Documentation Installation of the PDR code

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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

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FITS outputs PDR 1.2

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Graphical

interfaces PDR 1.2

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PDR Online PDR 1.2

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Documentation

Installation of the PDR code

Franck Le Petit

mardi 30 décembre 2008

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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.

src PDR

! Fortran source files

! Executables : stvz & prep

data

! Atomic and molecular data

! Density / Temperature profile files

! Specific incident radiation field files

! Line of sight extinction curves

Makefile ! Makefile used to compile the code

stvz ! Executable used to run the code

prep ! Executable used to read output files

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stvz : the executable of the Meudon PDR code

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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 :

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PDRLauncher : launch a graphical interface to provide input parameters and run the code

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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.

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PDR

src !

Fortran source files

! Makefile

! Executables : stvz & prep

data

! 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 out

! Binary, XML, FITS results files

PDRAnalyzer _! _Application_{to analyze results} PDRLauncher ! Application to run the code

GUIsrc

Results Scripts

! Ouputs of PDRAnalyzer in ASCII form

! Scripts for PDRAnalyzer

! Java source codes for GUI

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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 :

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compiler name

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compiler options

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Lapack and Blas location

At the end of this document, some informations concerning typical compilers are provided.

Commands :

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make : compile the code and produce two executables : stvz and prep.

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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

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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.

Note : If you are using intel fortran and have the MKL library, we recommend to use it since it is faster than vecLib.

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 ...

...

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Compilation of cfitsio

1- Download cfitsio at: http://heasarc.gsfc.nasa.gov/fitsio/ 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.