Documentation Installation of the PDR code

Transcription

1 Documentation Installation of the PDR code Franck Le Petit mardi 30 décembre 2008 Requirements Requirements depend on the way the code is run and on the version of the code. To install locally the Meudon PDR code, a fortran 90 compiler and Lapack and Blas libraries are necessary. Optional softwares are required to use the latest features of the Meudon PDR code. Output files used to be written in home-made binary files. To facilitate porting of output files, we now store results in FITS format. This requires the installation of the cfitsio library. Finally, we are developing graphical interfaces to facilitate the use of the Meudon PDR code. They are written in java and assume that java 1.5. is installed. Versions Fortran 90 Lapack & Blas cfitsio java 1.5 Astrogrid account Run locally PDR 1.2 and older FITS outputs PDR 1.2 Graphical interfaces PDR 1.2 PDR Online PDR 1.2 1

2 Files structure The Meudon PDR code can be used in command line mode and from version PDR 1.2 with graphical interfaces. Even if the graphical version is downloaded, the code can still be executed in command line mode. Command line mode In the version without graphical interfaces, the Meudon PDR code is structured in 3 directories src, data and out. PDR src! Fortran source files! Executables : stvz & prep Makefile! Makefile used to compile the code stvz! Executable used to run the code prep! Executable used to read output files data! Atomic and molecular data! Density / Temperature profile files! Specific incident radiation field files! Line of sight extinction curves pdr4.in! Input parameter file : pdr4.in chimie. chi! Chemistry file out! Results files produced by stvz in binary format! Extracted results produced by prep in ASCII format

3 During the compilation, two executables are produced in src : stvz : the executable of the Meudon PDR code prep : A code used to read outputs produced by stvz To run the code, go in src and run stvz. Input parameters are provided in the data/pdr4.in file. List of chemical species to be used and chemical reactions have to be provided in a data/*.chi file. Some examples are provided. It is possible to control some fine aspects of the treatment of atomic and molecular physics from other files in the data directory. This is explained in other documentations. Graphical User Interface mode In the GUI version, the three main directories are still present with a few other ones. The execution of the code and its outputs analyzer are directly done in the PDR directory running : PDRLauncher : launch a graphical interface to provide input parameters and run the code PDRAnalyzer : launch a graphical interface to open output files and navigate in the results. Output files have to be converted from binary to VO-TABLE + FITS format thanks to the Transfobin code. This GUI replaces the prep program. It can open results downloaded from the PDR database.

4 PDR src! Fortran source files! Makefile! Executables : stvz & prep data out! Input parameter file : pdr4.in! Chemistry file! Density / Temperature profile files! Specific incident radiation field files! Atomic and molecular data! Line of sight extinction curves! Binary, XML, FITS results files GUIsrc! Java source codes for GUI! ant file (compilation of GUI) PDRLauncher! Application to run the code PDRAnalyzer! Application to analyze results Scripts! Scripts for PDRAnalyzer Results! Ouputs of PDRAnalyzer in ASCII form

5 Compilation Compilation of the fortran code Required for Command line mode and GUI mode. A Makefile is provided in the src directory. It has to be modified accordingly to your configuration. Once executed, it should produce two executables stvz and prep. To configure the Makefile, provide : compiler name compiler options Lapack and Blas location At the end of this document, some informations concerning typical compilers are provided. Commands : make : compile the code and produce two executables : stvz and prep. make clean : clear executables, object files and modules. You can try you installation running the stvz code. Compilation of the graphical interfaces Required for GUI mode or to run the code online or to read results downloaded from the Meudon PDR code database. Compilation of Transfobin Required for GUI mode.

6 Tips for Makefile Intel fortran gfortran Using veclib on a Mac instead of Lapack and Blas If Xcode in installed on your Mac, you should also have the Veclib library installed. It contains a version of Lapack and Blas developed by Apple. To avoid a Lapack / Blas installation and instead use the veclib library. Makefile using veclib instead of standard Lapack and Blas # # GNU COMPILER: g95 # FC = g95 # Options and Path FFLAGS = -O -fno-second-underscore -Wall # No path for Lapack and Blas # For the links, call veclib with this syntax $(FC) stv1a.o $(OBJstv) -Wl,-framework -Wl,vecLib -o stvz $(FC) prep1.o $(OBJprep) $(OBJstv) -Wl,-framework -Wl,vecLib -o prep Note : If you are using intel fortran and have the MKL library, we recommend to use it since it is faster than veclib. veclib website : Reference/reference.html

7 Compilation of cfitsio 1- Download cfitsio at: 2- Follow their instructions to compile it: On a Mac OS X type first: export CFLAGS= -arch ppc -arch i386 -g -O2./configure make make install [optional] 3- Modify Makefileof the Meudon PDR code to point towards the libcfitsio.a file Note: It is recommanded to test the libcfitsio.a before using it. A test program is provided with the download of cfitsio files. In cfitsio directory: make testprog testprog > testprog.lis diff testprog.lis testprog.out cmp testprog.fit testprog.std No differences should be find.