Update documentation for use on Cray

Updating how to use compilers.yaml on Cray as well as setting up
external packages. Also includes what needs to be set up for usage on
Cray and explains what needs to be done to get Spack properly working.
Also explain the architecture spec and what it does.

2 files changed, 152 insertions, 70 deletions

diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst
index ec193e767d..199a7ef386 100644
--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -114,13 +114,13 @@ that the packages is installed:
 
    $ spack install mpileaks
    ==> Installing mpileaks
-   ==> mpich is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpich@3.0.4.
-   ==> callpath is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/callpath@1.0.2-5dce4318.
-   ==> adept-utils is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da.
+   ==> mpich is already installed in /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/mpich@3.0.4.
+   ==> callpath is already installed in /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/callpath@1.0.2-5dce4318.
+   ==> adept-utils is already installed in /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/adept-utils@1.0-5adef8da.
    ==> Trying to fetch from https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
    ######################################################################## 100.0%
-   ==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=chaos_5_x86_64_ib-59f6ad23/mpileaks-1.0.tar.gz
-   ==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=chaos_5_x86_64_ib-59f6ad23.
+   ==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-x86_64-debian7-59f6ad23/mpileaks-1.0.tar.gz
+   ==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-x86_64-debian7-59f6ad23.
    ==> No patches needed for mpileaks.
    ==> Building mpileaks.
 
@@ -128,7 +128,7 @@ that the packages is installed:
 
    ==> Successfully installed mpileaks.
      Fetch: 2.16s.  Build: 9.82s.  Total: 11.98s.
-   [+] /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpileaks@1.0-59f6ad23
+   [+] /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/mpileaks@1.0-59f6ad23
 
 The last line, with the ``[+]``, indicates where the package is
 installed.
@@ -230,7 +230,7 @@ Running ``spack find`` with no arguments lists installed packages:
 
    $ spack find
    ==> 74 installed packages.
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
    ImageMagick@6.8.9-10  libdwarf@20130729  py-dateutil@2.4.0
    adept-utils@1.0       libdwarf@20130729  py-ipython@2.3.1
    atk@2.14.0            libelf@0.8.12      py-matplotlib@1.4.2
@@ -256,7 +256,7 @@ Running ``spack find`` with no arguments lists installed packages:
    lcms@2.6              pixman@0.32.6      xz@5.2.0
    libdrm@2.4.33         py-dateutil@2.4.0  zlib@1.2.8
 
-   -- chaos_5_x86_64_ib / gcc@4.9.2 --------------------------------
+   -- linux-x86_64-debian7 / gcc@4.9.2 --------------------------------
    libelf@0.8.10  mpich@3.0.4
 
 Packages are divided into groups according to their architecture and
@@ -279,7 +279,7 @@ in more detail using ``spack find -d``, and by asking only to show
 
    $ spack find --deps libdwarf
    ==> 2 installed packages.
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
        libdwarf@20130729-d9b90962
            ^libelf@0.8.12
        libdwarf@20130729-b52fac98
@@ -295,7 +295,7 @@ want to know whether two packages' dependencies differ, you can use
 
    $ spack find -l libdwarf
    ==> 2 installed packages.
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
    libdwarf@20130729-d9b90962  libdwarf@20130729-b52fac98
 
 Now the ``libwarf`` installs have hashes after their names.  These are
@@ -309,14 +309,14 @@ use ``spack find -p``:
 
    $ spack find -p
    ==> 74 installed packages.
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
-       ImageMagick@6.8.9-10  /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/ImageMagick@6.8.9-10-4df950dd
-       adept-utils@1.0       /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da
-       atk@2.14.0            /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/atk@2.14.0-3d09ac09
-       boost@1.55.0          /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/boost@1.55.0
-       bzip2@1.0.6           /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/bzip2@1.0.6
-       cairo@1.14.0          /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/cairo@1.14.0-fcc2ab44
-       callpath@1.0.2        /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/callpath@1.0.2-5dce4318
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
+       ImageMagick@6.8.9-10  /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/ImageMagick@6.8.9-10-4df950dd
+       adept-utils@1.0       /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/adept-utils@1.0-5adef8da
+       atk@2.14.0            /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/atk@2.14.0-3d09ac09
+       boost@1.55.0          /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/boost@1.55.0
+       bzip2@1.0.6           /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/bzip2@1.0.6
+       cairo@1.14.0          /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/cairo@1.14.0-fcc2ab44
+       callpath@1.0.2        /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/callpath@1.0.2-5dce4318
    ...
 
 And, finally, you can restrict your search to a particular package
@@ -325,10 +325,10 @@ by supplying its name:
 .. code-block:: sh
 
    $ spack find -p libelf
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
-       libelf@0.8.11  /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.11
-       libelf@0.8.12  /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.12
-       libelf@0.8.13  /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.13
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
+       libelf@0.8.11  /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/libelf@0.8.11
+       libelf@0.8.12  /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/libelf@0.8.12
+       libelf@0.8.13  /home/gamblin2/spack/opt/linux-x86_64-debian7/gcc@4.4.7/libelf@0.8.13
 
 ``spack find`` actually does a lot more than this.  You can use
 *specs* to query for specific configurations and builds of each
@@ -338,7 +338,7 @@ package. If you want to find only libelf versions greater than version
 .. code-block:: sh
 
    $ spack find libelf@0.8.12:
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
        libelf@0.8.12  libelf@0.8.13
 
 Finding just the versions of libdwarf built with a particular version
@@ -348,7 +348,7 @@ of libelf would look like this:
 
    $ spack find -l libdwarf ^libelf@0.8.12
    ==> 1 installed packages.
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
    libdwarf@20130729-d9b90962
 
 We can also search for packages that have a certain attribute. For example,
@@ -460,19 +460,38 @@ editing your ``~/.spack/compilers.yaml`` file.  You can do this by running
 Each compiler configuration in the file looks like this::
 
     ...
-    chaos_5_x86_64_ib:
-      ...
-      intel@15.0.0:
+    compilers:
+      - compiler:
+          modules = []
+          operating_system: OS
+        paths:
           cc: /usr/local/bin/icc-15.0.024-beta
           cxx: /usr/local/bin/icpc-15.0.024-beta
           f77: /usr/local/bin/ifort-15.0.024-beta
           fc: /usr/local/bin/ifort-15.0.024-beta
-      ...
 
-The chaos_5_x86_64_ib string is an architecture string, and multiple
-compilers can be listed underneath an architecture.  The architecture
-string may be replaced with the string 'all' to signify compilers that
-work on all architectures.
+          spec: intel@15.0.0:
+
+If you're on a Cray system, the modules array will hold the names of the
+compiler module as well as the corresponding PrgEnv. For example, on Edison
+at NERSC the intel compiler looks just like this::
+    ...
+    - compiler:
+        modules:
+          - PrEnv-intel
+          - intel/15.0.109
+    ...
+
+The compiler paths will also look different on a Cray system. Since most 
+compilers are invoked using cc, CC and ftn, the paths for each compiler are
+replaced with their respective Cray compiler wrapper names::
+    ...
+    paths:
+      cc: cc
+      cxx: CC
+      f77: ftn
+      fc: ftn
+    ...
 
 For compilers, like ``clang``, that do not support Fortran, put
 ``None`` for ``f77`` and ``fc``::
@@ -488,10 +507,11 @@ list displayed by ``spack compilers``.
 
 You can also add compiler flags to manually configured compilers. The
 valid flags are ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``,
-``ldflags``, and ``ldlibs``. For example,::
+``ldflags``, and ``ldlibs``. For example::
 
     ...
-    chaos_5_x86_64_ib:
+    compilers:
+      - compiler:
       ...
       intel@15.0.0:
           cc: /usr/local/bin/icc-15.0.024-beta
@@ -546,8 +566,8 @@ More formally, a spec consists of the following pieces:
 boolean variants
 * ``name=<value>`` Optional compiler flag specifiers. Valid flag names are
 ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``.
-* ``arch=<value>`` Optional architecture specifier (``arch=bgq_os``)
-* ``^`` Dependency specs (``^callpath@1.1``)
+* ``target=<value> os=<value>`` Optional architecture specifier 
+(``target=haswell os=CNL10``) * ``^`` Dependency specs (``^callpath@1.1``)
 
 There are two things to notice here.  The first is that specs are
 recursively defined.  That is, each dependency after ``^`` is a spec
@@ -626,7 +646,7 @@ compilers, variants, and architectures just like any other spec.
 Specifiers are associated with the nearest package name to their left.
 For example, above, ``@1.1`` and ``%gcc@4.7.2`` associates with the
 ``callpath`` package, while ``@1.2:1.4``, ``%gcc@4.7.5``, ``+debug``,
-``-qt``, and ``arch=bgq_os`` all associate with the ``mpileaks`` package.
+``-qt``, and ``target=haswell os=CNL10`` all associate with the ``mpileaks`` package.
 
 In the diagram above, ``mpileaks`` depends on ``mpich`` with an
 unspecified version, but packages can depend on other packages with
@@ -758,14 +778,20 @@ in gnu autotools. If all flags are set, the order is
 Architecture specifiers
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-.. Note::
-
-   Architecture specifiers are part of specs but are not yet
-   functional. They will be in Spack version 1.0, due in Q3 2015.
-
 The architecture specifier looks identical to a variant specifier for a
-non-boolean variant. The architecture can be specified only using the
-reserved name ``arch`` (``arch=bgq_os``).
+non-boolean variant. The architecture can be specified by using the reserved
+words ``target`` and/or ``os`` (``target=x86-64 os=debian7``). 
+
+If you are on a Cray system, you can specify which target processor to 
+build with. For example, if you want to build against a compute node processor 
+with the compute node operating system, you would specify 
+``target=haswell os=CNL10``. Spack will then load the appropriate module for 
+the target. Additionally, Spack can also intepret the following values: 
+``be, backend, fe, frontend``. Backend is used for specifying the compute-node 
+processor and operating sytem, and frontend is used for login nodes. 
+If you decide to leave this field empty, Spack will use the 
+default architecture (compute nodes). The architecture spec is displayed as a 
+triplet of platform-target-operating_system. (``arch=linux-x86_64-debian7``)
 
 
 .. _sec-virtual-dependencies:
@@ -985,7 +1011,7 @@ of installed packages.
 
      $ module avail
 
-     ------- /home/gamblin2/spack/share/spack/modules/chaos_5_x86_64_ib --------
+     ------- /home/gamblin2/spack/share/spack/modules/linux-x86_64-debian7 --------
      adept-utils@1.0%gcc@4.4.7-5adef8da   libelf@0.8.13%gcc@4.4.7
      automaded@1.0%gcc@4.4.7-d9691bb0     libelf@0.8.13%intel@15.0.0
      boost@1.55.0%gcc@4.4.7               mpc@1.0.2%gcc@4.4.7-559607f5
@@ -1056,7 +1082,7 @@ Spack.  For example, this will add the ``mpich`` package built with
    $ spack use mpich %gcc@4.4.7
    Prepending: mpich@3.0.4%gcc@4.4.7 (ok)
    $ which mpicc
-   ~/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpich@3.0.4/bin/mpicc
+   ~/src/spack/opt/linux-x86_64-debian7/gcc@4.4.7/mpich@3.0.4/bin/mpicc
 
 Or, similarly with modules, you could type:
 
@@ -1089,8 +1115,8 @@ than one installed package matches it), then Spack will warn you:
 
    $ spack load libelf
    ==> Error: Multiple matches for spec libelf.  Choose one:
-   libelf@0.8.13%gcc@4.4.7 arch=chaos_5_x86_64_ib
-   libelf@0.8.13%intel@15.0.0 arch=chaos_5_x86_64_ib
+   libelf@0.8.13%gcc@4.4.7 arch=linux-x86_64-debian7
+   libelf@0.8.13%intel@15.0.0 arch=linux-x86_64-debian7
 
 You can either type the ``spack load`` command again with a fully
 qualified argument, or you can add just enough extra constraints to
@@ -1470,7 +1496,7 @@ an *extension*.  Suppose you have Python installed like so:
 
    $ spack find python
    ==> 1 installed packages.
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
    python@2.7.8
 
 .. _spack-extensions:
@@ -1483,7 +1509,7 @@ You can find extensions for your Python installation like this:
 .. code-block:: sh
 
    $ spack extensions python
-   ==> python@2.7.8%gcc@4.4.7 arch=chaos_5_x86_64_ib-703c7a96
+   ==> python@2.7.8%gcc@4.4.7 arch=linux-x86_64-debian7-703c7a96
    ==> 36 extensions:
    geos          py-ipython     py-pexpect    py-pyside            py-sip
    py-basemap    py-libxml2     py-pil        py-pytz              py-six
@@ -1495,7 +1521,7 @@ You can find extensions for your Python installation like this:
    py-h5py       py-numpy       py-pyqt       py-shiboken
 
    ==> 12 installed:
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
    py-dateutil@2.4.0    py-nose@1.3.4       py-pyside@1.2.2
    py-dateutil@2.4.0    py-numpy@1.9.1      py-pytz@2014.10
    py-ipython@2.3.1     py-pygments@2.0.1   py-setuptools@11.3.1
@@ -1511,8 +1537,8 @@ prefixes, and you can see this with ``spack find -p``:
 
    $ spack find -p py-numpy
    ==> 1 installed packages.
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
-       py-numpy@1.9.1  /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/py-numpy@1.9.1-66733244
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
+       py-numpy@1.9.1  /g/g21/gamblin2/src/spack/opt/linux-x86_64-debian7/gcc@4.4.7/py-numpy@1.9.1-66733244
 
 However, even though this package is installed, you cannot use it
 directly when you run ``python``:
@@ -1573,9 +1599,9 @@ installation:
 .. code-block:: sh
 
    $ spack activate py-numpy
-   ==> Activated extension py-setuptools@11.3.1%gcc@4.4.7 arch=chaos_5_x86_64_ib-3c74eb69 for python@2.7.8%gcc@4.4.7.
-   ==> Activated extension py-nose@1.3.4%gcc@4.4.7 arch=chaos_5_x86_64_ib-5f70f816 for python@2.7.8%gcc@4.4.7.
-   ==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7.
+   ==> Activated extension py-setuptools@11.3.1%gcc@4.4.7 arch=linux-x86_64-debian7-3c74eb69 for python@2.7.8%gcc@4.4.7.
+   ==> Activated extension py-nose@1.3.4%gcc@4.4.7 arch=linux-x86_64-debian7-5f70f816 for python@2.7.8%gcc@4.4.7.
+   ==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=linux-x86_64-debian7-66733244 for python@2.7.8%gcc@4.4.7.
 
 Several things have happened here.  The user requested that
 ``py-numpy`` be activated in the ``python`` installation it was built
@@ -1590,7 +1616,7 @@ packages listed as activated:
 .. code-block:: sh
 
    $ spack extensions python
-   ==> python@2.7.8%gcc@4.4.7  arch=chaos_5_x86_64_ib-703c7a96
+   ==> python@2.7.8%gcc@4.4.7  arch=linux-x86_64-debian7-703c7a96
    ==> 36 extensions:
    geos          py-ipython     py-pexpect    py-pyside            py-sip
    py-basemap    py-libxml2     py-pil        py-pytz              py-six
@@ -1602,14 +1628,14 @@ packages listed as activated:
    py-h5py       py-numpy       py-pyqt       py-shiboken
 
    ==> 12 installed:
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
    py-dateutil@2.4.0    py-nose@1.3.4       py-pyside@1.2.2
    py-dateutil@2.4.0    py-numpy@1.9.1      py-pytz@2014.10
    py-ipython@2.3.1     py-pygments@2.0.1   py-setuptools@11.3.1
    py-matplotlib@1.4.2  py-pyparsing@2.0.3  py-six@1.9.0
 
    ==> 3 currently activated:
-   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   -- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
    py-nose@1.3.4  py-numpy@1.9.1  py-setuptools@11.3.1
 
 
@@ -1670,7 +1696,7 @@ Spack currently needs to be run from a filesystem that supports
 ``flock`` locking semantics.  Nearly all local filesystems and recent
 versions of NFS support this, but parallel filesystems may be mounted
 without ``flock`` support enabled.  You can determine how your
-filesystems are mounted with ``mount -p``.  The output for a Lustre
+ filesystems are mounted with ``mount -p``.  The output for a Lustre
 filesystem might look like this:
 
 .. code-block:: sh
@@ -1691,7 +1717,7 @@ This issue typically manifests with the error below:
    Traceback (most recent call last):
    File "./spack", line 176, in <module>
      main()
-   File "./spack", line 154, in main
+   File "./spack", line 154,' in main
      return_val = command(parser, args)
    File "./spack/lib/spack/spack/cmd/find.py", line 170, in find
      specs = set(spack.installed_db.query(**q_args))
@@ -1709,6 +1735,20 @@ This issue typically manifests with the error below:
 
 A nicer error message is TBD in future versions of Spack.
 
+
+Spack on Cray
+-----------------------------
+
+Spack is able to detect compilers through the module avail command. Once it
+detects the compiler it writes the appropriate PrgEnv and compiler module 
+name to compilers.yaml and sets the paths to each compiler with Cray\'s 
+compiler wrapper names ie (cc, CC, ftn). During build time, Spack will
+load the correct PrgEnv and compiler module and will call either cc, CC
+or ftn. If you want to use default compilers for each PrgEnv and also be able
+to link to cray external modules, you will need to set up a packages.yaml 
+:ref:`Exernal Packages`<sec-external packages>
+
+
 Getting Help
 -----------------------
 
diff --git a/lib/spack/docs/configuration.rst b/lib/spack/docs/configuration.rst
index a6f876b2aa..b2e81e4334 100644
--- a/lib/spack/docs/configuration.rst
+++ b/lib/spack/docs/configuration.rst
@@ -70,20 +70,31 @@ directory. Here's an example of an external configuration:
    packages:
       openmpi:
          paths:
-            openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib: /opt/openmpi-1.4.3
-            openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib+debug: /opt/openmpi-1.4.3-debug
-            openmpi@1.6.5%intel@10.1 arch=chaos_5_x86_64_ib: /opt/openmpi-1.6.5-intel
+            openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3
+            openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debug
+            openmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel
 
 This example lists three installations of OpenMPI, one built with gcc,
 one built with gcc and debug information, and another built with Intel.
 If Spack is asked to build a package that uses one of these MPIs as a
 dependency, it will use the the pre-installed OpenMPI in
-the given directory.
+the given directory. Packages.yaml can also be used to specify modules
+
+Here's an example of an external configuration for cray modules:
+
+.. code-block:: yaml
+  packages:
+      mpich:
+        modules:
+            mpich@7.3.1%gcc@5.2.0 arch=cray_xc-haswell-CNL10: cray-mpich
+            mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-haswell-CNL10: cray-mpich
+
+
 
 Each ``packages.yaml`` begins with a ``packages:`` token, followed
-by a list of package names.  To specify externals, add a ``paths``
+by a list of package names.  To specify externals, add a ``paths`` or ``modules``
 token under the package name, which lists externals in a
-``spec : /path`` format.  Each spec should be as
+``spec: /path`` or ``spec: module-name`` format.  Each spec should be as
 well-defined as reasonably possible.  If a
 package lacks a spec component, such as missing a compiler or
 package version, then Spack will guess the missing component based
@@ -108,9 +119,9 @@ be:
   packages:
     openmpi:
       paths:
-        openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib: /opt/openmpi-1.4.3
-        openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib+debug: /opt/openmpi-1.4.3-debug
-        openmpi@1.6.5%intel@10.1 arch=chaos_5_x86_64_ib: /opt/openmpi-1.6.5-intel
+        openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3
+        openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debug
+        openmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel
       buildable: False
 
 The addition of the ``buildable`` flag tells Spack that it should never build
@@ -118,6 +129,9 @@ its own version of OpenMPI, and it will instead always rely on a pre-built
 OpenMPI.  Similar to ``paths``, ``buildable`` is specified as a property under
 a package name.
 
+If an external module is specified as not buildable, then Spack will load the
+external module into the build environment which can be used for linking.
+
 The ``buildable`` does not need to be paired with external packages.
 It could also be used alone to forbid packages that may be
 buggy or otherwise undesirable.
@@ -180,7 +194,35 @@ concretization rules.  A provider lists a value that packages may
 ``depend_on`` (e.g, mpi) and a list of rules for fulfilling that
 dependency.
 
+For Cray users, you can specify the default compiler that Spack will
+concretize too. If you want to use the Cray defaults, then set them
+under all: in packages.yaml. You can also specify concretization preferences
+to cray-mpich. Just set the cray-mpich external module as a preferred package,
+set buildable to False and set the preference of mpi to mpich.
+
+Here is an example of a full packages.yaml used at NERSC
 
+.. code-block:: sh
+   packages:
+    mpich:
+        modules:
+            mpich@7.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-mpich
+            mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-SuSE11-ivybridge: cray-mpich
+        buildable: False
+    netcdf:
+        modules:
+            netcdf@4.3.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-netcdf
+            netcdf@4.3.3.1%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge: cray-netcdf
+        buildable: False
+    hdf5:
+        paths:
+            hdf5@1.8.14%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-hdf5
+            hdf5@1.8.14%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge: cray-hdf5
+        buildable: False
+    all:
+        compiler: [gcc@5.2.0, intel@16.0.0.109]
+        providers:
+            mpi: [mpich, openmpi, intelmpi]ackages:
 
 Profiling
 ------------------