Development of an installation package for the EFIT++ code on
Contents
1. go on to illustrate how to create a debian package of the EFIT code This work also aims to be an actual installation manual Chapter 1 Installing EFIT As mentioned EFIT is a rewrite of EFIT code written by Lao Lang in FORTRAN 77 The implementation of EFIT is in a mix of C and Fortran 90 It is an excellent solution to the plasma boundary identification problem and to the reconstruction of the equilibrium in the Tokamak This chapter shows the download procedure the compiling and the running of the EFIT code 1 1 Download The first thing to do is to create a directory and to rename it efit Then you have to download the main development version of the EFIT code i e mkdir efit cd efit svn checkout https mastweb fusion org uk svnroot efit development trunk After which the EFIT source code and the make file will be located in the sre subdirectory 2 The main development version used is of October 2011 8 1 2 External libraries EFIT needs the following libraries to be compiled and installed Library Description Qt Contains many facilities including a DOM parser and a regular expression evaluator Blitz A C class library for scientific computing GSL Gnu scientific library numerical library for C and C IDAM Universal API for data access BOOST above version 1 35 C source libraries pspline Collection of Spline and H2. implemented in FORTRAN 77 has been installed on many Tokamaks However there has been a gradual diversification of the original source code as each installation was created by simply copying the EFIT source code In EFIT all machine dependencies have been removed and now reside either in local data files or in databases Thus the EFIT code has no pre set values and all configurable parameters need to be explicitly set by the user At present output is written to an HDFS file The implementation of EFIT is in a mix of C and Fortran 90 The user interface is written in C whereas the algorithmic elements i e the construction of the tabulated response functions and the calculation of the individual equilibria are written in Fortran 90 The reason for this mixed language approach is a consequence of how the EFIT project evolved rather than due to any inherent performance issues of FORTRAN compared to C The EFIT code sets out to compute the axisymmetric magnetic field distribution satisfying radial force balance in Tokamaks The EFIT field solution provides the best fit to user supplied synthetic and measured data relating to the magnetic fields taking account of the uncertainties in the data EFIT can calculate the magnitude of toroidal currents induced in conducting structures which may not have been explicitly measured In addition EFIT can model material with non linear finite permeability characteristics by using an ax
3. like and how it should act The Build section is where the actual building of the package begins Once the build button is pressed Debreate will gather all of the information inputted into each section and start the process 2 2 Creating the installation package of EFIT First you have to create the directory efiit that will turn out to be the content of the installation package Then you have to start Debreate in order to create the package itself 2 2 1 Creating the package structure You need to create a directory and name it efit This directory should contain e The src subdirectory containing all the source files of EFIT and the efitEnvironmentSettings sh script file e The lib subdirectory containing all the libraries and header files used to execute and to compile the program e The obj subdirectory containing all object files that are generated during the compilation of the EFIT source code This subdirectory must be specified by the 16 EFIT_LOCAL_OBJ_PATH variable in efitEnvironmentSettings sh script that is located in the src subdirectory e The bin subdirectory containing the executable file efit exe This subdirectory must be specified by EFIT_LOCAL_BIN_PATH variable in the efitEnvironmentSettings sh script located in the src subdirectory e The obj parallel subdirectory containing the data for parallel architecture This subdirectory must be specified by the EFIT_LOCAL_OBJECT_PA
4. the libraries can be found in section 1 2 PS Home efit lib f Q blitz boost efitxml gsl d ci hdf5 idam lapack libblas n Ad netcdf pspline qt4 x86_64 linux gnu Figure 3 Example of the lib subdirectory 18 Having the IDAM pspline netCDF C local version and efitxml libraries been regularly compiled and installed by the user they can be simply copied into the lib subdirectory While instead the libraries installed with Synaptic and therefore installed in the system directories can be copied to the Jib subdirectory only with administrator permissions Because of the large number of files to copy you should use the sudo nautilus command The system directories that contain these libraries are e usr include e usr lib e usr lib x86_64 linux gnu P3 Home efit lib Q Cerca Shi bl array gnu meta applics h array h jens re N ca ore CI bl ba Al gt AI ni ni co Co co array impl h array old h bench cc bench h benchext cc Ta FORI ei FOR ros bl osso ifnd bl bl nf bl defi n g Co benchext h blitz h bzconfig h bzdebug h compiler h Pr TIE PR FTIR 7 bl bl bl ies n config h etbase h extremum h funcs h indexexpr h Si A A libblitz a libblitz so libblitz s0 0 libblitz s0 0 0 0 limits hack h Figure 4 This figure shows some files of the Blitz library Header files static a extension and dynamically linked shared object so extension libr
5. However the long time needed both to compile the source code and to compile and install the external libraries the not simple library compiling procedure the use and the modification of a script make difficult the process of installing the EFIT code and in terms of time very inconvenient The creation of the debian package of EFIT code has brought significant improvements In fact with the newly created installation package we have the following significant advantages e Not having to compile the source code because it is already pre compiled e Not having to either download compile or install the libraries necessary to run EFIT because they are already included in the package Not having to create or to edit the script efitEnvironmentSettings sh because it has been conveniently modified for use by the user Possibility to be able to recompile the source code after any change Very short installation time that turns out to be even more significant when compared with the time needed both for the compilation of the source code and of the external libraries Possibility of having all the program files located in the same directory instead as 25 having them dispersed throughout the system as was the case with the standard procedure Therefore it is clear that the use of the installation package brings significant improvements both in terms of difficulty and in terms of speed of use Concerning the Debreate utility it has be
6. RALLEL_PATH variable in the efitEnvironmentSettings sh script located in the src subdirectory e The fest subdirectory containing a copy of efit exe located in the bin subdirectory the three data files efitOptions xml pfCircuits xml tokamakData xml and the copy of the efitEnvironmentSettings sh script located in the src subdirectory This subdirectory will contain the output file and will be used for testing PRB Home efit Q Cerca bin lib obj obj_parallel src test Figure 2 Structure of the efit directory Furthermore the efitEnvironmentSettings sh script must be properly edited so that all users can use it This script will be used to indicate the location of the libraries that are needed for the execution of the program 17 An example of instructions of this script after the appropriate modifications is the following BOOSTINC lib boost NETCDFINC lib netcdf include BOOSTLIB lib boost NETCDFLIB lib netcdf lib export C_LINCLUDE_PATH BOOSTINC NETCDFINC export CPLUS_ INCLUDE _PATH BOOSTINC NETCDFINC export LIBRARY PATH BOOSTLIB NETCDLIB export LD LIBRARY PATH BOOSTLIB NETCDLIB export EFIT_LOCAL_BIN_PATH bin export EFIT_LOCAL_OBJ_PATH obj export EFIT_LOCAL OBJECT_PARALLEL PATH obj_parallel As mentioned above all the libraries necessary to execute EFIT have to be placed inside the Jib subdirectory The list of all
7. UNIVERSITA becu STUDI pi NAPOLI FEDERICO Il Scuola Politecnica e delle Scienze di Base Corso di Laurea in Ingegneria Informatica Elaborato finale in Fondamenti di Sistemi Dinamici Development of an installation package for the EFIT code on Linux distributions Anno Accademico 2013 2014 Relatore Candidato Ch mo Prof Pietro Liguori Alfredo Pironti matr N46000088 Index Indesit EE dia OLA ee oad alga da Se ech cl gaat epee Set lira II Introdutioliasaasalaelesiolieeseiieenla a E EAE a aa A E ETE 4 Chapter I gt Installing EFFET iranica aio alia ii 8 LL Downloader esili cee ei edili eee Oe eda tated 8 1 2 External AAT OS eae pitti born linee doi iii liete tali aaa 9 CSERFA environment stino Sni ina e E E E E E EE E E E E R E 10 E OUTING tag serach E E A isntatizinnableaiprblassolazia 12 1 5 R n e n min ops caine a a E ii 12 Chapter 2 Development of the Installation Package 14 Be PODER AG 25 sed lela lel eh aed un a ee ae eh ie a luo aah ee 15 2 2 Creating the installation package of RPV lalla eee ta 16 2 2 1 Creating the package structure lai 16 2 2 Starine IDE DPC A Cy alert allinea 20 2 3 Installing and running the package ese cased e ela i 22 2 3 REMOVING the package alia ritirata 23 2 3 2 Recompiling the SOULCE OE raro ir 23 CONC US OTS seo ats ec es Aiea ce cs cei anaes peat ie aul el 25 BST Sia an cs laine 27 Introduction The possibility to use controlled nuclear fusion as a source of alt
8. a location in which the user has the read write and execute permissions For example if the package e g EFIT _10 2010_amd64 deb is located on your Desktop and you want to install it in your Home directory then you must use the following command dpkg deb x HOME Desktop EFIT _10 2010_amd64 deb HOME The result of the above mentioned operation is that the efit directory will be created in the chosen installation path This directory will contain all the files that were included in the package The overall time for the package installation will be merely a few seconds Regarding the execution of EFIT by using the terminal just move into the directory containing the efit exe executable file and run it after having first executed the efitEnvironmentSettings sh script 1 e cd efit test source efitEnvironmentSettings sh lefit exe 22 Execution of the script is necessary because it indicates the locations of the libraries that have been included in the package and which are essential for the execution of the EFIT code As previously explained the script has been conveniently modified so as to require no further editing by the user The program will begin to perform calculations based on the values contained in the input data file in the test subdirectory The output will be saved in the efitout hdf5 file 2 3 1 Removing the package You can easily remove EFIT by del
9. aries of each external library required have to be copied to the lib subdirectory Considering that files copied from system directories can be read written and performed only with administrator permissions you must change the permissions to all the files located in the efit directory and subdirectories To do this use the chmod command 7 GNOME Files formerly called Nautilus is the official file manager for the GNOME desktop 8 chmod is the command and system call which may change the access permissions to file system objects files and directories 19 If for example the efit directory has been created in the home directory then insert sudo chmod R 777 HOME efit 2 2 3 Starting Debreate Once created the efit directory containing everything that is needed for the package you have to start Debreate and particularly dwell on the Control Files and Build sections In the Control section you must specify the information required for the control file such as the name of the program the version your name your e mail address and the computer architecture for which the package is intended You can also enter information about the program in the Short Desciption and Long Description fields Debreate Debian Package Builder RI O gt Required Package EFIT Version 19 2011 Maintainer pietro Liguori Email pie liguori gmailcom Architecture amd64 Recommende
10. ctrical current into the plasma and making it interact with a magnetic field produced by external coils Furthermore the current induced into the plasma also provides to its heating by means of the Joule effect Central solenoid magnet Poloidal field magnet Toroidal field magnet Figure 1 Tokamak structure Unfortunately the equilibrium so achieved proves to be unstable and the ring of plasma in the Tokamak disintegrates in a time lapse still today considered to be too short and far from the necessary standards to make the fusion process energetically favourable Hence the need of a controller able to act upon the plasma s evolution over time so as to ensure it remains confined for as long as possible In view of this the importance of a plasma boundary identification algorithm is evident in order to control the position and the shape of the plasma itself EFIT Equilibrium Fitting is a computer code written by Lang Lao in FORTRAN 77 for the Tokomak and developed to translate measurements from plasma diagnostics into useful information like plasma geometry stored energy and electrical current profiles 5 The Grad Shafranov equilibrium equation which describes the force equilibrium inside a plasma is solved by using the available measurements as constraints on the toroidal electric current density The EFIT code is a substantial rewrite of the EFIT code originally written by Lang Lao The original version
11. d Section y Priority optional gt Short Description 7 5 _ B 7 The EFIT code sets out to compute the axisymmetic magnetic field distribution satisfying radial force balance in tokamaks Long Description The EFIT code sets out to compute the axisymmetic magnetic field distribution satisfying radial force balance in tokamaks The EFIT field solution provides the best fit to user supplied synthetic and measured data relating to the magnetic fields taking account of the uncertainties in the data EFIT can calculate the magnitude of toroidal currents induced in conducting structures which may not have been explcitly measured In addition EFIT can model material with non linear finite permeability characteristics using an axisymmetric treatment This version of EFIT is a substantial rewrite of the EFIT code originally written by Lang Lao for the DIII D tokamak Optional Source Homepage Essential no Figure 5 The Control section of Debreate In the Architecture field you have to select the same computer architecture on which the EFIT code has been compiled 20 In the Files section you must first select the custom option in Target and then digit the destination directory efit which will also become the package installation directory Then you must select the previously created directory efit on the left which is our package structure and finally you mu
12. en extremely useful in the development of the installation package In fact by having a very intuitive graphical interface it has made the development of the debian package of the EFIT code sufficiently easy 26 Bibliography 1 2 3 4 5 6 7 8 Alfredo Pironti Identificazione della frontiera di plasma in un Tokamak con l espansione di Legendre Fourier Academic Year1990 91 Lynton Appel EFIT user manual 2nd July 2010 Alfredo Pironti and Michael Walker Fusion Tokamaks and Plasma Control IEEE Control Systems Magazine October 2005 Volume 25 Number 5 Lynton Appel EFIT Equilibrium Reconstruction 2010 Debreate Usage Versione 0 3 Theory and Computational Sciences website https fusion gat com theory Efitdef October 2014 Official Ubuntu Documentation https help ubuntu com 12 04 index html November 2014 Debreate Debian Package Builder http debreate sourceforge net October 2014 27
13. ermite interpolation tools lapack Linear algebra package netCDF Common data format netCDF C local version Local version of the netCDF C library HDF5 Hierarchical data format BLAS Routines that provide standard building blocks for performing basic vector and matrix operations efitxml IDAM EFIT magnetics XML library xml2 Convert between XML HTML CSV and a line oriented format ICU Development files for International Components for Unicode You can easily install some of the required libraries by using Synaptic the Ubuntu package management system The following table shows which packages you have to install with Synaptic Library Package Name Qt libqt4 dev Blitz libblitz0 dev GSL libgsl0 dev BOOST libboost all dev lapack liblapack dev netCDF libnetcdf dev HDF5 libhdf5 serial dev BLAS libblas dev xml2 libxml2 ICU libicu dev As for the following libraries IDAM pspline netCDF C local version and efitxml they have to be downloaded compiled and then installed in locations where you have normal user privileges by using the terminal and by following the proper instructions The compilation procedure and the subsequent installation of the above mentioned libraries are relatively complicated and require a considerable amount of time 1 3 EFIT environment settings The locations of the executable files the include files the
14. ernative energy is one of the main objectives pursued by the scientific community for the benefits offered in terms of availability of raw materials and security In a fusion reaction two light atomic nuclei fuse by clashing together giving place to a heavier nucleus As atomic nuclei are positively charged they tend to repel each other and therefore for the fusion to take place they must have sufficient kinetic energy to overcome the repulsion itself Such energy can be provided to the nuclei by taking them to very high temperatures 4x10 K At such temperatures all gas atoms are dissociated into their constituents the nuclei and the electrons The electric charge density is such that the behaviour of the set of particles is totally governed by electromagnetic phenomena This set of ionized matter subject to electromagnetic actions is defined as plasma High temperature plasma is unconfinable by material walls therefore the confinement device has to be of inertial or of magnetic type The creation of a magnetic field configuration able to contain the plasma in a stable equilibrium has always represented a major problem in the production of energy by fusion The Tokamak Russian acronym for Toroidal Chamber and Magnetic Coil is a machine produced in the Soviet Union at the end of the sixties for the magnetic confinement of 4 plasma It is characterized by a toroidal geometry in which the equilibrium is achieved by inducing an ele
15. eters e pfCircuits xml describes active currents driven by pf supplies and passive currents induced by the active currents e tokamakData xml contains details of a particular Tokamak for example its geometry and measurement data 4 The source command in shell is used to execute commands from a file in the current shell This is useful to load function or variables stored in another file 12 These files have to be positioned in the directory specified by EFIT_LOCAL_BIN_PATH the directory where is located the efit exe file and are used both to provide the program input and to customize the output To run the program you must use the following commands cd efit bin source efitEnvironmentSettings sh lefit exe If execution of the program is successfully completed the efitOut hdf5 output file will be created in the same location of the efit exe file 13 Chapter 2 Development of the Installation Package This chapter shows how to create an installation package of the EFIT code for Linux distributions The Linux distribution used is Ubuntu 12 04 64 bit hence the procedure of creating a debian package deb extension will be shown Debian packages are standard UNIX archives that include two tar archives optionally compressed one archive holds the control information and another contains the program data To be able to create the package of the EFIT code the source code has to be co
16. eting the efit directory The cancellation does not require any special permissions 2 3 2 Recompiling the source code In addition to the libraries even the header files needed to compile the source code have been inserted inside the installation package Although this choice significantly increases the size of the debian package it gives the user the option to recompile the source code I contained in the src subdirectory This option might be useful if you should decide to change the source code In case you want to recompile the source code it is necessary to conveniently modify the Fortran Flags in line 33 of the efitEnvironmentSettings sh script positioned in the src subdirectory After this change you can recompile the source code with these commands cd efit src make clean make At the end of the recompilation process the efit exe file will be generate in the bin subdirectory You have to copy this file to the fest subdirectory before starting the program execution When recompiling the source code since all the libraries have been compiled with a 23 specific version of g and gfortran it is absolutely necessary to install the same compiler versions used and to uninstall any other installed version 10 Compiler versions used are g 4 6 and gfortran 4 6 24 Conclusions The EFIT code turns out to be extremely useful for those working in the field of nuclear fusion
17. for which the package is intended package description etc This section of Debreate has a field for the necessary entries of the control file The Dependencies and Conflicts section provides an interface to specify which packages are required for the correct installation The Files section is for specifying which files will make up the contents of the package In the Script section you can create scripts Maintainer scripts are executables that can dpkg is the software at the base of the package management system in the free operating system Debian and its numerous derivatives It is used to install remove and provide information about deb packages 15 be called during the installation and or removal processes In the Changelog section you can create the changelog file The changelog is a documentation of changes across different versions Changelogs are gzip compressed text files containing the information on the package changes The Copyright section is simply a plain text editor where the entire copyright license or a copyright declaration with the path to a common license available on the system can be declared In the Menu Launcher section you can create a single launcher to be installed to ust share applications These menu entries are normally based on text files that use the desktop extension and are often referred to as desktop files Desktop files contain information about what the launcher should look
18. isymmetric treatment In view of all this it is clear that EFIT turns out to be an excellent solution to the plasma boundary identification problem and to the reconstruction of the equilibrium in the Tokamak However the procedure of using the EFIT code is not easy In fact the long compilation time of the code together with the many external libraries needed and the not HDF5 is a file format designed to store and organize large amounts of numerical data 6 simple compilation procedure that requires a shell script and therefore addressed only to expert users in programming make not optimal the compilation procedure and the subsequent use of EFIT in terms of time and difficulty These reasons have led to the idea of creating an installation package that would solve the above mentioned problematic This study aims precisely to create an installation package of the EFIT code for Linux distributions and to highlight the advantages of its use rather than that of the standard procedure In the first chapter the standard procedure for the use of EFIT based on the compilation of the source code will be illustrate In the second chapter the procedure for creating the installation package of the EFIT code for Linux distributions the relevant installation directives and the program execution instructions will be illustrated The Linux distribution on which the research has been carried out is Ubuntu and therefore the study will
19. locations of the libraries are specified by the LIBRARY_PATH and LD_LIBRARY_PATH variables An example of instructions contained in the script that shows how to specify these variables is the following BOOSTINC usr include boost NETCDFINC HOME netcdf include BOOSTLIB usr lib NETCDFLIB HOME netcdf lib export C INCLUDE _PATH BOOSTINC NETCDFINC export CPLUS_INCLUDE_PATH BOOSTINC NETCDFINC export LIBRARY _PATH BOOSTLIB NETCDLIB export LD LIBRARY PATH BOOSTLIB NETCDLIB 11 In addition efitEnvironmentSettings sh must also contain an instruction declaring the Fortran Flags that specify the location of the mod file of the pspline and netcdf libraries e g export FFLAGS I home username pspline LINUX mod I home username netcdf include g 1 4 Compiling At this point you can compile the EFIT source files by first using the source command and then the make command i e cd efit src source efitEnvironmentSettings sh make In order to compile them you must have installed the gfortran and g compilers If the build is successful the object files and the efit exe executable file will be respectively generated in the locations specified by EFIT_LOCAL_OBJ_PATH and by EFIT_LOCAL BIN_PATH 1 5 Running To run the program you need the following data files e efitOptions xml contains data describing EFIT specific param
20. mpiled and the object files and the executable files have to be generated see Chapter 1 The installation package has been created by using Debreate an aid utility for the building of debian packages The goal is to make packaging for Debian based Linux distributions more appealing with an easy to use interface for creating distributable archives of applications artworks media and more 5 deb is the extension of the Debian software package format and the most often used name for such binary packages 14 2 1 Debreate First you have to download Debreate from the following URL http debreate sourceforge net Then you have to install this utility with the terminal by using the dpkg command e g sudo dpkg i debreate_version deb Debreate needs the python wxgtk2 8 library in order to work You can install it via the terminal or with the package management system After that you can execute the utility with the command debreate and start the creation and the customization of the package Debreate is divided into several sections that will be specifically considered The Control section of Debreate is where the control file is to be created The control file is a text file that is the core of the debian package This file contains all the package information needed by the package manager package name and version package maintainer s name and email address computer architecture
21. object files and the libraries required by EFIT are specified in a single shell script You have to name this script efitEnvironmentSettings sh and to place it in a location known to the system i e a location specified in the PATH environment variable 3 A shell script is a computer program designed to be run by the Unix terminal It is a text file that uses the sh extension and its first line has to start with bin sh 10 The location of the executable files is specified by the variable EFIT_LOCAL_BIN_PATH the location of the object files is specified by the variable EFIT_LOCAL_OBJ_PATH and the location of the data for parallel architectures by EFIT_LOCAL_OBJECT_PARALLEL_PATH An example of instructions in efitEnvironmentSettings sh that shows how to specify these variables is the following export EFIT_LOCAL_BIN_PATH HOME efit bin export EFIT _LOCAL_OBJ_PATH HOME efit obj export EFIT LOCAL _OBJECT_PARALLEL_PATH HOME efit obj_parallel sr By so doing the bin obj and obj parallel subdirectories located in the HOME efit directory respectively contain the executable files the object files and the files for parallel architectures It is also necessary to specify in the efitEnvironmentSettings sh script the locations of all the libraries and of the include files required by EFIT Include files must be specified in the C_LINCLUDE_PATH and CPLUS_INCLUDE_PATH variables while the
22. st press the Add button as shown in the figure below Debreate Debian Package Builder ee ee gt v Home directory Target gt i Documenti O bin O usr bin y I efit usr share bin usr local bin a a Custom gt lib gt obj i obj_parallel Gs nm aa gt src lig test efit test gt la EFIT efitEnvironmentSettings sh efit test gt li immagini efitEnvironmentSettings sh efit test gt fi Ironefit pfcircuits xml efit test gt local tokamakData xml efit test m sodolli efit exe Figure 6 The Files section of Debreate In the Build section click on the build button then choose the name of the package and the directory where you wish to save it Debreate Debian Package Builder Extra options Create mdSsums file Delete build tree _ Check package for errors with lintian Install package after build x Start building Figure 7 The Build section of Debreate 21 2 3 Installing and running the package Now it is possible to simply install the package by using the terminal with the following command dpkg deb x Package_Path Package_Name deb Installation_Path in which a the Package_Path indicates the debian package path b the Package_Name indicates the name of the debian package c the Installation_Path indicates the path where you want to install the program It is necessary to choose
Download Pdf Manuals
Related Search