The following are required to be installed before this code will work:
How to install everything is discussed below.
After the installation, you should be able to open a Python interpreter, and type:
import usadel1
If it doesn’t report errors (Traceback ...), installation was successful, and you can proceed to Scripting.
If you want to run tests for usadel1, go to tests/ directory and run:
test.py
Note that this will exercise most of the functionality, compare results to literature, and solve several “large” problems, and can take several hours to complete.
The most straightforward way to get all the prerequisites is to install either (both are free for academic use)
The former is bundled with C and Fortran 77/90 compilers, that is, all that you need. The latter is not, so you need to get compilers separately. I’d recommend using Python(x,y).
After the prerequisites are installed, edit install.bat and change the --fcompiler switch to match your Fortran compiler, and --compiler to match your C compiler (Python(x,y) comes with mingw32). Supported compiler choices are listed below.
Finally, run install.bat to compile and install the Usadel library.
Test if it works
Double-click on the sns_minigap_vs_phi.py script in the scripts subdirectory. It should start calculating the size of the minigap in an SNS junction.
Supported compilers
| F90 Compiler | |
|---|---|
| gnu95 | GNU Fortran recommended |
| absoft | Absoft Corp Fortran Compiler |
| compaq | Compaq Fortran Compiler |
| g95 | G95 Fortran Compiler |
| intel | Intel Fortran Compiler for 32-bit apps |
| intele | Intel Fortran Compiler for Itanium apps |
| intelem | Intel Fortran Compiler for EM64T-based apps |
| lahey | Lahey/Fujitsu Fortran 95 Compiler |
| nag | NAGWare Fortran 95 Compiler |
| pg | Portland Group Fortran Compiler |
| vast | Pacific-Sierra Research Fortran 90 Compiler |
| hpux | HP Fortran 90 Compiler |
| ibm | IBM XL Fortran Compiler |
| intelev | Intel Visual Fortran Compiler for Itanium apps |
| intelv | Intel Visual Fortran Compiler for 32-bit apps |
| mips | MIPSpro Fortran Compiler |
| sun | Sun or Forte Fortran 95 Compiler |
| C Compiler | |
|---|---|
| bcpp | Borland C++ Compiler |
| cygwin | Cygwin port of GNU C Compiler for Win32 |
| emx | EMX port of GNU C Compiler for OS/2 |
| intel | Intel C Compiler for 32-bit applications |
| intele | Intel C Itanium Compiler for Itanium-based applications |
| mingw32 | Mingw32 port of GNU C Compiler for Win32 |
| msvc | Microsoft Visual C++ |
| mwerks | MetroWerks CodeWarrior |
| unix | standard UNIX-style compiler |
Recent Linux distributions may have the necessary packages available.
Debian-based
Starting from Debian 4.0, including most versions of Ubuntu, you can easily install everything necessary:
apt-get install python-numpy python-scipy python-tables gfortran python-dev python-numpy-dev
Fedora/Redhat
yum install numpy scipy python-devel hdf5-develYou’ll need to compile Pytables yourself: get http://www.pytables.org/download/stable/tables-2.1.1.tar.gz and do:
tar xzf tables-2.1.1.tar.gz cd tables-2.1.1 python setup.py build su -c 'python setup.py install --skip-build --prefix=/usr/local'
This package
To build this Usadel package, do
cd usadel1 python setup.py config_fc --fcompiler=gnu95 --noarch build
and install with
sudo python setup.py install --skip-build --prefix=/usr/local
or:
su -c 'python setup.py install --skip-build --prefix=/usr/local'
Test if it works
Try to run:
cd usadel1/scripts python sns_minigap_vs_phi.py
It should start calculating the size of the minigap in an SNS junction.
In case prebuilt packages are not available on your platform (eg. on a cluster where the administrators don’t want to install additional software system-wide, or the installed software is too old), you need to build the prerequisites yourself. Unfortunately, this may take some more effort.
The easiest way is to install SPD:
http://code.google.com/p/spdproject/
which bundles most necessary parts in one piece that can be easily built from sources. Also binaries are available for many platforms.
SPD does not ship with HDF5 or PyTables libraries, so you’ll have to install them separately.
HDF5
Get ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.8.3.tar.gz
Do: (replace $SPD_PATH with the unpacked SPD directory)
cd $SPD_PATH tar xzf hdf5-1.8.3.tar.gz cd hdf5-1.8.3/ ./configure --prefix=$SPD_PATH/local --disable-parallel make make install
Pytables
Get http://www.pytables.org/download/pytables-2.1.1/tables-2.1.1.tar.gz
Install HDF5 first.
Do:
cd $SPD_PATH tar xzf tables-2.1.1.tar.gz cd tables-2.1.1 export HDF5_DIR=$SPD_PATH/local $SPD_PATH/local/bin/python setup.py install
This package
Do:
cd usadel1 $SPD_PATH/local/bin/python setup.py config_fc --fcompiler=gnu95 --noarch build $SPD_PATH/local/bin/python setup.py install --skip-build
Test if it works
Try to run:
cd usadel1/scripts export LD_LIBRARY_PATH=$SPD_PATH/local/lib $SPD_PATH/local/bin/python sns_minigap_vs_phi.py
It should start calculating the size of the minigap in an SNS junction.
If you do not want to use SPD, you can build everything manually, as instructed below.
Note that you also need BLAS, LAPACK, and Zlib libraries. It is very likely that these are already installed on a cluster used for scientific computations.
When everything is installed, you can run:
$HOME/local/bin/python some-script.py
to run scripts.
In case your Unix shell is CSH, instead of:
export VARIABLE=value
write:
setenv VARIABLE value
In general, before installing or running codes, do:
export PATH=$HOME/local/bin:$PATH export LD_LIBRARY_PATH=$HOME/local/lib export LIBRARY_PATH=$HOME/local/lib export CPATH=$HOME/local/include
zlib
Typically this is already installed (zlib.h is present), but if not, get ftp://ftp.hdfgroup.org/lib-external/zlib/1.2/src/zlib-1.2.3.tar.gz
Do:
cd $HOME mkdir $HOME/local tar xzf zlib-1.2.3.tar.gz cd zlib-1.2.3 ./configure --prefix=$HOME/local --shared make make install
Python
Get http://python.org/ftp/python/2.5.2/Python-2.5.2.tgz
Do:
cd $HOME mkdir $HOME/local tar xzf Python-2.5.2.tgz cd Python-2.5.2 ./configure --prefix=$HOME/local make make install
HDF5
Get ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.8.3.tar.gz
Do:
cd $HOME tar xzf hdf5-1.8.3.tar.gz cd hdf5-1.8.3/ ./configure --prefix=$HOME/local --disable-parallel make make install
Numpy
Get http://downloads.sourceforge.net/numpy/numpy-1.1.1.tar.gz?use_mirror=osdn
Do:
cd $HOME tar xzf numpy-1.1.1.tar.gz cd numpy-1.1.1 $HOME/local/bin/python setup.py install
Scipy
Get http://prdownloads.sourceforge.net/scipy/scipy-0.6.0.tar.gz?download
Do:
cd $HOME tar xzf scipy-0.6.0.tar.gz cd scipy-0.6.0 $HOME/local/bin/python setup.py install
If it complains about missing BLAS or LAPACK, try to point it at your BLAS/LAPACK libraries:
export BLAS=/usr/lib/libblas.so export LAPACK=/usr/lib/liblapack.so
the actual file names may be different on your system.
Pytables
Get http://www.pytables.org/download/pytables-2.1.1/tables-2.1.1.tar.gz
Install HDF5 first.
Do:
cd $HOME tar xzf tables-2.1.1.tar.gz cd tables-2.1.1 export HDF5_DIR=$HOME/local $HOME/local/bin/python setup.py install
This package
Do:
cd usadel1 $HOME/local/bin/python setup.py config_fc --fcompiler=gnu95 --noarch build $HOME/local/bin/python setup.py install --skip-build
Test if it works
Try to run:
cd usadel1/scripts $HOME/local/bin/python sns_minigap_vs_phi.py
It should start calculating the size of the minigap in an SNS junction.