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ARSC news items for linuxws
Contents
News Items
"news compilers" on 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
- f95 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
-Donald Bahls, 21 June 2006
[This news item valid until June 2007]
"news downtime" on linuxws
Downtime
========
This file contains a description of the next scheduled downtime
for preventive maintenance, and the most recent system downtime
and/or network interruption. All times are Alaska Time. Contact
consult@arsc.edu or 907-450-8602 for more information.
=======================================================================
NEXT SCHEDULED DOWNTIME(S)
-----------------------
25 JUN 2008 SCHEDULED DOWNTIME
machine(s): nanook ($HOME and $ARCHIVE_HOME server)
start time: 18:00
end time: 22:00
reason: Reboot to enable IPv6 functionality.
MOST RECENT DOWNTIME(S)
--------------------------
11 JUN 2008 SCHEDULED DOWNTIME
machine(s): nanook ($HOME and $ARCHIVE_HOME server)
start time: 18:00
end time: 22:00
reason: Firmware upgrades.
17 MAY 2008 SCHEDULED DOWNTIME
machine(s): Linux Workstations (and all ARSC systems)
start time: 17:00 MAY 17
end time: 17:00 MAY 18
reason: The machine room will undergo power maintenance.
16 APR 2008 SCHEDULED DOWNTIME
machine(s): Linux Workstations ($HOME, $ARCHIVE_HOME, $PROJECTS directories)
start time: 18:00
end time: 18:30
reason: The $HOME, $ARCHIVE_HOME and $PROJECTS directories will be
unmounted temporarily. Total duration of this outage should
be around 10 minutes.
09 APR 2008 SCHEDULED DOWNTIME
machine(s): Linux Workstations
start time: 18:00
end time: 22:00
reason: Possible disruption of network service during switch reboots.
27 MAR 2008 UNSCHEDULED DOWNTIME
machine(s): nanook ($HOME and $ARCHIVE_HOME server)
start time: 17:00
end time: 17:20
reason: Rebooted nanook to fix hanging $ARCHIVE_HOME file system
on linux workstations.
12 MAR 2008 SCHEDULED DOWNTIME
machine(s): nanook ($HOME and $ARCHIVE_HOME server)
start time: 18:00
end time: 22:00
reason: SL8500 firmware upgrade.
11 FEB 2008 SCHEDULED DOWNTIME
machine(s): linux workstations
start time: FEB 11, 17:00
end time: FEB 12, 17:00
reason: Emergency system maintenance.
Update: 13 FEB 2008
Maintenance is now completed on all publicly
accessible workstations.
23 JAN 2008 SCHEDULED DOWNTIME
machine(s): nanook and therefore all linux workstations
start time: 18:00
end time: 22:00
reason: Repair of lnxhome filesystem. Workstations may
temporarily hang during this maintenance.
* For a log of past downtimes, type: less /var/news/LOGS/downtime.log
Then press "space bar" to advance a page or "q" to quit.
==========================================================================
-Donald Bahls, 24 April 2006
[This news item valid until April 2007]
"news filezilla" on linuxws
Filezilla
=========
This news item is for users of the Filezilla ftp client which is
included with the HPCMP Kerberos kit for Windows.
Some users have reported problems connecting to the Linux Workstations
with the Filezilla client. Should you experience these problems
with Filezilla, try the following:
Option 1) Set the transfer mode to passive:
a) Select the menus "Edit | Settings"
b) Select the tree option "Firewall Settings "
c) Then check the passive mode check box
Option 2) Set the ftp protocol to sftp:
a) Select the menus "File | Site Manager"
b) Click "New Site" button. Enter the machine name.
c) Fill in the "host" (e.g. iceberg.arsc.edu)
d) Set "Servertype" to "SFTP using SSH2"
e) Set "Logontype" to "Normal"
f) Set the "User" to your username.
g) Click the "Connect" button to connect.
Sites entered in the Site Manager can be also be selected using the
leftmost icon on the Filezilla toolbar.
If you experience problems with the Filezilla client using these
recommendations, please report them to the ARSC help desk
(consult@arsc.edu).
-Donald Bahls, 22 February 2008
[This news item valid until February 2009]
"news idl" on linuxws
IDL at ARSC
===========
IDL is installed at ARSC on the Linux workstations and iceberg.
To run, you must first make sure the following two steps are done:
1) Files named idl_setup and idl_setup.ksh are
automatically created by the installation script. These
files contain appropriate definitions for IDL-related
environment variables and aliases. Users must set up their
accounts as shown below:
C-shell users add the line:
source /usr/local/pkg/idl/idl-6.2/idl/bin/idl_setup
source /usr/local/pkg/idl/idl-6.2/envi/bin/envi_setup
to your .cshrc files.
Korn shell users add the line:
. /usr/local/pkg/idl/idl-6.2/idl/bin/idl_setup.ksh
. /usr/local/pkg/idl/idl-6.2/envi/bin/envi_setup.ksh
to your .profile files.
Bash shell users add the line:
. /usr/local/pkg/idl/idl-6.2/idl/bin/idl_setup.bash
. /usr/local/pkg/idl/idl-6.2/envi/bin/envi_setup.bash
to your .bashrc files.
2) Make sure the license variable is set correctly, if not add this
line to the same file as listed above for your shell:
C-shell (csh, tcsh)
setenv LM_LICENSE_FILE 7111@license1.arsc.edu:7111@license.arsc.edu
Korn shell (ksh)
export LM_LICENSE_FILE=7111@license1.arsc.edu:7111@license.arsc.edu
Bash shell (bash)
export LM_LICENSE_FILE=7111@license1.arsc.edu:7111@license.arsc.edu
3) Some users have reported malloc errors with the 64 bit version
on envi and idl. We are currently investigating these errors.
Should you encounter a malloc error try using the 32 bit version of
idl or envi.
The "-32" flag will invoke the 32 bit executable:
e.g.
% idl -32
-Andrew Lee, 25 April 2006
[This news item valid until April 2007]
"news modules" on 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.
Before the modules package can be used, its init file must first 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
Once the modules init file has been sourced, the following commands
become 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
-Craig R. Stephenson, 27 November 2006
[This news item valid until November 2007]
"news software" on linuxws
software
========
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-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-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.
-Alec Bennett, 28 June 2007
[This news item valid until June 2008]
"news storage" on 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 256 MB
$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 'qcheck' command will show quota information for your $HOME
directory. This command requires that you have an account on
nanook, please contact the help desk should you need your account
activated.
* "qcheck -k" will show quota information in kilobytes rather than
blocks.
-- 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 nanook, files will be temporarily
unavailable when nanook goes down for maintenance. I/O performance
in this directory will 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.
-Donald Bahls, 19 June 2006
[This news item valid until June 2007]
These items were uploaded on 20080708 at 19:47:44. News items are available for other systems.
Arctic Region Supercomputing Center
PO Box 756020, Fairbanks, AK 99775 | voice: 907-450-8600 | email: 
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