Modify SLAC Central Linux Environment

Note: If you have not already done so, be sure you have
fulfilled the basic prerequisites for using SLAC Central Linux.
(See Prerequisites: Basic.)

.cshrc

If you plan to use SLAC Central Linux, you will need to set up your environment in one of the following two ways in order to access external libraries (root, clhep, etc.). Based upon .cshrc status from which you start, modify your login profile using one of the following procedures:

• If you are starting from the default .cshrc, which you received from the SCS with your new account, replace your default  .cshrc file with the file:

  /afs/slac.stanford.edu/g/glast/ground/scripts/user.cshrc

Note: If you are not familiar with Unix, Use the following procedure to update your .cshrc file:

Are you accessing SLAC Public from a Windows or Linux/Mac machine?

If you are coming from a windows machine, first:

Open a secure shell (e.g., PuTTY).

Log in to a SLAC Public Machine (e.g., yakut.slac.stanford.edu); see Public Machines at SLAC.

If you are coming from a Linux or a Mac machine, use a command-line ssh:

ssh -Y rhel5-32.slac.stanford.edu

Do not change directories (i.e., remain in your home directory for now).

At the $ prompt, enter:

cp /afs/slac.stanford.edu/g/glast/ground/scripts/user.cshrc ./.cshrc

Refer below to: SLAC Public Environment (after setup)

OR

• If you already have a .cshrc script with statements which you want to keep, you may use the group script by adding the following lines to the top of your .cshrc: 

  set interactive=${?prompt}
  if ( ${?LD_LIBRARY_PATH} != 1 ) then
        setenv  LD_LIBRARY_PATH

  endif
  setenv     GLASTROOT /afs/slac.stanford.edu/g/glast
  source  ${GLASTROOT}/ground/scripts/group.cshrc

SLAC Central Linux Environment (after setting up .cshrc)

A non-customized, Slac Public user environment should look similar to the one shown below after updating the .cshrc file.

Tip: After logging in to a Slac Central Linux machine, check the environment variables by entering the env|sort command at the $ prompt. When using the NFS User Space, you will need to make special note of the environment variables set up for:

Note: ROOT for GLAST variables are not included in the script files. If using ROOT on SLAC Public, you will also want to add those variables to your .cshrc file. (See Set ROOT Environment Variables: Linux.)

Examples of environment variables in a SLAC Central Linux user's home directory:

SCons Environment Variables

Setting up environment variables is less complicated when using SCons builds: there are only three that you must watch closely:

• BUILDS:
  • SCons versions are on the u35 disk.
  • The earlier CMT versions are on the u30 disk.

  When running on SLAC Central Linux with intent to use a Release Manager build, be sure that the BUILDS variable is pointing to u35:

  BUILDS=/nfs/farm/g/glast/u35/

• GLAST_EXT:

  For SCons (at the time this was written, 08-24-2010), the correct values are:

Note: The earlier CMT versions are at: /afs/slac/g/glast/ground/GLAST_EXT/rhel4_gcc34opt

Tip: It is strongly recommended that you routinely set GLAST_EXT when you login to SLAC Central Linux!

• INST_DIR:
• This path points to the directory where the package(s) you are working with are (or are to be) installed.

Example: Setup (when running Science Tools on SLAC Central Linux)

KIPAC's "xray" packages. While the default login shell when using SLAC Central Linux is tcsh, the Fermi LAT Science Tools are often used together with some of HEASOFT tools within the FTOOLS environment (e.g., ds9, fv, XSPEC, etc.) At SLAC, configurations of the HEASOFT packages are maintained by KIPAC and intended primarily for use in a bash shell. (See The KIPAC software collection.)

When running a setup script, first:

1. Refer to: SLAC Central Linux: Getting Started and then create a work directory (e.g., explore_LATdata) in your User Work Space.
   
2. SSH to a RHEL5-64 machine: ssh rhel5-64
3. Start a bash shell: bash
4. If you have not already done so:
   1. Use the emacs editor and create the following file:

2. Name the file .xrayrc and save it to your $HOME directory.

Note: The .xrayrc file works only when you are running in a bash shell. For more information on the .xrayrc file, see The KIPAC software collection page and scroll down to the section titled ~/.xrayrc Configuration File.

If this .xrayrc file is not in your $HOME directory when you run your setup script, you may experience problems when a Science Tool accesses the wrong version of an external library. To check if this file is in your ~HOME directory, issue the ls -a command. Periodically, you may wish to update this file as new HEASOFT versions are released.

5. Create a setup script similar to the example shown below and save it to your ~HOME directory, then run the setup script; for example: source setup_mypyLike_environment

Important: Be sure that the kipac packages are sourced before the ScienceTools. (If the kipac packages are sourced after sourcing the ScienceTools, applications using cfitsio will fail.)

Assumptions

• You are running SCons builds on SLAC Central Linux in a bash shell.
• You have the .xrayrc file in your ~HOME directory.
• The KIPAC tools are sourced before the Science Tools.
• The data files you are working with are located in your work directory.
• All commands will be issued from within your work directory.

Notes:

• If you are used to working in a tcsh shell, observe that the bash "export" command equates to the C shell's "setenv" command.

• You may also want to review SCons for Fermi LAT: An Overview.