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Add more documentation fix arch spec

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Added more documentation for Spack on Cray. Also fixed the architecture
spec to be linux-debian7-x86_64 since it was reversed in the previous
commit.
This commit is contained in:
Mario Melara 2016-06-30 16:59:36 -07:00
parent 26325fe812
commit d784d561fc
1 changed files with 185 additions and 85 deletions
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270
lib/spack/docs/basic_usage.rst
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@ -114,13 +114,13 @@ that the packages is installed:
$ spack install mpileaks
==> Installing mpileaks
==> 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.
==> mpich is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4.
==> callpath is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/callpath@1.0.2-5dce4318.
==> adept-utils is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/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=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.
==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-debian7-x86_64-59f6ad23/mpileaks-1.0.tar.gz
==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-debian7-x86_64-59f6ad23.
==> 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/linux-x86_64-debian7/gcc@4.4.7/mpileaks@1.0-59f6ad23
[+] /home/gamblin2/spack/opt/linux-debian7-x86_64/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.
-- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
-- linux-debian7-x86_64 / 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
-- linux-x86_64-debian7 / gcc@4.9.2 --------------------------------
-- linux-debian7-x86_64 / 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.
-- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
-- linux-debian7-x86_64 / 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.
-- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
-- linux-debian7-x86_64 / 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.
-- 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
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
ImageMagick@6.8.9-10 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/ImageMagick@6.8.9-10-4df950dd
adept-utils@1.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/adept-utils@1.0-5adef8da
atk@2.14.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/atk@2.14.0-3d09ac09
boost@1.55.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/boost@1.55.0
bzip2@1.0.6 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/bzip2@1.0.6
cairo@1.14.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/cairo@1.14.0-fcc2ab44
callpath@1.0.2 /home/gamblin2/spack/opt/linux-debian7-x86_64/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
-- 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
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
libelf@0.8.11 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.11
libelf@0.8.12 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.12
libelf@0.8.13 /home/gamblin2/spack/opt/linux-debian7-x86_64/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:
-- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
-- linux-debian7-x86_64 / 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.
-- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
libdwarf@20130729-d9b90962
We can also search for packages that have a certain attribute. For example,
@ -359,6 +359,7 @@ will find every installed package with a 'debug' compile-time option enabled.
The full spec syntax is discussed in detail in :ref:`sec-specs`.
.. _compiler-config:
Compiler configuration
-----------------------------------
@ -445,7 +446,7 @@ If you want to see specifics on a particular compiler, you can run
fc = /usr/local/bin/ifort-15.0.090
This shows which C, C++, and Fortran compilers were detected by Spack.
Notice also that we didn't have to be too specific about the
Notice also that we didn\'t have to be too specific about the
version. We just said ``intel@15``, and information about the only
matching Intel compiler was displayed.
@ -472,27 +473,6 @@ Each compiler configuration in the file looks like this::
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``::
@ -538,10 +518,10 @@ Spack, that descriptor is called a *spec*. Spack uses specs to refer
to a particular build configuration (or configurations) of a package.
Specs are more than a package name and a version; you can use them to
specify the compiler, compiler version, architecture, compile options,
and dependency options for a build. In this section, we'll go over
and dependency options for a build. In this section, we\'ll go over
the full syntax of specs.
Here is an example of a much longer spec than we've seen thus far::
Here is an example of a much longer spec than we\'ve seen thus far::
mpileaks @1.2:1.4 %gcc@4.7.5 +debug -qt arch=bgq_os ^callpath @1.1 %gcc@4.7.2
@ -778,20 +758,18 @@ in gnu autotools. If all flags are set, the order is
Architecture specifiers
~~~~~~~~~~~~~~~~~~~~~~~
The architecture specifier looks identical to a variant specifier for a
non-boolean variant. The architecture can be specified by using the reserved
words ``target`` and/or ``os`` (``target=x86-64 os=debian7``).
The architecture can be specified by using the reserved
words ``target`` and/or ``os`` (``target=x86-64 os=debian7``). You can also
use the triplet form of platform, operating system and processor.
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``)
.. code-block:: sh
spack install libelf arch=cray_xc-CNL10-haswell
Users on non-Cray systems won't have to worry about specifying the architecture.
Spack will autodetect what kind of operating system is on your machine as well
as the processor. For more information on how the architecture can be
used on Cray machines, check here :ref:`spack-cray`
.. _sec-virtual-dependencies:
@ -1011,7 +989,7 @@ of installed packages.
$ module avail
------- /home/gamblin2/spack/share/spack/modules/linux-x86_64-debian7 --------
------- /home/gamblin2/spack/share/spack/modules/linux-debian7-x86_64 --------
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
@ -1082,7 +1060,7 @@ 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/linux-x86_64-debian7/gcc@4.4.7/mpich@3.0.4/bin/mpicc
~/src/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4/bin/mpicc
Or, similarly with modules, you could type:
@ -1115,8 +1093,8 @@ 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=linux-x86_64-debian7
libelf@0.8.13%intel@15.0.0 arch=linux-x86_64-debian7
libelf@0.8.13%gcc@4.4.7 arch=linux-debian7-x86_64
libelf@0.8.13%intel@15.0.0 arch=linux-debian7-x86_64
You can either type the ``spack load`` command again with a fully
qualified argument, or you can add just enough extra constraints to
@ -1496,7 +1474,7 @@ an *extension*. Suppose you have Python installed like so:
$ spack find python
==> 1 installed packages.
-- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
python@2.7.8
.. _spack-extensions:
@ -1509,7 +1487,7 @@ 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=linux-x86_64-debian7-703c7a96
==> python@2.7.8%gcc@4.4.7 arch=linux-debian7-x86_64-703c7a96
==> 36 extensions:
geos py-ipython py-pexpect py-pyside py-sip
py-basemap py-libxml2 py-pil py-pytz py-six
@ -1521,7 +1499,7 @@ You can find extensions for your Python installation like this:
py-h5py py-numpy py-pyqt py-shiboken
==> 12 installed:
-- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
-- linux-debian7-x86_64 / 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
@ -1537,8 +1515,8 @@ prefixes, and you can see this with ``spack find -p``:
$ spack find -p py-numpy
==> 1 installed packages.
-- 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
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
py-numpy@1.9.1 /g/g21/gamblin2/src/spack/opt/linux-debian7-x86_64/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``:
@ -1599,9 +1577,9 @@ installation:
.. code-block:: sh
$ spack activate py-numpy
==> 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.
==> Activated extension py-setuptools@11.3.1%gcc@4.4.7 arch=linux-debian7-x86_64-3c74eb69 for python@2.7.8%gcc@4.4.7.
==> Activated extension py-nose@1.3.4%gcc@4.4.7 arch=linux-debian7-x86_64-5f70f816 for python@2.7.8%gcc@4.4.7.
==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=linux-debian7-x86_64-66733244 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
@ -1616,7 +1594,7 @@ packages listed as activated:
.. code-block:: sh
$ spack extensions python
==> python@2.7.8%gcc@4.4.7 arch=linux-x86_64-debian7-703c7a96
==> python@2.7.8%gcc@4.4.7 arch=linux-debian7-x86_64-703c7a96
==> 36 extensions:
geos py-ipython py-pexpect py-pyside py-sip
py-basemap py-libxml2 py-pil py-pytz py-six
@ -1628,14 +1606,14 @@ packages listed as activated:
py-h5py py-numpy py-pyqt py-shiboken
==> 12 installed:
-- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
-- linux-debian7-x86_64 / 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:
-- linux-x86_64-debian7 / gcc@4.4.7 --------------------------------
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
py-nose@1.3.4 py-numpy@1.9.1 py-setuptools@11.3.1
@ -1664,7 +1642,7 @@ dependencies, you can use ``spack activate -f``:
.. code-block:: sh
$ spack activate -f py-numpy
==> 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-numpy@1.9.1%gcc@4.4.7 arch=linux-debian7-x86_64-66733244 for python@2.7.8%gcc@4.4.7.
.. _spack-deactivate:
@ -1736,18 +1714,140 @@ This issue typically manifests with the error below:
A nicer error message is TBD in future versions of Spack.
.. _spack-cray:
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>
Spack differs slightly when used on a Cray system. The architecture spec
can differentiate between the front-end and back-end processor and operating system.
For example, on Edison at NERSC, the back-end target processor
is \"Ivy Bridge\", so you can specify to use the back-end this way:
.. code-block:: sh
spack install zlib target=ivybridge
You can also use the operating system to build against the back-end:
.. code-block:: sh
spack install zlib os=CNL10
Notice that the name includes both the operating system name and the major
version number concatenated together.
Alternatively, if you want to build something for the front-end,
you can specify the front-end target processor. The processor for a login node
on Edison is \"Sandy bridge\" so we specify on the command line like so:
.. code-block:: sh
spack install zlib target=sandybridge
And the front-end operating system is:
.. code-block:: sh
spack install zlib os=SuSE11
Cray compiler detection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Spack can detect compilers using two methods. For the front-end, we treat
everything the same. The difference lies in back-end compiler detection.
Back-end compiler detection is made via the Tcl 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 (i.e. cc, CC, ftn). During build time, Spack will load
the correct PrgEnv and compiler module and will call appropriate wrapper.
The compilers.yaml config file will also differ. There is a
modules section that is filled with the compiler\'s Programming Environment
and module name. On other systems, this field is empty []::
...
- compiler:
modules:
- PrgEnv-intel
- intel/15.0.109
...
As mentioned earlier, the compiler paths will 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
...
As opposed to an explicit path to the compiler executable. This allows Spack
to call the Cray compiler wrappers during build time.
For more on compiler configuration, check out :ref:`compiler-config`.
Setting defaults and using Cray modules
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If you want to use default compilers for each PrgEnv and also be able
to load cray external modules, you will need to set up a packages.yaml.
Here\'s an example of an external configuration for cray modules:
.. code-block:: yaml
packages:
mpi:
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
This tells Spack that for whatever package that depends on mpi, load the
cray-mpich module into the environment. You can then be able to use whatever
environment variables, libraries, etc, that are brought into the environment
via module load.
You can set the default compiler that Spack can use for each compiler type.
If you want to use the Cray defaults, then set them under *all:* in packages.yaml.
In the compiler field, set the compiler specs in your order of preference.
Whenever you build with that compiler type, Spack will concretize to that version.
Here is an example of a full packages.yaml used at NERSC
.. code-block:: yaml
packages:
mpi:
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:
modules:
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]
Here we tell spack that whenever we want to build with gcc use version 5.2.0 or
if we want to build with intel compilers, use version 16.0.0.109. We add a spec
for each compiler type for each cray modules. This ensures that for each
compiler on our system we can use that external module.
For more on external packages check out the section :ref:`sec-external_packages`.
Getting Help
-----------------------