install dir.