=========================
Download and Installation
=========================

**WARNING:** The Dacapo code is **not being maintained any longer** and should not be used for any new projects!
The Dacapo code download server no longer exists.

.. contents::
.. section-numbering::

Requirements
============

The new `ASE version 3 <https://wiki.fysik.dtu.dk/ase>`_ package, unless you have a very good reason for using the old ASE version 2.

**Warning** due to the unmaintained `Numeric <http://sourceforge.net/projects/numpy/files/Old%20Numeric/>`_ package, ASE2 does not work on 64-bit systems with python version > 2.4.
If this is you case please use the `jacapo` interface from the new `ase <https://wiki.fysik.dtu.dk/ase>`_ package.

If you already have an installation of the old `ASE2 <https://wiki.fysik.dtu.dk/ase2>`_ package, it is enough just installing the `Dacapo Python interface`_.

Installation
============

Installation of prebuilt binaries
----------------------------------

**Preferably** install as RPM/deb. Configure the repositories `<https://wiki.fysik.dtu.dk/ase/download.html#installation-with-package-manager-on-linux>`_
and install the **dacapo** package using your distribution package manager.
On Debian/Ubuntu you may need additionally to set the `DACAPOPATH`, `DACAPOEXE_SERIAL` and `DACAPOEXE_PARALLEL` variables.

**No** further steps are necessary, please stop reading now!

If installing manually on Ubuntu see old instructions https://listserv.fysik.dtu.dk/pipermail/campos/2010-June/002635.html

If you prefer to install from tarballs
the next section describes how the fortran program, pseudopotentials and python interface can be installed.

Dacapo fortran program and pseudopotentials
-------------------------------------------

This section describes how the fortran program and pseudopotential are installed.

From svn
--------

**WARNING:** The Dacapo code download server no longer exists.

This is the recommended method.
The commands below will fetch the whole dacapo fortran and python source, and pseudopotentials::

  cd
  svn checkout https://USER@svn.fysik.dtu.dk/projects/dacapo/trunk dacapo

where "USER@" part has to be skipped for anonymous access.

Alternatively, get the tar-ball (usually slightly outdated) here: `campos-dacapo`_.

Only for a reference the `Dacapo tar file`_ contains the ``2.7.7`` version.

.. _campos-dacapo: http://wiki.fysik.dtu.dk/dacapo-files/campos-dacapo-2.7.16.tar.gz

.. _Dacapo tar file: http://wiki.fysik.dtu.dk/dacapo-files//Dacapo-2.7.7.tar.gz

From RPM
--------

Preferably install as RPMS: see `Configure fys yum repository <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#configure-fys-yum-repository>`_.

**Warning**: the section below is outdated, please ignore it.

A pretty outdated Dacapo 2.7.7 `binary RPM`_ (tested and built using Pentium 4) can be used to install Dacapo on a Pentium 4 system.

.. _binary RPM: http://dcwww.camp.dtu.dk/campos/download/Dacapo-2.7.7-0.1.i386.rpm

This will install pseudopotentials in ``/usr/share/dacapo/psp`` and binary executables in ``/usr/bin``.


Dacapo binaries for different platforms
---------------------------------------

**Warning**: this section is outdated, please ignore it.

The page `dacapo binaries`_ list dacapo binaries for different platforms.

.. _dacapo binaries: binaries.html

Compling the fortran source code
--------------------------------

Compile the Dacapo source code by::

   cd src
   gmake <arch>           # Serial version
   gmake <arch> MP=mpi    # Parallel MPI version

where ``<arch>`` is one of:

.. list-table::
  :widths: 2 5

  * - ``pglinux``
    - Portland Group (PGI) *pgf90* compiler on Linux
  * - ``intellinux`` 
    - Intel *ifort* Fortran compiler version >=9.0 and MKL on Linux
  * - ``pathscale`` 
    - Pathscale EKOpath *pathf90* compiler for AMD64 and EM64T
  * - ``itanium`` 
    - Intel *ifort* compiler version >=9.0 on SGI Itanium2 Linux
  * - ``intelmac`` 
    - Intel *ifort* Fortran compiler + MKL, >= 9.x on Mac OS X
  * - ``g95linux`` 
    - GNU *g95* compiler on Linux
  * - ``gfortran_fnosecond_underscore``
    - gcc-gfortran-4.1.1 compiler on CentOS
  * - ``gfortran_fsecond_underscore``
    -  gcc-gfortran-4.2.1 compiler on Ubuntu
  * - ``sun_ss10`` 
    - Sun sparcstation 10/20)
  * - ``ibm_power3`` 
    - RS/6000 power3 node
  * - ``ibm_power2_wide`` 
    - RS/6000 wide power2 node
  * - ``ibm_power2_thin`` 
    - RS/6000 thin/thin2 power2 node
  * - ``sgi`` 
    - Silicon Graphics n32 ABI
  * - ``alpha`` 
    - Compaq/Digital Alpha

It is important to use the GNU ``gmake`` command on many UNIX systems, in stead of the
system's own ``make`` command which may be incompatible with our Makefile.

Please see also the `Notes for installation on specific computers`_ below.


Installing the pseudopotentials
-------------------------------

Get the pseudopotentials tar-ball here:  `campos-dacapo-pseudopotentials`_

.. _campos-dacapo-pseudopotentials: http://wiki.fysik.dtu.dk/dacapo-files/campos-dacapo-pseudopotentials-2.tar.gz

The dacapo fortran program adds the enviroment variable ``DACAPOPATH`` to the pseudopotential filename 
(if the file is not found in the current working directiory).
Copy all pseudopotentials to a directory and set the ``DACAPOPATH`` environment variable to this directory::

    cp *.pseudo /some/directory/
    setenv DACAPOPATH /some/directory/

Pseudopotential data files
--------------------------

Dacapo uses the `Vanderbilt ultra-soft pseudopotentials <http://www.physics.rutgers.edu/~dhv/uspp/>`_
which are read in from binary data files.
It is important to compile Dacapo and NetCDF with appropriate compiler flags to enable 
*fortran unformatted IEEE big-endian* data files.
Please consult this `note from Vanderbilt <http://www.physics.rutgers.edu/~dhv/uspp/uspp-736/Doc/FORMAT>`_.

Big-endian I/O is enabled in various compilers with compiler flags as follows:

 * **gfortran compiler:** ``-fconvert=big-endian -frecord-marker=4``

 * **Pathscale compiler:** ``-byteswapio``

 * **PGI compiler:** ``-byteswapio``

 * **Intel compiler:** ``-convert big_endian``

These flags should already be set in the Dacapo ``Makefile``.

Dacapo Python interface
-----------------------

**Warning** due to the unmaintained `Numeric <http://sourceforge.net/projects/numpy/files/Old%20Numeric/>`_ package, the Dacapo Python interface (as ASE 2) does not work on 64-bit systems with python version > 2.4.
If this is you case please ignore this section and use the dacapo interface from the new `ase <https://wiki.fysik.dtu.dk/ase>`_ package.

1) Get the latest version of the dacapo python interface by either of these two methods:

   a) svn (the commands below will fetch the whole dacapo fortran and python source, and pseudopotentials)::

        cd
        svn checkout https://USER@svn.fysik.dtu.dk/projects/dacapo/trunk dacapo
        cd dacapo/Python

   where "USER@" part has to be skipped for anonymous access.


   b) alternatively, get the tar-ball (usually slightly outdated) here: `Dacapo-0.9.4`_.

.. _Dacapo-0.9.4: http://wiki.fysik.dtu.dk/dacapo-files/Dacapo-0.9.4.tar.gz

2) Install with the standard setup.py script (if you have root permission)::

     python setup.py install

   If you do not have *root permission* use::

     python setup.py install --prefix=/some/where/in/your/path

   In this latter case you must set your ``PYTHONPATH`` environment variable,
   as directed by the ``setup.py`` script.

3) Alternative to step 2: Simply set the ``PYTHONPATH`` environment variable to your ``svn`` directory,
i.e. ${HOME}/dacapo/Python if you followed step 1.2).

==========================
Running Dacapo in parallel
==========================

Dacapo can run in parallel using the MPI parallel library. 
You need to compile a parallel executable:: 

    gmake <arch> MP=mpi

For getting dacapo to work in parallel with ASE you need to make a script 
`dacapo.run`, which should be executable and in your path. 
The `jacapo project <https://svn.fysik.dtu.dk/projects/ase/trunk/ase/calculators/jacapo/tools>`_
provides an example of such a script. PBS, Sun grid engine, and LoadLeveler batch systems are supported.

.. _LAM/MPI:  http://www.lam-mpi.org/
.. _Torque/PBS: http://www.clusterresources.com/pages/products/torque-resource-manager.php

OpenMPI
=======

For dacapo to run together with ASE_ you need a `dacapo.run` script in your path, that will 
start the correct dacapo executable. This `OpenMPI dacapo.run`_ script assumes you are running OpenMPI 
using the *Torque/PBS* batch system. 

.. _OpenMPI dacapo.run: http://dcwww.camp.dtu.dk/campos/download/dacapo_openmpi.run
.. _ASE: https://wiki.fysik.dtu.dk/ase

You might have to edit the location and names of the serial and parallel executable in this script, 
i.e the lines:: 

    # Name of serial and parallel DACAPO executables
    DACAPOEXE="dacapo_2.7.7.run"
    DACAPOEXE_PAR="dacapo_2.7.7_mpi.run"

If OpenMPI is not installed under ``/usr`` you will also have to change this in the script. 
    
Copy this script to ``/usr/local/bin/dacapo.run``.

============================================
Notes for installation on specific computers
============================================

Dacapo can be built on a large number of different systems and compilers.
This portability has been evolving over the years, and the supported systems are displayed by the command ``make`` in the
top level source code directory.
Below we give specific instructions for some systems which we actively use at our site.

If you would like to contribute new entries to the ``Makefile``, correct errors, or add complete instructions
for a new platform to the present Wiki page, please send an E-mail to support@fysik.dtu.dk.

If you would like to see how we install Dacapo etc. on our Niflheim Linux cluster and how we build RPM 
packages, please consult the `Niflheim Wiki <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS>`_.

**Note**: the most commond compilation/linking problem concerns using of incorrect underscoring convention,
when lot's of **undefined reference** errors appear, like::

  ../netcdf/gfortran_fsecond_underscore/netcdfinterface.o: In function `__netcdfinterface_MOD_local_error_handler': netcdfinterface.F:(.text+0xa3b): undefined reference to `nf_strerror__'

Please check your underscoring convention as described in this `post <https://listserv.fysik.dtu.dk/pipermail/ase-users/2009-September/000362.html>`_.

Opteron (gfortran compiler)
===========================

This build assumes you have the 
`ACML Math library <http://developer.amd.com/acml.aspx>`_ installed.
Below follows details on how to build the MPI, NetCDF and FFTW libraries needed by dacapo. 

NetCDF (Network common Data Format)
-----------------------------------

Download the `NetCDF software <http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_1/index.jsp>`_
and read the `NetCDF installation instructions <http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-install.html#Platform-Specific-Notes>`_.
NetCDF version 3.6.1 or later is supported.

Build netcdf like this::

   tar -zxf netcdf-3.6.1.tar.gz
   cd netcdf-3.6.1/src
   ./configure --prefix=/usr/local/netcdf3-3.6.1-1.gfortran \
               FC=gfortran FCFLAGS=-O2 CC=gcc CXX=c++ CPPFLAGS='-DNDEBUG -DpgiFortran -fPIC"'
   make

and then install running as root:: 

   make install

See also `niflheim note <https://wiki.fysik.dtu.dk/niflheim/Cluster_software#netcdf-network-common-data-form>`_ on building
a netcdf RPM.

FFTW (Fast Fourier Transform library)
-------------------------------------

Download version 2.1.5 `here <http://www.fftw.org/fftw-2.1.5.tar.gz>`_
Build FFTW like this:: 

  tar -zxf fftw-2.1.5.tar.gz
  cd fftw-2.1.5
  ./configure --prefix=/usr/local/fftw2-2.1.5-1.gfortran \
              F77=gfortran CC=gcc CFLAGS=-O3 FFLAGS=-O3 --enable-shared --enable-threads
  make 

and then as root:: 

  make install

OpenMPI
-------

`OpenMPI <http://www.open-mpi.org>`_ is an open source implementation of the MPI message passing standard.
Configure OpenMPI with::

  ./configure --prefix=/usr/local/openmpi-1.2.7.gfortran --with-tm=/usr/local FC=gfortran F77=gfortran CC=gcc CXX=g++ \
              FFLAGS=-O2 FCFLAGS=-O2 CFLAGS=-O2 CXXFLAGS=-O2

The flag ``--with-tm=/usr/local`` is used only with the Torque/PBS batch system (version 2.1 or later)
and enables Torque's very fast *Task Manager* startup of MPI processes.


Dacapo
------

Get dacapo `From svn`_, and go to `src` directory::

     cd dacapo/src
  
Set the environment variables for blas/lapack, NETCDF, and FFTW, for example:: 

     setenv BLASLAPACK "-L/opt/acml-4.0.1/gfortran64/lib -lacml -L/opt/acml-4.0.1/gfortran64/lib -lacml -lgfortran"
     setenv NETCDF /usr/local/netcdf3-3.6.1-1.gfortran/lib64
     setenv FFTW /usr/local/fftw2-2.1.5-1.gfortran/lib64

**Warning**: if you use netcdf >= 3.6.2 (which has fortran interface in libnetcdff.a) you need to modify the BLASLAPACK variable, for example::

    setenv BLASLAPACK "/usr/local/netcdf3-3.6.2-1.gfortran/lib64 -lnetcdff -lnetcdf -L/opt/acml-4.0.1/gfortran64/lib -lacml -L/opt/acml-4.0.1/gfortran64/lib -lacml -lgfortran"

Select the location of the MPI library which you want to use::

     setenv MPIDIR /usr/local/openmpi-1.2.7.gfortran
     setenv MPI_LIBDIR ${MPIDIR}/lib64
     setenv MPI_BINDIR ${MPIDIR}/bin
     setenv MPI_INCLUDEDIR ${MPIDIR}/include

Check the underscore convention:

 - netcdf < 3.6.2::

     nm ${NETCDF}/libnetcdf.a | grep "T nf_strerror_"

 - netcdf >= 3.6.2::

     nm ${NETCDF}/libnetcdff.a | grep "T nf_strerror_"

Perform the check also on the `${FFTW}/libfftw.a` file.

Now compile dacapo with correct underscoring convention (serial and parallel):: 

     make gfortran_fnosecond_underscore
     make gfortran_fnosecond_underscore MP=mpi 

Ignore warnings about type mismatch when compiling ``ms.F``, 
this is due to MPI expecting pointers to integer arrays for all data types.
 
Now copy the compiled executables to somewhere on your path, e.g.:: 

    cp gfortran_fnosecond_underscore_serial/dacapo.run /usr/local/bin/dacapo_<version>.run 
    cp gfortran_fnosecond_underscore_mpi/dacapo.run /usr/local/bin/dacapo_<version>_mpi.run


Opteron (Pathscale EKOpath compiler)
====================================

This build assumes you have the 
`Pathscale EKOpath Fortran compiler <http://www.pathscale.com/ekopath.html>`_ and the 
`ACML Math library <http://developer.amd.com/acml.aspx>`_ installed.
Below follows details on how to build the NetCDF and FFTW libraries needed by dacapo. 

NetCDF (Network common Data Format)
-----------------------------------

Download the `NetCDF software <http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_1/index.jsp>`_
and read the `NetCDF installation instructions <http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-install.html#Platform-Specific-Notes>`_.
NetCDF version 3.6.1 or later is supported.

Build netcdf like this::

   tar -zxf netcdf-3.6.1.tar.gz
   cd netcdf-3.6.1/src
   ./configure --prefix=/usr/local/netcdf3-3.6.1-1.pathscale \
               FC=pathf90 FCFLAGS=-byteswapio CC=pathcc CXX=pathCC CPPFLAGS='-DNDEBUG -DpgiFortran -fpic'
   make

and then install in /usr running as root:: 

   make install

See also `niflheim note <https://wiki.fysik.dtu.dk/niflheim/Cluster_software#netcdf-network-common-data-form>`_ on building
a netcdf RPM.

FFTW (Fast Fourier Transform library)
-------------------------------------

Download version 2.1.5 `here <http://www.fftw.org/fftw-2.1.5.tar.gz>`_
Build FFTW like this:: 

  tar -zxf fftw-2.1.5.tar.gz
  cd fftw-2.1.5
  ./configure --prefix=/usr/local/fftw2-2.1.5-1.pathscale \
              F77=pathf90 CC=pathcc CFLAGS=-O3 FFLAGS="-O3 --enable-shared --enable-threads"
  make 

and then as root:: 

  make install

OpenMPI
-------

`OpenMPI <http://www.open-mpi.org>`_ is an open source implementation of the MPI message passing standard.
Configure OpenMPI with::

  ./configure --prefix=/usr/local/openmpi-1.2.7.pathscale --with-tm=/usr/local \
              FC=pathf90 F77=pathf90 CC=pathcc CXX=pathCC \
              FFLAGS=-O2 FCFLAGS=-O2 CFLAGS=-O2 CXXFLAGS=-O2

The flag ``--with-tm=/usr/local`` is used only with the Torque/PBS batch system (version 2.1 or later)
and enables Torque's very fast *Task Manager* startup of MPI processes.


Dacapo
------

Get dacapo `From svn`_, and go to `src` directory::

     cd dacapo/src
  
Set the environment variables for blas/lapack, NETCDF, and FFTW, for example:: 

     setenv BLASLAPACK "-L/opt/acml-4.0.1/pathscale64/lib -lacml -L/opt/acml-4.0.1/pathscale64/lib -lacml -lgfortran"
     setenv NETCDF /usr/local/netcdf3-3.6.1-1.pathscale/lib64
     setenv FFTW /usr/local/fftw2-2.1.5-1.pathscale/lib64

Select the location of the MPI library which you want to use::

     setenv MPIDIR /usr/local/openmpi-1.2.7.pathscale
     setenv MPI_LIBDIR ${MPIDIR}/lib64
     setenv MPI_BINDIR ${MPIDIR}/bin
     setenv MPI_INCLUDEDIR ${MPIDIR}/include

Alternative locations may be specified, for example::

     setenv MPIDIR /usr/local/infinipath-2.0

Now compile dacapo (serial and parallel):: 

     make pathscale 
     make pathscale MP=mpi 

Ignore warnings about type mismatch when compiling ``ms.F``, 
this is due to MPI expecting pointers to integer arrays for all data types.
 
Now copy the compiled executables to somewhere on your path, e.g.:: 

    cp pathscale_serial/dacapo.run /usr/local/bin/dacapo_<version>.run 
    cp pathscale_mpi/dacapo.run /usr/local/bin/dacapo_<version>_mpi.run

Portland Group (PGI) compiler
=============================

Here we will build using the Portland Group's `PGI Workstation <http://www.pgroup.com/products/workpgi.htm>`_
version 6.2-4 Fortran compiler, and the MKL library.
 

NetCDF (Network common Data Format)
-----------------------------------

Download the `NetCDF software <http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_1/index.jsp>`_
and read the `NetCDF installation instructions <http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-install.html#Platform-Specific-Notes>`_.
NetCDF version 3.6.1 or later is supported.

Build netcdf like this::

   tar -zxf netcdf-3.6.1.tar.gz
   cd netcdf-3.6.1/src
   ./configure --prefix=/usr/local/netcdf3-3.6.1-1.pgi \
               FC=pgf90 FCFLAGS='-byteswapio -Msecond_underscore' CC=pgcc CXX=pgCC CPPFLAGS='-DNDEBUG -DpgiFortran'
   make

and then install as the *root* superuser:: 

   make install

FFTW (Fast Fourier Transform library)
-------------------------------------

Download `FFTW version 2.1.5 <http://www.fftw.org/fftw-2.1.5.tar.gz>`_ and build FFTW like this:: 

  tar -zxf fftw-2.1.5.tar.gz
  cd fftw-2.1.5
  ./configure --prefix=/usr/local/fftw2-2.1.5-1.pgi \
              F77=pgf90 CC=pgcc CFLAGS=-O3 FFLAGS="-O3 --enable-shared --enable-threads -Msecond_underscore"
  make 

and then install as the *root* superuser:: 

   make install


LAM-MPI
-------

**Warning**: These instructions are **outdated**.

We will here use the MPI library `LAM-MPI <http://www.lam-mpi.org/>`_

Download the `tarfile <http://www.lam-mpi.org/download/files/lam-7.1.2.tar.gz>`_ and build LAM-MPI 
for installation in ``/usr/local/lam-7.1.2-pgi`` and with the *ssh* remote-shell command, using:: 

   tar xzvf lam-7.1.2.tar.gz  
   cd lam-7.1.2
   setenv CPPFLAGS '-DNDEBUG -Df2cFortran'
   setenv F77 pgf90
   setenv FC  pgf90
   setenv FFLAGS '-byteswapio -Msecond_underscore'
   ./configure --prefix=/usr/local/lam-7.1.2-pgi/ --with-rsh="/usr/bin/ssh -a -x" CPPFLAGS='-DNDEBUG -Df2cFortran'  F77=pgf90 FC=pgf90  FFLAGS='-byteswapio -Msecond_underscore'
   make

and then install as the *root* superuser:: 

   make install

OpenMPI
-------

Alternatively to LAM-MPI, you may want to use OpenMPI.

`OpenMPI <http://www.open-mpi.org>`_ is an open source implementation of the MPI message passing standard.
Configure OpenMPI with::

  ./configure --prefix=/usr/local/openmpi-1.2.7.pgi --with-tm=/usr/local FC=pgf90 F77=pgf90 CC=pgcc CXX=pgCC \
              FFLAGS=-Msignextend FCFLAGS=-Msignextend \
              --with-wrapper-fflags=-Msignextend --with-wrapper-fcflags=-Msignextend"

The flag ``--with-tm=/usr/local`` is used only with the Torque/PBS batch system (version 2.1 or later)
and enables Torque's very fast *Task Manager* startup of MPI processes.

Dacapo
------

Get dacapo `From svn`_, and go to `src` directory::

     cd dacapo/src

Set the environment variables to use specific versions of LAPACK and BLAS::

   setenv BLASLAPACK '-L/opt/intel/mkl/9.0/lib/64 -lmkl_lapack -lmkl_ia64 -lguide -lpthread -lmkl'

and for 32 bit machines::

   setenv BLASLAPACK '-L/opt/intel/mkl/9.0/lib/32 -lmkl_lapack -lmkl_ia32 -lguide -lpthread -lmkl'

Also remember to set variables for where to find netCDF, FFTW::

     setenv NETCDF /usr/local/netcdf3-3.6.1-1.pgi/lib64
     setenv FFTW /usr/local/fftw2-2.1.5-1.pgi/lib64

Select the location of the MPI library which you want to use::

     setenv MPIDIR /usr/local/openmpi-1.2.7.pgi
     setenv MPI_LIBDIR ${MPIDIR}/lib64
     setenv MPI_BINDIR ${MPIDIR}/bin
     setenv MPI_INCLUDEDIR ${MPIDIR}/include

and compile like:: 

   make pglinux 
   make pglinux MP=mpi


Running Dacapo
--------------

If you get a runtime error from Dacapo similar to this one::

  relocation error: /usr/pgi/linux86/6.2/lib/libpthread.so.0: symbol _h_errno, version GLIBC_2.0 not defined in file libc.so.6 with link time reference

then this may possibly be a `problem with the PGI compiler installation <http://www.pgroup.com/userforum/viewtopic.php?t=207>`_.
You can use ``ldd dacapo.run`` to examine which shared libraries are needed, and if ``libpthread.so.0``
in the ``/usr/pgi`` tree is referenced, the recommended solution is to remove the soft-link 
``/usr/pgi/linux86/6.2/lib/libpthread.so.0`` (or whatever version you have).

Intel compiler
==============

The Intel Fortran and C/C++ compilers are installed on Intel CPUs such as Pentium-4, Xeon, Itanium etc.
The Intel MKL library contains highly optimized BLAS subroutines, among many other things.
It is strongly recommended that you use the latest version of the Intel compilers,
since many bugs in the past have caused a number of problems for Dacapo and other software packages.

Homepages: `Intel Fortran <http://developer.intel.com/software/products/compilers/flin/index.htm>`_
and `Intel C++ <http://developer.intel.com/software/products/compilers/clin/index.htm>`_
Compiler version 9.1.

Manuals in PDF format are in the 
`Intel Fortran guide <http://developer.intel.com/software/products/compilers/techtopics/for_ug_lnx.pdf>`_
and the `Intel C++ guide <http://developer.intel.com/software/products/compilers/techtopics/c_ug_lnx.pdf>`_.

Intel Math Kernel Library (MKL)
-------------------------------

The `Intel Math Kernel Library <http://developer.intel.com/software/products/mkl/>`_ (MKL) Version 9.0
with `MKL Manuals <http://developer.intel.com/software/products/mkl/docs/manuals.htm>`_.
A `MKL User Forum <http://softwareforums.intel.com/ids/board?board.id=MKL>`_
for the Intel Math Kernel Library is available.

MKL 9.0 contains may of the libraries required by Dacapo: 
`BLAS, LAPACK <,http://www.intel.com/cd/software/products/asmo-na/eng/266858.htm>`_
and `FFTW <http://www.intel.com/cd/software/products/asmo-na/eng/266852.htm>`_ 
(see `these notes <http://www.intel.com/software/products/mkl/docs/fftw_mkl_user_notes_2.htm>`_).

The FFTW library must be manually built (by the *root* superuser) according to the notes
`FFTW2.x to Intel(R) Math Kernel Library Wrappers <http://www.intel.com/software/products/mkl/docs/fftw2xmkl_notes.htm>`_.
For example, if MKL is installed in ``/opt/intel/mkl/9.0``,
the 32-bit FFTW library is built like this::

  cd /opt/intel/mkl/9.0/interfaces/fftw2xf
  make lib32

Now FFTW can be linked in using these loader flags::

  -L/opt/intel/mkl/9.0/lib/32 -lfftw2xf_intel

NetCDF (Network common Data Format)
-----------------------------------

Download the `NetCDF software <http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_1/index.jsp>`_
and read the `NetCDF installation instructions <http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-install.html#Platform-Specific-Notes>`_.
NetCDF version 3.6.1 or later is supported.

Build netcdf like for the Intel compiler with::

   tar -zxf netcdf-3.6.1.tar.gz
   cd netcdf-3.6.1/src
   ./configure --prefix=/usr/local/netcdf3-3.6.1-1.intel \
               FC=ifort CC=icc CXX=icpc CPPFLAGS='-DNDEBUG -DpgiFortran'
   make check

If make check fails with errors "Numeric conversion not representable" add the following flags
(see `<http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg02387.html>`_)::

   CFLAGS='-mp' FFLAGS='-mp'

FFTW (Fast Fourier Transform library)
-------------------------------------

The Intel MKL version of FFTW should be used as discussed above.

However, if for some reason you're unable to use MKL's FFTW, you should configure the FFTW library build with::

  ./configure --prefix=/usr/local/fftw2-2.1.5-1.intel \
              F77=ifort CC=icc CFLAGS=-O3 FFLAGS="-O3 --enable-shared --enable-threads"

OpenMPI
-------

Get the latest version source tar file from `OpenMPI <http://www.open-mpi.org>`_. 
You **must** use the Intel C++ compiler version October 5, 2006 (build 44) or later, see
`an OpenMPI FAQ <http://www.open-mpi.org/faq/?category=troubleshooting#intel-c++-9.1-compiler>`_.
(Note added: OpenMPI version 1.1.4 has a workaround for this bug, see the
`Release Notes <http://www.open-mpi.org/community/lists/announce/2007/01/0009.php>`_).

Configure OpenMPI with::

  ./configure --prefix=/usr/local/openmpi-1.2.7.intel --with-tm=/usr/local FC=ifort F77=ifort CC=icc CXX=icpc \
              FFLAGS=-O2 FCFLAGS=-O2 CFLAGS=-O2 CXXFLAGS=-O2
              

The flag ``--with-tm=/usr/local`` is used only with the Torque/PBS batch system (version 2.1 or later)
and enables Torque's very fast *Task Manager* startup of MPI processes.


Dacapo
------

You **must** use the Intel compiler version 9.1 (or later).  If you use older versions of the compiler,
bugs will give you a lot of troubles.

Get dacapo `From svn`_, and go to `src` directory::

     cd dacapo/src

Edit the ``Makefile`` section named ``intellinux`` if you want to modify the compiler flags to generate optimal code for your
particular Intel CPU, where the ``-x`` flag controls the code generation (see `man ifort <attachment:ifort.html>`_)::

  INTELLINUX_OPT = -O3 -xN

You should also select the Intel MKL library for your specific Intel CPU architecture::

   setenv BLASLAPACK '-L/opt/intel/mkl/9.0/lib/64 -lmkl_lapack -lmkl_ia64 -lguide -lpthread -lmkl'

and for 32 bit machines::

   setenv BLASLAPACK '-L/opt/intel/mkl/9.0/lib/32 -lmkl_lapack -lmkl_ia32 -lguide -lpthread -lmkl'


Set the environment variables to use specific versions Netcdf, FFTW and MPI::

     setenv NETCDF /usr/local/netcdf3-3.6.1-1.intel/lib64
     setenv FFTW /usr/local/fftw2-2.1.5-1.intel/lib64

Select the location of the MPI library which you want to use::

     setenv MPIDIR /usr/local/openmpi-1.2.7.intel
     setenv MPI_LIBDIR ${MPIDIR}/lib64
     setenv MPI_BINDIR ${MPIDIR}/bin
     setenv MPI_INCLUDEDIR ${MPIDIR}/include

Now build Dacapo::

  make intellinux
  make intellinux MP=mpi  # Parallel version


Running Dacapo
--------------

The default process stacksize limit may cause unexpected crashes of *Dacapo* at the point when all available
stack space has been exhausted.
Often this can be seen as the txt output freezes around the line::

  WFG: Setup initial potential 

Therefore you must increase the resource limits before running *Dacapo*::

  ulimit -s unlimited        # bash shell
  limit stacksize unlimited  # tcsh shell

**Preferably** instead of ``unlimited`` you could enter a number such as ``500000`` (500 MB, the largest required value required so far) so that you do not 
exhaust your system resources, or in case your system prohibits ``unlimited`` stack size.

You can set such commands in your personal login scripts (``.bashrc`` or ``.tcshrc``)
or in any scripts used to run the *Dacapo* executable.

Performance
===========

Below the average runtime in seconds of the `memory benchmark <https://wiki.fysik.dtu.dk/gpaw/devel/benchmarks.html#memory-benchmark>`_
obtained with different compilers/libraries is given.

Benchmark is performed on a reserved node by running the following command::

  export OMP_NUM_THREADS=1
  ulimit -s 500000
  time numactl --membind=0 --physcpubind=1 python H2Al110.py --code=dacapo --runs=3 2>&1 | tee run.log

Using physical CPU number 1 with the memory node number 0 turned out to be the the fastest combination.
For description of `numa` see `NUMACTL <https://computing.llnl.gov/LCdocs/chaos/index.jsp?show=s5.2.2>`_
and `libnuma <http://oss.sgi.com/projects/libnuma/>`_.

**Note**: "fftw2" denotes `FFTW 2.1.5 <http://www.fftw.org/fftw-2.1.5.tar.gz>`_ 

Dual-socket dual Core AMD Opteron(tm) Processor 285/2.6 GHz/2 GB RAM per core
-----------------------------------------------------------------------------

Date: 27 May 2009

**Note**: **mkl** version **10.1.2.024** was used. Standard deviations are found below 5 sec. "**N/A**" denotes the fact
that libraries are not available, "**-**" that tests were not performed. The number of SCF steps is 16 in all cases.

============================== ======== ========== ======= ======= ====== ======
blas/lapack/fftw : compiler    gfortran gfortran43 amd4.2  pathf90 ifort  g95
============================== ======== ========== ======= ======= ====== ======
acml-4.2.0/acml-4.2.0/fftw2    N/A      1179.8     --      1140.1  1147.7 N/A
acml-4.1.0/acml-4.1.0/fftw2    N/A      --         --      1102.0  --     N/A
acml-4.1.0/acml-4.1.0/mkl      N/A      --         --      1051.4  --     N/A
acml-4.0.1/acml-4.0.1/fftw2    --       N/A        --      1165.7  --     N/A
blas-3.0-37/lapack-3.0-37/fftw 1484.7   1399.4     --      --      --     --
goto-1.26/acml-4.2.0/fftw2     N/A      1220.3     1288.2  1118.6  1125.6 N/A
goto-1.26/acml-4.2.0/mkl       N/A      1180.9     --      --      --     N/A
goto-1.26/acml-4.0.1/fftw2     1312.2   N/A        --      --      --     N/A
atlas-3.8.3/lapack-3.2.1/fftw  --       1235.3     --      --      --     1362.7
mkl/mkl/fftw                   --       1256.4     --      --      1153.0 --
mkl/mkl/mkl                    --       1209.5     --      --      --     --
============================== ======== ========== ======= ======= ====== ======

**Warning**: problems with pathscale/gfortran43: acml-4.1.0 and acml-4.2.0 have been reported.
Linking dacapo against fftw built with `pathf90 Version 3.2 2008-06-16` compiled with `-Ofast` fails.

**Note**: compilation options of fftw are important: for comparison: pathf90 Version 3.2 2008-06-16, acml-4.0.1/acml-4.0.1/fftw2, with fftw
compiled with "-O0" option (no optimizations) results in 1966.7 seconds.

================================== ============================ ============================
compiler                           options                      options for fftw
================================== ============================ ============================
gfortran 4.1.2 20080704            -O3 -funroll-all-loops       -O3 -funroll-all-loops
gfortran43 4.3.2 20081007          -O3 -funroll-all-loops       -O3 -funroll-all-loops
gfortran 4.2.0-amd-barcelona-rhel4 -O3 -funroll-all-loops       -O3 -funroll-all-loops
pathf90 Version 3.2 2008-06-16     -Ofast                       -O3 -OPT:Ofast -ffast-math
ifort 11.0 083                     -xHOST -O3 -ipo -no-prec-div -xHOST -O3 -ipo -no-prec-div
g95 0.91-4 gcc 4.0.3               -O3                          -O3
================================== ============================ ============================