Installing FISPACT-II

From FISPACT-II Wiki
Jump to: navigation, search

FISPACT-II has been installed on various platforms and clusters around the world. Pre-compiled executables are supplied for several operating systems and compilers in the standard distributions. If you are unable to find a executable for your system, please post your details on the FISPACT-II forum or contact the project members directly.

*NIX installation

For those using a Linux, Unix or OSX system without a current version of FISPACT-II, a short guide for new installations is outlined below. We will assume that the user is installing the code in a homespace from some media directory.

Within your installation directory copy the full FISPACT-II media content and uncompress all tar.bz2 files with the provided uncompress script

mkdir ~/FISPACT-II
cd ~/FISPACT-II/
cp -R /media/FISPACT-II/ .
chmod -R u+w *
chmod +x libdatauncompress
./libdatauncompress

or directly

cd ENDFdata/
tar -xjvf decay.tar.bz2
rm decay.tar.bz2
tar -xjvf ...

Note that the full nuclear data files provided in FISPACT-II will require, when expanded, more than 40 Gb disc space. The QA suite can then be uncompressed, requiring around 1 Gb in total

chmod +x fispQAuncompress
./fispQAuncompress

Users who require source code access may request this directly from the UKAEA nuclear data manager, but FISPACT-II executables are provided for numerous operating systems with different compilers. For the following, we will take the ifort compiled executable for a 64-bit Linux system. Either copy the executable to your bin or produce a sybolic link

cd ~/bin
cp ~/FISPACT-II/fispact/exec/Linux/64-bit/ifort/fispact .

or

cd ~/bin
ln -s ~/FISPACT-II/fispact/exec/Linux/64-bit/ifort/fispact 

The set of QA tests will require an environment variable which points to the executable that has now been installed in /bin/

fispact=~/bin/fispact; export fispact

To run the test QA cases, master scripts have been privided which execute simulations within fispQA and fispQA2012, which can be initialised with

./runalltests your.times >& your.log

which will output the runtimes for the cases and terminal log. The QA folders also contain testresults/ folders which provide references for each case. Simply running

diff test81.out testresults/.

should identify any problems. Note that different compiler versions of the code may give minor numberical differences and that some test cases are specifically designed to give errors or warning messages.

Using a Virtual Linux machine

An alternative approach on any specific operating system is to download a virtual machine player (e.g., VmWare Player from [1] or VirtualBox from [2]) and install an operating system (e.g. Scientific Linux, Ubuntu, openSUSE) for which an executable is provided. Using one of the well-known Linux distributions, the installation instructions above may be followed. Note that FISPACT-II is distributed with several executables that are built and tested on those systems. Selection of one of those operating systems will ensure the simplest installation process.

Windows installation

The recommended way of running FISPACT-II on a computer using the Windows operating system is to install Cygwin (download from [3]). Cygwin contains native Windows programs and dll's that emulate Unix/Linux commands and allow the same commands to be used in Windows as in other operating systems. Statically prebuilt executables for running in both Cygwin and command prompt windows are also provided.

You can add all the Linux/Unix capabilities by selecting the appropriate Cygwin packages. Once this is done, you can work in exactly the same manner as described in the previous section for running the code, and for printing and plotting outputs.

Once Cygwin is installed (see below) and you have logged into it, then copy FISPACT-II to your home directory as described above *NIX systems. If the DVD drive on the Windows machine is d:, then copy FISPACT-II-3-00 using the command:

cp -R /cygdrive/d/* .

Installing Cygwin

To install Cygwin, do the following:

  1. download the installation program setup.exe from the Cygwin website
  2. run setup.exe, selecting download from internet, installation file directory and mirror. The default installation for all users only contains a minimal set of packages, and you need to add the following
    1. make: the GNU make utility
    2. gcc4-fortran: the GNU compilers
    3. binutils: utilities
    4. csh: the c-shell
    5. a2ps: the print utility
    6. your favourite editor (e.g. vim, emacs or xemacs)
  3. It is recommended that you also include the following packages in your Cygwin environment, so you have X11 terminal windows (xterm) and are able to plot and view your graphs (Note that when you select packages, the Cygwin installer will add extra packages needed to satisfy dependencies. Say yes to installing these extra packages):
    1. xinit: X11 initialisation package
    2. gnuplot: plotting program
    3. xpdf: pdf viewer
    4. ghostscript: postscript processing program
  4. If you want an alternative compiler, then g95 for Cygwin may be installed.

If you select the gcc compiler collection, you will get the gfortran compiler installed. Self extracting files containing binaries for g95 to run under Cygwin are available for download from [4].

Setting environment variables

Environment variables that put the FISPACT-II executable on PATH and that point to the executable used in the fispQA test scripts are needed for the usage to be as described in the User Manual. Different ways of setting these are described below; Cygwin will use environment variables from Windows, .bash_profile, .bashrc or the command line.

or the purposes of illustration, we shall assume that Cygwin is installed in c:\cygwin and that the fispact.exe executable we wish to use is stored in the directory c:\cygwin\home\wuser\bin, where wuser is the login name of the Windows user. If the executable is stored elsewhere, change the path accordingly.

The above assumes that the wuser home directory exists. Open a Cywin window by double clicking on the desktop icon, change to /home and list files by typing the following in the Cygwin terminal

cd /cygdrive/c/home
ls

If the home directory for wuser does not exist, then type the following

mkdir wuser
cd wuser
cp /cygdrive/c/etc/skel/.bash_profile .
cp /cygdrive/c/etc/skel/.bashrc .
mkdir bin

and copy the required version of fispact.exe into ~/bin.

Setting environment variables using .bashrc

Add the following lines to the .bashrc file for wuser:

PATH=$HOME/bin;$PATH
fispact=$HOME/bin/fispact.exe; export fispact

To invoke these, after opening the Cygwin window, log in as wuser:

login wuser
Password: **********

where the password is the same as the Windows password for wuser.

If, after logging in, wuser invokes X11 to get xterm:

startxwin

then the child xterm windows will inherit the environment variables.

Setting environment variables in a Cygwin or xterm window

To set environment variables that last the lifetime of the window, enter

PATH=$HOME/bin;$PATH
fispact=$HOME/bin/fispact.exe; export fispact

in the window.

Using prebuilt Windows executables

Two types of Windows executable are provided; statically linked IA32 and IA64. Executing the setup.exe for Cygwin automatically installs the Cygwin dynamically linked library, and it appears on the path if you use a Cygwin or xterm window. If you wish to run the Cygwin executables from a Windows Command window, then you need to add the directory containing cygwin1.dll to your path. The statically linked Windows executables will run from either Windows, Cygwin or xterm command windows. The Cygwin or xterm windows are recommended because they allow line widths greater than 80 characters, provide all the familiar UNIX commands and the subsidiary commands such as fp, fisprint and gnuplot can be run from them.

Compiling from source on Windows

The Intel fortran compiler for Windows uses the Microsoft VB linker rather than the gnu one. To compile Fispact using ifort under Windows, do the following:

  1. install the ifort compiler (e.g., Intel Parallel Studio XS 2015)
  2. copy FISPACT from the DVD to your workspace
  3. open a Visual Studio command prompt window

    The Intel compiler installation provides a command prompt that sets the environment variables needed for ifort. For the above example, this command prompt may be found in the start menu under

    All Programs|Intel Parallel Studio ..|Command Prompt|Parallel Studio ..|Intel64 Visual Studio 2010 mode

    for 64-bit compilation. For 32-bit compilation the "Intel64 Visual .." is replaced by "IA-32 Visual .." in the above menu selection.

  4. change directory to FISPACT\fispact\source\build_win
  5. execute the batch file
    build_ifort.bat
    to create executable fispact.exe
  6. in order to undertake the tests described above for Linux/Unix in the Cygwin environment, copy the fispact.exe to FISPACT\fispact\source\build

If you wish to use the ifort compiler from a Cygwin window, then follow the instructions given on the web page [5].

If g95 is being used without the Cygwin installation, then a g95 version of fispact.exe may be built in the build_win directory using the build_g95.bat batch file.

Running validation tests on Windows

If Cygwin is installed, running the program on a Windows machine is exactly the same as running it on a Linux or Unix machine.

If a virtual Linux machine is used, then the above instructions for Linux and Unix apply.

A limited number of batch files named fisprun.bat are also provided.