LHCb Software At Nikhef: Prepare for Workshop 22-24 June 2009

From LHCb Wiki
Revision as of 11:16, 18 June 2009 by Juancho (talk | contribs)
Jump to navigation Jump to search

Introduction

The B-Fys workshop will not take place at a high energy physics lab. For these reasons, it is recommended that people install a virtual machine on their laptops in order to be able to run LHCb software locally, without necessity of an internet connection. Whereas this is not a "standard" way of performing analysis at the moment, it might be beneficial to set this up anyway. In what follows, there are explanations on how to run either with an internet connection to nikhef, or with a local virtual machine. Once the installation has been done and the environment set correctly, running on the virtual machine should be the same as running at Nikhef.

Running at Nikhef

Logon at Nikhef 

ssh user@ribble.nikhef.nl
ssh stbc-16   (on stoomboot)

Set the environment

Here we set the environment for DaVinci, but it could also another LHCb application, like Bender or Panoramix. 

mkdir cmtuser
cd cmtuser
source /project/bfys/lhcb/sw/setup.sh   # for sh, bash, ksh, zsh
source /project/bfys/lhcb/sw/setup.csh  # for csh, tcsh
SetupProject --build-env DaVinci v23r1 # makes a DaVinci_v23r1 directory if one doesn't already exist
SetupProject DaVinci v23r1 # exports environment variables to the shell

(NB: zsh-users should add 'setopt SH_WORD_SPLIT' to their .zshrc )

Running on a virtual machine on your very own laptop

This assumes you have successfully installed a CernVM on your computer. The installation varies between Windows, Mac OS and Linux, so see section further down for instructions on how to set it up. It also assumes you have set up basic login scripts, and installed AFS, X11R6, CVS and SVN if necessary. Also note that you have to run an application like DaVinci, Bender or Panoramix at least once while connected to the network in order to cache the necessary software.

Log onto your CernVM

This could mean starting the virtual machine and CernVM, starting it and logging in "remotely" from a terminal (Linux, Mac) or Exceed (Windows). Linux/Mac 

ssh -XY -p 2222 CernVMUserName@localhost


AFS access

If you need access to CERN AFS areas, 

klog user@CERN>CH

Where user is your CERN AFS username. Note the upper case for the domain name. Be careful: Never do: ls /opt/ !! (It could start caching all atlas software...).

Set the environment

This is the same as in the remote login to Nikhef, except that the LHCb environment should be set when you log in if you have set up your CernVM correctly. 

SetupProject --build-env DaVinci v23r1 # makes a DaVinci_v23r1 directory if one doesn't already exist
SetupProject DaVinci v23r1 # exports environment variables to the shell

The main difference here is that if you do not have the necessary software installed, CernVM will pull it and cache it for you. So the first time you do this you should have an interned connection.

Running over some events on a DST or MicroDST

After the environment has been set (either by remote login to Nikhef or CERN, or in the local CernVM on your laptop, we can start some simple analysis:

Get a nice package full of example scripts (new Bender Examples package exists too...)

If you haven't already got an examples package, get it, as you might need to perform modifications to some of the scripts. This has to be done when you have access to the internet. 

getpack -p anonymous Ex/MicroDSTExample v2r5

cd ~/cmtuser/DaVinci_v23r1/Ex/MicroDSTExample/scripts
python -i MicroDSTReadingExample.py --input /data/bfys/h71/Workshop/SeqDC06selBs2JpsiPhiWithMC_50.0_Kevt_NoPVReFit.dst

Plot some of the histograms made by the script 

>>> massPlots[443].plot()
>>> massPlots[531].plot()
>>> massResPlots[531].plot()
>>> propTimePlots[531].plot()
>>> Ctrl-D

Some more examples, using Gaudi or Bender environments and example scripts. Note we run them directly without getpacking them. 

SetupProject Gaudi v21r0
python $GAUDIEXAMPLESROOT/python/HistoEx.py
SetupProject Bender v12r0
cd $BENDEREXAMPLEROOT/python/BenderExample/
./Phi.py

Introduction to Python

It is important that attendees make themselves familiar with the python programming language, at least at the level of writing simple scripts.

Extensive tutorial: Tutorial

Cheat Sheet: Cheat Sheet 


/user/h71> python
>>> hello = "Hello world"
>>> print hello
>>> Ctrl-D

Install a Virtual Machine on your laptop: CernVM

See talk by Pere Mato, slide 14: 17 March 2009

CernVM beginner's guide: CernVM beginner's guide


Windows

1) Download vmware player here 

Unzip and put CernVM in fixed place. For example C:\Program Files\CernVM
Start vmplayer from desktop
Open CernVM from C:\Program Files\CernVM
Open in browser: http://192.168.204.128:8004/
                 (your number might be different!)
Create account. For example: use lxplus username and password
Virtual organization: lhcb
Change memory allocation in vmware player
  -> troubleshoot
     -> change memory allocation
         -> 1024 MB



2) Start CernVM

Follow CernVM beginner's guide step by step: CernVM beginner's guide

Start Exceed + SSH 

Start exceed
Start ssh
Connect to vm with ssh to 192.168.204.128
     (Your number might be different!)
     (fink tunnel x11 connections in ssh!)


3) Create shared data folder on your laptop 

Make folder C:\Data
Change properties of C:\Data
   -> sharing
     -> network sharing without wizard
       V share
          name: Data
       V allow 

Edit the 2kB VMware configuration file (in C:\Program Files\CernVM\ ) and add:

sharedFolder.maxNum = "1"

sharedFolder0.present = "TRUE"
sharedFolder0.enabled = "TRUE" 
sharedFolder0.readAccess = "TRUE"
sharedFolder0.writeAccess = "TRUE"
sharedFolder0.hostPath = "C:\Data"
sharedFolder0.guestName = "data"
sharedFolder0.expiration = "session"

usb.autoConnect.device1 = ""

NB: after editing the configuration file, restart VMware Player

In VMware:
  -> Share folders
     -> o always enabled

Add the following line to /etc/fstab:
sudo emacs -nw /etc/fstab
     .host:/ /mnt/hgfs vmhgfs defaults 0 0

sudo ln -s /usr/sbin/mount.vmhgfs /sbin

I edited Phi.py and put input data location: /mnt/hgfs/data/Bs2DsK_1.dst )
Data can be found here:
/afs/cern.ch/lhcb/group/calo/ecal/vol10/DATA
(or ask Niels or Vanya for a copy...)

Starting CernVM 

Start VMware Player (don't select 'Open', but 'Recent')

Login to your CernVM with your SSH.

MAC

I have succesfully tried using VirtualBox, from Sun Microsystems. It is free, it works. Follow more or less the instructions in the ATLAS CernVM wiki

Download and untar CernVM 1.20

Get the one for VirtualBox from here. Unzip and untar it. And figure out where in your file system it is. This will be the boot image "disk" for the operating system so VirtualBox will need it for booting. This must be done *before* the VirtualBox step.

Get and set up VirtualBox

http://www.virtualbox.org/wiki/Downloads Install it following instructions run it and follow https://twiki.cern.ch/twiki/bin/view/Atlas/CernVMGuideVirtualBox I went for ~1542MB memory as my laptop has 4GB. 

Name:                 CernVM
OS Type:              Linux 2.6
Base Memory:          1532 MB
Video Memory:         6 MB

Hard Disks
IDE Primary Master: cernvm-1.2.0-x86.vmdk (Normal, 5.24 GB)

I had some problems getting it to find the disk image. I did lots of clicking around and it worked in the end. I cannot replicate the "locate the vmdk file" snapshots in the ATLAS VirtualBox wiki exactly. Maybe I'll try again to see.

For network setup, I used NAT following these instructions

Then I followed the rest of the steps here

Linux

Configuration of CernVM

This configuration of CernVM is platform independent. A few things need to be set up before we can start playing

Login scripts

If you want the LHCb environment to be correctly set by default each time you login, the following is necessary:

/opt/lhcb/group_login.sh (csh) has to be sourced at the end of the .bash_profile (.login)for bash (tcsh).

/opt/lhcb/group_shell.sh (.csh) SHOULD be sourced at the end of the .bashrc (.tcshrc). However, this doesn't work at the moment and Hubert claims it doesn't really make a difference for now.

The most important one for us, /opt/lhcb/LbLogin.sh (csh), should be sourced, I do this in my .bashrc (.tcshrc).

Installing missing software

I found that I was missing SVN, CVS and, less importantly for the workshop, AFS. To install these, it is necessary to get the packages: 

sudo conary update cvs
sudo conary update subversion
sudo conary update openafs=1.4.8-1-1
sudo conary update openafs-client=1.4.8-1-1
sudo conary update openafs-kernel=1.4.8-1-1

AFS has to be started: 

sudo /etc/init.d/afs start

If you are using C-shell, remember to do type 

rehash

to update the paths, otherwise you won't see cvs, klog, etc. until the next time you log it.

Retrieved from "https://wiki.nikhef.nl/lhcb/index.php?title=LHCb_Software_At_Nikhef:_Prepare_for_Workshop_22-24_June_2009&oldid=208"