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"LDAP Passwords" on linuxws
Last Updated: Mon, 20 May 2013 -Machines: linuxws pacman bigdipper fish
How to update your LDAP password ======================================== User authentication and login to ARSC systems uses University of Alaska (UA) passwords and follows the LDAP protocol to connect to the University's Enterprise Directory. Because of this, users must change their passwords using the UA Enterprise tools. While logging into ARSC systems, if you see the following message, please change your password on https://elmo.alaska.edu Password: Your are required to change your LDAP password immediately. Enter login(LDAP) password: Attempts to change your password on ARSC systems will fail. Please contact the ARSC Help Desk if you are unable to log into https://elmo.alaska.edu to change your login password.
"compilers" on linuxws
Last Updated: Wed, 21 Jun 2006 -Machines: linuxws
Compilers
========================================
The ARSC Linux Workstations have two suites of compilers available:
* The GNU Compiler suite version 4.0 including:
- gcc C compiler
- g++ C++ compiler
- gfortran Fortran 95 compiler
* The Portland Group (PGI) compiler suite version 6.1 including:
- pgcc C compiler
- pgCC C++ compiler
- pgf90 Fortran 90 compiler
- pgf95 Fortran 95 compiler
The PGI compilers require several environment variables to be set:
For ksh/bash users:
===================
export PGI=/usr/local/pkg/pgi/pgi-6.1
pgibase=${PGI}/linux86-64/6.1
export PATH=$PATH:${pgibase}/bin
if [ -z "$MANPATH" ]; then
export MANPATH=${pgibase}/man
else
export MANPATH=${pgibase}/man:$MANPATH
fi
if [ -z "$LD_LIBRARY_PATH" ]; then
export LD_LIBRARY_PATH=${pgibase}/lib
else
export LD_LIBRARY_PATH=${pgibase}/lib:$LD_LIBRARY_PATH
fi
unset pgibase
For csh/tcsh users:
===================
setenv PGI /usr/local/pkg/pgi/pgi-6.1/
set pgibase=${PGI}/linux86-64/6.1
setenv PATH ${PATH}:${pgibase}/bin
if ( ! ${?MANPATH} ) then
setenv MANPATH ${pgibase}/man
else
setenv MANPATH ${pgibase}/man:${MANPATH}
endif
if ( ! ${?LD_LIBRARY_PATH} ) then
setenv LD_LIBRARY_PATH ${pgibase}/lib
else
setenv LD_LIBRARY_PATH ${pgibase}/lib:${LD_LIBRARY_PATH}
endif
unset pgibase
"modules" on linuxws
Last Updated: Mon, 28 Dec 2009 -Machines: linuxws
Using the Modules Package
=========================
The modules package is used to prepare the environment for various
applications before they are run. Loading a module will set the
environment variables required for a program to execute properly.
Conversely, unloading a module will unset all environment variables
that had been previously set. This functionality is ideal for
switching between different versions of the same application, keeping
differences in file paths transparent to the user.
The following modules commands are available:
module avail - list all available modules
module load <pkg> - load a module file from environment
module unload <pkg> - unload a module file from environment
module list - display modules currently loaded
module switch <old> <new> - replace module <old> with module <new>
module purge - unload all modules
Before the modules package can be used in a script, its init file may
need to be sourced.
To do this using tcsh or csh, type:
source /usr/local/pkg/modules/init/<shell>
To do this using bash, ksh, or sh, type:
. /usr/local/pkg/modules/init/<shell>
For either case, replace <shell> with the shell you are using.
If your shell is bash, for example:
. /usr/local/pkg/modules/init/bash
Known Issues:
=============
2009-09-24 Accounts using bash that were created before 9/24/2009
are missing the default ~/.bashrc file. This may cause
the module command to be unavailable in some instances.
Should you experience this issue run the following:
# copy the template .bashrc to your account.
[ ! -f ~/.bashrc ] && cp /etc/skel/.bashrc ~
If you continue to experience issues, please contact the
ARSC Help Desk.
"pubkeys" on linuxws
Last Updated: Sun, 19 Dec 2010 -Machines: linuxws
Setting up SSH Public Authentication on Linux/UNIX Systems
===========================================================
SSH public key authentication is available on ARSC Academic systems
as an alternative to SecurID authentication. This method of authentication
allows you to log into ARSC Academic systems (e.g. pacman, midnight,
bigdipper) using a password, removing the need for a hardware
authentication mechanism. The following guide describes the procedure for
enabling SSH public key authentication for your workstation account.
Linux and Mac Systems Instructions
==================================
Step #1 - Generate an SSH Key Pair on Your Local System
Note: If you have existing SSH keys on your system, you may want to back
them up before generating a new key pair.
The SSH installation on your local system should have come with an
executable named "ssh-keygen". Use this command to generate an SSH
public/private key pair:
$ ssh-keygen
This program will prompt you for the location to save the key. The rest
of this guide will assume you chose the default location,
$HOME/.ssh/id_rsa.
You will then be prompted to enter a password. Please choose a long
password with multiple character classes (e.g., lowercase letters,
uppercase letters, numbers, and/or symbols). After you set your password,
the program will write two files to the location you specified:
Private Key: $HOME/.ssh/id_rsa
Public Key: $HOME/.ssh/id_rsa.pub
Do not share your private key. Take precautions to make sure others
cannot access your private key.
Step #2 - Transfer Your Public Key to Pacman, Midnight, Linux Workstations, etc.
ARSC has developed a tool, "ssh-keymanage", to help you comply with our
security policies while adding your SSH public keys to linux workstations.
When a public key is added to your account on the workstations, it must be
associated with a particular system that is allowed to authenticate with that
key. This is accomplished via SSH's "from=" clause, which is tied to a public
key when it is inserted into SSH's authorized_keys file.
The basic usage for adding a public key to a workstation with the
ssh-keymanage tool is:
ssh-keymanage --add <keyfile> --host <hostname>
This usage assumes that you have already transferred the public key you
generated in Step #1 to the workstation. You will also need to know your local
system's full hostname (e.g., "sysname.uaf.edu").
Alternatively, the following command can be used to transfer and add your
key to a workstation all at once:
cat ~/.ssh/id_rsa.pub | ssh -tt username@mallard.arsc.edu ssh-keymanage --add /dev/stdin --host sysname.uaf.edu
Step #3 - Enable SSH Public Key Authentication on Your Local System
Workstations are already configured to allow SSH public key authentication on
the server side, but you will need to make sure the SSH client on your local
machine is configured to allow SSH public key authentication. There are
several ways to do this, including:
a) Adding an option to your SSH command when you connect to a workstation:
ssh -o PubkeyAuthentication=yes username@mallard.arsc.edu
b) Adding the following to your $HOME/.ssh/config file as a long-term
solution:
Host mallard.arsc.edu
PubkeyAuthentication yes
Windows Instructions
====================
Step #1 - Generate an SSH Key Pair on Your Local System
Note: If you have existing SSH keys on your system, you may want to back
them up before generating a new key pair.
You will need to use PuTTY's "puttygen.exe" program to generate a key
pair. If you installed the HPCMP Kerberos Kit in the default location,
you can run this program by clicking Start -> Run and entering the
following into the "Open" text box:
"C:\Program Files\HPCMP Kerberos\puttygen.exe"
Next, click the "Generate" button in this program. This will prompt you
to move the mouse around to generate randomness to create a unique key
pair. This may take you a few minutes. Once this process is complete,
you will be shown the public key for your SSH key pair.
Please enter a password for your key pair by filling out both the "Key
passphrase" and "Confirm passphrase" text boxes. Choose a long password
with multiple character classes (e.g., lowercase letters, uppercase
letters, numbers, and/or symbols).
Then, click the "Save private key" button. You are free to choose the
file name and location of the private key. This guide will assume you
saved the private key as "private.ppk" in your "My Documents" folder. Do
not share your private key. Take precautions to make sure others cannot
access your private key. Proceed to Step #2, but do not close the "PuTTY
Key Generator" yet.
Step #2 - Transfer Your Public Key to the workstations
Log into a workstation with your SecurID card and open your favorite text
editor. Copy the text in the "Public key for pasting into OpenSSH
authorized_keys file" text area on the "PuTTY Key Generator" window.
Paste this text into the text editor on a workstation and save this to a
temporary file. This guide will assume you named the file "pubkey".
ARSC has developed a tool, "ssh-keymanage", to help you comply with our
security policies while adding your SSH public keys to a workstation. When a
public key is added to your account on the workstation, it must be associated
with a particular system that is allowed to authenticate with that key. This
is accomplished via SSH's "from=" clause, which is tied to a public key
when it is inserted into SSH's authorized_keys file.
The basic usage for adding a public key to the workstation with the
ssh-keymanage tool is:
ssh-keymanage --add <keyfile> --host <hostname>
You will need to know your local system's full hostname (e.g.,
"sysname.uaf.edu"). For example:
ssh-keymanage --add pubkey --host sysname.uaf.edu
This command will report whether the key was successfully added. Once the
public key has been added, type "exit" to close PuTTY.
Step #3 - Add Your Private Key to PuTTY
Launch PuTTY again. Click the + sign next to "SSH", under the
"Connection" category. Click the "Auth" section under the SSH
subcategory. Click the "Browse..." button under "Private key file for
authentication" and select your private key file, "private.ppk". Go back
to the "Session" category and enter workstation name under "Host Name".
If you do not want to enter your private key every time you run PuTTY, you
may wish to save your session settings by entering a name under "Saved
Sessions" (e.g., "Workstation (pubkey auth)") and clicking "Save". The next
time you run PuTTY, you can reload these settings by selecting your saved
session and clicking "Load".
Finally, click "Open". Instead of being prompted for a SecurID passcode,
you should be prompted for the password you set on your key pair in
Step #1. Enter your key pair password. You should now be logged into
the workstation.
"software" on linuxws
Last Updated: Tue, 17 Feb 2009 -Machines: linuxws
Software on Linuxws
========================================
matlab: matlab-R2012a (2012-12-07)
Matlab version R2012a is now available to UAF users via modules:
module load matlab/R2012a
comsol: comsol-4.3a (2012-12-07)
The newest comsol release is now available to UAF users via modules:
module load comsol/4.3a
R: R-2.15.0 and R-2.15.1 (2012-08-03)
The two newest releases of R are now available.
Load the module to access your preferred version:
module load r/2.15.0
module load r/2.15.1
totalview: totalview-8.10.0-0 (2012-05-23)
The newest release of the Totalview Debugger is now available with
CUDA support. Load the module to access the newest version:
module load totalview/8.10.0-0
python: python-2.7.2 (2012-04-20)
Version 2.7.2 of python is now available via modules
module load python/2.7.2
idl/envi: idl-8.1 (2012-02-10)
Idl/envi version 8.1 is now available via modules
module load idl/8.1
comsol: comsol-4.2a.update2 (2012-01-13)
The newest comsol release is now available via modules
module load comsol/4.2a.update2
totalview: totalview.8.9.1-0 (2011-12-08)
Totalview Debugger version 8.9.1-0 is now available on the linux
workstations. Launch the softwar by first loading the module:
module load totalview/8.9.1-0
matlab: matlab-R2011b (2011-12-06)
Matlab version R2011b is now available to UAF users and
can be loaded via modules:
module load matlab/R2011b
R: R version 2.13.2 (2011-11-28)
A newer version is now available via modules:
module load r/2.13.2
comsol: comsol-4.2a (2011-11-02)
The newest comsol release is now available via modules
module load comsol/4.2a
automake: automake-1.11.1 (2011-11-01)
Automake version 1.11.1 has been installed in the following location:
/usr/local/pkg/automake/automake-1.11.1/bin
autoconf: autoconf-2.68 (2011-11-01)
Autoconf version 2.68 has been installed in the following location:
/usr/local/pkg/autoconf/autoconf-2.68/bin
visit: visit 2.3.2 (2011-10-17)
Visit 2.3.2 is now available available on Linux Workstation
via modules:
module load visit/2.3.2
ncl: ncl 6.0.0 (2011-10-17)
NCL 6.0.0 is now available available on Linux Workstation
via modules:
module load ncl/6.0.0
ncview: ncview 2.0 (2011-07-19)
Ncview version 2.0 is now available via modules
module load ncview/2.0
abaqus: abaqus 6.11 (2011-07-19)
The newest abaqus release is now available via modules
module load abaqus/6.11
comsol: comsol-4.2 (2011-06-08)
The new comsol release is now available via modules
module load comsol/4.2
matlab: matlab-7.10.0 (R2010a) (2010-10-20)
Matlab 7.10.0 is now available to UAF users. A module is
available for this software and can be loaded with:
module load matlab-7.10.0
After loading the module, type 'matlab' at the prompt
to open a new matlab session.
mexnc: mexnc-r3240 (aka mexcdf) (2010-10-07)
Mexnc/mexcdf is now available. To use this software
with matlab, first load the matlab-7.8.0 module
then enter the following at the matlab prompt:
addpath /usr/local/pkg/mexnc/mexcdf-r3240/mexnc
comsol: comsol-4.0a (2010-09-20)
The newest version of comsol is now available in
/usr/local/pkg/comsol/comsol-4.0a.
idl: idl-7.1 (2010-05-17)
idl 7.1 is now available on the linux workstations. A
module is available as idl-7.1 for use.
gsl: gsl-1.13 GNU Scientific Library 1.13 (2010-01-14)
The newest version of GSL is now available. This version
was compiled using the GNU compiler and is now available
on the Workstations in the following location:
/usr/local/pkg/gsl/gsl-1.13/
pgi: pgi-9.0.4 (2010-01-11)
The pgi 9.0.4 compiler is now available via the
pgi-9.0.4 module.
paraview: paraview-3.6.2 (2010-01-11)
Paraview 3.6.2 is now available via the paraview-3.6.2
module.
vapor: vapor-1.5.0 (2009-10-21)
Vapor 1.5.0 is now available via the vapor-1.5.0 module.
paraview: paraview-3.6.1 (2009-10-20)
Paraview 3.6.1 is now available via the paraview-3.6.1
module.
idv: idv-2.7u2 (2009-10-20)
idv 2.7 update 2 is now available via the idv-2.7u2 module.
subversion: subversion-1.6.3 (2009-09-03)
The latest version of subversion is available via the
subversion-1.6.3 module.
google-earth: google-earth-5.0 (2009-08-31)
Google Earth 5.0 is now available on the Workstations in the
following location:
/usr/local/pkg/google-earth/google-earth-5.0
ncl: ncl-5.1.1 (2009-08-05)
The latest version of ncl is now available via the "ncl-5.1.1"
module.
git: git-1.6.1.3 (2009-07-28)
git 1.6.1.3 is now available. This package is available
by loading the "git-1.6.1.3" module.
abaqus: Abaqus 6.9 (2009-07-09)
Abaqus 6.9 is now available. This package is available
by loading the "abaqus-6.9" module.
matlab: matlab-7.8.0 (2009-06-19)
Matlab 7.8.0 is now available. A module is
available for this software and can be loaded with:
module load matlab-7.8.0
After loading the module, type 'matlab' at the prompt
to open a new matlab session.
cmake: cmake-2.6.4
The latest version of cmake is available via the cmake-2.6.4
module.
blender: blender-2.48a
Blender 2.48a is now available on the Workstations. It is
available in a module, as blender-2.48a
avizo: avizo-6.0 (2009-04-30)
Avizo 6.0 is now available in the following directory:
/usr/local/pkg/avizo/avizo60
visit: visit-1.11.2 (2009-04-29)
VisIt 1-11.2 is now available via the "visit-1.11.2" module.
ncl: ncl-5.1.0 (2009-04-29)
The latest version of ncl is now available via the "ncl-5.1.0"
module.
paraview: paraview-3.4.0 (2009-03-10)
Paraview 3.4.0 is now available. It can be accessed with the
paraview-3.4.0 module file and is located in the
/usr/local/pkg/paraview/paraview-3.4.0 directory.
visit: visit-1.11.1 (2009-03-02)
VisIt is now available in /usr/local/pkg/visit/visit-1.11.1
Module files are available as both "visit" and "visit-1.11.1"
comsol: comsol-3.5a (2009-02-06)
The newest version of comsol is now available in
/usr/local/pkg/comsol/comsol-3.5a. This version appears
to resolve the previous errors when starting the software.
matlab: matlab-7.7.0 (2009-02-05)
The latest version of Matlab is available for
use by loading the matlab-7.7.0 module.
matlab: matlab-7.6.0 (2008-07-24)
The latest version of Matlab is available for
use by loading the matlab-7.6.0 module.
paraview: paraview-3.0.2 (2007-09-19)
Paraview version 3.0.2 has been installed into
/usr/local/pkg/paraview/paraview-3.0.2. It is
available via a module (paraview-3.0.2).
acml: acml-3.6.0 & acml-4.0.0 AMD Core Math Library (2007-09-14)
The ACML has been installed and is available in
/usr/local/pkg/acml. The following versions were installed:
acml-3.6.0.gcc
acml-3.6.0.pgi
acml-4.0.0.gcc
These libraries are available as of Sep 14th, 2007 and
the current link was set to point to acml-3.6.0.gcc.
idv: idv-2.2: Integrated Data Viewer (2007-07-28)
The new version of idv(2.2) has been installed
in /usr/local/pkg/idv/idv-2.2 and will be made
the default version on July 12th, 2007.
"storage" on linuxws
Last Updated: Mon, 19 Jun 2006 -Machines: linuxws
Linux Workstation Storage
========================================
The environment variables listed below represent paths. They are
expanded to their actual value by the shell, and can be used in commands
(i.e. ls $ARCHIVE). From the command prompt the value and the variable
are usually interchangeable. However, in non-shell settings like ftp
you will need to use the actual path, not the variable.
In the listing below, $USER is an environment variable holding your
ARSC username.
Filesystem Purpose Purged Backed Up Quota
------------- ---------------------- ------- ---------- ------
$HOME shared filesystem No Yes 4 GB
$WRKDIR temp filesystem Yes No None (1)
$WORKDIR
$SCRATCH
$ARCHIVE long term storage No Yes None
$ARCHIVE_HOME
NOTES:
(1) Use is limited by the available space on the disk.
Environment Variable Definitions
=================================
Variable Definition
-------------- ---------------------
$HOME /u1/uaf/$USER or
/u2/wes/$USER or
/u2/red/$USER
$WRKDIR /scratch/$USER
$WORKDIR /scratch/$USER
$SCRATCH /scratch/$USER
$ARCHIVE /archive/$HOME
$ARCHIVE_HOME /archive/$HOME
-- Home directories are intended primarily for basic account info
(e.g. dotfiles). Please use $WRKDIR (your /scratch/$USER directory)
for compiles, inputs, outputs, etc.
* The 'quota' command will show quota information for your $HOME
directory.
-- The $WRKDIR or $SCRATCH directories are local to each machine. (On the
Linux Workstations these two variables both point to the same
location.) When moving to another machine you will also need to move
your files. This file system not backed up, files not accessed in
over 30 days are purged (deleted).
-- Your $SCRATCH directory is not created by default. If one does
not exist on the machine you are using, type 'mkdir $SCRATCH' to
create one.
-- Purging: Files not accessed in over 30 days in $WRKDIR ($SCRATCH)
directories are purged, and these directories are not backed up.
Please store what you want to keep in $ARCHIVE.
-- Long-term backed up storage is only available in your $ARCHIVE
directory. No other directories are backed up. As this is an
NFS-mounted filesystem from bigdipper, files will be temporarily
unavailable when bigdipper is taken down for maintenance. I/O
performance in this directory may be much slower. Compiles and runs in
$ARCHIVE are not recommended.
See http://www.arsc.edu/support/howtos/storage.html for more information
on storage policies at ARSC.