Tag Archive | macosx

MacOSX: Solution to PYTHIA / HBOOK Problem in Cernlib

Last month, I was trying to compile some pythia codes to calculate snutau (scalar tau) cross section, Pt and eta distributions. But unfortunately my trusted g77 compiler insistently rejected to compile my code with the following errors:

Undefined symbols:
"_pylist_", referenced from:
_MAIN__ in ccJ7qu36.o
"_pyevnt_", referenced from:
_MAIN__ in ccJ7qu36.o
"_pyinit_", referenced from:
_MAIN__ in ccJ7qu36.o
"_hropen_", referenced from:
_MAIN__ in ccJ7qu36.o
"_hlimit_", referenced from:
_MAIN__ in ccJ7qu36.o
"_pystat_", referenced from:
_MAIN__ in ccJ7qu36.o
_MAIN__ in ccJ7qu36.o
"_pydata_", referenced from:
___g77_forceload_0.0 in ccJ7qu36.o
"_hfill_", referenced from:
_MAIN__ in ccJ7qu36.o
_MAIN__ in ccJ7qu36.o
_MAIN__ in ccJ7qu36.o
"_hrout_", referenced from:
_MAIN__ in ccJ7qu36.o
"_hbook1_", referenced from:
_MAIN__ in ccJ7qu36.o
_MAIN__ in ccJ7qu36.o
_MAIN__ in ccJ7qu36.o
"_hrend_", referenced from:
_MAIN__ in ccJ7qu36.o
ld: symbol(s) not found
collect2: ld returned 1 exit status

After a little research about HBOOK technology, i discovered that it’s a quite old component even before Fortran 77 and the only way to make it run in this way is to include Cernlib components while compiling. But that didn’t work either for MacOsX because probably MacosX version of Cernlib doesn’t support HBOOK libraries although it’s possible for Linux.

Anyway why do we have to use HBOOK? At the end of the day, we just want to have some data files to draw using Paw or Root and it’s possible using Pythia’s own components. So the principle must be “Use Pythia Commands to get an Output file because that’s the easiest way!” Here is my solution: I changed all HBOOK commands to PY..s in my code below and it worked perfect.

Write “g77 -o mycode.x -w mycode.f libpythia6421.a” to compile.

C...All real arithmetic in double precision.
C...Three Pythia functions return integers, so need declaring.
C...Parameter statement to help give large particle numbers
C...(left- and righthanded SUSY, technicolor, excited fermions,
C...extra dimensions).
      PARAMETER (KSUSY1=1000000,KSUSY2=2000000,KTECHN=3000000,
C...EXTERNAL statement links PYDATA on most machines.
C...The event record.
C...Particle properties + some flavour parameters.
C...Decay information.
C...Selection of hard scattering subprocesses.
C...Supersymmetry parameters.

C....Real definitions...
C ....rapidity: YX

C...First section: initialization.

C...Select generic SUSY generation.
C...39:all MSSM processes except Higgs prod.
C...41:stop pair(ISUB=261-265), 42:slepton pair(201-214), 45:sbottom(281-296)
C...ISUB=210,211,212 for slepton+sneutrino

C...Set SUSY parameters in SUGRA scenario.
      IMSS(1)=2		!mSUGRA parameters given to PYTHIA
      RMSS(8)=230D0	!m_0
      RMSS(1)=360D0	!m_1/2
      RMSS(5)=10D0	!tan(beta)
      RMSS(4)=1D0	!sign(mu)
      RMSS(16)=0D0	!A_0

      do kk=1949,1974

C...Channels for W boson
      do kw=206,208

C...If interested only in cross sections and resonance decays:
C...switch on/off initial and final state radiation,
C...multiple interactions and hadronization.
      MSTP(11)=0	! 1:QED radiation
      MSTP(61)=0	! 2:ISR
      MSTP(71)=0	! 1:FSR
      MSTP(81)=0	! 1:multiple int.
      MSTP(111)=0 	! 1:hadronization

C...Initialization for the LHC.
       CALL PYINIT('CMS','e-','e+',3000D0)

C...List resonance data: decay channels, widths etc.
       CALL PYSTAT(2)

C...Book Histograms
	CALL PYBOOK(10,'PT',100,0D0,1000D0)
	CALL PYBOOK(20,'ETA',100,-5D0,5D0)
	CALL PYBOOK(30,'MTAUTAU',100,0D0,2000D0)


C...Second section: event loop.

C...Loop over the number of events.
       DO 200 IEV=1,NEV
        IF(MOD(IEV,500).EQ.0) WRITE(6,*)
     &  'Now at event number',IEV

C...Event generation.
         CALL PYEVNT

C...List first few events.
          IF(IEV.LE.5) CALL PYLIST(1)

C...Fill the masses of interesting (s)particles.
C...Fill pt of particle
       DO I=1,N
C...Catch tau- lepton
       IF((K(I,2).EQ.15).AND.(K(I,1).EQ.1)) THEN

       CALL PYFILL(10,DBLE(PTX),1D0)
C......       CALL HFILL(10,PTX,0.,1.)
C......       CALL HFILL(20,ETAX,0.,1.)
C...Catch tau+ lepton
       IF((K(I,2).EQ.-15).AND.(K(I,1).EQ.1)) THEN
     .   +2.0*(ptaupx*ptaumx+ptaupy*ptaumy+ptaupz*ptaumz)))
C...       CALL HFILL(30,XMTAU,0.,1.)

C...End of documentation and event loops.


C...Third section: produce output and end.

C...Cross section table.
       CALL PYSTAT(1)

C...Histogram close
C...       CALL HROUT(0,ICYCLE,' ')
C...       CALL HREND('SUSY')


       CALL PYDUMP(3,11,1,IHI)
       CALL PYDUMP(3,22,1,IHI)
       CALL PYDUMP(3,33,1,IHI)


Cernlib Manual Installation

If you are using Unix/Linux based operating system and having difficulties for installing CERNLIB, the best way is to try the simplest way: manual installation.

1- ) Go to http://cernlib.web.cern.ch/cernlib/version.html and click “compressed tar files” link which is proper with your system.

2-) cd / (open your root folder)

3-) mkdir cern

4-) copy 3 tar files that you’ve already downloaded (cernlib.tar.gz, cernbin.tar.gz, include.tar.gz)  into cern folder you created.

5-) Go into your Cern folder you’ve already created and write the command:
tar -xvf cernlib.tar
tar -xvf cernbin.tar
tar -xvf include.tar
6-) Create symbolic links in this folder:
ln -s 2006 pro
ln -s 2006 new
(If you don’t have a folder 2006, change it with the name you have exp: 2004,2005,2007…etc)

7-) Now you should set some system variables: write “export” on the command line to see all fixed system variables and their values which has been declared in the past.

8 ) You must change the variables related to CERN. So either write following commands on the command line or add them into your /etc/bashrc file (for unix). If you add them into your /etc/baschrc file, you won’t need to set these variables everytime you open your computer.

export CERN=<Your Cern Directory>
export CERN_ROOT=<Your Cern Directory>
export CERNLIB=$CERN/pro/lib
export CERNBIN=$CERN/pro/bin

IMPORTANT: Please check your environmental variables by writing “export” in your command line. If you installed Cernlib by Fink or apt-get before, you may not get correct CERN_ROOT, CERNLIB or CERNBIN variables. In this case, open corresponding bashrc/profile files and edit your CERN variables. For fink, edit cernlib… csh, sh files under /sw/etc/profile.d folder.

MacOSX: Manage Programs that Automatically Launch at Startup

Mac Os X operating system has different options to manage startup items. If you have already installed skype, some messengers, orb or some agents, you may not want to use them at the startup of your computer. To inactivate these processes, actually you should remove your login accounts related to corresponding process. So;

  • Open System Preferences (if it’s not in your Dock, you can go to Apple > System Preferences at the top of the screen)
  • From the System Preferences screen, click the “Accounts” icon under the “System” settings.
  • For each account, there is a “Login Items” tab where you can add and remove programs to automatically launch at startup. If you cannot edit your Login Items there it is one of two things:
    • You do not have proper access to edit the person’s account you are looking at.
    • You have proper access, but you need to “Click the lock to make changes.” Just look at the padlock icon at the bottom-left corner of the page. If it’s locked, that’s what you need to do.
  • MacOSX: Installing PAW and PAW++

    Normally, PAW and PAW++ comes after your cernlib installation. If you didn’t install cernlib before, all you need to do is writing the following command in your terminal window

    $ fink install cernlib

    Click here to learn how you can install package manager ‘FINK’ on your Macbook.

    As a more advanced version of PAW, you can use PAW++ only if you also have the right components installed. Otherwise you will get an error like;

    dyld: Library not loaded: /sw/lib/libXm.2.dylib
    Referenced from: /usr/bin/paw++
    Reason: image not found
    Trace/BPT trap

    SW is your fink folder. So the error prompts that you have a missing library file related with lesstif package. So write the following;

    $ fink install lesstif

    In a few minutes later, fink will download and install your missing library files and you can run paw++ writing it in your terminal window.

    Running ROOT on Lxplus Server of CERN

    Mac OsX terminal window has powerful features than any other operating systems but if you are working on a remote server you need to know a little more about it.

    If you are using MacOSX and if you are connecting lxplus@cern using regular command ssh, the first thing you will observe is that your system cannot open X11 window which is needed by ROOT. To overcome this problem, you should connect using either

    ssh -X username@lxplus.cern.ch
    ssh -Y username@lxplus.cern.ch

    X option, provides you a ssh connection forwarding X11. And Y option, provides a ssh connection Forwarding trusted X11.

    After you logged in using your user name and password, you have 2 options to run ROOT.

    1 -) Entering ROOT variables below:

    export ROOTSYS=/afs/cern.ch/sw/lcg/app/releases/ROOT/5.28.00/i686-slc5-gcc43-opt/root
    export PATH=$PATH:$ROOTSYS/bin

    2-) Or just source Athena Framework and setup root from Athena: (Note that Athena consists much more than ROOT)

    export AtlasSetup=/afs/cern.ch/atlas/software/releases/16.6.0/AtlasSetup
    alias asetup='source $AtlasSetup/scripts/asetup.sh'
    asetup 16.6.0

    –Recently this procedure has been changed and became eaiser. Please google for sourcing Athena framework–

    Then just write “root” and start your analysis.

    Installing Scientific Packages on Mac OS X

    If you decided to buy a Macbook, the first thing you need to know may be that “It’s not a Big Mac at all but rather it’s a Mac”. Don’t even think you can eat all the Mac Universe that goes around and is almost parallel to our universe. It even may take quite a lot of time to figure out what kind of a trouble you have, especially if you are someone in the scientific era. Don’t forget that some says “People who buy Macs are the same people who said BETA is better than VHS 15 years ago”.

    For an average physicist like me, it may be long term run to build a useful system on Macbook.
    Here is a list of softwares that a scientist may need:

    gcc, g++, gfortran, g77, f77,Java, …etc.

    Package Managers:

    MacPorts, Fink, Darwin, RPM, Apt-get, …etc.

    Analysis Softwares:

    ROOT, Jas3, Aida, Octave, …etc.

    Computing Softwares:

    Mathematica, Matlab, …etc.

    Physics Phenomenology Softwares:

    Comphep, Calchep, Pythia, Fluka, Geant4, Madx,
    Isajet, Prospino …etc.

    Depended Packages:

    Cernlib, Openmotif, X11, Latex …etc.

    Office Tools:

    Excel, Text Editors, Presentation tools, PDF, DVI, PS viewers, …etc.

    Web Browsers

    Mozilla Firefox, Internet Explorer, Safari, Opera, Netscape, …etc.

    Next the main question comes up! How to install these softwares on Mac Os X 10.5.x ??

    Here is a prescription for beginners:
    (1). First of all, install compilers
    (2). Install some package managers
    (3). Install other software packages using compilers and installed package managers.


    GCC Compiler Installation: Use Macbook installation DVD, you will find a package called Xcode in the DVD, if you search for it. Just install Xcode development tool and your gcc compiler will also comes with it. Then open a terminal window and just write “gcc”. If its error turns like “no input file”, it means you successfully installed the gcc compiler.
    Or you can check its location by writing “which gcc” on the command line.

    G77 Compiler Installation: Unfortunately you may not find g77 support combining with any other packages or package managers. So you should install it manually:

    • Download tar file which is most suitable for your computer g77-intel-bin.tar.gz (Intel Mac only) or g77-bin.tar.gz (PowerPC only)
    • Open a terminal window and write “gunzip g77-bin.tar.gz”
    • Write “sudo tar -xvf g77-bin.tar -C /.” for install the spesific files into your usr/bin/ folder.

    Gfortran Compiler Installation: There’s an dmg installation file for gfortran compiler. So you should download and install it by just clicking on it.


    MacPorts Installation:

    MacPorts provides an open-source software for managing, compiling, installing, upgrading packages which include libraries, utilities on the Mac Os X operating system. One can easily install MacPorts downloading its dmg file and just click on it. After installation you can open a terminal and learn basic Macport commands writing “man port” . Recently for Mac users, MacPorts seem to be the most powerful package manager with almost 8000 packages. Some useful MacPorts commands are;

    • port list : Get the lists of all packages so that one can choose the package name before installation.
    • port upgrade <pkgname> : Upgrades the specific packages with newest versions.
    • port search <pkgname>: Search the package name (or a part of it) in the complete list of packages. You can make wild card searches like *root* or *X11*..etc.
    • port install <pkgname>: –Most used MacPort command- downloads, compiles, stages and installs the package you entered.
    • port installed: Shows the installed packages on your computer.
    • port uninstall <pkgname>: Deactivate the package.
    • port deps: Shows you the dependencies of a package with other packages.
    For complete list of commands, please read the documentation of MacPorts here.

    FINK Installation:

    Fink automates the process of downloading the binary package, or downloading source package, applying a patch, compling, and installing it. As a package manager, fink is the most advanced unix based software and one can easily find its documentations through web. There is an impressive number of applications you can install via fink. Fink was designed carefully as to not disturb or modify the system. It can be uninstalled with a single command ‘sudo rm -r /sw’ You definitely want f77, imagemagick, ghostscript for X, ispell, xdvi, and gimp if you want to edit graphics or xv to preview them.

    To download Fink visit http://www.finkproject.org and install its dmg file on your Macbook.

    • Open a terminal window and write “fink” to learn its usage and options.
    • Write “apt-get” (Fink also installs apt-get package)
    • Fink downloads packages from mirror servers around the world. So I strictly recommend you to configure mirror settings. Write “fink configure” to configure mirror options. Fink will start to ask you questions about configurations. Press “Enter” for default values. When it asks a question about mirror choose “4- Nearest mirrors from your continent”. Choose your country. And answer all other questions to complete configuration definitions. If you cannot download packages from chosen mirrors while installations, you should reconfigure these settings.
    • Fink supports stable packages as well as the unstable ones which are not tested or has some exceptions during their running process. To see the supported package list write “fink list” on your command line.
    • To be able to install unstable packages write “fink configure” and activate unstable package option when it asks you about stable/unstable packages. Press “Enter” to give default answers to other questions.
    • To download and install a package write “sudo fink install packagename” on the command line. (ex. “sudo fink install cernlib”)
    • WARNING: Fink automatically finds the dependencies of packages and usually downloads a set of package. That may probably extand your installation time. So i do not recommend anyone to download huge packages -ex. ROOT- via fink. Because it may take quite a lot of time with the related other packages like gcc4, X11, openmotif, …etc.


    CERNLIB Installation:

    • First, make sure you installed fink and the compilers gcc, g77.
    • Open a terminal window and write “sudo fink install cernlib”
    • Fink will download and install cernlib in a few minutes.
    • Write “cernlib” on terminal window and see related cernlib locations. If you get an error message, make sure you installed fink and the compilers properly.

    OR you may prefer to install Cernlib Manually to avoid non-standard installation.

    COMPHEP Installation:

    • Visit Comphep’s website, be a member and then download its .tar files.
    • Make sure you installed the compilers gcc and g77 properly.
    • Open a terminal window in the folder that comphep’s .tar file exits.
    • Write “sudo tar -xvf comphep-4.5.1.tar”
    • Write “cd comphep-4.5.1”
    • Write “./configure”
    • Follow the commands and write “make” to complete installation.
    • Write “make setup WDIR=calculations” to create a user file called calculations.
    • To run the application write “cd calculations” and “./comphep”

    ROOT Installation:

    • Download ROOT analysis framewok visiting ROOT official web site at CERN. If you’r obsessed to perfection, you should download the latest version for your system. (Mac OS X intel or power pc)
    • To open the related .tar file write “sudo tar -xvf root_v5-1.24.00.macosx105-i386-gcc-4.0.tar” on the command line.
    • Write “cd rroot_v5-1.24.00.macosx105-i386-gcc-4.0”
    • Write “./confgure –help” and “./configure” to make installation settings.
    • Write “make” and complete the installation.

    You can also set environmental variables to run root for anytime you open a terminal window by writing “root” command. To edit bash and add environmental variables;

    • Open a termianl window and write “cd /” to go root directory.
    • Write “sudo nano etc/bashrc” to open a editor to edit bash profile.
    • Add the following lines in to bashrc file, save and exit (CTRL-O and CTRL-X)
      • export ROOTSYS=/usr/local/root
      • export DYLD_LIBRARY_PATH=$ROOTSYS/lib
      • export PATH=$PATH:$ROOTSYS/bin
    • You should change $ROOTSYS variable (first line) if you installed ROOT framework in to another directory.

    General Instructions for Installations:

    • Download the software in tarball.
    • Decompress tarball writing “sudo tar -zxvf <software>.tar”
    • Write “./install” or “./configure” if you have such shell files to run.
    • Write “make” and start compiling.
    • Trace errors if you have any.

    I strongly recommend you to register Apple’s developer website http://developer.apple.com/ for recent updates and development tools.