Merge branch 'develop' into mplegendre-multi_pkgsrc_roots

Conflicts: lib/spack/spack/__init__.py lib/spack/spack/directives.py lib/spack/spack/packages.py
2015-11-04 18:09:59 -08:00
parent 6dff42be09 1c4ef29962
commit 55662eca69
93 changed files with 2989 additions and 284 deletions
--- a/lib/spack/docs/conf.py
+++ b/lib/spack/docs/conf.py
@@ -149,7 +149,7 @@
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = [('show_copyright', False)]
+html_theme_options = { 'logo_only' : True }

 # Add any paths that contain custom themes here, relative to this directory.
 html_theme_path = ["_themes"]
@@ -163,12 +163,12 @@

 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+html_logo = '../../../share/spack/logo/spack-logo-white-text-48.png'

 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+html_favicon = '../../../share/spack/logo/favicon.ico'

 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -222,7 +222,7 @@ def working_dir(dirname, **kwargs):

 def touch(path):
    """Creates an empty file at the specified path."""
-    with closing(open(path, 'a')) as file:
+    with open(path, 'a') as file:
        os.utime(path, None)


--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -88,10 +88,7 @@ def index_by(objects, *funcs):
    result = {}
    for o in objects:
        key = f(o)
-        if key not in result:
-            result[key] = [o]
-        else:
-            result[key].append(o)
+        result.setdefault(key, []).append(o)

    for key, objects in result.items():
        result[key] = index_by(objects, *funcs[1:])
--- a/lib/spack/llnl/util/lock.py
+++ b/lib/spack/llnl/util/lock.py
@@ -0,0 +1,175 @@
+##############################################################################
+# Copyright (c) 2013-2015, 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
+##############################################################################
+import os
+import fcntl
+import errno
+import time
+import socket
+
+# Default timeout in seconds, after which locks will raise exceptions.
+_default_timeout = 60
+
+# Sleep time per iteration in spin loop (in seconds)
+_sleep_time = 1e-5
+
+
+class Lock(object):
+    def __init__(self,file_path):
+        self._file_path = file_path
+        self._fd = None
+        self._reads = 0
+        self._writes = 0
+
+
+    def _lock(self, op, timeout):
+        """This takes a lock using POSIX locks (``fnctl.lockf``).
+
+        The lock is implemented as a spin lock using a nonblocking
+        call to lockf().
+
+        On acquiring an exclusive lock, the lock writes this process's
+        pid and host to the lock file, in case the holding process
+        needs to be killed later.
+
+        If the lock times out, it raises a ``LockError``.
+        """
+        start_time = time.time()
+        while (time.time() - start_time) < timeout:
+            try:
+                if self._fd is None:
+                    self._fd = os.open(self._file_path, os.O_RDWR)
+
+                fcntl.lockf(self._fd, op | fcntl.LOCK_NB)
+                if op == fcntl.LOCK_EX:
+                    os.write(self._fd, "pid=%s,host=%s" % (os.getpid(), socket.getfqdn()))
+                return
+
+            except IOError as error:
+                if error.errno == errno.EAGAIN or error.errno == errno.EACCES:
+                    pass
+                else:
+                    raise
+            time.sleep(_sleep_time)
+
+        raise LockError("Timed out waiting for lock.")
+
+
+    def _unlock(self):
+        """Releases a lock using POSIX locks (``fcntl.lockf``)
+
+        Releases the lock regardless of mode. Note that read locks may
+        be masquerading as write locks, but this removes either.
+
+        """
+        fcntl.lockf(self._fd,fcntl.LOCK_UN)
+        os.close(self._fd)
+        self._fd = None
+
+
+    def acquire_read(self, timeout=_default_timeout):
+        """Acquires a recursive, shared lock for reading.
+
+        Read and write locks can be acquired and released in arbitrary
+        order, but the POSIX lock is held until all local read and
+        write locks are released.
+
+        Returns True if it is the first acquire and actually acquires
+        the POSIX lock, False if it is a nested transaction.
+
+        """
+        if self._reads == 0 and self._writes == 0:
+            self._lock(fcntl.LOCK_SH, timeout)   # can raise LockError.
+            self._reads += 1
+            return True
+        else:
+            self._reads += 1
+            return False
+
+
+    def acquire_write(self, timeout=_default_timeout):
+        """Acquires a recursive, exclusive lock for writing.
+
+        Read and write locks can be acquired and released in arbitrary
+        order, but the POSIX lock is held until all local read and
+        write locks are released.
+
+        Returns True if it is the first acquire and actually acquires
+        the POSIX lock, False if it is a nested transaction.
+
+        """
+        if self._writes == 0:
+            self._lock(fcntl.LOCK_EX, timeout)   # can raise LockError.
+            self._writes += 1
+            return True
+        else:
+            self._writes += 1
+            return False
+
+
+    def release_read(self):
+        """Releases a read lock.
+
+        Returns True if the last recursive lock was released, False if
+        there are still outstanding locks.
+
+        Does limited correctness checking: if a read lock is released
+        when none are held, this will raise an assertion error.
+
+        """
+        assert self._reads > 0
+
+        if self._reads == 1 and self._writes == 0:
+            self._unlock()      # can raise LockError.
+            self._reads -= 1
+            return True
+        else:
+            self._reads -= 1
+            return False
+
+
+    def release_write(self):
+        """Releases a write lock.
+
+        Returns True if the last recursive lock was released, False if
+        there are still outstanding locks.
+
+        Does limited correctness checking: if a read lock is released
+        when none are held, this will raise an assertion error.
+
+        """
+        assert self._writes > 0
+
+        if self._writes == 1 and self._reads == 0:
+            self._unlock()      # can raise LockError.
+            self._writes -= 1
+            return True
+        else:
+            self._writes -= 1
+            return False
+
+
+class LockError(Exception):
+    """Raised when an attempt to acquire a lock times out."""
+    pass
--- a/lib/spack/llnl/util/tty/colify.py
+++ b/lib/spack/llnl/util/tty/colify.py
@@ -33,8 +33,7 @@
 from StringIO import StringIO

 from llnl.util.tty import terminal_size
-from llnl.util.tty.color import clen
-
+from llnl.util.tty.color import clen, cextra

 class ColumnConfig:
    def __init__(self, cols):
@@ -42,7 +41,6 @@ def __init__(self, cols):
        self.line_length = 0
        self.valid = True
        self.widths = [0] * cols   # does not include ansi colors
-        self.cwidths = [0] * cols  # includes ansi colors

    def __repr__(self):
        attrs = [(a,getattr(self, a)) for a in dir(self) if not a.startswith("__")]
@@ -66,8 +64,6 @@ def config_variable_cols(elts, console_width, padding, cols=0):
    # Get a bound on the most columns we could possibly have.
    # 'clen' ignores length of ansi color sequences.
    lengths = [clen(e) for e in elts]
-    clengths = [len(e) for e in elts]
-
    max_cols = max(1, console_width / (min(lengths) + padding))
    max_cols = min(len(elts), max_cols)

@@ -85,7 +81,6 @@ def config_variable_cols(elts, console_width, padding, cols=0):
                if conf.widths[col] < (length + p):
                    conf.line_length += length + p - conf.widths[col]
                    conf.widths[col]  = length + p
-                    conf.cwidths[col] = clengths[i] + p
                    conf.valid = (conf.line_length < console_width)

    try:
@@ -118,7 +113,6 @@ def config_uniform_cols(elts, console_width, padding, cols=0):

    config = ColumnConfig(cols)
    config.widths = [max_len] * cols
-    config.cwidths = [max_clen] * cols

    return config

@@ -147,9 +141,6 @@ def colify(elts, **options):
    method=<string>   Method to use to fit columns.  Options are variable or uniform.
                      Variable-width columns are tighter, uniform columns are all the
                      same width and fit less data on the screen.
-
-    len=<func>        Function to use for calculating string length.
-                      Useful for ignoring ansi color. Default is 'len'.
    """
    # Get keyword arguments or set defaults
    cols         = options.pop("cols", 0)
@@ -199,9 +190,6 @@ def colify(elts, **options):
        raise ValueError("method must be one of: " + allowed_methods)

    cols = config.cols
-    formats = ["%%-%ds" % width for width in config.cwidths[:-1]]
-    formats.append("%s")  # last column has no trailing space
-
    rows = (len(elts) + cols - 1) / cols
    rows_last_col = len(elts) % rows

@@ -209,7 +197,9 @@ def colify(elts, **options):
        output.write(" " * indent)
        for col in xrange(cols):
            elt = col * rows + row
-            output.write(formats[col] % elts[elt])
+            width = config.widths[col] + cextra(elts[elt])
+            fmt = '%%-%ds' % width
+            output.write(fmt % elts[elt])

        output.write("\n")
        row += 1
--- a/lib/spack/llnl/util/tty/color.py
+++ b/lib/spack/llnl/util/tty/color.py
@@ -158,6 +158,11 @@ def clen(string):
    return len(re.sub(r'\033[^m]*m', '', string))


+def cextra(string):
+    """"Length of extra color characters in a string"""
+    return len(''.join(re.findall(r'\033[^m]*m', string)))
+
+
 def cwrite(string, stream=sys.stdout, color=None):
    """Replace all color expressions in string with ANSI control
       codes and write the result to the stream.  If color is
--- a/lib/spack/spack/init.py
+++ b/lib/spack/spack/init.py
@@ -29,25 +29,27 @@
 import llnl.util.tty as tty

 # This lives in $prefix/lib/spack/spack/__file__
-prefix = ancestor(__file__, 4)
+spack_root = ancestor(__file__, 4)

 # The spack script itself
-spack_file = join_path(prefix, "bin", "spack")
+spack_file = join_path(spack_root, "bin", "spack")

 # spack directory hierarchy
-etc_path       = join_path(prefix, "etc")
-lib_path       = join_path(prefix, "lib", "spack")
+lib_path       = join_path(spack_root, "lib", "spack")
 build_env_path = join_path(lib_path, "env")
 module_path    = join_path(lib_path, "spack")
 compilers_path = join_path(module_path, "compilers")
 test_path      = join_path(module_path, "test")
 hooks_path     = join_path(module_path, "hooks")
-var_path       = join_path(prefix, "var", "spack")
+var_path       = join_path(spack_root, "var", "spack")
 stage_path     = join_path(var_path, "stage")
 packages_path  = join_path(var_path, "packages")
+share_path     = join_path(spack_root, "share", "spack")
+
+prefix = spack_root
 opt_path       = join_path(prefix, "opt")
 install_path   = join_path(opt_path, "spack")
-share_path     = join_path(prefix, "share", "spack")
+etc_path       = join_path(prefix, "etc")

 #
 # Setup the spack.repos namespace
@@ -65,6 +67,12 @@
 db = spack.packages.PackageFinder(*_repo_paths)
 sys.meta_path.append(db)

+#
+# Set up the installed packages database
+#
+from spack.database import Database
+installed_db = Database(install_path)
+
 #
 # Paths to mock files for testing.
 #
--- a/lib/spack/spack/architecture.py
+++ b/lib/spack/spack/architecture.py
@@ -23,13 +23,13 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import platform as py_platform
+import re
+import platform

 from llnl.util.lang import memoized

 import spack
 import spack.error as serr
-from spack.version import Version


 class InvalidSysTypeError(serr.SpackError):
@@ -59,14 +59,11 @@ def get_sys_type_from_environment():
    return os.environ.get('SYS_TYPE')


-def get_mac_sys_type():
-    """Return a Mac OS SYS_TYPE or None if this isn't a mac."""
-    mac_ver = py_platform.mac_ver()[0]
-    if not mac_ver:
-        return None
-
-    return "macosx_%s_%s" % (
-        Version(mac_ver).up_to(2), py_platform.machine())
+def get_sys_type_from_platform():
+    """Return the architecture from Python's platform module."""
+    sys_type = platform.system() + '-' + platform.machine()
+    sys_type = re.sub(r'[^\w-]', '_', sys_type)
+    return sys_type.lower()


@memoized
@@ -74,7 +71,7 @@ def sys_type():
    """Returns a SysType for the current machine."""
    methods = [get_sys_type_from_spack_globals,
               get_sys_type_from_environment,
-               get_mac_sys_type]
+               get_sys_type_from_platform]

    # search for a method that doesn't return None
    sys_type = None
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -317,4 +317,9 @@ def child_fun():
        # message.  Just make the parent exit with an error code.
        pid, returncode = os.waitpid(pid, 0)
        if returncode != 0:
-            sys.exit(1)
+            raise InstallError("Installation process had nonzero exit code."
+                .format(str(returncode)))
+
+
+class InstallError(spack.error.SpackError):
+    """Raised when a package fails to install"""
--- a/lib/spack/spack/cmd/init.py
+++ b/lib/spack/spack/cmd/init.py
@@ -124,7 +124,7 @@ def elide_list(line_list, max_num=10):


 def disambiguate_spec(spec):
-    matching_specs = spack.db.get_installed(spec)
+    matching_specs = spack.installed_db.query(spec)
    if not matching_specs:
        tty.die("Spec '%s' matches no installed packages." % spec)

--- a/lib/spack/spack/cmd/deactivate.py
+++ b/lib/spack/spack/cmd/deactivate.py
@@ -54,7 +54,7 @@ def deactivate(parser, args):
    if args.all:
        if pkg.extendable:
            tty.msg("Deactivating all extensions of %s" % pkg.spec.short_spec)
-            ext_pkgs = spack.db.installed_extensions_for(spec)
+            ext_pkgs = spack.installed_db.installed_extensions_for(spec)

            for ext_pkg in ext_pkgs:
                ext_pkg.spec.normalize()
--- a/lib/spack/spack/cmd/diy.py
+++ b/lib/spack/spack/cmd/diy.py
@@ -58,36 +58,38 @@ def diy(self, args):
    if len(specs) > 1:
        tty.die("spack diy only takes one spec.")

-    spec = specs[0]
-    if not spack.db.exists(spec.name):
-        tty.warn("No such package: %s" % spec.name)
-        create = tty.get_yes_or_no("Create this package?", default=False)
-        if not create:
-            tty.msg("Exiting without creating.")
+    # Take a write lock before checking for existence.
+    with spack.installed_db.write_transaction():
+        spec = specs[0]
+        if not spack.db.exists(spec.name):
+            tty.warn("No such package: %s" % spec.name)
+            create = tty.get_yes_or_no("Create this package?", default=False)
+            if not create:
+                tty.msg("Exiting without creating.")
+                sys.exit(1)
+            else:
+                tty.msg("Running 'spack edit -f %s'" % spec.name)
+                edit_package(spec.name, True)
+                return
+
+        if not spec.version.concrete:
+            tty.die("spack diy spec must have a single, concrete version.")
+
+        spec.concretize()
+        package = spack.db.get(spec)
+
+        if package.installed:
+            tty.error("Already installed in %s" % package.prefix)
+            tty.msg("Uninstall or try adding a version suffix for this DIY build.")
            sys.exit(1)
-        else:
-            tty.msg("Running 'spack edit -f %s'" % spec.name)
-            edit_package(spec.name, True)
-            return

-    if not spec.version.concrete:
-        tty.die("spack diy spec must have a single, concrete version.")
+        # Forces the build to run out of the current directory.
+        package.stage = DIYStage(os.getcwd())

-    spec.concretize()
-    package = spack.db.get(spec)
+        # TODO: make this an argument, not a global.
+        spack.do_checksum = False

-    if package.installed:
-        tty.error("Already installed in %s" % package.prefix)
-        tty.msg("Uninstall or try adding a version suffix for this DIY build.")
-        sys.exit(1)
-
-    # Forces the build to run out of the current directory.
-    package.stage = DIYStage(os.getcwd())
-
-    # TODO: make this an argument, not a global.
-    spack.do_checksum = False
-
-    package.do_install(
-        keep_prefix=args.keep_prefix,
-        ignore_deps=args.ignore_deps,
-        keep_stage=True)   # don't remove source dir for DIY.
+        package.do_install(
+            keep_prefix=args.keep_prefix,
+            ignore_deps=args.ignore_deps,
+            keep_stage=True)   # don't remove source dir for DIY.
--- a/lib/spack/spack/cmd/extensions.py
+++ b/lib/spack/spack/cmd/extensions.py
@@ -80,7 +80,7 @@ def extensions(parser, args):
    colify(ext.name for ext in extensions)

    # List specs of installed extensions.
-    installed  = [s.spec for s in spack.db.installed_extensions_for(spec)]
+    installed = [s.spec for s in spack.installed_db.installed_extensions_for(spec)]
    print
    if not installed:
        tty.msg("None installed.")
--- a/lib/spack/spack/cmd/find.py
+++ b/lib/spack/spack/cmd/find.py
@@ -54,6 +54,16 @@ def setup_parser(subparser):
        '-L', '--very-long', action='store_true', dest='very_long',
        help='Show dependency hashes as well as versions.')

+    subparser.add_argument(
+        '-u', '--unknown', action='store_true', dest='unknown',
+        help='Show only specs Spack does not have a package for.')
+    subparser.add_argument(
+        '-m', '--missing', action='store_true', dest='missing',
+        help='Show missing dependencies as well as installed specs.')
+    subparser.add_argument(
+        '-M', '--only-missing', action='store_true', dest='only_missing',
+        help='Show only missing dependencies.')
+
    subparser.add_argument(
        'query_specs', nargs=argparse.REMAINDER,
        help='optional specs to filter results')
@@ -113,6 +123,7 @@ def fmt(s):
                if hashes:
                    string += gray_hash(s, hlen) + ' '
                string += s.format('$-_$@$+', color=True)
+
                return string
            colify(fmt(s) for s in specs)

@@ -136,11 +147,21 @@ def find(parser, args):
        if not query_specs:
            return

+    # Set up query arguments.
+    installed, known = True, any
+    if args.only_missing:
+        installed = False
+    elif args.missing:
+        installed = any
+    if args.unknown:
+        known = False
+    q_args = { 'installed' : installed, 'known' : known }
+
    # Get all the specs the user asked for
    if not query_specs:
-        specs = set(spack.db.installed_package_specs())
+        specs = set(spack.installed_db.query(**q_args))
    else:
-        results = [set(spack.db.get_installed(qs)) for qs in query_specs]
+        results = [set(spack.installed_db.query(qs, **q_args)) for qs in query_specs]
        specs = set.union(*results)

    if not args.mode:
--- a/lib/spack/spack/cmd/info.py
+++ b/lib/spack/spack/cmd/info.py
@@ -65,11 +65,21 @@ def print_text_info(pkg):
        print "None"
    else:
        pad = padder(pkg.variants, 4)
+
+        maxv = max(len(v) for v in sorted(pkg.variants))
+        fmt = "%%-%ss%%-10s%%s" % (maxv + 4)
+
+        print "    " + fmt % ('Name',   'Default',   'Description')
+        print
        for name in sorted(pkg.variants):
            v = pkg.variants[name]
-            print "    %s%s" % (
-                pad(('+' if v.default else '-') + name + ':'),
-                "\n".join(textwrap.wrap(v.description)))
+            default = 'on' if v.default else 'off'
+
+            lines = textwrap.wrap(v.description)
+            lines[1:] = ["      " + (" " * maxv) + l for l in lines[1:]]
+            desc = "\n".join(lines)
+
+            print "    " + fmt % (name, default, desc)

    print
    print "Dependencies:"
--- a/lib/spack/spack/cmd/install.py
+++ b/lib/spack/spack/cmd/install.py
@@ -71,10 +71,11 @@ def install(parser, args):
    specs = spack.cmd.parse_specs(args.packages, concretize=True)
    for spec in specs:
        package = spack.db.get(spec)
-        package.do_install(
-            keep_prefix=args.keep_prefix,
-            keep_stage=args.keep_stage,
-            ignore_deps=args.ignore_deps,
-            make_jobs=args.jobs,
-            verbose=args.verbose,
-            fake=args.fake)
+        with spack.installed_db.write_transaction():
+            package.do_install(
+                keep_prefix=args.keep_prefix,
+                keep_stage=args.keep_stage,
+                ignore_deps=args.ignore_deps,
+                make_jobs=args.jobs,
+                verbose=args.verbose,
+                fake=args.fake)
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -65,7 +65,7 @@ def module_find(mtype, spec_array):
        tty.die("You can only pass one spec.")
    spec = specs[0]

-    specs = [s for s in spack.db.installed_package_specs() if s.satisfies(spec)]
+    specs = spack.installed_db.query(spec)
    if len(specs) == 0:
        tty.die("No installed packages match spec %s" % spec)

@@ -86,7 +86,7 @@ def module_find(mtype, spec_array):
 def module_refresh():
    """Regenerate all module files for installed packages known to
       spack (some packages may no longer exist)."""
-    specs = [s for s in spack.db.installed_known_package_specs()]
+    specs = [s for s in spack.installed_db.query(installed=True, known=True)]

    for name, cls in module_types.items():
        tty.msg("Regenerating %s module files." % name)
--- a/lib/spack/spack/cmd/reindex.py
+++ b/lib/spack/spack/cmd/reindex.py
@@ -0,0 +1,31 @@
+##############################################################################
+# Copyright (c) 2013-2015, 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
+##############################################################################
+from external import argparse
+import spack
+
+description = "Rebuild Spack's package database."
+
+def reindex(parser, args):
+    spack.installed_db.reindex(spack.install_layout)
--- a/lib/spack/spack/cmd/test-install.py
+++ b/lib/spack/spack/cmd/test-install.py
@@ -0,0 +1,211 @@
+##############################################################################
+# 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
+##############################################################################
+from external import argparse
+import xml.etree.ElementTree as ET
+import itertools
+import re
+import os
+import codecs
+
+import llnl.util.tty as tty
+from llnl.util.filesystem import *
+
+import spack
+from spack.build_environment import InstallError
+from spack.fetch_strategy import FetchError
+import spack.cmd
+
+description = "Treat package installations as unit tests and output formatted test results"
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '-j', '--jobs', action='store', type=int,
+        help="Explicitly set number of make jobs.  Default is #cpus.")
+    
+    subparser.add_argument(
+        '-n', '--no-checksum', action='store_true', dest='no_checksum',
+        help="Do not check packages against checksum")
+    
+    subparser.add_argument(
+        '-o', '--output', action='store', help="test output goes in this file")
+    
+    subparser.add_argument(
+        'package', nargs=argparse.REMAINDER, help="spec of package to install")
+
+
+class JunitResultFormat(object):
+    def __init__(self):
+        self.root = ET.Element('testsuite')
+        self.tests = []
+        
+    def add_test(self, buildId, testResult, buildInfo=None):
+        self.tests.append((buildId, testResult, buildInfo))
+    
+    def write_to(self, stream):
+        self.root.set('tests', '{0}'.format(len(self.tests)))
+        for buildId, testResult, buildInfo in self.tests:
+            testcase = ET.SubElement(self.root, 'testcase')
+            testcase.set('classname', buildId.name)
+            testcase.set('name', buildId.stringId())
+            if testResult == TestResult.FAILED:
+                failure = ET.SubElement(testcase, 'failure')
+                failure.set('type', "Build Error")
+                failure.text = buildInfo
+            elif testResult == TestResult.SKIPPED:
+                skipped = ET.SubElement(testcase, 'skipped')
+                skipped.set('type', "Skipped Build")
+                skipped.text = buildInfo
+        ET.ElementTree(self.root).write(stream)
+
+
+class TestResult(object):
+    PASSED = 0
+    FAILED = 1
+    SKIPPED = 2
+    
+
+class BuildId(object):
+    def __init__(self, spec):
+        self.name = spec.name
+        self.version = spec.version
+        self.hashId = spec.dag_hash()
+    
+    def stringId(self):
+        return "-".join(str(x) for x in (self.name, self.version, self.hashId))
+
+    def __hash__(self):
+        return hash((self.name, self.version, self.hashId))
+    
+    def __eq__(self, other):
+        if not isinstance(other, BuildId):
+            return False
+            
+        return ((self.name, self.version, self.hashId) == 
+            (other.name, other.version, other.hashId))
+
+
+def fetch_log(path):
+    if not os.path.exists(path):
+        return list()
+    with codecs.open(path, 'rb', 'utf-8') as F:
+        return list(line.strip() for line in F.readlines())
+
+
+def failed_dependencies(spec):
+    return set(childSpec for childSpec in spec.dependencies.itervalues() if not 
+        spack.db.get(childSpec).installed)
+
+
+def create_test_output(topSpec, newInstalls, output, getLogFunc=fetch_log):
+    # Post-order traversal is not strictly required but it makes sense to output 
+    # tests for dependencies first.
+    for spec in topSpec.traverse(order='post'):
+        if spec not in newInstalls:
+            continue
+
+        failedDeps = failed_dependencies(spec)
+        package = spack.db.get(spec)
+        if failedDeps:
+            result = TestResult.SKIPPED
+            dep = iter(failedDeps).next()
+            depBID = BuildId(dep)
+            errOutput = "Skipped due to failed dependency: {0}".format(
+                depBID.stringId())
+        elif (not package.installed) and (not package.stage.source_path):
+            result = TestResult.FAILED
+            errOutput = "Failure to fetch package resources."
+        elif not package.installed:
+            result = TestResult.FAILED
+            lines = getLogFunc(package.build_log_path)
+            errMessages = list(line for line in lines if
+                re.search('error:', line, re.IGNORECASE))
+            errOutput = errMessages if errMessages else lines[-10:]
+            errOutput = '\n'.join(itertools.chain(
+                    [spec.to_yaml(), "Errors:"], errOutput, 
+                    ["Build Log:", package.build_log_path]))
+        else:
+            result = TestResult.PASSED
+            errOutput = None
+        
+        bId = BuildId(spec)
+        output.add_test(bId, result, errOutput)
+
+
+def test_install(parser, args):
+    if not args.package:
+        tty.die("install requires a package argument")
+
+    if args.jobs is not None:
+        if args.jobs <= 0:
+            tty.die("The -j option must be a positive integer!")
+
+    if args.no_checksum:
+        spack.do_checksum = False        # TODO: remove this global.
+    
+    specs = spack.cmd.parse_specs(args.package, concretize=True)
+    if len(specs) > 1:
+        tty.die("Only 1 top-level package can be specified")
+    topSpec = iter(specs).next()
+    
+    newInstalls = set()
+    for spec in topSpec.traverse():
+        package = spack.db.get(spec)
+        if not package.installed:
+            newInstalls.add(spec)
+    
+    if not args.output:
+        bId = BuildId(topSpec)
+        outputDir = join_path(os.getcwd(), "test-output")
+        if not os.path.exists(outputDir):
+            os.mkdir(outputDir)
+        outputFpath = join_path(outputDir, "test-{0}.xml".format(bId.stringId()))
+    else:
+        outputFpath = args.output
+    
+    for spec in topSpec.traverse(order='post'):
+        # Calling do_install for the top-level package would be sufficient but
+        # this attempts to keep going if any package fails (other packages which
+        # are not dependents may succeed)
+        package = spack.db.get(spec)
+        if (not failed_dependencies(spec)) and (not package.installed):
+            try:
+                package.do_install(
+                    keep_prefix=False,
+                    keep_stage=True,
+                    ignore_deps=False,
+                    make_jobs=args.jobs,
+                    verbose=True,
+                    fake=False)
+            except InstallError:
+                pass
+            except FetchError:
+                pass
+   
+    jrf = JunitResultFormat()
+    handled = {}
+    create_test_output(topSpec, newInstalls, jrf)
+
+    with open(outputFpath, 'wb') as F:
+            jrf.write_to(F)
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -53,51 +53,52 @@ def uninstall(parser, args):
    if not args.packages:
        tty.die("uninstall requires at least one package argument.")

-    specs = spack.cmd.parse_specs(args.packages)
+    with spack.installed_db.write_transaction():
+        specs = spack.cmd.parse_specs(args.packages)

-    # For each spec provided, make sure it refers to only one package.
-    # Fail and ask user to be unambiguous if it doesn't
-    pkgs = []
-    for spec in specs:
-        matching_specs = spack.db.get_installed(spec)
-        if not args.all and len(matching_specs) > 1:
-            tty.error("%s matches multiple packages:" % spec)
-            print
-            display_specs(matching_specs, long=True)
-            print
-            print "You can either:"
-            print "  a) Use a more specific spec, or"
-            print "  b) use spack uninstall -a to uninstall ALL matching specs."
-            sys.exit(1)
+        # For each spec provided, make sure it refers to only one package.
+        # Fail and ask user to be unambiguous if it doesn't
+        pkgs = []
+        for spec in specs:
+            matching_specs = spack.installed_db.query(spec)
+            if not args.all and len(matching_specs) > 1:
+                tty.error("%s matches multiple packages:" % spec)
+                print
+                display_specs(matching_specs, long=True)
+                print
+                print "You can either:"
+                print "  a) Use a more specific spec, or"
+                print "  b) use spack uninstall -a to uninstall ALL matching specs."
+                sys.exit(1)

-        if len(matching_specs) == 0:
-            if args.force: continue
-            tty.die("%s does not match any installed packages." % spec)
+            if len(matching_specs) == 0:
+                if args.force: continue
+                tty.die("%s does not match any installed packages." % spec)

-        for s in matching_specs:
+            for s in matching_specs:
+                try:
+                    # should work if package is known to spack
+                    pkgs.append(s.package)
+
+                except spack.packages.UnknownPackageError, e:
+                    # The package.py file has gone away -- but still want to uninstall.
+                    spack.Package(s).do_uninstall(force=True)
+
+        # Sort packages to be uninstalled by the number of installed dependents
+        # This ensures we do things in the right order
+        def num_installed_deps(pkg):
+            return len(pkg.installed_dependents)
+        pkgs.sort(key=num_installed_deps)
+
+        # Uninstall packages in order now.
+        for pkg in pkgs:
            try:
-                # should work if package is known to spack
-                pkgs.append(s.package)
-
-            except spack.packages.UnknownPackageError, e:
-                # The package.py file has gone away -- but still want to uninstall.
-                spack.Package(s).do_uninstall(force=True)
-
-    # Sort packages to be uninstalled by the number of installed dependents
-    # This ensures we do things in the right order
-    def num_installed_deps(pkg):
-        return len(pkg.installed_dependents)
-    pkgs.sort(key=num_installed_deps)
-
-    # Uninstall packages in order now.
-    for pkg in pkgs:
-        try:
-            pkg.do_uninstall(force=args.force)
-        except PackageStillNeededError, e:
-            tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True))
-            print
-            print "The following packages depend on it:"
-            display_specs(e.dependents, long=True)
-            print
-            print "You can use spack uninstall -f to force this action."
-            sys.exit(1)
+                pkg.do_uninstall(force=args.force)
+            except PackageStillNeededError, e:
+                tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True))
+                print
+                print "The following packages depend on it:"
+                display_specs(e.dependents, long=True)
+                print
+                print "You can use spack uninstall -f to force this action."
+                sys.exit(1)
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -227,14 +227,32 @@ def find(cls, *path):
        for d in dicts:
            all_keys.update(d)

-        compilers = []
+        compilers = {}
        for k in all_keys:
            ver, pre, suf = k
+
+            # Skip compilers with unknown version.
+            if ver == 'unknown':
+                continue
+
            paths = tuple(pn[k] if k in pn else None for pn in dicts)
            spec = spack.spec.CompilerSpec(cls.name, ver)
-            compilers.append(cls(spec, *paths))

-        return compilers
+            if ver in compilers:
+                prev = compilers[ver]
+
+                # prefer the one with more compilers.
+                prev_paths = [prev.cc, prev.cxx, prev.f77, prev.fc]
+                newcount  = len([p for p in paths      if p is not None])
+                prevcount = len([p for p in prev_paths if p is not None])
+
+                # Don't add if it's not an improvement over prev compiler.
+                if newcount <= prevcount:
+                    continue
+
+            compilers[ver] = cls(spec, *paths)
+
+        return list(compilers.values())


    def __repr__(self):
--- a/lib/spack/spack/database.py
+++ b/lib/spack/spack/database.py
@@ -0,0 +1,628 @@
+##############################################################################
+# Copyright (c) 2013-2015, 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
+##############################################################################
+"""Spack's installation tracking database.
+
+The database serves two purposes:
+
+  1. It implements a cache on top of a potentially very large Spack
+     directory hierarchy, speeding up many operations that would
+     otherwise require filesystem access.
+
+  2. It will allow us to track external installations as well as lost
+     packages and their dependencies.
+
+Prior ot the implementation of this store, a direcotry layout served
+as the authoritative database of packages in Spack.  This module
+provides a cache and a sanity checking mechanism for what is in the
+filesystem.
+
+"""
+import os
+import time
+import socket
+
+from external import yaml
+from external.yaml.error import MarkedYAMLError, YAMLError
+
+import llnl.util.tty as tty
+from llnl.util.filesystem import *
+from llnl.util.lock import *
+
+import spack.spec
+from spack.version import Version
+from spack.spec import Spec
+from spack.error import SpackError
+
+# DB goes in this directory underneath the root
+_db_dirname = '.spack-db'
+
+# DB version.  This is stuck in the DB file to track changes in format.
+_db_version = Version('0.9')
+
+# Default timeout for spack database locks is 5 min.
+_db_lock_timeout = 60
+
+
+def _autospec(function):
+    """Decorator that automatically converts the argument of a single-arg
+       function to a Spec."""
+    def converter(self, spec_like, *args, **kwargs):
+        if not isinstance(spec_like, spack.spec.Spec):
+            spec_like = spack.spec.Spec(spec_like)
+        return function(self, spec_like, *args, **kwargs)
+    return converter
+
+
+class InstallRecord(object):
+    """A record represents one installation in the DB.
+
+    The record keeps track of the spec for the installation, its
+    install path, AND whether or not it is installed.  We need the
+    installed flag in case a user either:
+
+        a) blew away a directory, or
+        b) used spack uninstall -f to get rid of it
+
+    If, in either case, the package was removed but others still
+    depend on it, we still need to track its spec, so we don't
+    actually remove from the database until a spec has no installed
+    dependents left.
+
+    """
+    def __init__(self, spec, path, installed, ref_count=0):
+        self.spec = spec
+        self.path = str(path)
+        self.installed = bool(installed)
+        self.ref_count = ref_count
+
+    def to_dict(self):
+        return { 'spec'      : self.spec.to_node_dict(),
+                 'path'      : self.path,
+                 'installed' : self.installed,
+                 'ref_count' : self.ref_count }
+
+    @classmethod
+    def from_dict(cls, spec, dictionary):
+        d = dictionary
+        return InstallRecord(spec, d['path'], d['installed'], d['ref_count'])
+
+
+class Database(object):
+    def __init__(self, root, db_dir=None):
+        """Create a Database for Spack installations under ``root``.
+
+        A Database is a cache of Specs data from ``$prefix/spec.yaml``
+        files in Spack installation directories.
+
+        By default, Database files (data and lock files) are stored
+        under ``root/.spack-db``, which is created if it does not
+        exist.  This is the ``db_dir``.
+
+        The Database will attempt to read an ``index.yaml`` file in
+        ``db_dir``.  If it does not find one, it will be created when
+        needed by scanning the entire Database root for ``spec.yaml``
+        files according to Spack's ``DirectoryLayout``.
+
+        Caller may optionally provide a custom ``db_dir`` parameter
+        where data will be stored.  This is intended to be used for
+        testing the Database class.
+
+        """
+        self.root = root
+
+        if db_dir is None:
+            # If the db_dir is not provided, default to within the db root.
+            self._db_dir = join_path(self.root, _db_dirname)
+        else:
+            # Allow customizing the database directory location for testing.
+            self._db_dir = db_dir
+
+        # Set up layout of database files within the db dir
+        self._index_path = join_path(self._db_dir, 'index.yaml')
+        self._lock_path  = join_path(self._db_dir, 'lock')
+
+        # Create needed directories and files
+        if not os.path.exists(self._db_dir):
+            mkdirp(self._db_dir)
+
+        if not os.path.exists(self._lock_path):
+            touch(self._lock_path)
+
+        # initialize rest of state.
+        self.lock = Lock(self._lock_path)
+        self._data = {}
+
+
+    def write_transaction(self, timeout=_db_lock_timeout):
+        """Get a write lock context manager for use in a `with` block."""
+        return WriteTransaction(self, self._read, self._write, timeout)
+
+
+    def read_transaction(self, timeout=_db_lock_timeout):
+        """Get a read lock context manager for use in a `with` block."""
+        return ReadTransaction(self, self._read, None, timeout)
+
+
+    def _write_to_yaml(self, stream):
+        """Write out the databsae to a YAML file.
+
+        This function does not do any locking or transactions.
+        """
+        # map from per-spec hash code to installation record.
+        installs = dict((k, v.to_dict()) for k, v in self._data.items())
+
+        # database includes installation list and version.
+
+        # NOTE: this DB version does not handle multiple installs of
+        # the same spec well.  If there are 2 identical specs with
+        # different paths, it can't differentiate.
+        # TODO: fix this before we support multiple install locations.
+        database = {
+            'database' : {
+                'installs' : installs,
+                'version' : str(_db_version)
+            }
+        }
+
+        try:
+            return yaml.dump(database, stream=stream, default_flow_style=False)
+        except YAMLError as e:
+            raise SpackYAMLError("error writing YAML database:", str(e))
+
+
+    def _read_spec_from_yaml(self, hash_key, installs, parent_key=None):
+        """Recursively construct a spec from a hash in a YAML database.
+
+        Does not do any locking.
+        """
+        if hash_key not in installs:
+            parent = read_spec(installs[parent_key]['path'])
+
+        spec_dict = installs[hash_key]['spec']
+
+        # Build spec from dict first.
+        spec = Spec.from_node_dict(spec_dict)
+
+        # Add dependencies from other records in the install DB to
+        # form a full spec.
+        for dep_hash in spec_dict[spec.name]['dependencies'].values():
+            child = self._read_spec_from_yaml(dep_hash, installs, hash_key)
+            spec._add_dependency(child)
+
+        return spec
+
+
+    def _read_from_yaml(self, stream):
+        """
+        Fill database from YAML, do not maintain old data
+        Translate the spec portions from node-dict form to spec form
+
+        Does not do any locking.
+        """
+        try:
+            if isinstance(stream, basestring):
+                with open(stream, 'r') as f:
+                    yfile = yaml.load(f)
+            else:
+                yfile = yaml.load(stream)
+
+        except MarkedYAMLError as e:
+            raise SpackYAMLError("error parsing YAML database:", str(e))
+
+        if yfile is None:
+            return
+
+        def check(cond, msg):
+            if not cond: raise CorruptDatabaseError(self._index_path, msg)
+
+        check('database' in yfile, "No 'database' attribute in YAML.")
+
+        # High-level file checks
+        db = yfile['database']
+        check('installs' in db, "No 'installs' in YAML DB.")
+        check('version'  in db, "No 'version' in YAML DB.")
+
+        # TODO: better version checking semantics.
+        version = Version(db['version'])
+        if version != _db_version:
+            raise InvalidDatabaseVersionError(_db_version, version)
+
+        # Iterate through database and check each record.
+        installs = db['installs']
+        data = {}
+        for hash_key, rec in installs.items():
+            try:
+                # This constructs a spec DAG from the list of all installs
+                spec = self._read_spec_from_yaml(hash_key, installs)
+
+                # Validate the spec by ensuring the stored and actual
+                # hashes are the same.
+                spec_hash = spec.dag_hash()
+                if not spec_hash == hash_key:
+                    tty.warn("Hash mismatch in database: %s -> spec with hash %s"
+                             % (hash_key, spec_hash))
+                    continue    # TODO: is skipping the right thing to do?
+
+                # Insert the brand new spec in the database.  Each
+                # spec has its own copies of its dependency specs.
+                # TODO: would a more immmutable spec implementation simplify this?
+                data[hash_key] = InstallRecord.from_dict(spec, rec)
+
+            except Exception as e:
+                tty.warn("Invalid database reecord:",
+                         "file:  %s" % self._index_path,
+                         "hash:  %s" % hash_key,
+                         "cause: %s" % str(e))
+                raise
+
+        self._data = data
+
+
+    def reindex(self, directory_layout):
+        """Build database index from scratch based from a directory layout.
+
+        Locks the DB if it isn't locked already.
+
+        """
+        with self.write_transaction():
+            old_data = self._data
+            try:
+                self._data = {}
+
+                # Ask the directory layout to traverse the filesystem.
+                for spec in directory_layout.all_specs():
+                    # Create a spec for each known package and add it.
+                    path = directory_layout.path_for_spec(spec)
+                    self._add(spec, path, directory_layout)
+
+                self._check_ref_counts()
+
+            except:
+                # If anything explodes, restore old data, skip write.
+                self._data = old_data
+                raise
+
+
+    def _check_ref_counts(self):
+        """Ensure consistency of reference counts in the DB.
+
+        Raise an AssertionError if something is amiss.
+
+        Does no locking.
+        """
+        counts = {}
+        for key, rec in self._data.items():
+            counts.setdefault(key, 0)
+            for dep in rec.spec.dependencies.values():
+                dep_key = dep.dag_hash()
+                counts.setdefault(dep_key, 0)
+                counts[dep_key] += 1
+
+        for rec in self._data.values():
+            key = rec.spec.dag_hash()
+            expected = counts[key]
+            found = rec.ref_count
+            if not expected == found:
+                raise AssertionError(
+                    "Invalid ref_count: %s: %d (expected %d), in DB %s."
+                    % (key, found, expected, self._index_path))
+
+
+    def _write(self):
+        """Write the in-memory database index to its file path.
+
+        Does no locking.
+
+        """
+        temp_file = self._index_path + (
+            '.%s.%s.temp' % (socket.getfqdn(), os.getpid()))
+
+        # Write a temporary database file them move it into place
+        try:
+            with open(temp_file, 'w') as f:
+                self._write_to_yaml(f)
+            os.rename(temp_file, self._index_path)
+        except:
+            # Clean up temp file if something goes wrong.
+            if os.path.exists(temp_file):
+                os.remove(temp_file)
+            raise
+
+
+    def _read(self):
+        """Re-read Database from the data in the set location.
+
+        This does no locking.
+        """
+        if os.path.isfile(self._index_path):
+            # Read from YAML file if a database exists
+            self._read_from_yaml(self._index_path)
+
+        else:
+            # The file doesn't exist, try to traverse the directory.
+            # reindex() takes its own write lock, so no lock here.
+            self.reindex(spack.install_layout)
+
+
+    def _add(self, spec, path, directory_layout=None):
+        """Add an install record for spec at path to the database.
+
+        This assumes that the spec is not already installed. It
+        updates the ref counts on dependencies of the spec in the DB.
+
+        This operation is in-memory, and does not lock the DB.
+
+        """
+        key = spec.dag_hash()
+        if key in self._data:
+            rec = self._data[key]
+            rec.installed = True
+
+            # TODO: this overwrites a previous install path (when path !=
+            # self._data[key].path), and the old path still has a
+            # dependent in the DB. We could consider re-RPATH-ing the
+            # dependents.  This case is probably infrequent and may not be
+            # worth fixing, but this is where we can discover it.
+            rec.path = path
+
+        else:
+            self._data[key] = InstallRecord(spec, path, True)
+            for dep in spec.dependencies.values():
+                self._increment_ref_count(dep, directory_layout)
+
+
+    def _increment_ref_count(self, spec, directory_layout=None):
+        """Recursively examine dependencies and update their DB entries."""
+        key = spec.dag_hash()
+        if key not in self._data:
+            installed = False
+            path = None
+            if directory_layout:
+                path = directory_layout.path_for_spec(spec)
+                installed = os.path.isdir(path)
+
+            self._data[key] = InstallRecord(spec.copy(), path, installed)
+
+            for dep in spec.dependencies.values():
+                self._increment_ref_count(dep)
+
+        self._data[key].ref_count += 1
+
+    @_autospec
+    def add(self, spec, path):
+        """Add spec at path to database, locking and reading DB to sync.
+
+        ``add()`` will lock and read from the DB on disk.
+
+        """
+        # TODO: ensure that spec is concrete?
+        # Entire add is transactional.
+        with self.write_transaction():
+            self._add(spec, path)
+
+
+    def _get_matching_spec_key(self, spec, **kwargs):
+        """Get the exact spec OR get a single spec that matches."""
+        key = spec.dag_hash()
+        if not key in self._data:
+            match = self.query_one(spec, **kwargs)
+            if match:
+                return match.dag_hash()
+            raise KeyError("No such spec in database! %s" % spec)
+        return key
+
+
+    @_autospec
+    def get_record(self, spec, **kwargs):
+        key = self._get_matching_spec_key(spec, **kwargs)
+        return self._data[key]
+
+
+    def _decrement_ref_count(self, spec):
+        key = spec.dag_hash()
+
+        if not key in self._data:
+            # TODO: print something here?  DB is corrupt, but
+            # not much we can do.
+            return
+
+        rec = self._data[key]
+        rec.ref_count -= 1
+
+        if rec.ref_count == 0 and not rec.installed:
+            del self._data[key]
+            for dep in spec.dependencies.values():
+                self._decrement_ref_count(dep)
+
+
+    def _remove(self, spec):
+        """Non-locking version of remove(); does real work.
+        """
+        key = self._get_matching_spec_key(spec)
+        rec = self._data[key]
+
+        if rec.ref_count > 0:
+            rec.installed = False
+            return rec.spec
+
+        del self._data[key]
+        for dep in rec.spec.dependencies.values():
+            self._decrement_ref_count(dep)
+
+        # Returns the concrete spec so we know it in the case where a
+        # query spec was passed in.
+        return rec.spec
+
+
+    @_autospec
+    def remove(self, spec):
+        """Removes a spec from the database.  To be called on uninstall.
+
+        Reads the database, then:
+
+          1. Marks the spec as not installed.
+          2. Removes the spec if it has no more dependents.
+          3. If removed, recursively updates dependencies' ref counts
+             and remvoes them if they are no longer needed.
+
+        """
+        # Take a lock around the entire removal.
+        with self.write_transaction():
+            return self._remove(spec)
+
+
+    @_autospec
+    def installed_extensions_for(self, extendee_spec):
+        """
+        Return the specs of all packages that extend
+        the given spec
+        """
+        for s in self.query():
+            try:
+                if s.package.extends(extendee_spec):
+                    yield s.package
+            except UnknownPackageError as e:
+                continue
+            # skips unknown packages
+            # TODO: conditional way to do this instead of catching exceptions
+
+
+    def query(self, query_spec=any, known=any, installed=True):
+        """Run a query on the database.
+
+        ``query_spec``
+            Queries iterate through specs in the database and return
+            those that satisfy the supplied ``query_spec``.  If
+            query_spec is `any`, This will match all specs in the
+            database.  If it is a spec, we'll evaluate
+            ``spec.satisfies(query_spec)``.
+
+        The query can be constrained by two additional attributes:
+
+        ``known``
+            Possible values: True, False, any
+
+            Specs that are "known" are those for which Spack can
+            locate a ``package.py`` file -- i.e., Spack "knows" how to
+            install them.  Specs that are unknown may represent
+            packages that existed in a previous version of Spack, but
+            have since either changed their name or been removed.
+
+        ``installed``
+            Possible values: True, False, any
+
+            Specs for which a prefix exists are "installed". A spec
+            that is NOT installed will be in the database if some
+            other spec depends on it but its installation has gone
+            away since Spack installed it.
+
+        TODO: Specs are a lot like queries.  Should there be a
+              wildcard spec object, and should specs have attributes
+              like installed and known that can be queried?  Or are
+              these really special cases that only belong here?
+
+        """
+        with self.read_transaction():
+            results = []
+            for key, rec in self._data.items():
+                if installed is not any and rec.installed != installed:
+                    continue
+                if known is not any and spack.db.exists(rec.spec.name) != known:
+                    continue
+                if query_spec is any or rec.spec.satisfies(query_spec):
+                    results.append(rec.spec)
+
+            return sorted(results)
+
+
+    def query_one(self, query_spec, known=any, installed=True):
+        """Query for exactly one spec that matches the query spec.
+
+        Raises an assertion error if more than one spec matches the
+        query. Returns None if no installed package matches.
+
+        """
+        concrete_specs = self.query(query_spec, known, installed)
+        assert len(concrete_specs) <= 1
+        return concrete_specs[0] if concrete_specs else None
+
+
+    def missing(self, spec):
+        with self.read_transaction():
+            key =  spec.dag_hash()
+            return key in self._data and not self._data[key].installed
+
+
+class _Transaction(object):
+    """Simple nested transaction context manager that uses a file lock.
+
+    This class can trigger actions when the lock is acquired for the
+    first time and released for the last.
+
+    Timeout for lock is customizable.
+    """
+    def __init__(self, db, acquire_fn=None, release_fn=None,
+                 timeout=_db_lock_timeout):
+        self._db = db
+        self._timeout = timeout
+        self._acquire_fn = acquire_fn
+        self._release_fn = release_fn
+
+    def __enter__(self):
+        if self._enter() and self._acquire_fn:
+            self._acquire_fn()
+
+    def __exit__(self, type, value, traceback):
+        if self._exit() and self._release_fn:
+            self._release_fn()
+
+
+class ReadTransaction(_Transaction):
+    def _enter(self):
+        return self._db.lock.acquire_read(self._timeout)
+
+    def _exit(self):
+        return self._db.lock.release_read()
+
+
+class WriteTransaction(_Transaction):
+    def _enter(self):
+        return self._db.lock.acquire_write(self._timeout)
+
+    def _exit(self):
+        return self._db.lock.release_write()
+
+
+class CorruptDatabaseError(SpackError):
+    def __init__(self, path, msg=''):
+        super(CorruptDatabaseError, self).__init__(
+            "Spack database is corrupt: %s.  %s" %(path, msg))
+
+
+class InvalidDatabaseVersionError(SpackError):
+    def __init__(self, expected, found):
+        super(InvalidDatabaseVersionError, self).__init__(
+            "Expected database version %s but found version %s"
+            % (expected, found))
--- a/lib/spack/spack/directives.py
+++ b/lib/spack/spack/directives.py
@@ -238,13 +238,10 @@ def patch(pkg, url_or_filename, level=1, when=None):
    if when is None:
        when = pkg.name
    when_spec = parse_anonymous_spec(when, pkg.name)
-
-    if when_spec not in pkg.patches:
-        pkg.patches[when_spec] = [Patch(pkg, pkg.name, url_or_filename, level)]
-    else:
-        # if this spec is identical to some other, then append this
-        # patch to the existing list.
-        pkg.patches[when_spec].append(Patch(pkg, pkg.name, url_or_filename, level))
+    cur_patches = pkg.patches.setdefault(when_spec, [])
+    # if this spec is identical to some other, then append this
+    # patch to the existing list.
+    cur_patches.append(Patch(pkg, url_or_filename, level))


@directive('variants')
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -32,7 +32,6 @@
 from external import yaml

 import llnl.util.tty as tty
-from llnl.util.lang import memoized
 from llnl.util.filesystem import join_path, mkdirp

 from spack.spec import Spec
@@ -187,14 +186,9 @@ def hidden_file_paths(self):

    def relative_path_for_spec(self, spec):
        _check_concrete(spec)
-        enabled_variants = (
-            '-' + v.name for v in spec.variants.values()
-            if v.enabled)
-
-        dir_name = "%s-%s%s-%s" % (
+        dir_name = "%s-%s-%s" % (
            spec.name,
            spec.version,
-            ''.join(enabled_variants),
            spec.dag_hash(self.hash_len))

        path = join_path(
@@ -263,7 +257,6 @@ def create_install_directory(self, spec):
        self.write_spec(spec, spec_file_path)


-    @memoized
    def all_specs(self):
        if not os.path.isdir(self.root):
            return []
@@ -274,7 +267,6 @@ def all_specs(self):
        return [self.read_spec(s) for s in spec_files]


-    @memoized
    def specs_by_hash(self):
        by_hash = {}
        for spec in self.all_specs():
--- a/lib/spack/spack/error.py
+++ b/lib/spack/spack/error.py
@@ -55,8 +55,8 @@ def die(self):

    def __str__(self):
        msg = self.message
-        if self.long_message:
-            msg += "\n    %s" % self.long_message
+        if self._long_message:
+            msg += "\n    %s" % self._long_message
        return msg

 class UnsupportedPlatformError(SpackError):
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -438,9 +438,16 @@ def stage(self):
            raise ValueError("Can only get a stage for a concrete package.")

        if self._stage is None:
+            # Construct a mirror path (TODO: get this out of package.py)
            mp = spack.mirror.mirror_archive_path(self.spec)
-            self._stage = Stage(
-                self.fetcher, mirror_path=mp, name=self.spec.short_spec)
+
+            # Construct a path where the stage should build..
+            s = self.spec
+            stage_name = "%s-%s-%s" % (s.name, s.version, s.dag_hash())
+
+            # Build the stage
+            self._stage = Stage(self.fetcher, mirror_path=mp, name=stage_name)
+
        return self._stage


@@ -563,9 +570,12 @@ def installed(self):
    @property
    def installed_dependents(self):
        """Return a list of the specs of all installed packages that depend
-           on this one."""
+           on this one.
+
+        TODO: move this method to database.py?
+        """
        dependents = []
-        for spec in spack.db.installed_package_specs():
+        for spec in spack.installed_db.query():
            if self.name == spec.name:
                continue
            for dep in spec.traverse():
@@ -785,6 +795,7 @@ def cleanup():
                         "Manually remove this directory to fix:",
                         self.prefix)

+
        def real_work():
            try:
                tty.msg("Building %s." % self.name)
@@ -844,6 +855,10 @@ def real_work():
        # Do the build.
        spack.build_environment.fork(self, real_work)

+        # note: PARENT of the build process adds the new package to
+        # the database, so that we don't need to re-read from file.
+        spack.installed_db.add(self.spec, self.prefix)
+
        # Once everything else is done, run post install hooks
        spack.hooks.post_install(self)

@@ -862,6 +877,14 @@ def do_install_dependencies(self, **kwargs):
            dep.package.do_install(**kwargs)


+    @property
+    def build_log_path(self):
+        if self.installed:
+            return spack.install_layout.build_log_path(self.spec)
+        else:
+            return join_path(self.stage.source_path, 'spack-build.out')
+
+
    @property
    def module(self):
        """Use this to add variables to the class's module's scope.
@@ -916,6 +939,7 @@ def do_uninstall(self, force=False):

        # Uninstalling in Spack only requires removing the prefix.
        self.remove_prefix()
+        spack.installed_db.remove(self.spec)
        tty.msg("Successfully uninstalled %s." % self.spec.short_spec)

        # Once everything else is done, run post install hooks
--- a/lib/spack/spack/packages.py
+++ b/lib/spack/spack/packages.py
@@ -363,6 +363,11 @@ def get(self, spec, new=False):
        return self._instances[spec]


+    def purge(self):
+        """Clear entire package instance cache."""
+        self._instances.clear()
+
+
    @_autospec
    def providers_for(self, vpkg_spec):
        if self._provider_index is None:
@@ -396,6 +401,7 @@ def filename_for_package_name(self, pkg_name):
        """
        validate_module_name(pkg_name)
        pkg_dir = self.dirname_for_package_name(pkg_name)
+
        return join_path(pkg_dir, package_file_name)


--- a/lib/spack/spack/patch.py
+++ b/lib/spack/spack/patch.py
@@ -41,12 +41,8 @@ class Patch(object):
    """This class describes a patch to be applied to some expanded
       source code."""

-    def __init__(self, pkg, pkg_name, path_or_url, level):
-        print pkg, pkg.name, type(pkg)
-        print "pkg:", dir(pkg.__module__)
-        print "NAMESPACE", pkg.namespace()
-
-        self.pkg_name = pkg_name
+    def __init__(self, pkg, path_or_url, level):
+        self.pkg_name = pkg.name
        self.path_or_url = path_or_url
        self.path = None
        self.url = None
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -641,7 +641,9 @@ def prefix(self):


    def dag_hash(self, length=None):
-        """Return a hash of the entire spec DAG, including connectivity."""
+        """
+        Return a hash of the entire spec DAG, including connectivity.
+        """
        yaml_text = yaml.dump(
            self.to_node_dict(), default_flow_style=True, width=sys.maxint)
        sha = hashlib.sha1(yaml_text)
@@ -711,7 +713,7 @@ def from_yaml(stream):
        try:
            yfile = yaml.load(stream)
        except MarkedYAMLError, e:
-            raise SpackYAMLError("error parsing YMAL spec:", str(e))
+            raise SpackYAMLError("error parsing YAML spec:", str(e))

        for node in yfile['spec']:
            name = next(iter(node))
@@ -2012,4 +2014,4 @@ def __init__(self, provided, required):

 class SpackYAMLError(spack.error.SpackError):
    def __init__(self, msg, yaml_error):
-        super(SpackError, self).__init__(msg, str(yaml_error))
+        super(SpackYAMLError, self).__init__(msg, str(yaml_error))
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -261,7 +261,8 @@ def fetch(self):
                tty.debug(e)
                continue
        else:
-            tty.die("All fetchers failed for %s" % self.name)
+            errMessage = "All fetchers failed for %s" % self.name
+            raise fs.FetchError(errMessage, None)


    def check(self):
--- a/lib/spack/spack/test/init.py
+++ b/lib/spack/spack/test/init.py
@@ -56,7 +56,10 @@
              'spec_yaml',
              'optional_deps',
              'make_executable',
-              'configure_guess']
+              'configure_guess',
+              'unit_install',
+              'lock',
+              'database']


 def list_tests():
@@ -76,7 +79,7 @@ def run(names, verbose=False):
            if test not in test_names:
                tty.error("%s is not a valid spack test name." % test,
                          "Valid names are:")
-                colify(test_names, indent=4)
+                colify(sorted(test_names), indent=4)
                sys.exit(1)

    runner = unittest.TextTestRunner(verbosity=verbosity)
--- a/lib/spack/spack/test/database.py
+++ b/lib/spack/spack/test/database.py
@@ -0,0 +1,352 @@
+##############################################################################
+# Copyright (c) 2013-2015, 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
+##############################################################################
+"""
+These tests check the database is functioning properly,
+both in memory and in its file
+"""
+import tempfile
+import shutil
+import multiprocessing
+
+from llnl.util.lock import *
+from llnl.util.filesystem import join_path
+
+import spack
+from spack.database import Database
+from spack.directory_layout import YamlDirectoryLayout
+from spack.test.mock_packages_test import *
+
+from llnl.util.tty.colify import colify
+
+def _print_ref_counts():
+    """Print out all ref counts for the graph used here, for debugging"""
+    recs = []
+
+    def add_rec(spec):
+        cspecs = spack.installed_db.query(spec, installed=any)
+
+        if not cspecs:
+            recs.append("[ %-7s ] %-20s-" % ('', spec))
+        else:
+            key = cspecs[0].dag_hash()
+            rec = spack.installed_db.get_record(cspecs[0])
+            recs.append("[ %-7s ] %-20s%d" % (key[:7], spec, rec.ref_count))
+
+    with spack.installed_db.read_transaction():
+        add_rec('mpileaks ^mpich')
+        add_rec('callpath ^mpich')
+        add_rec('mpich')
+
+        add_rec('mpileaks ^mpich2')
+        add_rec('callpath ^mpich2')
+        add_rec('mpich2')
+
+        add_rec('mpileaks ^zmpi')
+        add_rec('callpath ^zmpi')
+        add_rec('zmpi')
+        add_rec('fake')
+
+        add_rec('dyninst')
+        add_rec('libdwarf')
+        add_rec('libelf')
+
+    colify(recs, cols=3)
+
+
+class DatabaseTest(MockPackagesTest):
+
+    def _mock_install(self, spec):
+        s = Spec(spec)
+        pkg = spack.db.get(s.concretized())
+        pkg.do_install(fake=True)
+
+
+    def _mock_remove(self, spec):
+        specs = spack.installed_db.query(spec)
+        assert(len(specs) == 1)
+        spec = specs[0]
+        spec.package.do_uninstall(spec)
+
+
+    def setUp(self):
+        super(DatabaseTest, self).setUp()
+        #
+        # TODO: make the mockup below easier.
+        #
+
+        # Make a fake install directory
+        self.install_path = tempfile.mkdtemp()
+        self.spack_install_path = spack.install_path
+        spack.install_path = self.install_path
+
+        self.install_layout = YamlDirectoryLayout(self.install_path)
+        self.spack_install_layout = spack.install_layout
+        spack.install_layout = self.install_layout
+
+        # Make fake database and fake install directory.
+        self.installed_db = Database(self.install_path)
+        self.spack_installed_db = spack.installed_db
+        spack.installed_db = self.installed_db
+
+        # make a mock database with some packages installed note that
+        # the ref count for dyninst here will be 3, as it's recycled
+        # across each install.
+        #
+        # Here is what the mock DB looks like:
+        #
+        # o  mpileaks     o  mpileaks'    o  mpileaks''
+        # |\              |\              |\
+        # | o  callpath   | o  callpath'  | o  callpath''
+        # |/|             |/|             |/|
+        # o |  mpich      o |  mpich2     o |  zmpi
+        #   |               |             o |  fake
+        #   |               |               |
+        #   |               |______________/
+        #   | .____________/
+        #   |/
+        #   o  dyninst
+        #   |\
+        #   | o  libdwarf
+        #   |/
+        #   o  libelf
+        #
+
+        # Transaction used to avoid repeated writes.
+        with spack.installed_db.write_transaction():
+            self._mock_install('mpileaks ^mpich')
+            self._mock_install('mpileaks ^mpich2')
+            self._mock_install('mpileaks ^zmpi')
+
+
+    def tearDown(self):
+        super(DatabaseTest, self).tearDown()
+        shutil.rmtree(self.install_path)
+        spack.install_path = self.spack_install_path
+        spack.install_layout = self.spack_install_layout
+        spack.installed_db = self.spack_installed_db
+
+
+    def test_005_db_exists(self):
+        """Make sure db cache file exists after creating."""
+        index_file = join_path(self.install_path, '.spack-db', 'index.yaml')
+        lock_file = join_path(self.install_path, '.spack-db', 'lock')
+
+        self.assertTrue(os.path.exists(index_file))
+        self.assertTrue(os.path.exists(lock_file))
+
+
+    def test_010_all_install_sanity(self):
+        """Ensure that the install layout reflects what we think it does."""
+        all_specs = spack.install_layout.all_specs()
+        self.assertEqual(len(all_specs), 13)
+
+        # query specs with multiple configurations
+        mpileaks_specs = [s for s in all_specs if s.satisfies('mpileaks')]
+        callpath_specs = [s for s in all_specs if s.satisfies('callpath')]
+        mpi_specs =      [s for s in all_specs if s.satisfies('mpi')]
+
+        self.assertEqual(len(mpileaks_specs), 3)
+        self.assertEqual(len(callpath_specs), 3)
+        self.assertEqual(len(mpi_specs),      3)
+
+        # query specs with single configurations
+        dyninst_specs =  [s for s in all_specs if s.satisfies('dyninst')]
+        libdwarf_specs = [s for s in all_specs if s.satisfies('libdwarf')]
+        libelf_specs =   [s for s in all_specs if s.satisfies('libelf')]
+
+        self.assertEqual(len(dyninst_specs),  1)
+        self.assertEqual(len(libdwarf_specs), 1)
+        self.assertEqual(len(libelf_specs),   1)
+
+        # Query by dependency
+        self.assertEqual(len([s for s in all_specs if s.satisfies('mpileaks ^mpich')]),  1)
+        self.assertEqual(len([s for s in all_specs if s.satisfies('mpileaks ^mpich2')]), 1)
+        self.assertEqual(len([s for s in all_specs if s.satisfies('mpileaks ^zmpi')]),   1)
+
+
+    def test_015_write_and_read(self):
+        # write and read DB
+        with spack.installed_db.write_transaction():
+            specs = spack.installed_db.query()
+            recs = [spack.installed_db.get_record(s) for s in specs]
+
+        for spec, rec in zip(specs, recs):
+            new_rec = spack.installed_db.get_record(spec)
+            self.assertEqual(new_rec.ref_count, rec.ref_count)
+            self.assertEqual(new_rec.spec,      rec.spec)
+            self.assertEqual(new_rec.path,      rec.path)
+            self.assertEqual(new_rec.installed, rec.installed)
+
+
+    def _check_db_sanity(self):
+        """Utiilty function to check db against install layout."""
+        expected = sorted(spack.install_layout.all_specs())
+        actual = sorted(self.installed_db.query())
+
+        self.assertEqual(len(expected), len(actual))
+        for e, a in zip(expected, actual):
+            self.assertEqual(e, a)
+
+
+    def test_020_db_sanity(self):
+        """Make sure query() returns what's actually in the db."""
+        self._check_db_sanity()
+
+
+    def test_030_db_sanity_from_another_process(self):
+        def read_and_modify():
+            self._check_db_sanity()  # check that other process can read DB
+            with self.installed_db.write_transaction():
+                self._mock_remove('mpileaks ^zmpi')
+
+        p = multiprocessing.Process(target=read_and_modify, args=())
+        p.start()
+        p.join()
+
+        # ensure child process change is visible in parent process
+        with self.installed_db.read_transaction():
+            self.assertEqual(len(self.installed_db.query('mpileaks ^zmpi')), 0)
+
+
+    def test_040_ref_counts(self):
+        """Ensure that we got ref counts right when we read the DB."""
+        self.installed_db._check_ref_counts()
+
+
+    def test_050_basic_query(self):
+        """Ensure that querying the database is consistent with what is installed."""
+        # query everything
+        self.assertEqual(len(spack.installed_db.query()), 13)
+
+        # query specs with multiple configurations
+        mpileaks_specs = self.installed_db.query('mpileaks')
+        callpath_specs = self.installed_db.query('callpath')
+        mpi_specs =      self.installed_db.query('mpi')
+
+        self.assertEqual(len(mpileaks_specs), 3)
+        self.assertEqual(len(callpath_specs), 3)
+        self.assertEqual(len(mpi_specs),      3)
+
+        # query specs with single configurations
+        dyninst_specs =  self.installed_db.query('dyninst')
+        libdwarf_specs = self.installed_db.query('libdwarf')
+        libelf_specs =   self.installed_db.query('libelf')
+
+        self.assertEqual(len(dyninst_specs),  1)
+        self.assertEqual(len(libdwarf_specs), 1)
+        self.assertEqual(len(libelf_specs),   1)
+
+        # Query by dependency
+        self.assertEqual(len(self.installed_db.query('mpileaks ^mpich')),  1)
+        self.assertEqual(len(self.installed_db.query('mpileaks ^mpich2')), 1)
+        self.assertEqual(len(self.installed_db.query('mpileaks ^zmpi')),   1)
+
+
+    def _check_remove_and_add_package(self, spec):
+        """Remove a spec from the DB, then add it and make sure everything's
+           still ok once it is added.  This checks that it was
+           removed, that it's back when added again, and that ref
+           counts are consistent.
+        """
+        original = self.installed_db.query()
+        self.installed_db._check_ref_counts()
+
+        # Remove spec
+        concrete_spec = self.installed_db.remove(spec)
+        self.installed_db._check_ref_counts()
+        remaining = self.installed_db.query()
+
+        # ensure spec we removed is gone
+        self.assertEqual(len(original) - 1, len(remaining))
+        self.assertTrue(all(s in original for s in remaining))
+        self.assertTrue(concrete_spec not in remaining)
+
+        # add it back and make sure everything is ok.
+        self.installed_db.add(concrete_spec, "")
+        installed = self.installed_db.query()
+        self.assertEqual(len(installed), len(original))
+
+        # sanity check against direcory layout and check ref counts.
+        self._check_db_sanity()
+        self.installed_db._check_ref_counts()
+
+
+    def test_060_remove_and_add_root_package(self):
+        self._check_remove_and_add_package('mpileaks ^mpich')
+
+
+    def test_070_remove_and_add_dependency_package(self):
+        self._check_remove_and_add_package('dyninst')
+
+
+    def test_080_root_ref_counts(self):
+        rec = self.installed_db.get_record('mpileaks ^mpich')
+
+        # Remove a top-level spec from the DB
+        self.installed_db.remove('mpileaks ^mpich')
+
+        # record no longer in DB
+        self.assertEqual(self.installed_db.query('mpileaks ^mpich', installed=any), [])
+
+        # record's deps have updated ref_counts
+        self.assertEqual(self.installed_db.get_record('callpath ^mpich').ref_count, 0)
+        self.assertEqual(self.installed_db.get_record('mpich').ref_count, 1)
+
+        # put the spec back
+        self.installed_db.add(rec.spec, rec.path)
+
+        # record is present again
+        self.assertEqual(len(self.installed_db.query('mpileaks ^mpich', installed=any)), 1)
+
+        # dependencies have ref counts updated
+        self.assertEqual(self.installed_db.get_record('callpath ^mpich').ref_count, 1)
+        self.assertEqual(self.installed_db.get_record('mpich').ref_count, 2)
+
+
+    def test_090_non_root_ref_counts(self):
+        mpileaks_mpich_rec = self.installed_db.get_record('mpileaks ^mpich')
+        callpath_mpich_rec = self.installed_db.get_record('callpath ^mpich')
+
+        # "force remove" a non-root spec from the DB
+        self.installed_db.remove('callpath ^mpich')
+
+        # record still in DB but marked uninstalled
+        self.assertEqual(self.installed_db.query('callpath ^mpich', installed=True), [])
+        self.assertEqual(len(self.installed_db.query('callpath ^mpich', installed=any)), 1)
+
+        # record and its deps have same ref_counts
+        self.assertEqual(self.installed_db.get_record('callpath ^mpich', installed=any).ref_count, 1)
+        self.assertEqual(self.installed_db.get_record('mpich').ref_count, 2)
+
+        # remove only dependent of uninstalled callpath record
+        self.installed_db.remove('mpileaks ^mpich')
+
+        # record and parent are completely gone.
+        self.assertEqual(self.installed_db.query('mpileaks ^mpich', installed=any), [])
+        self.assertEqual(self.installed_db.query('callpath ^mpich', installed=any), [])
+
+        # mpich ref count updated properly.
+        mpich_rec = self.installed_db.get_record('mpich')
+        self.assertEqual(mpich_rec.ref_count, 0)
--- a/lib/spack/spack/test/lock.py
+++ b/lib/spack/spack/test/lock.py
@@ -0,0 +1,266 @@
+##############################################################################
+# Copyright (c) 2013-2015, 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
+##############################################################################
+"""
+These tests ensure that our lock works correctly.
+"""
+import unittest
+import os
+import tempfile
+import shutil
+from multiprocessing import Process
+
+from llnl.util.lock import *
+from llnl.util.filesystem import join_path, touch
+
+from spack.util.multiproc import Barrier
+
+# This is the longest a failed test will take, as the barriers will
+# time out and raise an exception.
+barrier_timeout = 5
+
+
+class LockTest(unittest.TestCase):
+
+    def setUp(self):
+        self.tempdir = tempfile.mkdtemp()
+        self.lock_path = join_path(self.tempdir, 'lockfile')
+        touch(self.lock_path)
+
+
+    def tearDown(self):
+         shutil.rmtree(self.tempdir, ignore_errors=True)
+
+
+    def multiproc_test(self, *functions):
+        """Order some processes using simple barrier synchronization."""
+        b = Barrier(len(functions), timeout=barrier_timeout)
+        procs = [Process(target=f, args=(b,)) for f in functions]
+        for p in procs: p.start()
+        for p in procs:
+            p.join()
+            self.assertEqual(p.exitcode, 0)
+
+
+    #
+    # Process snippets below can be composed into tests.
+    #
+    def acquire_write(self, barrier):
+        lock = Lock(self.lock_path)
+        lock.acquire_write()  # grab exclusive lock
+        barrier.wait()
+        barrier.wait() # hold the lock until exception raises in other procs.
+
+    def acquire_read(self, barrier):
+        lock = Lock(self.lock_path)
+        lock.acquire_read()  # grab shared lock
+        barrier.wait()
+        barrier.wait() # hold the lock until exception raises in other procs.
+
+    def timeout_write(self, barrier):
+        lock = Lock(self.lock_path)
+        barrier.wait() # wait for lock acquire in first process
+        self.assertRaises(LockError, lock.acquire_write, 0.1)
+        barrier.wait()
+
+    def timeout_read(self, barrier):
+        lock = Lock(self.lock_path)
+        barrier.wait() # wait for lock acquire in first process
+        self.assertRaises(LockError, lock.acquire_read, 0.1)
+        barrier.wait()
+
+
+    #
+    # Test that exclusive locks on other processes time out when an
+    # exclusive lock is held.
+    #
+    def test_write_lock_timeout_on_write(self):
+        self.multiproc_test(self.acquire_write, self.timeout_write)
+
+    def test_write_lock_timeout_on_write_2(self):
+        self.multiproc_test(self.acquire_write, self.timeout_write, self.timeout_write)
+
+    def test_write_lock_timeout_on_write_3(self):
+        self.multiproc_test(self.acquire_write, self.timeout_write, self.timeout_write, self.timeout_write)
+
+
+    #
+    # Test that shared locks on other processes time out when an
+    # exclusive lock is held.
+    #
+    def test_read_lock_timeout_on_write(self):
+        self.multiproc_test(self.acquire_write, self.timeout_read)
+
+    def test_read_lock_timeout_on_write_2(self):
+        self.multiproc_test(self.acquire_write, self.timeout_read, self.timeout_read)
+
+    def test_read_lock_timeout_on_write_3(self):
+        self.multiproc_test(self.acquire_write, self.timeout_read, self.timeout_read, self.timeout_read)
+
+
+    #
+    # Test that exclusive locks time out when shared locks are held.
+    #
+    def test_write_lock_timeout_on_read(self):
+        self.multiproc_test(self.acquire_read, self.timeout_write)
+
+    def test_write_lock_timeout_on_read_2(self):
+        self.multiproc_test(self.acquire_read, self.timeout_write, self.timeout_write)
+
+    def test_write_lock_timeout_on_read_3(self):
+        self.multiproc_test(self.acquire_read, self.timeout_write, self.timeout_write, self.timeout_write)
+
+
+    #
+    # Test that exclusive locks time while lots of shared locks are held.
+    #
+    def test_write_lock_timeout_with_multiple_readers_2_1(self):
+        self.multiproc_test(self.acquire_read, self.acquire_read, self.timeout_write)
+
+    def test_write_lock_timeout_with_multiple_readers_2_2(self):
+        self.multiproc_test(self.acquire_read, self.acquire_read, self.timeout_write, self.timeout_write)
+
+    def test_write_lock_timeout_with_multiple_readers_3_1(self):
+        self.multiproc_test(self.acquire_read, self.acquire_read, self.acquire_read, self.timeout_write)
+
+    def test_write_lock_timeout_with_multiple_readers_3_2(self):
+        self.multiproc_test(self.acquire_read, self.acquire_read, self.acquire_read, self.timeout_write, self.timeout_write)
+
+
+    #
+    # Longer test case that ensures locks are reusable. Ordering is
+    # enforced by barriers throughout -- steps are shown with numbers.
+    #
+    def test_complex_acquire_and_release_chain(self):
+        def p1(barrier):
+            lock = Lock(self.lock_path)
+
+            lock.acquire_write()
+            barrier.wait() # ---------------------------------------- 1
+            # others test timeout
+            barrier.wait() # ---------------------------------------- 2
+            lock.release_write()   # release and others acquire read
+            barrier.wait() # ---------------------------------------- 3
+            self.assertRaises(LockError, lock.acquire_write, 0.1)
+            lock.acquire_read()
+            barrier.wait() # ---------------------------------------- 4
+            lock.release_read()
+            barrier.wait() # ---------------------------------------- 5
+
+            # p2 upgrades read to write
+            barrier.wait() # ---------------------------------------- 6
+            self.assertRaises(LockError, lock.acquire_write, 0.1)
+            self.assertRaises(LockError, lock.acquire_read, 0.1)
+            barrier.wait() # ---------------------------------------- 7
+            # p2 releases write and read
+            barrier.wait() # ---------------------------------------- 8
+
+            # p3 acquires read
+            barrier.wait() # ---------------------------------------- 9
+            # p3 upgrades read to write
+            barrier.wait() # ---------------------------------------- 10
+            self.assertRaises(LockError, lock.acquire_write, 0.1)
+            self.assertRaises(LockError, lock.acquire_read, 0.1)
+            barrier.wait() # ---------------------------------------- 11
+            # p3 releases locks
+            barrier.wait() # ---------------------------------------- 12
+            lock.acquire_read()
+            barrier.wait() # ---------------------------------------- 13
+            lock.release_read()
+
+
+        def p2(barrier):
+            lock = Lock(self.lock_path)
+
+            # p1 acquires write
+            barrier.wait() # ---------------------------------------- 1
+            self.assertRaises(LockError, lock.acquire_write, 0.1)
+            self.assertRaises(LockError, lock.acquire_read, 0.1)
+            barrier.wait() # ---------------------------------------- 2
+            lock.acquire_read()
+            barrier.wait() # ---------------------------------------- 3
+            # p1 tests shared read
+            barrier.wait() # ---------------------------------------- 4
+            # others release reads
+            barrier.wait() # ---------------------------------------- 5
+
+            lock.acquire_write() # upgrade read to write
+            barrier.wait() # ---------------------------------------- 6
+            # others test timeout
+            barrier.wait() # ---------------------------------------- 7
+            lock.release_write()  # release read AND write (need both)
+            lock.release_read()
+            barrier.wait() # ---------------------------------------- 8
+
+            # p3 acquires read
+            barrier.wait() # ---------------------------------------- 9
+            # p3 upgrades read to write
+            barrier.wait() # ---------------------------------------- 10
+            self.assertRaises(LockError, lock.acquire_write, 0.1)
+            self.assertRaises(LockError, lock.acquire_read, 0.1)
+            barrier.wait() # ---------------------------------------- 11
+            # p3 releases locks
+            barrier.wait() # ---------------------------------------- 12
+            lock.acquire_read()
+            barrier.wait() # ---------------------------------------- 13
+            lock.release_read()
+
+
+        def p3(barrier):
+            lock = Lock(self.lock_path)
+
+            # p1 acquires write
+            barrier.wait() # ---------------------------------------- 1
+            self.assertRaises(LockError, lock.acquire_write, 0.1)
+            self.assertRaises(LockError, lock.acquire_read, 0.1)
+            barrier.wait() # ---------------------------------------- 2
+            lock.acquire_read()
+            barrier.wait() # ---------------------------------------- 3
+            # p1 tests shared read
+            barrier.wait() # ---------------------------------------- 4
+            lock.release_read()
+            barrier.wait() # ---------------------------------------- 5
+
+            # p2 upgrades read to write
+            barrier.wait() # ---------------------------------------- 6
+            self.assertRaises(LockError, lock.acquire_write, 0.1)
+            self.assertRaises(LockError, lock.acquire_read, 0.1)
+            barrier.wait() # ---------------------------------------- 7
+            # p2 releases write & read
+            barrier.wait() # ---------------------------------------- 8
+
+            lock.acquire_read()
+            barrier.wait() # ---------------------------------------- 9
+            lock.acquire_write()
+            barrier.wait() # ---------------------------------------- 10
+            # others test timeout
+            barrier.wait() # ---------------------------------------- 11
+            lock.release_read()   # release read AND write in opposite
+            lock.release_write()  # order from before on p2
+            barrier.wait() # ---------------------------------------- 12
+            lock.acquire_read()
+            barrier.wait() # ---------------------------------------- 13
+            lock.release_read()
+
+        self.multiproc_test(p1, p2, p3)
--- a/lib/spack/spack/test/unit_install.py
+++ b/lib/spack/spack/test/unit_install.py
@@ -0,0 +1,121 @@
+##############################################################################
+# 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
+##############################################################################
+import unittest
+import itertools
+
+import spack
+test_install = __import__("spack.cmd.test-install", 
+    fromlist=["BuildId", "create_test_output", "TestResult"])
+
+class MockOutput(object):
+    def __init__(self):
+        self.results = {}
+    
+    def add_test(self, buildId, passed=True, buildInfo=None):
+        self.results[buildId] = passed
+    
+    def write_to(self, stream):
+        pass
+
+class MockSpec(object):
+    def __init__(self, name, version, hashStr=None):
+        self.dependencies = {}
+        self.name = name
+        self.version = version
+        self.hash = hashStr if hashStr else hash((name, version))
+    
+    def traverse(self, order=None):
+        allDeps = itertools.chain.from_iterable(i.traverse() for i in 
+            self.dependencies.itervalues())
+        return set(itertools.chain([self], allDeps))
+    
+    def dag_hash(self):
+        return self.hash 
+
+    def to_yaml(self):
+        return "<<<MOCK YAML {0}>>>".format(test_install.BuildId(self).stringId())
+
+class MockPackage(object):
+    def __init__(self, buildLogPath):
+        self.installed = False
+        self.build_log_path = buildLogPath
+
+specX = MockSpec("X", "1.2.0")
+specY = MockSpec("Y", "2.3.8")
+specX.dependencies['Y'] = specY
+pkgX = MockPackage('logX')
+pkgY = MockPackage('logY')
+bIdX = test_install.BuildId(specX)
+bIdY = test_install.BuildId(specY)
+
+class UnitInstallTest(unittest.TestCase):
+    """Tests test-install where X->Y"""
+
+    def setUp(self):
+        super(UnitInstallTest, self).setUp()
+        
+        pkgX.installed = False
+        pkgY.installed = False
+
+        pkgDb = MockPackageDb({specX:pkgX, specY:pkgY})
+        spack.db = pkgDb
+
+    def tearDown(self):
+        super(UnitInstallTest, self).tearDown()
+        
+    def test_installing_both(self):
+        mo = MockOutput()
+        
+        pkgX.installed = True
+        pkgY.installed = True
+        test_install.create_test_output(specX, [specX, specY], mo, getLogFunc=test_fetch_log)
+        
+        self.assertEqual(mo.results, 
+            {bIdX:test_install.TestResult.PASSED, 
+            bIdY:test_install.TestResult.PASSED})
+
+    def test_dependency_already_installed(self):
+        mo = MockOutput()
+        
+        pkgX.installed = True
+        pkgY.installed = True
+        test_install.create_test_output(specX, [specX], mo, getLogFunc=test_fetch_log)
+        
+        self.assertEqual(mo.results, {bIdX:test_install.TestResult.PASSED})
+
+    #TODO: add test(s) where Y fails to install
+
+class MockPackageDb(object):
+    def __init__(self, init=None):
+        self.specToPkg = {}
+        if init:
+            self.specToPkg.update(init)
+        
+    def get(self, spec):
+        return self.specToPkg[spec]
+
+def test_fetch_log(path):
+    return []
+
--- a/lib/spack/spack/url.py
+++ b/lib/spack/spack/url.py
@@ -209,8 +209,8 @@ def parse_version_offset(path):
        # e.g. foobar-4.5.1
        (r'-((\d+\.)*\d+)$', stem),

-        # e.g. foobar-4.5.1b
-        (r'-((\d+\.)*\d+\-?([a-z]|rc|RC|tp|TP)\d*)$', stem),
+        # e.g. foobar-4.5.1b, foobar4.5RC, foobar.v4.5.1b
+        (r'[-._]?v?((\d+\.)*\d+[-._]?([a-z]|rc|RC|tp|TP?)\d*)$', stem),

        # e.g. foobar-4.5.0-beta1, or foobar-4.50-beta
        (r'-((\d+\.)*\d+-beta(\d+)?)$', stem),
--- a/lib/spack/spack/util/multiproc.py
+++ b/lib/spack/spack/util/multiproc.py
@@ -27,9 +27,11 @@
 than multiprocessing.Pool.apply() can.  For example, apply() will fail
 to pickle functions if they're passed indirectly as parameters.
 """
-from multiprocessing import Process, Pipe
+from multiprocessing import Process, Pipe, Semaphore, Value
 from itertools import izip

+__all__ = ['spawn', 'parmap', 'Barrier']
+
 def spawn(f):
    def fun(pipe,x):
        pipe.send(f(x))
@@ -43,3 +45,49 @@ def parmap(f,X):
    [p.join() for p in proc]
    return [p.recv() for (p,c) in pipe]

+
+class Barrier:
+    """Simple reusable semaphore barrier.
+
+    Python 2.6 doesn't have multiprocessing barriers so we implement this.
+
+    See http://greenteapress.com/semaphores/downey08semaphores.pdf, p. 41.
+    """
+    def __init__(self, n, timeout=None):
+        self.n = n
+        self.to = timeout
+        self.count = Value('i', 0)
+        self.mutex = Semaphore(1)
+        self.turnstile1 = Semaphore(0)
+        self.turnstile2 = Semaphore(1)
+
+
+    def wait(self):
+        if not self.mutex.acquire(timeout=self.to):
+            raise BarrierTimeoutError()
+        self.count.value += 1
+        if self.count.value == self.n:
+            if not self.turnstile2.acquire(timeout=self.to):
+                raise BarrierTimeoutError()
+            self.turnstile1.release()
+        self.mutex.release()
+
+        if not self.turnstile1.acquire(timeout=self.to):
+            raise BarrierTimeoutError()
+        self.turnstile1.release()
+
+        if not self.mutex.acquire(timeout=self.to):
+            raise BarrierTimeoutError()
+        self.count.value -= 1
+        if self.count.value == 0:
+            if not self.turnstile1.acquire(timeout=self.to):
+                raise BarrierTimeoutError()
+            self.turnstile2.release()
+        self.mutex.release()
+
+        if not self.turnstile2.acquire(timeout=self.to):
+            raise BarrierTimeoutError()
+        self.turnstile2.release()
+
+
+class BarrierTimeoutError: pass
--- a/lib/spack/spack/virtual.py
+++ b/lib/spack/spack/virtual.py
@@ -73,10 +73,8 @@ def update(self, spec):
        for provided_spec, provider_spec in pkg.provided.iteritems():
            if provider_spec.satisfies(spec, deps=False):
                provided_name = provided_spec.name
-                if provided_name not in self.providers:
-                    self.providers[provided_name] = {}

-                provider_map = self.providers[provided_name]
+                provider_map = self.providers.setdefault(provided_name, {})
                if not provided_spec in provider_map:
                    provider_map[provided_spec] = set()

@@ -133,9 +131,7 @@ def _cross_provider_maps(self, lmap, rmap):
                if lp_spec.name == rp_spec.name:
                    try:
                        const = lp_spec.copy().constrain(rp_spec,deps=False)
-                        if constrained not in result:
-                            result[constrained] = set()
-                        result[constrained].add(const)
+                        result.setdefault(constrained, set()).add(const)
                    except spack.spec.UnsatisfiableSpecError:
                        continue
        return result