L3/BooNE/LIGO Linux Information

What's New

• We now have a documentation wiki which some users have write-access to.
• How to burn a CD-R/CD-RW/DVD-R/DVD-RW on Gallatin (instructions may differ depending on the machine you use.
  1. Prepare an ISO image. You need an empty directory with enough space to hold all your data /tmp/mydata, and your data that you want to burn is in the directory ~/data. You'll need to copy it all to the /tmp/mydata directory:

     tcsh> cp -a ~/data/* /tmp/mydata

     Then, create the ISO image:

     tcsh> cd /tmp/mydata
     tcsh> mkisofs -o /tmp/mydataimage.iso -l -R -L -V "" -P "" -p "" -A "" .

  2. Insert blank or re-writable media in top DVD drive.
  3. Burn the disk:

     tcsh> cdrecord dev=1,0,0 -v speed=8 -pad -data /tmp/mydataimage.iso

• Intel Optimized compilers and libraries installed. The C/C++ compiler is icc, the Fortran compiler is ifc. The Math Kernel libraries are installed in ${INTEL_MKL_LIBDIR}. To use any of these libraries, you will need to add some options to your compilation command, e.g.

  icc -Wl,-R,${INTEL_CC_LIBDIR},-R,${INTEL_MKL_LIBDIR} -I${INTEL_CC_INCLUDEDIR} -I${INTEL_MKL_INCLUDEDIR} myprogram.C

  The "-Wl,-R,..." options are to tell the linker where the shared libraries are. (I haven't figured out how to modify a system wide setting to search for libraries.)
  A bit of experimenting seems to show that I need to use the LD_LIBRARY_PATH environment variable. That variable is now set in a system-wide cshrc file. Just type echo $LD_LIBRARY_PATH to see its current value. If it's undefined, log out and then back in, or just start up a new terminal. Just source your ~/.cshrc to get the new path and environment variables. There is also a debugger install, called idb. Browse the directories for documentation and examples.
• GRID tools are installed on Tenaya, Halfdome and Tioga. You will need GRID credentials to use the GRID.
• Notes on local disk space
• Access to home directories from Windows machines now available.
• Basic instructions on setting up your own web page.
• New web-mail system in place.

Available Applications

Local Disk Space

Each machine has local (not backed up) disk space for temporary data storage. There is about 10 GB of space per machine, except for Tenaya which has less. The directory on all machines is /storage. Local disk is useful if you would like to reduce I/O overhead for your code: I/O access to your home directory is via the network, which has much less bandwidth and higher latency than local disk.

This storage area is also available to other machines via the network. Simply change directory to /automnt/machine_name/storage to access any machine's storage area.

User Setup

Mail

Click the link above for instructions on setting up your email program. OR, try our web-mail system, instead.

Printers

Most printers are available. There seems to be a problem printing to ocsbw, though, and the problem is not resolved, yet. (2002-Feb-01)

Personal Web space

All your HTML files should live in ~/public_html/, and they should have world-readable permissions. (Do chmod -R ugo+r ~/public_html to accomplish this. You should not have to do this unless you have changed the default.)

OpenOffice.org (was StarOffice)

OpenOffice.org is the open-source replacement for StarOffice. It has very good support for Microsoft Office documents. To use OpenOffice.org, you need to run an initial setup in your home directory:

                /usr/local/OpenOffice.org/program/setup 

and then choose "Standard Workstation Installation" when prompted.

Migrating from HPs

The HP home directories are NFS mounted on Tenaya. To find out which directory on Tenaya your HP home is, type the following while logged into your HP account:

                df -k ~

The result should be something like:

            /n/physics/mhpbob/std2 (mhpbob.physics.lsa.umich.edu:/usr/vg01/std2) :  2975394 total allocated Kb
                                              711484 free allocated Kb
                                             2263910 used allocated Kb
                                                  76 % allocation used

The value in parentheses, mhpbob.physics.lsa.umich.edu:/usr/vg01/std2 in the above example, will determine which directory on Tenaya your HP files are. In the above example, your home directory will be in:

            /tmp_mnt/mhpbob/std2/username

This will obviate the need for sftp.

Passwords

To change your password for all the Linux machines, log into Tenaya and use the "passwd" command. Do not use "yppasswd" on any machine (including Tenaya), or "passwd" on any machine (not including Tenaya).

Note: It is recommended that you change your password on the Linux machines as soon as you get your account. Doing this will store your password in a more secure format. The default format is quite easily crackable.

Local Disk Space

Each machine (except Tenaya) has two partitions for temporary data storage. This will remove NFS bottlenecks from your running time. The partitions are called /storage and /scratch. Of these two, /storage is backed up while /scratch is not.

Windows [New]

You may access your Linux home directory from a Windows machine. Your username will be same as in Linux, but your password will be independent of the Linux password. To connect, type

          \\tenaya\your_username

or

          \\tenaya.physics.lsa.umich.edu\your_username

Windows Partition (for dual-boot machines)

If your machine is a dual-boot machine, there will be a VFAT (Win95) partition that will be accessible to you. The partition is in the directory /win2kdata. You may share files between Linux and Windows by storing them on that partition, which will be the D: drive under Windows. Another solution is to use the Windows access feature described in the previous item.