I Do Linux

Fedora 16 Xfce on an Eee PC

2012-01-19T22:04:00.002-05:00

Here are some notes from a recent install of Fedora 16, 64-bit, on an Asus Eee PC 1015PEM Seashell netbook. This system has a 64-bit 1.5 GHz Intel Atom N550 processor. I skipped Gnome 3 and went with the Xfce Spin.

Create installation media by downloading the ISO of the Fedora 16 Xfce Spin 64-bit. A bootable USB drive can be prepared with liveusb-creator. To boot the installer, insert the prepared liveusb drive into the left USB port and hit the Esc key after powering on. This brings up the boot menu where the drive can be selected. The Linux install should be mostly defaults, except that disk encryption and a grub password should be enabled.

After an install and reboot, plug into a wired network connection, install the RPM Fusion software repository, do the first big system software update, then install some additional packages. Note that kmod-wl from RPM Fusion provides the driver for the Broadcom wireless card after a reboot.

# yum -y install yum-fastestmirror
# yum -y update
# yum localinstall --nogpgcheck \
http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-stable.noarch.rpm \
http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-stable.noarch.rpm
# yum install kmod-wl akmod-wl krb5-workstation tkinter \
python-setuptools ipython mysql-workbench gconf-editor git \
subversion ethtool liveusb-creator telnet freeglut-devel \
gcc gcc-c++ SDL-devel rdesktop thunderbird thunderbird-enigmail \
vim fortune-mod lsb redhat-lsb-graphics qt-x11 powertop dosbox \
tigervnc tigervnc-server audacity-freeworld rdiff-backup \
samba-client rtorrent unrar \
libreoffice-writer libreoffice-calc libreoffice-impress \
screen nmap net-snmp-utils wireshark-gnome iptraf strace sysstat \
gimp rpmdevtools yum-utils ncurses-devel \
libpng-devel mednafen jwhois java-1.6.0-openjdk-plugin wget \
ddrescue wodim vlc mplayer mencoder grip lame easytag id3v2 \
lm_sensors xterm xorg-x11-xinit-session xorg-x11-apps

The biggest tip with a 10" netbook is to consolidate and auto-hide menus/toolbars for maximum screen real estate. And when sitting at a desk, use a full-sized LCD monitor. The screen space issue is one of the main reasons I went with Xfce over Gnome 3. Gnome 3 wastes too much screen space with wide toolbars and window borders.

The trackpad is nice, supporting one, two and three-finger tapping. Enable this in the Xfce mouse preferences is not possible, though. Adding three lines to a config file fixes this, for easy copy-and-paste the way it was meant to be. On Linux, mouse button-one is highlight/select, copy being automatic, and button-three is paste. With a touchpad this is a double-tap with one finger and drag to select text, then a two-finger tap to paste.

/usr/share/X11/xorg.conf.d/50-synaptics.conf

Section "InputClass"
        Identifier "touchpad catchall"
        Driver "synaptics"
        MatchIsTouchpad "on"
        MatchDevicePath "/dev/input/event*"
        Option "TapButton1" "1"
        Option "TapButton2" "2"
        Option "TapButton3" "3"
EndSection

Now, one could stop here and be finished, but I'm interested in tweaking for power saving features, like the Super Hybrid Engine (SuperHE) features of this model.
To enable the Asus SuperHE power saving, we add a few scripts to the power management system.

/etc/pm/power.d/asus_she_power

#!/bin/sh
# /etc/pm/power.d/asus_she_power

cpufv="/sys/devices/platform/eeepc-wmi/cpufv"
lcd="/sys/devices/virtual/thermal/cooling_device4/cur_state"

case "$1" in
    true)
        echo "Super Hybrid Engine ENABLED"
        echo 2 > $cpufv
        echo 8 > $lcd
    ;;
    false)
        echo "Super Hybrid Engine DISABLED"
        echo 0 > $cpufv
        echo 0 > $lcd
    ;;
esac

exit 0

/etc/pm/sleep.d/asus_she_sleep

#!/bin/sh
# /etc/pm/sleep.d/asus_she_sleep
 
battery="/proc/acpi/ac_adapter/AC0/state"
ac="/sys/bus/acpi/drivers/ac/ACPI0003:00/power_supply/AC0/online"
 
case "$1" in
    thaw)
        if (test -e $battery); then
            if grep off-line "$battery" > /dev/null; then
                /etc/pm/power.d/asus_she_power true
            fi
        elif (test -e $ac); then
            if grep 0 "$ac" > /dev/null; then
                /etc/pm/power.d/asus_she_power true
            fi
        else
            /etc/pm/power.d/asus_she_power false
        fi
esac
 
exit 0

These two above scripts will trigger when plugging power and waking from suspend respectively. Don't forget to make them executable:

# chmod +x /etc/pm/sleep.d/asus_she_sleep /etc/pm/power.d/asus_she_power

With an SSD, we want to enable the noop scheduler. Edit /etc/default/grub and add the elevator option to the kernel line:

GRUB_TIMEOUT=5
GRUB_DISTRIBUTOR="Fedora"
GRUB_DEFAULT=saved
GRUB_CMDLINE_LINUX="rd.md=0 rd.dm=0  KEYTABLE=us rd.lvm.lv=vg_foo/lv_swap quiet rd.luks.uuid=luks-xxxxxxxx-xxxx-xxxx-xxxx SYSFONT=latarcyrheb-sun16 rhgb rd.lvm.lv=vg_foo/lv_root LANG=en_US.UTF-8 elevator=noop"

And rebuild the grub configuration:

# grub2-mkconfig -o /boot/grub2/grub.cfg

Enable noatime on ext4 file systems, and tmpfs for temporary directories in /etc/fstab:

/dev/mapper/vg_foo-lv_root / ext4 defaults,noatime 1 1
tmpfs /tmp tmpfs defaults,nodev,nosuid,size=256M 0 0
tmpfs /var/tmp tmpfs defaults,nodev,nosuid,size=64M 0 0
tmpfs /var/log tmpfs defaults,nodev,nosuid,size=32M 0 0

Some additional power and SDD saving tweaks:

# touch /etc/rc.d/rc.local
# chmod +x /etc/rc.d/rc.local

/etc/rc.d/rc.local

echo 1 > /proc/sys/vm/swappiness
echo 50 > /proc/sys/vm/vfs_cache_pressure
echo 1500 > /proc/sys/vm/dirty_writeback_centisecs
echo 20 > /proc/sys/vm/dirty_ratio
echo 10 > /proc/sys/vm/dirty_background_ratio
echo 0 > /proc/sys/kernel/nmi_watchdog
echo 1 > /sys/devices/system/cpu/sched_smt_power_savings
echo 1 > /sys/module/snd_hda_intel/parameters/power_save
echo 5 > /proc/sys/vm/laptop_mode
#echo noop > /sys/block/sda/queue/scheduler 
#for I in /sys/devices/system/cpu/cpu?/cpufreq/scaling_governor; do echo 'ondemand' >$I; done
#echo min_power > /sys/class/scsi_host/host0/link_power_management_policy
#ethtool -s eth0 wol d
#modprobe sdhci
#for I in `find /sys -name autosuspend -exec echo {} \;`; do echo "0" >"$I"; done
for I in `find /sys/devices -wholename "*pci*power/control" |grep -v "usb2"`; do echo 'auto' >"$I"; done

Disable some unused services on a laptop client machine:

# for s in abrtd-ccpp abrt-oops abrt-vmcore abrtd atd auditd avahi-daemon fcoe ip6tables iscsi livesys-late livesys lldpad mdmonitor-takeover sendmail sm-client; do echo $s; systemctl disable $s.service; done

If restoring a home directory from backup, with SELinux enabled, make sure to restore the security context of the home directories:

# restorecon -vr /home

Google Chrome is an excellent browser for a netbook. It is a very efficient in terms of performance speed and screen utilization. Download the rpm package from the Google website, then install it with yum to get all dependencies.

$ sudo yum install ~/Downloads/google-chrome-stable_current_x86_64.rpm

Skype is a must for video chat and international voice calling. Download the RPM from the Skype website, then use yum to install.

$ sudo yum install ~/Downloads/skype-2.2.0.35-fedora.i586.rpm

If you use Google Talk for chat, the voice and video plugin will allow you to do video calling to other Talk users and Android phones as well.

$ sudo yum install ~/Downloads/google-talkplugin_current_x86_64.rpm

To get the latest version of 64-bit Flash, install the Adobe repo, then the plugin package.

# yum install http://linuxdownload.adobe.com/adobe-release/adobe-release-x86_64-1.0-1.noarch.rpm
# yum install flash-plugin

One gripe I have about the Xfce desktop is that it uses Xscreensaver, which has the ugliest circa-1980 unlock screen. I found if the xscreensaver packages were removed and X reloaded, the system will default to the much nicer gnome-screensaver. Note that there is no auto-lock or preferences with this option. I manually use a Lock Screen button on my toolbar panel.

# yum remove xscreensaver*

If using Thunderbird, you may have to tell it to use Chrome for web links with this quick fix:

$ xdg-mime query default x-scheme-handler/http
$ xdg-mime default google-chrome.desktop x-scheme-handler/http
$ xdg-mime default google-chrome.desktop x-scheme-handler/https

You can change video modes from the command line when cabling to an external monitor or video projector. Stick these aliases into your ~/.bashrc file:

alias vga='xrandr --fb 1280x1624 --output LVDS1 --primary --mode 1024x600 --rate 60 --pos 0x0 --panning 0x0 --output VGA1 --mode 1280x1024 --rate 60 --pos 0x1024 --above LVDS1'
alias mir='xrandr --fb 1280x1024 --output LVDS1 --primary --mode 1024x600 --rate 60 --pos 0x0 --panning 1280x1024 --output VGA1 --mode 1280x1024 --rate 60 --pos 0x0 --same-as LVDS1'
alias lcd='xrandr --fb 1024x600  --output LVDS1 --primary --mode 1024x600 --rate 60 --output VGA1 --off'

After using Xfce for a few days, I'm liking it.

For further details on Fedora 16, I recommend reading the Release Notes, particularly the section on Changes for System Administrators.

Grid Engine Config Tips

2011-12-17T16:30:00.000-05:00

Here are some of the Grid Engine configuration steps we should take on a new install. I recommend doing all of these from the very beginning, to prevent changes that may change or break user workflow.

There is one thing I will always do with a new compute cluster, and that is enable hard memory limits. Users are usually not too keen on any kind of limit, because jobs will eventually run into them. Once you realize limits ensures node stability and uptime, users will want them. Without limits, one bad job can crash a node and bring down many other jobs.

To enable hard memory limits, we modify the complex configuration to make h_vmem requestable.

# qconf -mc
h_vmem              h_vmem     MEMORY      <=    YES         YES        1g       0

Once this complex is set, it is a good idea to define a default option for qsub in the /usr/global/sge/default/common/sge_request file. When enabling h_vmem, we should also set a default value for h_stack. h_vmem sets a limit on virtual memory, while h_stack sets a limit on stack space for binary execution. Without a sufficient value for h_stack, programs like Python, Matlab or IDL will fail to start.

-q all.q
-l h_vmem=1g
-l h_stack=128m

If we want to manually set values for each individual node, like slots and memory, a for-loop is very helpful.

# qconf -rattr exechost complex_values slots=8,h_vmem=8g node01
# for ((I=1; I <= 16 ; I++)); do 
> NODE=`printf "node%02d\n" $I`
> MEM=`ssh $NODE 'free -b |grep Mem |cut -d" " -f 5'`
> SWAP=`ssh $NODE 'free -b |grep Swap |cut -d" " -f 4'`
> VMEM=`echo $MEM+$SWAP|bc`
> qconf -rattr exechost complex_values slots=8,h_vmem=$VMEM $NODE
> done

To submit a job with a 4 gig limit, use the -l command line option.

$ qsub -l h_vmem=4g -l h_stack=256m myjob.sh

To see available memory, use qstat.

$ qstat -F h_vmem

It is also a good idea to place limits on the amount of memory any single process on the login node may allocate, in the /etc/security/limits.conf file. This example will limit any user in the clusterusers group to 4 gigs per process. Anything larger should be ran via qlogin. When adding new users, make sure to add them to this group.

# limit any process to 4GB = 1024*1024*4KB = 4194304
@clusterusers      hard    rss             4194304
@clusterusers      hard    as              4194304

Not only should there be a limit on memory, there should also be a limit on how many jobs a single user may submit and run simultaneously.

# qconf -msconf
 max_reservation 128
 maxujobs 128

If the queue will be accepting multi-slot parallel jobs, slot reservation should be enabled to prevent starvation, by submitting multi-slot jobs with the “-R y" option.

To enable a simple fairshare policy between all users, there are only three options to check:

# qconf -mconf
enforce_user auto
auto_user_fshare 100
# qconf -msconf
weight_tickets_functional 10000

To be a bit more verbose, we should collect some job scheduler info.

# man sched_conf
# qconf -msconf
 schedd_job_info true

Now we can see why or why not a job is scheduled.

$ qstat -j 427997
$ qacct -j 427997

If we plan to allow graphical GUI programs in the queue, we must setup a qlogin wrapper script with proper X11 forwarding.

# vim /usr/global/sge/qlogin_wrapper
# chmod +x /usr/global/sge/qlogin_wrapper

qlogin_wrapper:

#!/bin/sh
HOST=$1
PORT=$2
shift
shift
echo /usr/bin/ssh -Y -p $PORT $HOST
/usr/bin/ssh -Y -p $PORT $HOST

Set the qlogin wrapper and ssh shell:

# qconf -mconf
 qlogin_command /usr/global/sge/qlogin_wrapper
 qlogin_daemon /usr/sbin/sshd -i

Here are some handy aliases I find useful in my ~/.bashrc file:

alias qconf-all='qconf -mq all.q'
alias qconf-offline='echo "all.q@nodeXX" ; \qconf -rattr queue slots 0' # all.q@node23
alias qconf-online='echo "all.q@nodeXX" ; \qconf -rattr queue slots 8' # all.q@node23
alias qstat-errors='\qstat -f -explain E'
alias qstat-summary='\qstat -g c'
alias qstat-mem='qstat -F h_vmem'
alias qstat-ext='qstat -ext'
alias qstat-io='qstat -ext | awk '"'"'{print $11 "  " $5 "  " $1}'"'"' | grep -v "\-\-" | sort -n'
alias qmod-clear='\qmod -c "*"'

And done. If you have some must-do configuration steps, please post them in the comments bellow.

GPGPU with AMD

2011-12-14T19:41:00.003-05:00

GPGPU (General Purpose Graphics Processing Unit) is a high performance computing solution which off-loads heavy floating-point computation to the video card. OpenCL is a cross-platform cross-vendor solution for parallel computing with various kinds of coprocessors such a GPU video card.

Here, we will be configuring an AMD FireStream 9250 GPU Compute Accelerator which provides over 1 TFLOPS of computing power. The target operating system is Scientific Linux 6 x86_64, which is Red Hat Enterprise Linux 6 compatible.

You can verify the model of GPU installed with the lspci command:

# lspci | grep VGA
07:00.0 VGA compatible controller: ATI Technologies Inc RV770 [FireStream 9250]

To find the latest graphics driver, head over to the AMD driver download page. The current version is the AMD Catalyst 11.12 Proprietary Linux x86 Display Driver. Once we have the URL of the driver we can begin.

# mkdir /usr/local/src/amd ; cd /usr/local/src/amd
# wget http://www2.ati.com/drivers/linux/ati-driver-installer-11-12-x86.x86_64.run
# chmod +x ati-driver-installer-11-12-x86.x86_64.run
# ./ati-driver-installer-11-12-x86.x86_64.run --buildpkg RedHat/RHEL6_64a
# yum -y install fglrx64_p_i_c-8.92-1.x86_64.rpm
# aticonfig --initial -f

We may need to tweak the GDM setting to allow remote users access to the GPU with the /etc/gdm/custom.conf config file:

[servers]
0=Rendering
[server-Rendering]
command=/usr/bin/Xorg -br -ac -audit 0
flexible=true

An we also may need to allow permissions to direct rendering for shell users in the /etc/X11/xorg.conf config file:

Section "DRI"
Mode 0666
EndSection

Now to restart the display and verify that the FireGL module is in use.

# killall -9 gdm-binary
# lsmod | grep fgl
fglrx                3154329  49
# grep FireGL /var/log/Xorg.0.log
(II) Module fglrx: vendor="FireGL - ATI Technologies Inc."
(II) Module fglrxdrm: vendor="FireGL - ATI Technologies Inc."
(II) fglrx(0):     Desc: ATI FireGL DRM kernel module

Install the AMD APP SDK v2.5 with OpenCL:

# wget http://developer.amd.com/Downloads/AMD-APP-SDK-v2.5-lnx64.tgz
# mkdir AMD-APP-SDK-v2.5-lnx64 ; cd AMD-APP-SDK-v2.5-lnx64
# tar xzvf 
# ./Install-AMD-APP.sh

Install GPU-enabled BLAS and FFT, the AMD Accelerated Parallel Processing Math Libraries (APPML) v1.4.

# cd /usr/local/src/amd
# wget http://developer.amd.com/Downloads/clAmdBlas-1.4.182-Linux.tar.gz
# wget http://developer.amd.com/Downloads/clAmdFft-1.4.182-Linux.tar.gz
# wget http://developer.amd.com/Downloads/LUDOpenCLBLAS-Linux.zip
# wget http://developer.amd.com/Downloads/ObjectDetection-Linux.zip
# mkdir clAmdBlas-1.4.182-Linux ; cd clAmdBlas-1.4.182-Linux
# tar xzvf ../clAmdBlas-1.4.182-Linux.tar.gz
# ./install-clAmdBlas-1.4.182.sh
# cd ..
# mkdir clAmdFft-1.4.182-Linux ; cd clAmdFft-1.4.182-Linux
# tar xzvf ../clAmdFft-1.4.182-Linux.tar.gz
# ./install-clAmdFft-1.4.182.sh

Verify everything is functioning.

# . /etc/profile.d/ati-fglrx.sh
# . /opt/clAmdBlas-1.4.182/appmlEnv.sh
# /opt/clAmdBlas-1.4.182/bin64/clBlasVersion 
clAmdBlas version 1.4.182
# /opt/clAmdBlas-1.4.182/bin64/example_sgemm 
Result:
21370 22040 22710 
37070 38240 39410 
52770 54440 56110 
68470 70640 72810 
# /opt/clAmdBlas-1.4.182/bin64/example_strsm 
Result:
-1.17478e+00 -7.83188e-01 -3.91593e-01 1.51806e-06 3.91595e-01 
-4.03831e-01 -2.69220e-01 -1.34610e-01 5.98375e-07 1.34612e-01 
-2.06611e-01 -1.37741e-01 -6.88705e-02 2.98023e-07 6.88705e-02 
9.31818e+00 9.54545e+00 9.77273e+00 1.00000e+01 1.02273e+01
# . /opt/clAmdFft-1.4.182/appmlEnv.sh
# /opt/clAmdFft-1.4.182/bin64/clAmdFft.Client
                Client Test *****PASS*****

Read more about it all at the AMD OpenCL Zone.

How Much Work Can a Cluster Do?

2011-11-01T16:00:00.000-04:00

If we take a 32 node computer cluster, with each compute node averaging over 2 amps under high load, add in some extra amps for storage and network components, all running on 208 volt, we could be pulling over 90 amps total.

current x voltage = power
 amps  x  volts   = watts
   90A  x  208V   = 18720W

Wikipedia say, "A laborer over the course of an 8-hour day can sustain an average output of about 75 watts." So a 32 node HPC cluster is roughly equivalent to 250 laborers that never sleep!

Watt - Wikipedia

Easy Backup of MySQL Databases

2011-10-12T15:03:00.000-04:00

Real Men don't make backups. They upload it via ftp and let the world mirror it.
-- Linus Torvalds

Here is a simple method for doing daily backups of all MySQL databases on a server. This method will save a separate file for each database, every morning at 4AM, into a file named with the host, database and date. This method is extremely convenient for quick restores, to any day within the last two weeks.

Create a mysql backup user and grant database permissions. Then set the backup script to run every day at 4AM with cron.

# adduser mysqlbackup
# mysql -u root -p -e "GRANT SELECT, LOCK TABLES ON *.* TO 'mysqlbackup'@'localhost' IDENTIFIED BY 'XXXXXXX;"
# echo "0 4 * * * /home/mysqlbackup/mysqlbackup.sh" |crontab -u mysqlbackup
# touch /home/mysqlbackup/mysqlbackup.sh ; chmod +x /home/mysqlbackup/mysqlbackup.sh

Set the backup user mysql password, replacing XXXXXX with your own password, in the .my.cnf file.

/home/mysqlbackup/.my.cnf

[client]
password=XXXXXXX

/home/mysqlbackup/mysqlbackup.sh

#!/bin/sh

### get the hostname
MYHOST="`hostname -s`"

### individually dump all databases with timestamps
for I in `mysql -e "show databases;" |egrep -v '^Database$|hold$'`; do
        ### dump and compress
        mysqldump --quote-names --opt $I |gzip -cf >/home/mysqlbackup/$MYHOST-$I-`date +%Y%m%d`.sql.gz
        ### remove two-week old dumps
        rm -f /home/mysqlbackup/$MYHOST-$I-`date +%Y%m%d --date="-14 days"`.sql.gz
done

I recommend running the script at least once by hand to check functionality.

# su - mysqlbackup
$ /home/mysqlbackup/mysqlbackup.sh
$ exit

Now that you have daily database dumps, to do a restore you simply cat the dump file to the mysql client. The current database will be dropped and rebuilt from the file selected. Here is an example of restoring the database importantstuff on host foo from 4AM on 2011, April 30th.

# zcat /home/mysqlbackup/foo-importantstuff-20110430.sql.gz |mysql -u root -p importantstuff

It's easy. Do your backups!

Auto Update Kernel Modules with DKMS

2011-10-05T15:49:00.000-04:00

I had a brand new Dell OptiPlex 990 desktop computer that had just been installed with Scientific Linux 6. Enterprise Linux runs great on these things, except I was getting a lot of network errors.

# lspci | grep Ethernet
00:19.0 Ethernet controller: Intel Corporation 82579LM Gigabit Network Connection (rev 04)

Sep 11 03:59:47 foo kernel: e1000e: em1 NIC Link is Down
Sep 11 03:59:47 foo NetworkManager[1760]:  (em1): carrier now OFF (device state 8, deferring action for 4 seconds)
Sep 11 03:59:47 foo kernel: e1000e 0000:00:19.0: em1: Reset adapter

The solution was to update to the latest Intel Wired Ethernet e1000e driver, currently version 1.6.2. It is easy enough to download, un-tar, and make install the package, but it will be ignored after a new kernel is installed.

Dynamic Kernel Module Support (DKMS) is an easy solution to such a problem. Since we are replacing a kernel module that is included in the stock kernel RPM package, we want to be sure that the updated driver will be built and installed automatically whenever a new kernel is booted.

DKMS is easy to install with the EPEL repository enabled. Here we are enabling EPEL on Scientific Linux 6, then yum installing the DKMS package:

# rpm -ihv http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm
# yum install dkms

We must download and prepare the latest module source code by moving the source code to a /usr/src/MODULENAME-VERSION directory, then create a dkms.conf file within:

# cd /usr/local/src
# wget http://downloads.sourceforge.net/project/e1000/e1000e%20stable/1.6.2/e1000e-1.6.2.tar.gz
# tar xzvf e1000e-1.6.2.tar.gz
# mv e1000e-1.6.2/src /usr/src/e1000e-1.6.2
# vim /usr/src/e1000e-1.6.2/dkms.conf

dkms.conf:

PACKAGE_NAME="e1000e"
PACKAGE_VERSION="1.6.2"
BUILT_MODULE_NAME[0]="e1000e"
DEST_MODULE_LOCATION[0]="/kernel/drivers/net/e1000e/"
AUTOINSTALL="yes"

Now that we have the source code in place, we tell DKMS to maintain, build and install the module:

# dkms add -m e1000e -v 1.6.2
# dkms build -m e1000e -v 1.6.2
# dkms install -m e1000e -v 1.6.2
# chkconfig dkms_autoinstaller on

We must change the search order for modules to allow "weak modules" to load before the built-in modules by editing the /etc/depmod.d/dist.conf file:

search updates extra weak-updates built-in

This last step ensures that when rebooting into a new kernel, the custom module will be loaded instead of the RPM packaged module.

NX - A Fast Remote Linux Desktop

2011-08-30T14:59:00.018-04:00

Many Linux users are familiar with X11 forwarding via SSH, or VNC for remote desktop sharing. SSH can tunnel X Windows from your remote host to the local X server display. And VNC can remotely share the desktop seen on the monitor or start a completely new desktop in the background. Similarly, NoMachine (NX) can do the same things, with the bonus of a faster compression algorithm for a more responsive GUI.

I had avoided NX because it seemed confusing and difficult to install. Now, NX has a free client, node and server download, all of which is easy to install and use. These steps work on the latest CentOS 5 and Fedora 15.

Download the latest NX Free Edition client, node and server RPMs from www.nomachine.com/download.php and install them on your server:

# rpm -ihv nxclient-3.5.0-7.x86_64.rpm nxnode-3.5.0-6.x86_64.rpm nxserver-3.5.0-8.x86_64.rpm

On your client system, just install the client RPM:

# rpm -ihv nxclient-3.5.0-7.x86_64.rpm

Now you may log into your server by providing your username and password.

NX provides a much more responsive remote desktop, especially over low speed and high latency connections. There are also many options for choosing Gnome vs KDE, or even just a single program for your session. Give it a try.

There is also an option for sharing your desktop with multiple other users, called shadowing in NX terminology. The primary user logs in and starts a new Unix session. Then another user logs in with a Shadow session, selecting the session of the primary user. This is great for remote collaboration with trusted colleagues that have an account on the same server.

Make sure to check out Getting Started with NX. Also, detailed instructions and troubleshooting for installing the repository version of NX can be found at CentOS Wiki HowTos/FreeNX.

UPDATE: I have found that the free NX server download from nomachine.com is more functional than the one provided in the repositories. In particular, shadowing was broken in the repo version. Shadowing is the desktop session sharing feature of NX. So, I do not recommend using yum to install NX. NX Free Edition seems to be limited to two users, though.

LinuxCon Live Stream

2011-08-17T15:46:00.001-04:00

Didn't get a plane ticket to Vancouver for LinuxCon North America 2011? Well, there is a live video stream.

North America 2011 | Live Video Streaming

CentOS 6 Available

2011-07-11T09:39:00.005-04:00

One of my favorite, license fee-free, Red Hat Enterprise Linux rebuilds is now available. CentOS is completely RHEL-compatible, with a different logo. Read all about it:

Of particular note is that the i386 DVD image is a bit too big to fit on a DVD+R, so use a DVD-R. When the live CDs are released in a few days, be sure to give liveusb-creator a try to make a bootable USB thumb drive.

If you want a Linux distribution with great backwards compatibility, solid updates, a long support cycle (7+ years), that is tested on enterprise server hardware, then CentOS should be at the top of your list. It turns out that CentOS is the distribution of choice for 30% of web servers.

Fedora 15 is Out

2011-05-25T11:05:00.005-04:00

The latest and greatest of Linux, Fedora 15, has been released. Get your copy now!

Check out the release notes for more info.

So I tried Fedora 15 beta with the new Gnome 3 desktop, on my netbook. I didn't like the default Gnome desktop. I reverted back to Fedora 14. A netbook really needs a screen-space efficient window manager. I want all toolbars to be consolidated and hide when not needed. So what are other's doing? Time to switch to the LXDE or XFCE spins?

Video Tour of the Facebook Server Room

2011-04-21T11:38:00.003-04:00

If you didn't already know, Facebook runs on a Linux software stack which utilizes Apache, MySQL, Memcached, PHP, as well as many other open source technologies.

Facebook also happens to be doing some interesting things in their data centers, with the Open Data Center Alliance and Open Compute Project.

See behind the scenes in this video of Facebook data center hot isle containment.

via Data Center Knowledge

20 Year of Linux

2011-04-12T12:59:00.001-04:00

Grid Engine is Alive and Well

2011-04-08T13:54:00.002-04:00

Now that the pieces are falling into place, after Oracle's acquisition of Sun Microsystems, we can see that open source can vendor-proof central pieces of your software infrastructure. Grid Engine is alive and well, with a blog, a mailing list, a git repository, and even commercial support from Univa.

I'd like to give a big THANK YOU to Dag over at Bioteam, for being so active and providing courtesy binaries for CentOS Linux and Mac OS X.

Source code repositories can also be found from the Open Grid Scheduler and Son of Grid Engine projects.

Speech Input

2011-03-23T15:17:00.005-04:00

Testing speech input with Chrome 11. Neat.

Amazon EC2 for HPC

2011-03-15T12:32:00.007-04:00

I've been sitting on this for a while now. I did quite a lot of testing with Amazon EC2, Elastic Cloud Computing, to determine if replacing an on-site rack of high performance computing cluster hardware with cloud computing resources is feasible. Utilizing the Fabric and Boto Python modules, I have build a command line utility for automating cluster deployments within the cloud. The cluster utilizes a Red Hat Enterprise Linux-compatible operating system with Grid Engine for job queuing. Initial testing targeted the large HPC instance types, but I have since been able to substitute in micro instances for faster and more economical testing of deployments.

This slideshow covers the the basic terminology, and compares the cost of purchasing and maintaining a rack of equipment versus cloud fees.

Executive summary: Yes, an on-site rack of equipment can be replaced with cloud computing resources, while continuing to utilize existing workflows. The cost to a university for EC2 is competitive with in-house hardware, when factoring in data center and maintenance costs. The cost to faculty is prohibitively expensive for cloud, since university overhead is paid up-front. Data locality is a big concern. An added benefit of cloud computing is hardware abstraction, meaning that staff time is focused instead on system configuration and software deployment.

Fedora 14 on an Eee PC 1015PEM

2011-03-09T16:26:00.041-05:00

Here are some notes from a recent install of Fedora 14, 32-bit, on an Asus Eee PC 1015PEM Seashell netbook. This system has a 64-bit 1.5 GHz Intel Atom N550 processor, but things like Skype may have problems with 64-bit. I'll go 64-bit when Fedora 15 is released.

The 1GB memory chip was upgraded to a Crucial 2GB, 204-pin SODIMM, DDR3 PC3-10600 memory module. This was easily done by unscrewing the small panel on the bottom of the system and un-clipping the existing chip. The hard disk drive was also upgraded to a Corsair Nova 32GB 2.5" SSD, which was not-so-easily done. Replacing the drive involving removing the keyboard, prying apart plastic and removing many screws. I thought I was going to snap it to pieces! A tool, like the one in these disassembly photos, would have been handy.
Installation media is created on a USB drive with liveusb-creator. To boot the installer, insert the liveusb drive and hit esc after powering on. This brings up the boot menu where the usb drive can be selected. The install should be mostly defaults, except that disk encryption and a grub password should be enabled.

After an install and reboot, plug into a wired ethernet connection, install the RPM Fusion software repository, do the first big system software update, then install and remove some packages. Note that kmod-wl from RPM Fusion provides the driver for the Broadcom wireless card after a reboot.

# yum -y install yum-fastestmirror
# yum -y update
# yum localinstall --nogpgcheck \
http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-stable.noarch.rpm \
http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-stable.noarch.rpm
# yum -y install kmod-wl akmod-wl krb5-workstation tkinter \
python-setuptools ipython mysql-workbench gconf-editor git \
subversion ethtool liveusb-creator telnet freeglut-devel \
gcc gcc-c++ SDL-devel rdesktop thunderbird thunderbird-enigmail \
vim fortune-mod lsb redhat-lsb-graphics qt-x11 powertop dosbox \
tigervnc tigervnc-server audacity-freeworld rdiff-backup \
xscreensaver-extras-gss tempest-gnome-screensaver \
samba-client rtorrent unrar \
openoffice.org-writer openoffice.org-calc openoffice.org-impress \
screen nmap net-snmp-utils wireshark-gnome iptraf strace sysstat \
rfkill mono gimp rpmdevtools yum-utils ncurses-devel \
libpng-devel mednafen jwhois java-1.6.0-openjdk-plugin wget \
ddrescue wodim vlc mplayer mencoder grip lame easytag id3v2 \
lm_sensors xterm xorg-x11-xinit-session xorg-x11-apps
# yum remove alsa-plugins-pulseaudio

The biggest tip with a 10" netbook is to consolidate and auto-hide menus/toolbars for maximum screen real estate. And use a full-sized LCD monitor when sitting at a desk.

Now, one could stop here and be finished, but I'm interested in tweaking for power saving features, like the Super Hybrid Engine (SuperHE) features of this model. Currently, the acpi_osi and acpi_backlight kernel options must be added to get the /sys/devices/platform/eeepc/cpufv device functional. Add the kernel options in /boot/grub/grub.conf:

kernel /vmlinuz-2.6.35.11-83.fc14.i686 ro root=/dev/mapper/vg_foo-lv_root rd_LUKS_UUID=luks-xxx-xxx-xxx rd_LVM_LV=vg_foo/lv_root rd_LVM_LV=vg_foo/lv_swap rd_NO_MD rd_NO_DM LANG=en_US.UTF-8 SYSFONT=latarcyrheb-sun16 KEYBOARDTYPE=pc KEYTABLE=us rhgb quiet elevator=noop acpi_osi=Linux acpi_backlight=vendor

Enable noatime on ext4 file systems, and tmpfs for temp directories in /etc/fstab:

/dev/mapper/vg_foo-lv_root / ext4 defaults,noatime 1 1
tmpfs /tmp tmpfs defaults,size=256M 0 0
tmpfs /var/tmp tmpfs defaults,size=64M 0 0
tmpfs /var/log tmpfs defaults,size=32M 0 0

Add some power tweak commands, mostly from powertop, to /etc/rc.d/rc.local

### some power and ssd saving tweaks
echo noop > /sys/block/sda/queue/scheduler 
echo 0 > /proc/sys/vm/swappiness
echo 50 > /proc/sys/vm/vfs_cache_pressure
echo 1500 > /proc/sys/vm/dirty_writeback_centisecs
echo 20 > /proc/sys/vm/dirty_ratio
echo 10 > /proc/sys/vm/dirty_background_ratio
echo 1 > /sys/devices/system/cpu/sched_smt_power_savings
echo 10 > /sys/module/snd_hda_intel/parameters/power_save
echo 5 > /proc/sys/vm/laptop_mode
echo ondemand > /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor
echo ondemand > /sys/devices/system/cpu/cpu1/cpufreq/scaling_governor
echo ondemand > /sys/devices/system/cpu/cpu2/cpufreq/scaling_governor
echo ondemand > /sys/devices/system/cpu/cpu3/cpufreq/scaling_governor
cat /sys/devices/system/cpu/cpu0/cpufreq/ondemand/sampling_rate_max > /sys/devices/system/cpu/cpu0/cpufreq/ondemand/sampling_rate
echo min_power > /sys/class/scsi_host/host0/link_power_management_policy
ethtool -s eth0 wol d
for I in `find /sys -name autosuspend -exec echo {} \;` ; do echo "0" > "$I" ; done
/sbin/rfkill block bluetooth
echo 0 > /proc/sys/kernel/nmi_watchdog

Install the Jupiter package with Eee PC support to automatically tweak many of the above settings, including SuperHE.

Disable some unused services:

# for s in abrtd atd auditd avahi-daemon ip6tables iscsi iscsid mdmonitor portreserve livesys livesys-late; do echo "chkconfig $s off"; chkconfig $s off; done

If restoring a home directory from backup, with SELinux enabled, make sure to restore the security context of the home directories:

# restorecon -vr /home

Google Chrome Beta is an excellent browser for a netbook. It is a very efficient in terms of performance speed and screen usage. To enable the built-in flash plugin, go to the URL about:plugins, expand details, and enable Flash.

Skype is a must for video chat and international voice calling. To get automatic updates, create a repo file for yum in /etc/yum.repos.d/skype.repo:

[skype]
name=Skype Repository
baseurl=http://download.skype.com/linux/repos/fedora/updates/i586/
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-skype

And to get get the latest Adobe Reader, install the adobe repo rpm:

# yum localinstall --nogpgcheck http://linuxdownload.adobe.com/adobe-release/adobe-release-i386-1.0-1.noarch.rpm
# yum -y install AdobeReader_enu

Someone on a mailing list pointed out that the "Windows" key can be made more useful by mapping it as a main menu key:

# xmodmap -e 'remove mod4 = Super_L' 
# gconftool-2 --set /apps/metacity/global_keybindings/panel_main_menu --type=string 'Super_L'

The trackpad is nice, supporting one, two and three-finger tapping. Enable this in the Gnome mouse preferences, for easy copy-and-paste the way it was meant to be. On Linux, mouse button one is highlight/select, copy being automatic, and button three is paste. With a trackpad this is double-tap and drag one finger to select text, then a three-finger single-tap to paste.

To update the bios, here are my notes:

update bios 1015PE.ROM on fat16 drive
http://support.asus.com/download/
unzip 1015PE-ASUS-0904.zip
insert a free usb memory stick, assuming it is sdb...
umount /dev/sdb1
parted -s -- /dev/sdb mklabel msdos
parted -s -- /dev/sdb mkpartfs primary fat16 0 32
mount -t vfat -o fat=16 /dev/sdb1 /mnt
cp 1015PE-ASUS-0904.ROM /mnt/1015PE.ROM
umount /dev/sdb1
reboot with the usb drive & power plugged in
hit alt+f2 first thing at post
if all is well, it will get past reading 1015PE.ROM
allow the update to complete! ~10 minutes

You can change video modes from the command line. Stick these into ~/.bashrc:

alias vga='xrandr --fb 1280x1624 --output LVDS1 --primary --mode 1024x600 --rate 60 --pos 0x0 --panning 0x0 --output VGA1 --mode 1280x1024 --rate 60 --pos 0x1024 --above LVDS1'
alias mir='xrandr --fb 1280x1024 --output LVDS1 --primary --mode 1024x600 --rate 60 --pos 0x0 --panning 1280x1024 --output VGA1 --mode 1280x1024 --rate 60 --pos 0x0 --same-as LVDS1'
alias lcd='xrandr --fb 1024x600  --output LVDS1 --primary --mode 1024x600 --rate 60 --output VGA1 --off'

Other things done:

Recover LDAP Auth on Mac OS X

2011-02-21T17:01:00.002-05:00

I have an entire rack of Apple Xserve nodes, running Mac OS X 10.5. The Xserve is fond of refusing to reboot, crashing, and corrupting the Open Directory LDAP database when under high load. Here is a quick fix:

$ su -
# tar cvzf ldap-YYYYMMDD.tar.gz /var/db/openldap
# rm /var/db/openldap/openldap-data/log.0*
# launchctl unload /System/Library/LaunchDaemons/org.openldap.slapd.plist
# /usr/bin/db_recover -h /var/db/openldap/openldap-data
# launchctl load /System/Library/LaunchDaemons/org.openldap.slapd.plist
# slapcat | less

ATLAS NumPy SciPy Build on RHEL 6

2011-02-21T14:39:00.002-05:00

This is a build log for the latest ATLAS (ATLAS/BLAS/LAPACK), NumPy, and SciPy on Red Hat Enterprise Linux 6. Please note that this was attempted many times, following the documentation, but there were still errors when importing certain functions. The big tip is to edit site.cfg before building and installing numpy.
Here is an example of some of the errors we would see with a mis-configured build:

from scipy.optimize import fsolve
import scipy.integrate as integrate
from scipy.integrate import odeint
ImportError: /usr/local/scipy/lib64/python2.6/site-packages/scipy/optimize/_lbfgsb.so: undefined symbol: ATL_dcopy
ImportError: /usr/local/scipy/lib64/python2.6/site-packages/scipy/integrate/_odepack.so: undefined symbol: ATL_idamax
ImportError: /usr/local/scipy/lib64/python2.6/site-packages/scipy/integrate/_odepack.so: undefined symbol: daxpy_

Here is a log of commands for a successful build. We install each package into its own version-numbered directory, soft-linking to the current version and then setting the user environment variables.

# cd /usr/local/src
# wget http://www.netlib.org/lapack/lapack-3.3.0.tgz
# tar xzvf lapack-3.3.0.tgz
# cd lapack-3.3.0
# cp INSTALL/make.inc.gfortran make.inc
# vim make.inc
add -fPIC to OPTS and NOOPT
# make 2>&1 | tee log.make
# make blaslib lapacklib tmglib lapack_testing 2>&1 | tee log.makeall

# cd /usr/local/src
# wget http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%29/3.9.35/atlas3.9.35.tar.bz2
# tar xjvf atlas3.9.35.tar.bz2
# mv ATLAS atlas-3.9.35
# cd atlas-3.9.35
# mkdir ATLAS_LINUX ; cd ATLAS_LINUX
# cpufreq-selector -g performance
# ../configure -Fa alg -fPIC -Si cputhrchk 0 --prefix=/usr/local/atlas-3.9.35 --with-netlib-lapack-tarfile=/usr/local/src/lapack-3.3.0.tgz 2>&1 | tee log.config
# make 2>&1 | tee log.make
THIS WILL TAKE HOURS TO MAKE!
# make install 2>&1 | tee log.install
# cd /usr/local ; ln -s atlas-3.9.35 atlas
# export LD_LIBRARY_PATH=/usr/local/atlas/lib:$LD_LIBRARY_PATH

# cd /usr/local/src
# wget http://cdnetworks-us-2.dl.sourceforge.net/project/numpy/NumPy/1.5.1/numpy-1.5.1.tar.gz
# tar xzvf numpy-1.5.1.tar.gz
# cd numpy-1.5.1
# cp site.cfg.example site.cfg
# vim site.cfg
[DEFAULT]
library_dirs = /usr/local/atlas/lib
include_dirs = /usr/local/atlas/include
[atlas]
atlas_libs = lapack, f77blas, cblas, atlas
# python setup.py build 2>&1 | tee log.build
# python setup.py install --prefix=/usr/local/numpy-1.5.1 2>&1 | tee log.install
# cd /usr/local ; ln -s numpy-1.5.1 numpy
# export PYTHONPATH=$PYTHONPATH:/usr/local/numpy/lib64/python2.6/site-packages
# export PATH=/usr/local/numpy/bin:$PATH
# python /usr/local/numpy/lib64/python2.6/site-packages/numpy/distutils/system_info.py

# cd /usr/local/src
# wget http://cdnetworks-us-2.dl.sourceforge.net/project/scipy/scipy/0.9.0rc3/scipy-0.9.0rc3.tar.gz
# tar xzvf scipy-0.9.0rc3.tar.gz
# cd scipy-0.9.0rc3
# python setup.py build 2>&1 | tee log.build
# python setup.py install --prefix=/usr/local/scipy-0.9.0rc3 2>&1 | tee log.install
# cd /usr/local ; ln -s scipy-0.9.0rc3 scipy

Some references:

DD-WRT on Buffalo WHR-HP-GN

2011-02-12T13:07:00.027-05:00

I recently bought two Buffalo Technology WHR-HP-GN AirStation Wireless-N 150 High Power Router & Access Point units to upgrade my home network. The chipset of this router is an Atheros 7240 @ 400 MHz. I installed the latest DD-WRT firmware for maximum functionality. Specifically, I installed the BrainSlayer-V24-preSP2/12-24-10-r15962 webflash firmware.
This little router out-performs my old Linksys WRT54GL that had high-gain antennas. There is a problem, though. About once a day, the wireless signal drops out and dies with an error: Resetting; Code: 01

I'll see if I can post a bug report on the forum or trac. In the meantime, the quick-fix is to add a cron entry to the router:

*/2 * * * * root [ ! -z "`dmesg -c | tail | grep Resetting`" ] && (logger -p info "Bouncing ath0" && ifconfig ath0 down && ifconfig ath0 up)

Thanks go to King Lee for the fix.
Update: Filed a bug report, Ticket #1500.

Update: There is a new firmware, 03-17-11-r16454.
Update: Yet more new firmwares. I'm going to try the latest Brainslayer 06-14-11-r17201 firmware or the official Buffalo 2011-06-06 17135 Alpha firmware.

FINAL Update: I am done wasting my time with DD-WRT and these Atheros-based routers. Recent forum post show a lot of people with dropping wireless problems, and no solution. I am now the happy owner of an Asus RT-N16 running the latest Tomato USB firmware. Done and done.

Quick Dell OpenManage Email Alerts

2011-02-03T15:41:00.008-05:00

Dell OpenManage does not provide a simple way to set a catch-all email alert for platform and storage events. With these few steps, we can configure OpenManage to send an email on any alert.
First, we must create a simple shell script to send the email.

/usr/local/bin/om-alert.sh

#!/bin/sh
HOST=`hostname`
EMAIL="my_admin@my_network.net"
echo "There has been an OpenManage ALERT detected on $HOST.  Please login to the web interface to see details." | mail $EMAIL -s "OM ALERT $HOST"

We can set individual alerts:

# chmod +x /usr/local/bin/om-alert.sh
# omconfig system alertaction
# omconfig system alertaction -?
# omconfig system alertaction event=powersupply execappath=/usr/local/bin/om-alert.sh
# omconfig system alertaction event=storagesyswarn alert=true broadcast=true execappath=/usr/local/bin/om-alert.sh
# omreport system alertaction

Or we can set console, broadcast and email for all alerts.

# for I in `omconfig system alertaction | sed 's/ *(.*)//; s/>.*//; s/.*[:<] *// ; s/|/ /g;'`; do 
echo $I; 
omconfig system alertaction event=$I alert=true broadcast=true execappath="/usr/local/bin/om-alert.sh"
done

NCO netCDF Operators Build Log

2011-02-03T13:38:00.007-05:00

This is a build log for the netCDF Operators and dependencies: hdf5, netcdf4, udunits2, and antlr2. This build uses the Intel compiler version 11, but gcc will also work. This is for CentOS 5 / RHEL 5 x86_64.

The netCDF Operators, NCO, are a suite of programs known as operators.
The operators facilitate manipulation and analysis of self-describing
data stored in the freely available netCDF and HDF formats.

NCO runs on all major UNIX systems and MS Windows.
NCO requires only an ANSI-compliant C99 compiler.
NCO can be built and installed with the standard GNU autotools
./configure mechanism or with a custom Makefile.
-- http://nco.sourceforge.net/README

This build required many dependencies and many attempts with undocumented options. Here, we are installing into the /usr/global/ directory, which is a shared filesystem on our cluster.

# cd /usr/global/src
# wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.5-patch1.tar.bz2
# tar xjf hdf5-1.8.5-patch1.tar.bz2 ; cd hdf5-1.8.5-patch1
# CC=icc FC=ifort CXX=icpc ./configure \
--prefix=/usr/global/hdf5-1.8.5-patch1-i11 \
--enable-fortran \
--enable-cxx \
--with-pic 2>&1 | tee log.config
# make 2>&1 | tee log.make
# make install 2>&1 | tee log.install

# cd /usr/global/src
# wget http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.1.tar.gz
# tar xzf netcdf-4.1.1.tar.gz ; cd netcdf-4.1.1
# CC=icc FC=ifort F77=ifort CXX=icpc ./configure \
--prefix=/usr/global/netcdf-4.1.1-i11 \
--enable-fortran \
--enable-f77 \
--enable-cxx \
--with-hdf5=/usr/global/hdf5-1.8.5-patch1-i11 \
--with-pic 2>&1 | tee log.config
# make 2>&1 | tee log.make
# make install 2>&1 | tee log.install

# cd /usr/global/src
# wget http://www.antlr2.org/download/antlr-2.7.7.tar.gz
# tar xzf antlr-2.7.7.tar.gz ; cd antlr-2.7.7
# CC=icc CXX=icpc ./configure \
--prefix=/usr/global/antlr-2.7.7-i11 \
--disable-csharp \
--disable-java \
--disable-python 2>&1 | tee log.config
# make 2>&1 | tee log.make
# make install 2>&1 | tee log.install

# cd /usr/global/src
# wget ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.1.20.tar.gz
# tar xzf udunits-2.1.20.tar.gz ; cd udunits-2.1.20
# CC=icc CXX=icpc F77=ifort ./configure \
--prefix=/usr/global/udunits-2.1.20-i11 2>&1 | tee log.config
# make 2>&1 | tee log.make
# make install 2>&1 | tee log.install

# export LD_LIBRARY_PATH=/usr/global/hdf5-1.8.5-patch1-i11/lib:$LD_LIBRARY_PATH
# export PATH=/usr/global/hdf5-1.8.5-patch1-i11/bin:$PATH
# export LD_LIBRARY_PATH=/usr/global/netcdf-4.1.1-i11/lib:$LD_LIBRARY_PATH
# export PATH=/usr/global/netcdf-4.1.1-i11/bin:$PATH
# export LD_LIBRARY_PATH=/usr/global/antlr-2.7.7-i11/lib:$LD_LIBRARY_PATH
# export PATH=/usr/global/antlr-2.7.7-i11/bin:$PATH
# export LD_LIBRARY_PATH=/usr/global/udunits-2.1.20-i11/lib:$LD_LIBRARY_PATH
# export PATH=/usr/global/udunits-2.1.20-i11/bin:$PATH
# ln -s /usr/global/antlr-2.7.7-i11/include/antlr /usr/local/include/
# yum -y install expat-devel

# cd /usr/global/src
# wget http://nco.sourceforge.net/src/nco-4.0.6.tar.gz
# tar xzf nco-4.0.6.tar.gz ; nco-4.0.6
# CC=icc CXX=icpc \
NETCDF_INC=/usr/global/netcdf-4.1.1-i11/include \
NETCDF_LIB=/usr/global/netcdf-4.1.1-i11/lib \
HDF5_LIB_DIR=/usr/global/hdf5-1.8.5-patch1-i11/lib \
CFLAGS="-I/usr/global/hdf5-1.8.5-patch1-i11/include \
-L/usr/global/hdf5-1.8.5-patch1-i11/lib \
-I/usr/global/antlr-2.7.7-i11/include \
-L/usr/global/antlr-2.7.7-i11/lib" \
LDFLAGS="-L/usr/global/antlr-2.7.7-i11/lib \
-lhdf5_hl -lhdf5 -lstdc++" \
UDUNITS2_PATH=/usr/global/udunits-2.1.20-i11 \
./configure \
--prefix=/usr/global/nco-4.0.6-i11 \
--disable-shared \
--enable-netcdf-4 2>&1 | tee log.config
# make 2>&1 | tee log.make
# make install 2>&1 | tee log.install

Easy.

Red Hat Enterprise Linux 6 Released

2010-11-11T14:02:00.002-05:00

The latest version of Linux from Red Hat is out. This should be your number one choice for server, virtual and cloud deployments in an enterprise environment.

Open Source Animation

2010-10-05T10:05:00.002-04:00

I studied computer animation for a while, and was the only one in my class using Linux. My tool of choice was Blender, which has come a long way since then. Check out Sintel, the new short film produced by Durian, the Blender open movie project.

The movie itself, and all of the work of the Durian team in the past 18 months will be released under the Creative Commons Attribution license, free for everyone to distribute, learn from or re-use. The 4-disc DVD set will provide all data to be able to recreate and rerender the film in its entirety.

Dear Oracle

2010-10-01T10:16:00.002-04:00

Dear Oracle,

Please get your strategy together. The community behind the Sun open source projects, like Grid Engine and Lustre, will be looking for other solutions if you do not maintain an open development model. Don't burn the community that has been your customer base, beta testers and code contributors. Our time, attention and money can be taken elsewhere.

Signed,

Scientists

Researchers

Systems Integrators

HPC Specialists

Systems Programmers

Your customers

Check out "Lustre settles into post-Oracle life" over at Network World.

E-Waste

2010-09-20T09:40:00.001-04:00

Here's a short and direct video on electronics waste.