Albert's Academic Blog

how to see Ubuntu OS version

2012-01-07T17:43:00.001-10:00

lsb_release -a

To release-upgrade:

sudo do-release-upgrade -d

To find a certain type of files and copy to current dir.

2011-12-12T09:38:00.002-10:00

find -name "p*.pdf" -exec cp {} ./ \;

Install style files in LyX

2011-11-29T21:31:00.001-10:00

http://flukylogs.blogspot.com/2009/09/install-style-files-in-lyx.html

LyX is a frontend to LaTeX and so installation of any style file in LyX essentially mean: (1) installation of that style file in underlying LaTeX; and then (2) getting that style file work in LyX (using LyX layout files). Installation method for different types of style files are given below:

Install LaTeX class (.cls)
create new directory with name under /usr/share/texmf-texlive/tex/latex/
copy .cls file (& other files, if present) in the new directory
sudo texhash
create a file .layout in ~/.lyx/layouts
edit the layout file according to the instructions given in Chapter 5 of "Customizing LyX: Features for the Advanced User" (Help->Customization in LyX).
open LyX and click 'tools -> Reconfigure' and restart LyX when done. The new Document Class should be available now.
For Example, to install IEEEconf class file, download the zip files from here. Create .cls file by executing 'latex IEEEconf.ins'. Copy the folder IEEEconf to /usr/share/texmf-texlive/tex/latex/. Run sudo texhash. Find IEEEtran.layout file & copy it to a new file named IEEEconf.layout in ~/.lyx/layouts (IEEEconf and IEEEtran are very similar, so IEEEtran-layout file can be used as layout file for IEEEconf). Edit the the second line in IEEEconf.layout from
# \DeclareLaTeXClass{article (IEEEtran)}
to
# \DeclareLaTeXClass{article (IEEEconf)}
and it should turn up when you reconfigure LyX.

Install LaTeX style (.sty)

Style file (.sty) is an addition to class files (.cls) files and they provides special formatting rules which overrides the similar rules in class files, if present. So each style file must be associated with a class file. Installation process is similar to that of class files (see previous section of this post). Layout files (step 5 above) have different format. Instructions are given in Chapter 5 of "Customizing LyX: Features for the Advanced User" (Help->Customization in LyX).

For Example, to install ACRA style file, download the files from here. Copy the file acra.sty to /usr/share/texmf-texlive/tex/latex/ACRA/. Run sudo texhash. Find article.layout file & copy it to a new file named acra.layout in ~/.lyx/layouts (acra.sty uses "article" class). Edit the the second line in acra.layout from
# \DeclareLaTeXClass{article}
to
# \DeclareLaTeXClass[article, acra.sty]{article (ACRA)}
Then add in next line

Preamble
\usepackage{acra}
EndPreamble

and it should turn up when you reconfigure LyX.

Install BibTeX Style (.bst)
create new directory with name under /usr/share/texmf-texlive/bibtex/bst/
copy .bst file (& other files, if present) in the new directory
sudo texhash
open LyX and click 'tools -> Reconfigure' and restart LyX when done.
open LyX and click 'tools -> TeX Information' and choose BibTex Styles. Click 'Rescan' The new BibTeX should be available now.

How to develop software as a team using subversion

2011-11-28T17:54:00.001-10:00

http://wiki.developerforce.com/page/Using_Force.com_with_Subversion_for_Team_Development

How To Set Up Debian Linux File and Print Servers

2011-11-21T16:45:00.001-10:00

http://www.aboutdebian.com/lan.htm

How to generate video tutorial using Ubuntu

2011-11-01T22:02:00.003-10:00

Recording all desktop action (Can record compiz-fusion, effects, movies, audio, mouse, etc, etc.)

1 - RECORDING
Install application: (Type in terminal) sudo apt-get install gtk-recordmydesktop
Running: go to menu: "Applications" ---> "Sound & Video" ---> "gtk-recordMyDesktop" (You can read more about it, here: LINK )
Stop Recording: Click in the small grey square icon (next to time and date bar)
Movies are saved at: /home/yourname/out.ogg

2 - CONVERTING TO OTHER VIDEO FORMATS
Convert OGG video to AVI format: WinFF for GTK (ffmpeg Gnome based GUI) OR Check brennydoogles, next posts!

3 - EDITING THE SAVED VIDEOS
Install application: (Type in terminal) sudo apt-get install kino
Running: go to menu: "Applications" ---> "Sound & Video" ---> "Kino"
[Added in Jan 2010] OR OpenShot - New open source video editor here: http://www.openshotvideo.com/ (I haven´t tried it yet)

4 - SHARE IT
Final Video Example: brennydoogles turotial video about "AIM In Virtualbox" here
My Videos: here

from http://ubuntuforums.org/showthread.php?t=617006

pdfcrop

2011-10-21T12:38:00.002-10:00

pdfcrop myfile.pdf

from http://alexsleat.co.uk/2011/01/25/using-pdfcrop-to-remove-white-margins-ubuntu/

How to upgrade Ubuntu from 10.4 to 11.10.

2011-10-20T13:31:00.002-10:00

http://www.unixmen.com/linux-tutorials/linux-distributions/linux-distributions4-ubuntu/1933-how-to-upgrade-from-ubuntu-1004-1010-1104-to-ubuntu-1110-oneiric-ocelot-desktop-a-server

XMind web browser does not show

2011-10-18T12:40:00.002-10:00

Install Eclipse

That's all!

XMind scroll problem

2011-10-18T12:39:00.002-10:00

cgoise

View profile

More options Apr 7, 9:48 pm

XMind (and other Eclipse applications) do currently not show up in the
new global menu, which is used in Ubuntu Natty Narwhale (11.04).
See here: https://bugs.launchpad.net/ubuntu/+source/eclipse/+bug/688136
Workarounds for this type problems can be found on the following site:
http://askubuntu.com/questions/6784/is-it-possible-to-make-indicator-...

In essence: the command to run XMind from the command line is now:
"APPMENU_DISPLAY_BOTH=1 /usr/local/xmind/xmind"
(without quotes)

The site does not mention how to start applications affected by this
bug from the main menu, which requires a slightly different command.
This can be done by changing the command in the main menu to:
"/bin/sh -c 'APPMENU_DISPLAY_BOTH=1 /usr/local/xmind/xmind'"
(again without quotes).
The program 'alacarte' can be used for this, just as in previous gnome
version.

This specific setting (APPMENU_DISPLAY_BOTH=1) causes the normal AND
the global menu to be shown. It will be therefore noticed when the bug
is fixed, so the main menu can be resetted.

from http://groups.google.com/group/xmind/browse_thread/thread/bd2badc7f785c254/f3af24cd09888116?lnk=gst&q=xmind+11.04#f3af24cd09888116

Regards

how to install nautilus-terminal

2011-10-08T14:01:00.001-10:00

http://software.flogisoft.com/nautilus-terminal/en/

to convert column to row

2011-10-07T15:18:00.000-10:00

in any directory with files and directories

$ ls -1 | sed ':a;N;$!ba;s/\n/ /g'

will show a row with information

broadcom STA

2011-10-02T09:25:00.001-10:00

root@nostalgia:~/Desktop/broadcom# pwd
/home/albertsk/Desktop/broadcom

root@nostalgia:~/Desktop/broadcom# ll
total 20
drwxr-xr-x 4 albertsk albertsk 4096 2011-10-01 17:33 ./
drwxr-xr-x 3 albertsk albertsk 4096 2011-10-01 17:31 ../
drwxr-xr-x 2 albertsk albertsk 4096 2010-12-14 15:58 lib/
-rw-r--r-- 1 albertsk albertsk 1134 2010-12-14 15:58 Makefile
drwxr-xr-x 5 albertsk albertsk 4096 2010-12-14 15:58 src/

root@nostalgia:~/Desktop/broadcom# make -C /lib/modules/2.6.38-8-generic/build M=`pwd` clean
root@nostalgia:~/Desktop/broadcom# make -C /lib/modules/2.6.38-8-generic/build M=`pwd`

root@nostalgia:~/Desktop/broadcom# rmmod bcm43xx b43 b43legacy ndiswrapper
ERROR: Module bcm43xx does not exist in /proc/modules
ERROR: Module b43legacy does not exist in /proc/modules
ERROR: Module ndiswrapper does not exist in /proc/modules
root@nostalgia:~/Desktop/broadcom# apt-get remove ndiswrapper-common
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package ndiswrapper-common

root@nostalgia:~/Desktop/broadcom# modprobe ieee80211_crypt_tkip
FATAL: Module ieee80211_crypt_tkip not found.

cp wl.ko /lib/modules/2.6.38-8-generic/kernel/net/wireless/

root@nostalgia:~/Desktop/broadcom# cp wl.ko /lib/modules/2.6.38-8-generic/kernel/net/wireless/
root@nostalgia:~/Desktop/broadcom# depmod -a

insmod /lib/modules/2.6.38-8-generic/kernel/net/wireless/wl.ko

make -C /lib/modules/2.6.38-8-generic/build M=`pwd` clean

root@nostalgia:~/Desktop/broadcom# rmmod wl
root@nostalgia:~/Desktop/broadcom#
root@nostalgia:~/Desktop/broadcom#
root@nostalgia:~/Desktop/broadcom#
root@nostalgia:~/Desktop/broadcom# insmod /lib/modules/2.6.38-8-generic/kernel/net/wireless/wl.ko
root@nostalgia:~/Desktop/broadcom# depmod -a

Wireless setup when you install Ubuntu on HP mini

2011-10-02T01:28:00.002-10:00

http://www.linuxquestions.org/questions/blog/frandalla-68463/patching-802-11-linux-sta-driver-for-kernel-2-6-37-3558/

HP mini netbook no wireless

2011-10-01T20:33:00.001-10:00

sudo apt-get install bcmwl-kernel-source

from HP mini netbook no wireless

beamer->xouranl ->lecture

2011-10-01T10:13:00.002-10:00

Recently I purchased Wacom Intuos4 small, which allows me to electronically write anything on digital note. Windows has Windows Journal Note and Smartnotebook is an excellent software with 30 days of evaluation period.

On the other hand, Ubuntu provides the best solution since I am making my presentation slides using beamer. Once you make a pdf file using beamer, open xournal on Ubuntu and just open the pdf file. The software xournal will smoothly convert the pdf to xoj format. You can start lecturing!.

generate pdf using beamer or use any pdf file
start xournal and open the pdf file.
enjoy electronic writing!

So, simple and easy!

How to Import Xfig Figures in Your LaTeX Files

2011-09-18T18:06:00.002-10:00

http://epb.lbl.gov/xfig/latex_and_xfig.html

How to join multiple .avi or .mpg files

2011-09-12T23:55:00.000-10:00

cat 1.mpg 2.mpg > 3.mpg

http://www.arsgeek.com/2006/08/07/how-to-join-multiple-avi-or-mpg-files/

Submit a long running job via an LSF script file

2011-09-05T08:13:00.001-10:00

2. Submit a long running job via an LSF script file

An alternative way of the bsub command line is to use an LSF script file as follows

Usage: bsub < jobfile

where the jobfile is a job script file. A sample LSF jobfile might contain lines like the following:

#BSUB -J jobname
#BSUB -oo outfile.%J
#BSUB -eo errorfile.%J
myprog

If you prefer to have the job output sent to you via email, you can specify an email address instead of specifying output and error file names:

#BSUB -J jobname
#BSUB -u userid@missouri.edu
myprog

You can also use #BSUB comments to specify any other bsub command options that you want to include, and multiple options can be specified on a single #BSUB comment line. An advantage of this method is that all the command options are saved in the job script file so that they are not forgotten.

from: http://umbc.rnet.missouri.edu/resources/Submitting_Jobs_via_LSF.html

modifying-allowed-upload-types-in-wordpress

2011-09-01T13:51:00.002-10:00

http://chrismeller.com/2007/07/modifying-allowed-upload-types-in-wordpress

How to put a background image only on one beamer slide

2011-08-29T10:50:00.001-10:00

http://blog.nguyenvq.com/2011/08/24/background-image-in-latex-beamer-presentation/

remove color after word search in vi editor

2011-08-26T14:54:00.003-10:00

http://www.linuxquestions.org/questions/linux-newbie-8/remove-color-after-word-search-in-vi-editor-264760/

How to increase upload file size of wordpress in Ubuntu

2011-08-23T21:41:00.000-10:00

Login as a root
Go to /etc/php5/apache2
Open php.ini and add the following two lines

upload_max_filesize = 64M;
post_max_size = 32M;

Make sure that you added semi-colon at the end of each line.

How to includepdf files to SmartNotebook

2011-08-23T20:48:00.000-10:00

I have landscape pdf files for teaching. Here is steps to include the pdf file into SmartNotbook software.

1. Open a pdf file (landscape)
2. Rotate all the pages 180 degrees, so upside down.
3. Print the pdf to "SmartNotebook Document Writer" printer driver.
4. Once the pdf file is converted, it will be automatically loaded to SmartNotebook software in a correct way. Otherwise you have to rotate each page after loading.

The simplest way to print text and pdf files through ssh

2011-08-22T17:02:00.001-10:00

If you want to print "b.pdf" to a remote Linux box connected to a printer, then

$ cat b.pdf | ssh username@myserver.domain.com "lp -"

A script can be easier to use

#!/bin/bash
cat $1 | ssh username@myserver.domain.com "lp -"

Here is a better guide: http://docs.ocf.berkeley.edu/wiki/How_to_print_through_SSH

Your PHP installation appears to be missing the MySQL extension which is required.

2011-08-20T10:12:00.000-10:00

Here is how to solve the message:
"Your PHP installation appears to be missing the MySQL extension which is required."

prompt> sudo apt-get install php5-mysql

http://www.webtechquery.com/index.php/2010/03/php-installation-appears-to-be-missing-the-mysql-extension/

How to add US Holidays to iPad

2011-08-17T20:02:00.001-10:00

http://www.mac512.com/ipad/ipadQuestionsAnswers_files/Adding_US_holidays_to_the_iPad_.html

how to sync more than one google calendar to iPhone

2011-08-17T19:16:00.002-10:00

Using LDAP

http://gigaom.com/apple/ipad-quick-tip-enabling-multiple-google-calendars/

https://www.google.com/calendar/iphoneselect

Useful pbs tutorial

2011-08-15T23:12:00.000-10:00

In a pbs script for qsub,

echo ${JOB_ID}

http://cac.engin.umich.edu/resources/systems/nyxV2/pbs.html

How to disable blinking cursor of gnome terminal of Ubuntu 11.04

2011-08-15T21:21:00.000-10:00

gconftool-2 -s /apps/gnome-terminal/profiles/Default/cursor_blink_mode -t string off

from http://www.jurta.org/en/prog/noblink

splitting vim editor windows horizontally

2011-08-13T10:29:00.000-10:00

Press :split to split horizontally the currently edited file into two Vi editor windows.

Press :split file2 to split the Vi editor windows horizontally. The upper Vi editor windows access to file2 while the bottom Vi editor windows access to the currently edited file.

While in splitting mode, press CTRL+WW to switch between split Vi editor window. Copy between files made even easier in split Vi editor windows - just copy the block of lines and press CTRL+WW switching to target file then press p to paste the copied lines.

To close splitted windows press :q.

from http://bloggerdigest.blogspot.com/2006/09/vi-editor-quick-reference.html

tortoise SVN + sshkey authorization using Putty

2011-05-30T16:03:00.000-10:00

The key point is to put session name (not host name)

svn+ssh://[username]@[putty saved session name]/path/to/repository

http://www.vectorns.com/blog/11-tortoisesvn-over-ssh-on-windows-via-putty

mounting hfsplus file type on Ubuntu

2011-05-18T13:44:00.001-10:00

Following packages are requried:

sudo apt-get install hfsplus hfsutils hfsprogs

check the file system:

mkfs.hfsplus -J /dev/sdc3

mount -t hfsplus /dev/sdc3 /media/mybook -o rw,nosuid,nodev,uhelper=hal

or put the following line in /etc/fstab

/dev/sdc3 /media/mybook hfsplus rw,nosuid,nodev,uhelper=hal 0 0

To tar and gzip directories

2011-05-06T09:09:00.000-10:00

#!/bin/sh

for dirs in AAA BBB CCC
do
tar cvf $dirs.tar $dirs ; gzip $dirs.tar
done

Linux / Unix Command: zip

2011-05-06T08:52:00.002-10:00

When given the name of an existing zip archive, zip will replace identically named entries in the zip archive or add entries for new names. For example, if fooz.zip exists and contains foo/file1 and foo/file2, and the directory foo contains the files foo/file1 and foo/file3, then:

: zip -r fooz foo

will replace foo/file1 in fooz.zip and add foo/file3 to fooz.zip. After this, fooz.zip contains foo/file1, foo/file2, and foo/file3, with foo/file2 unchanged from before.

http://linux.about.com/od/commands/l/blcmdl1_zip.htm

How to use UHthesis2e in Lyx

2011-04-26T11:58:00.003-10:00

=== Ubuntu ===

Become a root by
$ sudo bash

Go to the latex directory (/usr/share/texmf-texlive/tex/latex)
$ cd /usr/share/texmf-texlive/tex/latex

Make a uhthesis directory
$ mkdir uhthesis
$ cd uhthesis

Copy uhthesis setup files to the dir.
$ cp /somewhere/uhthesis2e.cls ./
$ cp /somewhere/uht10.clo       ./
$ cp /somewhere/uht11.clo       ./
$ cp /somewhere/uht12.clo       ./

Go to
$ /usr/share/lyx/layouts
$ vi uhthesis2e.layout

Add following lines
#% Do not delete the line below; configure depends on this
# \DeclareLaTeXClass[uhthesis2e]{article (uhthesis2e)}
# Input general definitions
Input stdclass.inc

Start Lyx and in Lyx
do: Tools > Reconfigure ; Restart Lyx.

And you will see "article (uhthesis2e)"
Now you should be able to use the document class in LyX as usual:
Document > Settings > Document Class > Document Class > article (uhthesis2e)

Download UHthesis2e.zip

gcc and OpenFOAM

2011-04-20T11:03:00.045-10:00

I also find a couple of links that may be useful to you to compile gcc and OpenFOAM. (by Shengmeng at Platform Inc.)

(Link 1) http://www.cfd-online.com/Forums/blogs/wyldckat/385-automated-scripts-building-gcc-4-4-x-4-5-x-using-openfoam-1-7-series.html

(Link 2: discussion forum) http://www.cfd-online.com/Forums/openfoam-installation/73629-openfoam-installation-redhat-enterprise-linux-5-a.html

(Link 3: OpenFOAM in CentOS) http://sourceforge.net/apps/mediawiki/centfoam/index.php?title=Main_Page

I followed the steps in link 1 and so far so good.

First, Using yum in RHEL, I downloaded and installed flex, texinfo, byacc, and bison.

$ yum install -y flex flex++ --downloadonly --downloaddir=/home/albertsk/packages/
$ rpm -i /home/albertsk/packages/flex-2.5.4a-41.fc6.x86_64.rpm

$ yum install -y bison --downloadonly --downloaddir=/home/albertsk/packages/$ rpm -i /home/albertsk/packages/bison-2.3-2.1.x86_64.rpm

$ yum install -y byacc --downloadonly --downloaddir=/home/albertsk/packages/
$ rpm -i /home/albertsk/packages/byacc-1.9-29.2.2.x86_64.rpm

Second, I downloaded build-gcc_v4.tar.gz (5.7 KB, 12 views) and used the script to install other utilities such as gcc, gmp, mpfr and mpc. During this process, I defined set FOAM_INST_DIR under my $HOME directory, which is quite important to "source etc/bashrc" for compiling environment.

Third, I went to OpenFOAM/OpenFOAM-1.7.1 directory and execute
$ ./Allwmake

which is still going on for about a half day.

Fourth, later on I found that not all the executable files are built and got error message that says "/usr/lib/libstdc++.so.6: version `GLIBCXX_3.4.9' not found". None of web information is directly useful, so I search the library and found an newer version at

ThirdParty-1.7.1/platforms/linux64/gcc-4.3.3/lib64/libstdc++.so.6.0.10

So, I copied libstdc++.so.6.0.10 to /usr/lib/ and make a newer link

ln -sf libstdc++.so.6.0.10 libstdc++.so.6

(The file libstdc++.so.6.0.10 should be copied to all the compute nodes and the link should be updated once a serial OpenFOAM test is done in fractal.)

Fifth, I got 4 errors in config such as

configure: error: no vtf3.h found; check path for VTF3 package first...
configure: error: no bfd.h found; check path for BFD package first...
configure: error: no libiberty.h found; check path for LIBERTY package first...
configure: error: no papi.h found; check path for PAPI package first...

This link seems to have a solution: http://www.cfd-online.com/Forums/openfoam-installation/80787-missing-vtf3-h-bpatch-h-papi-h.html

vtf3 library problem can be solved. See
http://anirban.org/cs521/ass7/
Download VTF library and extract & copy to a convenient location.

For bfd.h, it is found at
/home/albertsk/OpenFOAM/ThirdParty-1.7.1/platforms/build-linux64Gcc/binutils-2.20.1/bfd/bfd.h
/home/albertsk/OpenFOAM/ThirdParty-1.7.1/platforms/linux64/gcc-4.5.2/include/bfd.h
/home/usr/local/binutils-2.21/include/bfd.h
Perhaps, these directories should be included in "INCLUDE" environment.

For iberty package, it is because binutils-devel is not installed.
http://www.rootninja.com/configuring-and-making-oprofile-for-a-custom-kernel-on-fedora/
/home/albertsk/OpenFOAM/ThirdParty-1.7.1/binutils-2.20.1/include/libiberty.h
/home/albertsk/OpenFOAM/ThirdParty-1.7.1/gcc-4.5.2/include/libiberty.h

How Do I Find Out CPU is 32bit or 64bit?

2011-04-20T10:02:00.001-10:00

$ grep flags /proc/cpuinfo
$ cat /proc/cpuinfo
$ lshw -C cpu

CPU Modes:

lm flag means Long mode cpu - 64 bit CPU
Real mode 16 bit CPU
Protected Mode is 32-bit CPU

How do I tell if 32 bit or 64 bit ubuntu is installed on a machine?

2011-04-20T09:40:00.002-10:00

file /sbin/init

Encoding from multiple input image files (JPEG, PNG, TGA, etc.)

2011-04-18T12:22:00.002-10:00

http://www.mplayerhq.hu/DOCS/HTML/en/menc-feat-enc-images.html

6.8. Encoding from multiple input image files (JPEG, PNG, TGA, etc.)

MEncoder is capable of creating movies from one or more JPEG, PNG, TGA, or other image files. With simple framecopy it can create MJPEG (Motion JPEG), MPNG (Motion PNG) or MTGA (Motion TGA) files.

Explanation of the process:

MEncoder decodes the input image(s) with libjpeg (when decoding PNGs, it will use libpng).
MEncoder then feeds the decoded image to the chosen video compressor (DivX4, Xvid, FFmpeg msmpeg4, etc.).

Examples. The explanation of the -mf option is in the man page.

Creating an MPEG-4 file from all the JPEG files in the current directory:

mencoder mf://*.jpg -mf w=800:h=600:fps=25:type=jpg -ovc lavc \
    -lavcopts vcodec=mpeg4:mbd=2:trell -oac copy -o output.avi

Creating an MPEG-4 file from some JPEG files in the current directory:

mencoder mf://frame001.jpg,frame002.jpg -mf w=800:h=600:fps=25:type=jpg \
    -ovc lavc -lavcopts vcodec=mpeg4:mbd=2:trell -oac copy -o output.avi

Creating an MPEG-4 file from explicit list of JPEG files (list.txt in current directory contains the list of files to use as source, one per line):

mencoder mf://@list.txt -mf w=800:h=600:fps=25:type=jpg \
    -ovc lavc -lavcopts vcodec=mpeg4:mbd=2:trell -oac copy -o output.avi

You can mix different types of images, regardless of the method you use — individual filenames, wildcard or file with list — provided of course they have the same dimensions. So you can e.g. take title frame from PNG file, and then put a slideshow of your JPEG photos.

Creating a Motion JPEG (MJPEG) file from all the JPEG files in the current directory:

mencoder mf://*.jpg -mf w=800:h=600:fps=25:type=jpg -ovc copy -oac copy -o output.avi

Creating an uncompressed file from all the PNG files in the current directory:

mencoder mf://*.png -mf w=800:h=600:fps=25:type=png -ovc raw -oac copy -o output.avi

Note

Width must be integer multiple of 4, it is a limitation of the RAW RGB AVI format.

Creating a Motion PNG (MPNG) file from all the PNG files in the current directory:

mencoder mf://*.png -mf w=800:h=600:fps=25:type=png -ovc copy -oac copy -o output.avi

Creating a Motion TGA (MTGA) file from all the TGA files in the current directory:

mencoder mf://*.tga -mf w=800:h=600:fps=25:type=tga -ovc copy -oac copy -o output.avi

Subversion Commands and Scripts

2011-04-06T09:42:00.003-10:00

Subversion Commands and Scripts
http://www.yolinux.com/TUTORIALS/Subversion.html

Basic SVN Commands
http://www.linuxfromscratch.org/blfs/edguide/chapter03.html

svn status

svn status. This command prints the status of working directories and files. If you have made local changes, it'll show your locally modified items. If you use the --verbose switch, it will show revision information on every item. With the --show-updates (-u) switch, it will show any server out-of-date information.

$ svn ci -m " any message"
$ svn update
$ svn status

will show files that are not subversioned with "?" in front.

Reference sheet for natbib usage

2011-04-05T21:20:00.002-10:00

http://merkel.zoneo.net/Latex/natbib.php

The natbib package has two basic citation commands, \citet and \citep for textual and parenthetical citations, respectively. There also exist the starred versions \citet* and \citep* that print the full author list, and not just the abbreviated one. All of these may take one or two optional arguments to add some text before and after the citation.

\citet{jon90}     -->     Jones et al. (1990)
\citet[chap. 2]{jon90}     -->     Jones et al. (1990, chap. 2)
\citep{jon90}     -->     (Jones et al., 1990)
\citep[chap. 2]{jon90}     -->     (Jones et al., 1990, chap. 2)
\citep[see][]{jon90}     -->     (see Jones et al., 1990)
\citep[see][chap. 2]{jon90}     -->     (see Jones et al., 1990, chap. 2)
\citet*{jon90}     -->     Jones, Baker, and Williams (1990)
\citep*{jon90}     -->     (Jones, Baker, and Williams, 1990)

ls exclude

2011-04-04T21:38:00.002-10:00

http://www.unix.com/shell-programming-scripting/100038-ls-exclude-pattern.html

# See all files ending in .html
ls | grep "\.html$"
# see all files not ending in .html
ls | grep -v "\.html$"

crontab how to

2011-04-03T23:21:00.000-10:00

https://help.ubuntu.com/community/CronHowto

01,31 04,05 1-15 1,6 * /usr/bin/somedirectory/somecommand

The above example will run /usr/bin/somedirectory/somecommand
at 01 and 31 minuts
past the hours of 4:00am and 5:00am
on the 1st through the 15th
of every January and June.

Jaws parallel job submission

2011-03-31T11:11:00.000-10:00

#!/bin/bash
#PBS -l walltime=24:00:00
# selecting 2 nodes = 2 * 4 = 8 processors for use, mpiprocs needs to equal ncpus and doesn't exceed 4
#PBS -l select=2:mpiprocs=4:ncpus=4
# scatter required
#PBS -l place=scatter
# account required
#PBS -A yout_project_number

cd $PBS_O_WORKDIR
echo "RUNNING ON: `/usr/bin/uniq $PBS_NODEFILE`"
mpirun_jaws -np 8 interFoam -parallel > $WORKDIR/test_case/

Clone Remote Subversion Repositories With svnsync

2011-03-28T10:13:00.000-10:00

http://www.thoughtspark.org/node/10

Create your local repository: svnadmin create PATH
Create an empty pre-revprop-change hook script: echo "#!/bin/bash" > PATH/hooks/pre-revprop-change
Make the pre-revprop-change hook script executable: chmod +x PATH/hooks/pre-revprop-change
Initialize svnsync: svnsync init file:⁄⁄⁄PATH URL_TO_REPO_ROOT_TO_CLONE
Synchronize: svnsync sync DEST_URL

(Note: "DEST_URL" is the url to the Subversion repository you created in step 1.)

CFD Online

2011-03-25T22:55:00.001-10:00

http://www.cfd-online.com/

How to install OpenFOAM in Mac

2011-03-24T23:08:00.005-10:00

Preparations

Obtain the necessary software through MacPorts.
- libtool
Obtain the latest version of XCode.
- This may be available on your Max OS X Install CD/DVD.
- Available online at http://developer.apple.com/technologies/xcode.html.
  - Note: You will need to sign in with your Apple ID and password to access the download.
Obtain the latest version of XQuartz from http://xquartz.macosforge.org/.
Obtain the latest version of Qt from http://qt.nokia.com/downloads/qt-for-open-source-cpp-development-on-mac-os-x.
- Note: You do not need the full SDK. The "QT libraries" download is sufficient, and will include qmake.
Obtain the latest version of CMake from http://www.cmake.org/cmake/resources/software.html

here we go.

But I was NOT able to install OpenFOAM on my Mac.

Installation of Elmer CFD using Intel Compilers ver. 12

2011-03-24T13:03:00.001-10:00

All most all routines are compiled with some warning and recommendation messages.

Two key things should be done to compile files in fem/src.

1. "CONTIGUOUS" option should be disabled in configure files, Makefile files, and especially acx_elmer.m4.

2. The following directory should be included in $LD_LIBRARY_PATH

/opt/intel/composerxe-2011.2.137/compiler/lib/ia32/

3. By running 'make check' in fem, I got 154 passes out of 163:

Making check in src
make[1]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem/src'
Making check in view3d
make[2]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem/src/view3d'
make[2]: Nothing to be done for `check'.
make[2]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem/src/view3d'
Making check in viewaxis
make[2]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem/src/viewaxis'
make[2]: Nothing to be done for `check'.
make[2]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem/src/viewaxis'
Making check in binio
make[2]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem/src/binio'
Making check in test
make[3]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem/src/binio/test'
make writetest readtest
make[4]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem/src/binio/test'
ifort -I.. -O -fPIC -I. -Ibinio -c -o writetest.o writetest.f90
ifort -I.. -O -fPIC -I. -Ibinio -L. -L/opt/elmer/intel/lib -o writetest writetest.o ../libbinio.a -L. -ldl -L/opt/elmer/intel/lib -lm
ifort -I.. -O -fPIC -I. -Ibinio -c -o readtest.o readtest.f90
ifort -I.. -O -fPIC -I. -Ibinio -L. -L/opt/elmer/intel/lib -o readtest readtest.o ../libbinio.a -L. -ldl -L/opt/elmer/intel/lib -lm
make[4]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem/src/binio/test'
make check-TESTS
make[4]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem/src/binio/test'
cp writetest.sh run-writetest
chmod a+x run-writetest
cp readtest.sh run-readtest
chmod a+x run-readtest
PASS: run-writetest
PASS: run-readtest
==================
All 2 tests passed
==================
make[4]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem/src/binio/test'
make[3]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem/src/binio/test'
make[3]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem/src/binio'
make[3]: Nothing to be done for `check-am'.
make[3]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem/src/binio'
make[2]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem/src/binio'
make[2]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem/src'
make[2]: Nothing to be done for `check-am'.
make[2]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem/src'
make[1]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem/src'
Making check in tests
make[1]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem/tests'
make check-TESTS
make[2]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem/tests'
$ELMER_HOME undefined, setting it to ../src
test 1 :                   1dtests              [PASSED], CPU time=0.12
test 2 :                   1sttime              [PASSED], CPU time=0.5
test 3 :                   2ndtime              [PASSED], CPU time=0.92
test 4 :                AdvReactDG              [PASSED], CPU time=1.23
test 5 :            BlockLinElast1              [PASSED], CPU time=1.62
test 6 :             BlockPoisson1              [PASSED], CPU time=1.76
test 7 :             BlockPoisson2              [PASSED], CPU time=1.88
test 8 :             BlockPoisson3              [PASSED], CPU time=2.32
test 9 :         CapacitanceMatrix              [PASSED], CPU time=2.6
test 10 :                 CavityLid             [PASSED], CPU time=3.26
test 11 :                CavityLid2             [PASSED], CPU time=7.56
test 12 :         CoordinateScaling             [PASSED], CPU time=7.69
test 13 :           CoupledPoisson1             [PASSED], CPU time=7.81
test 14 :           CoupledPoisson2             [PASSED], CPU time=8.93
test 15 :           CoupledPoisson3             [PASSED], CPU time=9.07
test 16 :           CoupledPoisson4             [PASSED], CPU time=9.21
test 17 :           CoupledPoisson5             [PASSED], CPU time=9.38
test 18 :           CoupledPoisson6             [PASSED], CPU time=9.52
test 19 :           CoupledPoisson7             [PASSED], CPU time=9.66
test 20 :           CoupledPoisson8             [PASSED], CPU time=9.81
test 21 :           CoupledPoisson9             [PASSED], CPU time=9.95
test 22 :           CurvedBndryPFEM             [PASSED], CPU time=10.06
test 23 :      DivergenceAnalytic2D             [PASSED], CPU time=10.82
test 24 :         ElastElstat1DBeam             [PASSED], CPU time=11.02
test 25 :           ElastElstatBeam             [PASSED], CPU time=11.49
test 26 :        ElasticLubrication             [PASSED], CPU time=14.59
test 27 :     ExtrusionStructured2D             [PASSED], CPU time=18.16
test 28 :               HeatControl             [PASSED], CPU time=18.29
test 29 :              HeatControl2             [PASSED], CPU time=18.51
test 30 :                   HeatGap             [PASSED], CPU time=18.67
test 31 :              HelmholtzBEM             [PASSED], CPU time=19.34
test 32 :             HelmholtzEdge             [PASSED], CPU time=19.63
test 33 :              HelmholtzFEM             [PASSED], CPU time=19.9
test 34 :             HelmholtzFace             [PASSED], CPU time=20.21
test 35 :          InductionHeating             [PASSED], CPU time=20.7
test 36 :         InductionHeating2             [PASSED], CPU time=21.56
test 37 :                    L2norm look at [L2norm/test.log] for details
test 38 :         LimitDisplacement             [PASSED], CPU time=24.44
test 39 :          LimitTemperature             [PASSED], CPU time=28.97
test 40 :         LimitTemperature2             [PASSED], CPU time=31.52
test 41 :     LubricationTunedForce             [PASSED], CPU time=32.45
test 42 :         MeshRefineGrading             [PASSED], CPU time=36.8
test 43 :         NaturalConvection             [PASSED], CPU time=43.66
test 44 :        NormalTangentialBC             [PASSED], CPU time=45.72
test 45 : OptimizeSimplexFourHeaters            [PASSED], CPU time=50.37
test 46 :               PhaseChange             [PASSED], CPU time=53.94
test 47 :              PhaseChange2             [PASSED], CPU time=54.86
test 48 :              PhaseChange3             [PASSED], CPU time=55.8
test 49 :                PoissonBEM             [PASSED], CPU time=55.95
test 50 :                 PoissonDG             [PASSED], CPU time=56.2
test 51 :               PoissonPFEM             [PASSED], CPU time=56.32
test 52 :                PorousPipe             [PASSED], CPU time=57.32
test 53 :                      Q1Q0             [PASSED], CPU time=57.53
test 54 :              RichardsDyke             [PASSED], CPU time=62.57
test 55 :             RichardsDyke2             [PASSED], CPU time=72.15
test 56 :          RigidMeshMapper1             [PASSED], CPU time=72.74
test 57 :          RigidMeshMapper2             [PASSED], CPU time=73.25
test 58 :              RotatingFlow             [PASSED], CPU time=74.21
test 59 :                   Step_ke             [PASSED], CPU time=76.6
test 60 :                   Step_ns             [PASSED], CPU time=77.14
test 61 :                   Step_sa             [PASSED], CPU time=87.75
test 62 :            Step_sst-kw-wf             [PASSED], CPU time=107.02
test 63 :               Step_stokes             [PASSED], CPU time=107.21
test 64 :         Step_stokes_block             [PASSED], CPU time=107.49
test 65 :                  Step_v2f             [PASSED], CPU time=132.67
test 66 :                StokesPFEM             [PASSED], CPU time=132.89
test 67 :                StokesProj             [PASSED], CPU time=133.45
test 68 :       StrainCalculation01             [PASSED], CPU time=133.91
test 69 :       StrainCalculation02             [PASSED], CPU time=142.01
test 70 :            ThermalBiMetal             [PASSED], CPU time=142.23
test 71 :           ThermalBiMetal2             [PASSED], CPU time=142.49
test 72 :           ThermalCompress             [PASSED], CPU time=143.41
test 73 :                 TimeAdapt             [PASSED], CPU time=145.49
test 74 :                   WaveEqu             [PASSED], CPU time=145.69
test 75 :               adaptivity1 look at [adaptivity1/test.log] for details
test 76 :               adaptivity2 look at [adaptivity2/test.log] for details
test 77 :               adaptivity3 look at [adaptivity3/test.log] for details
test 78 :               adaptivity4 look at [adaptivity4/test.log] for details
test 79 :               adaptivity5 look at [adaptivity5/test.log] for details
test 80 :                 adv_diff1             [PASSED], CPU time=146.93
test 81 :                 adv_diff2             [PASSED], CPU time=147.93
test 82 :                 adv_diff3             [PASSED], CPU time=150.8
test 83 :                 adv_diff4             [PASSED], CPU time=155.33
test 84 :                    amultg             [PASSED], CPU time=156.72
test 85 :                   amultg2             [PASSED], CPU time=157.24
test 86 :              beam-springs             [PASSED], CPU time=158.1
test 87 :                 bentonite             [PASSED], CPU time=158.24
test 88 :                   bodydir             [PASSED], CPU time=158.38
test 89 :                  bodyload             [PASSED], CPU time=158.5
test 90 :                  buckling             [PASSED], CPU time=161.1
test 91 :               channel_v2f             [PASSED], CPU time=167.67
test 92 :                   coating             [PASSED], CPU time=171.88
test 93 :                   current             [PASSED], CPU time=172.19
test 94 :      current_heat_control             [PASSED], CPU time=173.04
test 95 :                 dft-water             [PASSED], CPU time=173.04
test 96 :               diffuser_sa             [PASSED], CPU time=184.22
test 97 :              diffuser_sst             [PASSED], CPU time=191.64
test 98 :              diffuser_v2f             [PASSED], CPU time=208.07
test 99 :             el_adaptivity look at [el_adaptivity/test.log] for details
test 100 :                elasticity            [PASSED], CPU time=208.79
test 101 :                    elstat            [PASSED], CPU time=213.32
test 102 :             elstat_source            [PASSED], CPU time=213.57
test 103 :                fluxsolver            [PASSED], CPU time=213.71
test 104 :               fluxsolver2            [PASSED], CPU time=213.86
test 105 :                  freesurf            [PASSED], CPU time=214.75
test 106 :              freesurf_axi            [PASSED], CPU time=216.2
test 107 :              freesurf_int            [PASSED], CPU time=217.16
test 108 :              freesurf_ltd            [PASSED], CPU time=223.7
test 109 :                  fsi_beam            [PASSED], CPU time=225.51
test 110 :         fsi_beam_optimize            [PASSED], CPU time=230.94
test 111 :                   fsi_box            [PASSED], CPU time=233.11
test 112 :                  fsi_box2            [PASSED], CPU time=234.68
test 113 :                 geomstiff            [PASSED], CPU time=234.96
test 114 :                    gmultg look at [gmultg/test.log] for details
test 115 :                    heateq            [PASSED], CPU time=235.56
test 116 :                heateq-par            [PASSED], CPU time=235.69
test 117 :               heateq_bdf2            [PASSED], CPU time=235.97
test 118 :               heateq_bdf3            [PASSED], CPU time=236.25
test 119 :                 levelset1            [PASSED], CPU time=240.49
test 120 :                 levelset2            [PASSED], CPU time=243.06
test 121 :             linearsolvers            [PASSED], CPU time=243.35
test 122 :       linearsolvers_cmplx            [PASSED], CPU time=244.61
test 123 :                 marangoni            [PASSED], CPU time=244.8
test 124 :                  mgdyn_bh            [PASSED], CPU time=278.71
test 125 :            mgdyn_harmonic            [PASSED], CPU time=290.79
test 126 :              mgdyn_steady            [PASSED], CPU time=299.57
test 127 :               mgdyn_torus            [PASSED], CPU time=304.96
test 128 :           mgdyn_transient            [PASSED], CPU time=335.68
test 129 :                       mhd            [PASSED], CPU time=338.38
test 130 :                      mhd2            [PASSED], CPU time=342
test 131 :                 multimesh look at [multimesh/test.log] for details
test 132 :                   normals            [PASSED], CPU time=342.13
test 133 :                   passive            [PASSED], CPU time=342.97
test 134 :                 periodic1            [PASSED], CPU time=343.15
test 135 :                 periodic2            [PASSED], CPU time=343.32
test 136 :         periodic_explicit            [PASSED], CPU time=344.99
test 137 :    periodic_nonconforming            [PASSED], CPU time=345.15
test 138 :              periodic_rot            [PASSED], CPU time=345.31
test 139 :                     piezo            [PASSED], CPU time=345.5
test 140 :                    plates            [PASSED], CPU time=345.66
test 141 :                  pointdir            [PASSED], CPU time=345.79
test 142 :                 pointload            [PASSED], CPU time=345.92
test 143 :                 radiation            [PASSED], CPU time=346.17
test 144 :                radiation2            [PASSED], CPU time=346.41
test 145 :               radiation2d            [PASSED], CPU time=348.41
test 146 :               radiation3d            [PASSED], CPU time=354.35
test 147 :                    reload            [PASSED], CPU time=355.48
test 148 :                 reynolds1            [PASSED], CPU time=357.86
test 149 :                 reynolds2            [PASSED], CPU time=358.5
test 150 :                 reynolds3            [PASSED], CPU time=362.48
test 151 :                  rgdblock            [PASSED], CPU time=364.92
test 152 :                 rot_aniso            [PASSED], CPU time=368.66
test 153 :                   rotflow            [PASSED], CPU time=369.54
test 154 :               savescalars            [PASSED], CPU time=369.98
test 155 :                     shell            [PASSED], CPU time=370.25
test 156 :                    shell2            [PASSED], CPU time=370.72
test 157 :                staged_sim            [PASSED], CPU time=372.15
test 158 :               streamlines            [PASSED], CPU time=372.58
test 159 :                    stress            [PASSED], CPU time=372.92
test 160 :                 structmap            [PASSED], CPU time=373.09
test 161 :                    tresca            [PASSED], CPU time=373.31
test 162 :                  vortex2d            [PASSED], CPU time=374.73
test 163 :                  vortex3d            [PASSED], CPU time=376.67
Tests completed, passed: 154 out of total 163 tests
Cumulative CPU time used in test: 376.67 s
PASS: runtests
==================
All 1 tests passed
==================
make[2]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem/tests'
make[1]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem/tests'
make[1]: Entering directory `/home/albertsk/packages/elmerfem-intel/fem'
make[1]: Leaving directory `/home/albertsk/packages/elmerfem-intel/fem'

Coding Guidelines for Intel® Architectures

2011-03-24T09:42:00.000-10:00

Do J
Do I

is better than

Do I
Do J

http://www.ncsa.illinois.edu/UserInfo/Resources/Software/Intel/Compilers/8.1/f_ug2/code_arch.htm

Mesh generation (free) software

2011-03-23T10:24:00.000-10:00

CALCULIX: A Free Software Three-Dimensional Structural Finite Element Program

Gmsh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities

NETGEN: an automatic 3d tetrahedral mesh generator.

capturing messages from configure and make

2011-03-21T16:16:00.000-10:00

To capture the output of the configure and make steps you can use the script command or the following technique if using a Bourne style shell:

shell$ ./configure {options} 2>&1 | tee config.out
shell$ make all 2>&1              | tee make.out
shell$ make install 2>&1          | tee make-install.out

or if using a csh style shell:

shell% ./configure {options} |& tee config.out
shell% make all              |& tee make.out
shell% make install          |& tee make-install.out

cluster pach update using yum and repoman

2011-03-17T15:17:00.001-10:00

Best Practice for Patching Individual Packages in PCM

Document Number	1-1F6K86
Product	Platform OCS/PCM
Affected Version	1.2* 2.0* 2.1*
OS	Linux
Category	Installation/Upgrade
Date Created	Jan 21 2009, 10:15 PM
Last Update	Nov 10 2010, 11:14 AM
Keywords	Update, patch, rhn, repopatch, kernel,

Topic

Best Practice for Patching Individual Packages in PCM

Issue Description

I need to update the kernel package on my PCM cluster with the latest and greatest avaialbe on RHN.

Solution Detail

Often, it is necessary to apply patches to your PCM cluster. Some patches fix security issues, while other patches offer bug fixes and feature improvements. Patches can be applied in two ways.

1. One way is to use kusu-repopatch tool to download and install all available patches for your Operating System. This has the advantage of having your cluster nodes always at the "latest and greatest" version level. There are a few down sides with this approach, namely that updating large number of packages is more risky and can break your production environment, and also if you are using Platform OFED for InfiniBand support, kusu-repopatch cannot be used due to dependency issues. This last point is only valid for PCM versions < 2.1. In 2.1, this issue is addressed, and kusu-repopatch can safely be used even with Platform OFED kit installed.

2. The other way is to download the individual packages manually using yum command, and then add them to your PCM repository. The advantage is that updates can be done very quickly and relatively safely. The disadvantage is that not all of your packages are at the "latest and greatest" version level.

This article describes the second approach, That is, how to patch individual packages in your PCM cluster. As a working example, the article shows how to patch the kernel package.

If you are interested in using kusu-repopatch to patch all the packages, please refer to the article titled "Best Practice for Patching PCM Clusters with kusu-repopatch."

0. Before you begin

Before applying any patches to your production environment, you should take some precautions in case something goes wrong. In your PCM cluster you can take advantage of repository snapshots and node group templates to apply your updates in a safe way.

NOTE: In older version of PCM (< 2.0) the above commands did not have the "kusu-" prefix. For example, repoman vs. kusu-repoman. To determine which version of PCM cluster you are using,you can look at the output of cat /etc/kusu-release.

1. Use kusu-repoman command to get the name of your production repository. For example,

pcm201installer:~ # kusu-repoman -l
Repo name:      sles-10.3-x86_64
Repository:     /depot/repos/1000
Installers:     192.168.1.1;172.27.1.43
Ostype:         sles-10-x86_64
Kits:           base-2.0-1-x86_64, sles-10.3-x86_64,
                nagios-2.12-7-x86_64, ofed-2.0-1-x86_64,
                PCM_GUI-2.0-1-x86_64, platform-hpc-2.0-2-x86_64,
                platform-isf-ac-1.0-1-x86_64, platform-lsf-7.0.6-1-x86_64,
                platform-mpi-7.1-1-x86_64, platform-rtm-2.0.1-1-x86_64

The name of the repository is sles-10.3-x86_64, and it has an ID of 1000. The repository is located under /depot/repos/1000/ directory, and it was created during PCM installation.

2. Create a snapshot of your production repository with kusu-repoman command. This will create a new repository with ID 1001 under /depot/repos/1001/ directory.

# kusu-repoman -r -s

3. Create a new node group which is a copy of your production node group with kusu-ngedit command. You can use kusu-nghosts -l command to determine the name of your production node group, first. Then, use kusu-ngedit to create a copy called compute-patchtest, like this:

# kusu-ngedit -c compute-rhel-5.4-x86-64 -n compute-patchtest

4. Associate the compute-patchtest node group with snapshot repository using the kusu-ngedit command.

5. Move a single node to compute-patchtest node group using kusu-nghosts command.

1. Register with Red Hat Network (RHN)

Fist step is to to register your cluster to Red Hat Network. If you are using SLES, then please use equivalent procedure to register for online updates. If you are using CentOS or SCL, then you do not need to register your cluster, but you might need to enable the online repository in /etc/yum.repos.d/ directory.

Do following to register your cluster with RHN:

1. run rhn_register on your Installer node

2. Update the /opt/kusu/etc/updates.conf file and enter valid username/password to login to RHN as well as Server ID (a.k.a RHN System ID).

NOTE: Server ID is not needed if you are running PCM version < 2.0.

2. Download and Install the Patches

Yum will, by default, download and install the updated packages. However, since PCM will be responsible for installing the updated packages on cluster nodes, we just need yum to download the package, and not install them. For this, you need to download the downloadonly plugin for yum. Follow these steps to download and install the kernel patches.

1. Download the downloadonly plugin from RHN:

# yum -y install yum-downloadonly

2. Create a snapshot of your production repository. Best practice is to always test the updates prior to applying them to production repository. Therefore, you should first create a snapshot of your production repository and .....

3. Download latest kernel packages from RHN. There are three packages which you must update: kernel, kernel-devel and kernel-headers. The packages must be downloaded to /depot/contrib/1001/ directory; this is where PCM will look for custom RPMs associated with snapshot repository (id = 1001).

# yum update -y kernel kernel-devel kernel-headers --downloadonly --downloaddir=/depot/contrib/1001/

4. Update the snapshot repository:

# kusu-repoman -ur "name of snapshot repository"

This will create appropriate symbolic links in /depot/repos/1001/Server/ directory, and it may take up to 10 minutes to complete. The symbolic links to the latest kernel packages are shown below:

[root@pcm201installer ~]# ll /depot/repos/1000/Server/kernel-*
lrwxrwxrwx 1 root root 59 Oct 21 12:13 /depot/repos/1000/Server/kernel-2.6.18-194.17.1.el5.x86_64.rpm -> ../../../contrib/1000/kernel-2.6.18-194.17.1.el5.x86_64.rpm

lrwxrwxrwx 1 root root 65 Oct 21 12:13 /depot/repos/1000/Server/kernel-devel-2.6.18-194.17.1.el5.x86_64.rpm -> ../../../contrib/1000/kernel-devel-2.6.18-194.17.1.el5.x86_64.rpm
lrwxrwxrwx 1 root root 67 Oct 21 12:13 /depot/repos/1000/Server/kernel-headers-2.6.18-194.17.1.el5.x86_64.rpm -> ../../../contrib/1000/kernel-headers-2.6.18-194.17.1.el5.x86_64.rpm

5. Install the patches on nodes in the compute-testpatch node group. Use the kusu-cfmsync command to install the patches "on-the-fly" - there is no need to re-provision the nodes to install the patches in PCM. However, if you have patched the kernel, you need to reboot the nodes using kusu-boothost command to boot them with the new kernel.

# kusu-cfmsync -n compute-testpatch -u
# kusu-boothost -r "hostname of patched node"

3. Test the Patches and Install in Production Environment

The only thing that remains is to test the patches work ok for nodes in compute-testpatch node group. Do as much testing as required to convince yourself that your production applications will work with OK after the patches were applied. For example, you may wish to do the following tests:

Test that nodes in compute-testpatch node group can be re-provisioned correctly
Test that patched packages are installed after re-provisioning. For kernel patches, run uname -r command to make sure kernel version is the latest one.
If you have patched the Installer node as well, then you can run command like kusu-genconfig nodes and make sure you get a list of all node hostnames in you cluster. This will confirm that PCM tools can communicate to the cluster database

Once you are satisfied that the patches are safe to roll out to your production environment, you can follow the steps outlined in section 2 "Download and Install the Patches" to patch your production repository. The only difference is that now you should specify your production node group and installer node group name when you apply the updates via kusu-cfmsync -u

Raster3D version 2.9.2 installation on Ubuntu Marverik

2011-03-04T15:32:00.000-10:00

Install Raster3D_2.9-2/

Install

Tiff ftp://ftp.remotesensing.org/pub/libtiff/tiff-3.9.4.zip
gdlib http://www.libgd.org/releases/gd-2.0.35.tar.gz

Other graphic library

sudo apt-get install libjpeg-dbg
sudo apt-get install libjpeg-dev
sudo apt-get install libpng-dev libpng12-0-dev libpng3-dev libpngwriter libpngwriter-dev libtk-png-perl pnmtopng
sudo apt-get install xutils-dev

iPhone

2011-03-02T15:34:00.000-10:00

How to use iPhone in Ubuntu

cmake installation

2011-02-28T23:31:00.001-10:00

Download cmake (cmake-2.8.4.tar.gz) from here.
Unzip using "tar zxvof cmake-2.8.4.tar.gz"
cd cmake-2.8.4
./bootstrap
make
make install

For compute nodes, use script Docmake.

OpenFOAM = Ubuntu/Debian Pack Installation

2011-02-28T17:45:00.002-10:00

http://www.openfoam.com/download/ubuntu.php

Customize LSF configuration files in OCS/PCM

2011-01-14T08:28:00.002-10:00

Customize LSF configuration files in OCS/PCM

Document Number	1-1GMJYZ
Product	Platform OCS/PCM
Version	1.2, 1.2a, 1.2b, 1.2.1, 2.0.1
OS	Linux
Category	Product Usage
Date Created	Apr 02 2009, 04:37 PM
Last Update	Oct 22 2010, 02:01 PM
Keywords	Customize LSF configuration files in OCS/PCM

Topic

Customize LSF configuration files in OCS/PCM

Problem Description

After PCM LSF Kit is installed, the first thing you usually do is to customize LSF configuration according to the actual needs of your site.

For example, you may want to customize lsb.queues file to add your own queue definition, or you may need to define a special resource which is only available on several nodes. In the later case, you will need to customize lsf.shared file and lsf.cluster file.

This article provides you with the steps and some examples of how to customize LSF configuration in different PCM/OCS versions.

Solution Detail

Customize LSF in PCM 2.0, PCM 1.2a, PCM 1.2b, PCM 1.2.1

In the versions listed above, all the LSF configuration changes should be done through template files.

The templates for lsf.* files are under /etc/cfm/templates/lsf/.

# pwd
/etc/cfm/templates/lsf
# ll
total 32
-r--r--r-- 1 lsfadmin root 1770 Dec 1 03:11 default.lsf.cluster
-r--r--r-- 1 lsfadmin root 1479 Dec 1 03:11 default.lsf.conf
lrwxrwxrwx 1 root root 16 Mar 12 14:53 default.lsf.conf.master -> default.lsf.conf
lrwxrwxrwx 1 root root 16 Mar 12 14:53 default.lsf.conf.slave -> default.lsf.conf
-r--r--r-- 1 lsfadmin root 12766 Dec 1 03:11 default.lsf.shared
drwxr-xr-x 3 lsfadmin root 4096 Mar 12 14:53 ego
drwxr-xr-x 3 lsfadmin root 4096 Mar 12 14:53 lsbatch

The templates for lsb.* files are under/etc/cfm/templates/lsf/lsbatch/default/configdir/.

# pwd
/etc/cfm/templates/lsf/lsbatch/default/configdir
# ll
total 80
-r--r--r-- 1 lsfadmin root 21388 Dec 1 03:11 lsb.applications
-r--r--r-- 1 lsfadmin root 2912 Dec 1 03:11 lsb.hosts
-r--r--r-- 1 lsfadmin root 1196 Dec 1 03:11 lsb.modules
-r--r--r-- 1 lsfadmin root 1547 Dec 1 03:11 lsb.nqsmaps
-r--r--r-- 1 lsfadmin root 1454 Dec 1 03:11 lsb.params
-r--r--r-- 1 lsfadmin root 20801 Dec 1 03:11 lsb.queues
-r--r--r-- 1 lsfadmin root 6025 Dec 1 03:11 lsb.resources
-r--r--r-- 1 lsfadmin root 1279 Dec 1 03:11 lsb.serviceclasses
-r--r--r-- 1 lsfadmin root 899 Dec 1 03:11 lsb.users

If you need to customize any file, make changes in the relative template file. After you save the changes to the template file, run addhost -u which will propagate the changes to nodes and restart LSF services.

What needs to be highlighted is default.lsf.cluster file. In this template file, you cannot find the host information like what you have in /opt/lsf/conf/lsf.cluster.<cluster_name> file.

If you need to modify the host section of lsf.cluster file, you have to first manually type in the host information or copy the host information over from /opt/lsf/conf/lsf.cluster.<cluster_name> file, then make changes.

By default, the default.lsf.cluster file looks like this:

Begin   Host
HOSTNAME model    type        server r1m mem swp RESOURCES    #Keywords
......
#orange   !        SUNSOL       1     3.5 1    2   (sparc bsd)   #Example
#prune    !        !            1     3.5 1    2   (convex)
XXX_lsfmc_XXX   !   !   1   3.5   ()   ()   (mg)
End     Host

Let's take an example that you need to change the r1m value of a compute node compute-0 from the default value 3.5 to 4.0. You need to manually type the following information for compute-0 in the file:

compute-0 ! ! 1 4.0 () () (mg)
End Host

Run addhost -u after you make the change.

Customize LSF in OCS 5.3/PCM 1.2 and OCS 5.1

Due to some bug in LSF Kit shipped with OCS 5.3/PCM 1.2 and OCS 5.1, you need to follow different steps to customize LSF configuration files from PCM 2.0, PCM 1.2a, PCM 1.2b and PCM 1.2.1.

Steps to customize lsf.* files such as lsf.conf, lsf.shared, except for the host section oflsf.cluster file:

1. Make changes to the relative files in /etc/cfm/templates/lsf/
For example, modify default.lsf.conf if you need to customize lsf.conf file.

2. Run addhost -u

Steps to customize lsb.* files such as lsb.hosts, lsb.users:

1. Make changes to the files in /etc/cfm/installer-rhel-5-x86_64/opt/lsf/conf/lsbatch/<clustername>/configdir/

2. Run cfmsync -fp

Steps to customize lsf.cluster file:

Due to the bug mentioned above, there are problems in customizing the host section oflsf.cluster file in OCS 5.3/PCM 1.2 and OCS 5.1. For other sections, you can follow the same steps with customizing lsf.conf file.

To customize the host section of lsf.cluster file, you can do that through /etc/cfm/installer-rhel-5-x86_64/opt/lsf/conf/lsf.cluster file and run "cfmsync -fp". But the changes will be overwritten if addhost -u is called. Please contact Platform PCM Support to require a fix if you really need to customize the host section of lsf.cluster file. Upgrading your cluster to a higher version can also solve the issue and it is recommended.

Note:

Changing the files in /opt/lsf/conf only works temporarily. Configuration changes are rolled back if cfmsync is called by other actions, such as ngedit.

LSF license file renew

2011-01-13T15:18:00.000-10:00

Copy a new license file (e.g., license_new.dat") to LSF_ENVDIR.
Change LSF_LICENSE_FILE pointing to the new license file.
Restart LIM using "lsadmin reconfig"(or stop and start LSF deamons on LSF master host)
Run followings to confirm: lsid, lsload, bhosts

LaTex symbols: space and carriage return

2011-01-11T11:12:00.000-10:00

To show space as upward square cup:

\newcommand{\spc}{$_{\sqcup}$}

To show the enter key character using "mathabx" package
\usepackage{mathabx}

\newcommand{\enter}{$\dlsh$}

rsync excluding .svn dir

2010-12-30T15:57:00.005-10:00

rsync -av --exclude=".svn" -e ssh A B

The TeX Catalogue OnLine, Entry for titleref, Home Edition

2010-12-27T16:43:00.000-10:00

The TeX Catalogue OnLine, Entry for titleref, Home Edition

to increase section number by 2

2010-12-23T09:53:00.002-10:00

\addtocounter{section}{2}

pdfpages to include pdf files into LaTex

2010-12-23T09:30:00.001-10:00

\usepackage{pdfpages}
\usepackage{fancyhdr}

\includepdf[pages=-, pagecommand={\thispagestyle{fancy}}]{PeerEvalScanned.pdf}

\includepdf[pages=-, fitpaper=true, pagecommand={\thispagestyle{fancy}},addtolist={1,figure,{some interesting}, TEformNumeric}]{TE/TEformNumeric.pdf}

Natbib reference sheet

2010-12-22T12:17:00.001-10:00

Natbib reference sheet

\citet{jon90} --> Jones et al. (1990)

\citet[chap. 2]{jon90} --> Jones et al. (1990, chap. 2)

\citep{jon90} --> (Jones et al., 1990)

\citep[chap. 2]{jon90} --> (Jones et al., 1990, chap. 2)

\citep[see][]{jon90} --> (see Jones et al., 1990)

\citep[see][chap. 2]{jon90} --> (see Jones et al., 1990, chap. 2)

\citet*{jon90} --> Jones, Baker, and Williams (1990)

\citep*{jon90} --> (Jones, Baker, and Williams, 1990)

How to use nomenclature

2010-12-21T11:21:00.000-10:00

Put \usepackage[〈options〉]{nomencl} in the preamble of your document.
Put \makenomenclature in the preamble of your document.
Issue the \nomenclature command (see Section 2.2) for each symbol you want to have included in the nomenclature list. The best place for this command is immediately after you introduce the symbol for the ﬁrst time.
Put \printnomenclature at the place you want to have your nomenclature list.

\documentclass[12pt]{article}

\usepackage{nomencl}

\makenomenclature

\begin{document}

\maketitle

\tableofcontents

\printnomenclature

\nomenclature{$N$}{The number of particles}

\end{document}

To compile do followings in Unix prompt:

makeindex 〈ﬁlename〉.nlo -s nomencl.ist -o 〈ﬁlename〉.nls

TAR a large disk image

2010-12-17T10:42:00.000-10:00

http://bit.ly/11m9K6

Particle variables

2010-12-17T09:20:00.000-10:00

for i = 1, np

Particle radius

AP(i)

Translational Coordinates and Uelocities, Acceleration

CX(i), UX(i), AX(i)
CY(i), UY(i), AY(i)
CX(i), UZ(i), AZ(i)

Rotational Euler-coordinates and Welocities (omega), Bacceleration (Boosting rotation)

EX(i), WX(i), BX(i)
EY(i), WY(i), BY(i)
EX(i), WZ(i), BZ(i)

Version Control Demystified, Part 2: A Subversion Primer

2010-12-14T09:30:00.000-10:00

Version Control Demystified, Part 2: A Subversion Primer

anthony.liekens.net » LaTeX » Degrees Notation

2010-12-13T08:49:00.001-10:00

anthony.liekens.net » LaTeX » Degrees Notation: "\usepackage{gensymb}"

anthony.liekens.net » LaTeX » Degrees Notation

2010-12-13T08:49:00.000-10:00

anthony.liekens.net » LaTeX » Degrees Notation: "\usepackage{gensymb}"

mathmode - How to get a little frac - TeX - LaTeX - Stack Exchange

2010-12-10T09:51:00.001-10:00

\usepackage{amsmath}
\tfrac{x}{y}

mathmode - How to get a little frac - TeX - LaTeX - Stack Exchange: "amsmath"

Red Hat Enterprise Linux-Specific Information

2010-12-08T14:49:00.000-10:00

Red Hat Enterprise Linux-Specific Information: "[Ctrl]-[C]"

KCB's LaTeX files

2010-12-04T22:35:00.000-10:00

KCB's LaTeX files: "\timestamp"

LaTeX Tools and Templates

2010-12-04T22:31:00.000-10:00

LaTeX Tools and Templates

periodic boundary conditions

2010-12-04T00:26:00.000-10:00

1, 2, 3, ..., L-1, L

i + 1 => mode ( i , L) + 1
i + 2 => mode ( i+1, L) + 1

i - 1 => mode ( i - 2 + L , L ) + 1

i - 2 => mode ( i - 3 + L , L ) + 1

Octave/MATLAB basics

2010-12-03T21:36:00.000-10:00

Octave/MATLAB basics

Getting to Grips with Latex - Tables - Latex Tutorials by Andrew Roberts @ School of Computing, University of Leeds

2010-12-03T21:07:00.000-10:00

Getting to Grips with Latex - Tables - Latex Tutorials by Andrew Roberts @ School of Computing, University of Leeds: "\begin{center}
\begin{tabular}{ l | c || r | }
\hline
1 & 2 & 3 \\ \hline
4 & 5 & 6 \\ \hline
7 & 8 & 9 \\
\hline
\end{tabular}
\end{center}"

LaTeX:Commands - AoPSWiki

2010-12-03T15:11:00.002-10:00

LaTeX:Commands - AoPSWiki

LaTex \newcommand

2010-12-03T13:25:00.003-10:00

\newcommand{\dd}{\mathrm{d}}
\newcommand{\dt}{\mathrm{d}t}
\newcommand{\tr}{\mathrm{tr}}
\newcommand{\bmcal}[1]{\bm{\mathcal{#1}}}

\newcommand{\mycolor}{white}%purple, white
\newcommand{\mypause}{\pause}%
\newcommand{\justmoment}{\mypause}
%
\newcommand{\tcol}[1]{\textsf{\textcolor{\mycolor}{#1}}}
\newcommand{\tcolred}[1]{\textsf{\textcolor{red}{#1}}}
\newcommand{\tcolpurple}[1]{\textbf{\textcolor{purple}{#1}}}
\newcommand{\tcolul}[1]{\underline{\textbf{\textcolor{\mycolor}{#1}}}}
\newcommand{\tcolep}[1]{\emph{\textbf{\textcolor{\mycolor}{#1}}}}
\newcommand{\tcolmath}[1]{{\textcolor{\mycolor}{#1}}}
\newcommand{\tcolmathblue}[1]{{\textcolor{blue}{#1}}}
\newcommand{\tcolmathbf}[1]{\mathbf{\textcolor{\mycolor}{#1}}}
\newcommand{\tcolmathrm}[1]{\mathrm{\textcolor{\mycolor}{#1}}}
\newcommand{\textrtblue}[1]{\textrt{\textcolor{blue}{#1}}}
%\newcommand{\tcol}[1]{\textbf{\textcolor{white}{#1}}}
%\newcommand{\tcolmath}[1]{\mathbf{\textcolor{white}{#1}}}
%
\newcommand{\dbar}{d\mkern-6mu\mathchar'26}
\newcommand{\degree}{\textdegree}
\newcommand{\FigurePath}{/Users/albertsk/svn2009/Library/Figures}
\newcommand{\xunit}{\mathbf{i}}
\newcommand{\yunit}{\mathbf{j}}
\newcommand{\zunit}{\mathbf{k}}
\newcommand{\ii}{\mathbf{i}}
\newcommand{\jj}{\mathbf{j}}
\newcommand{\kk}{\mathbf{k}}
\newcommand{\textrt}[1]{\textit{\textrm{#1}}}
\newcommand{\paren}[1]{\left[{#1}\right]}
\newcommand{\prn}[1]{\left({#1}\right)}
\newcommand{\jmitem}{\justmoment \item}
\newcommand{\pitem}{\justmoment \item}
\newcommand{\lb}{\ \mathrm{lb}}
\newcommand{\ft}{\ \mathrm{ft}}
\newcommand{\inch}{\ \mathrm{in}}
\newcommand{\lbft}{\ \mathrm{lb}\cdot\mathrm{ft}}
\newcommand{\N}{\ \mathrm{N}}
\newcommand{\kN}{\ \mathrm{kN}}
\newcommand{\kip}{\ \mathrm{kip}}
\newcommand{\mm}{\ \mathrm{mm}}
\newcommand{\m}{\ \mathrm{m}}
\newcommand{\Nm}{\ \mathrm{N}\cdot\mathrm{m}}
\newcommand{\comment}[1]{}
\newcommand{\skipframe}[1]{}
\newcommand{\myvspace}{3cm}
\newcommand{\commentvspace}[1]{\vspace{\myvspace}}
\newcommand{\myfirstsection}{1}
\newcommand{\D}{\mathrm{d}}
\newcommand{\second}{\,\mathrm{sec}}
\newcommand{\minute}{\,\mathrm{min}}
\newcommand{\minutes}{\,\mathrm{mins}}
\newcommand{\hour}{\,\mathrm{hr}}
\newcommand{\hours}{\,\mathrm{hrs}}
\newcommand{\Pe}{\mathrm{Pe}}
\newcommand{\Plus}{^{+}}
\newcommand{\PlusPlus}{^{2+}}
\newcommand{\Minus}{^{-}}
\newcommand{\MinusMinus}{^{2-}}
\newcommand{\subs}[1]{$_{#1}$}
\newcommand{\supers}[1]{$^{#1}$}
\newcommand{\mailto}[1]{\href{mailto:#1}{#1}}

bug in "find" command in Linux

2010-11-19T21:55:00.001-10:00

One should put single quotations for the wild card option.

> find $HOME -name '*.tcl'

This command is to find any file whose extension is tcl under the home directory including all the sub-directories.

shell script

2010-11-17T13:52:00.001-10:00

This script read a directory, zip the directory, and create directory.zip file.
And it send the zip file to specific location in my Mac computer using scp.

==========

#!/bin/sh
echo $1
zip -r $1 $1
scp $1.zip albertsk@stokes.eng.hawaii.edu:/Users/albertsk/Desktop/On-going/Presentations/APS-DFD/simulations/

Latex: how to change footnote symbols

2010-11-15T15:21:00.001-10:00

Arabic numerals, e.g., 1, 2, 3... \renewcommand{\thefootnote}{\arabic{footnote}}
Roman numerals (lowercase), e.g., i, ii, iii...\renewcommand{\thefootnote}{\roman{footnote}}
Roman numerals (uppercase), e.g., I, II, III... \renewcommand{\thefootnote}{\Roman{footnote}} Alphabetic (lowercase), e.g., a, b, c...
\renewcommand{\thefootnote}{\alph{footnote}} Alphabetic (uppercase), e.g., A, B, C...
\renewcommand{\thefootnote}{\Alph{footnote}} A sequence of nine symbols (try it and see!)
\renewcommand{\thefootnote}{\fnsymbol{footnote}}

LaTex: Long arrow

2010-11-15T15:20:00.000-10:00

If

\longrightarrow

is not sufficiently long, try


\[ \xrightarrow{\hspace*{3cm}} \]

PDF to Keynote (pdftokeynote)

2010-11-13T17:17:00.000-10:00

For people who enjoys LaTex presentation, beamer, this free software "pdftokeynote"provides an excellent link between pdf and keynote. A pdf presentation is prepared using beamer with full functionality of math typesetting. Once the final pdf file is made, then pdftokeynote can convert the pdf file with a number of slides to a Keynote file. Each Keynote page includes a pdf image of the presentation. Only slide transition is possible in Keynote.

http://www.cs.hmc.edu/~oneill/freesoftware/pdftokeynote.html

Thesis Acknowledgement | Thesis Acknowledgement Sample

2010-08-25T10:50:00.000-10:00

Thesis Acknowledgement | Thesis Acknowledgement Sample

Student t distribution table

2010-08-25T09:09:00.003-10:00

Eigenvalues of an Inverse Matrix

2010-06-10T15:40:00.000-10:00

If lambda is an eigen value of a matrix A, then
1/lambda is an eigen value of the inverse matrix of A.

http://en.wikipedia.org/wiki/Inverse_eigenvalues_theorem

AMBER on Macintosh: Installing g95 or gfortran with MacPorts

2010-05-03T15:05:00.001-10:00

Here is how to install gfortran on Mac using macport.

sudo port install g95

if not working

sudo port install gcc45 +gfortran

AMBER on Macintosh: Installing g95 or gfortran with MacPorts

Migration – MacPorts

2010-05-02T09:10:00.000-10:00

After I installed Snow Leopard, macport was not working well, especially when I tried to install texmacs and octave. Below is the site that showed me the entire step to fresh MacPort by reinstalling everything again.

Migration – MacPorts: "sudo ./restore_ports.tcl myports.txt"

LaTeX/Packages/Listings - Wikibooks, collection of open-content textbooks

2010-04-28T07:30:00.003-10:00

A way to easily convert FORTRAN code to LaTex

LaTeX/Packages/Listings - Wikibooks, collection of open-content textbooks

\documentclass[11pt]{article}
%\usepackage{geometry} % See geometry.pdf to learn the layout options. There are lots.
%\geometry{letterpaper} % ... or a4paper or a5paper or ...
%\geometry{landscape} % Activate for for rotated page geometry
%\usepackage[parfill]{parskip} % Activate to begin paragraphs with an empty line rather than an indent
%\usepackage{graphicx}
%\usepackage{amssymb}
%\usepackage{epstopdf}
\usepackage{listings}
\lstset{ %
language= Fortran, % choose the language of the code
basicstyle=\footnotesize, % the size of the fonts that are used for the code
basicstyle=\scriptsize,
numbers=left, % where to put the line-numbers
numberstyle=\footnotesize, % the size of the fonts that are used for the line-numbers
numberstyle=\scriptsize, % the size of the fonts that are used for the line-numbers
stepnumber=2, % the step between two line-numbers. If it's 1 each line will be numbered
numbersep=5pt, % how far the line-numbers are from the code
%backgroundcolor=\color{white}, % choose the background color. You must add \usepackage{color}
%showspaces=false, % show spaces adding particular underscores
%showstringspaces=false, % underline spaces within strings
%showtabs=false, % show tabs within strings adding particular underscores
frame=single, % adds a frame around the code
tabsize=2, % sets default tabsize to 2 spaces
captionpos=b, % sets the caption-position to bottom
breaklines=true, % sets automatic line breaking
breakatwhitespace=false, % sets if automatic breaks should only happen at whitespace
title=\lstname, % show the filename of files included with \lstinputlisting; also try caption instead of title
escapeinside={\%*}{*)} % if you want to add a comment within your code
%morekeywords={*,...} % if you want to add more keywords to the set
}
%\DeclareGraphicsRule{.tif}{png}{.png}{`convert #1 `dirname #1`/`basename #1 .tif`.png}

\title{Brief Article}
\author{The Author}
%\date{} % Activate to display a given date or no date

\begin{document}
\maketitle
%\section{}
%\subsection{}

\lstinputlisting[language=Fortran]{pGrand_hsnj.f}
\lstinputlisting[language=Fortran]{pHydroTort_FT_F.f90}

\end{document}

How to add a new rpm using repoman

2010-03-11T10:06:00.003-10:00

I needed to install pdftk rpm in my RHEL 5 host using repoman. Here is one that I figured out.

1. Download a necessary rpm from any source.

2. Copy the rpm file to a sub-directory under /deport/. In my case, it is
/depot/contrib/rhel/5/x86_64/

3. Type and enter:

ngedit

and follow instruction.

To manually update repository, type/enter:

repoman -r "Repo for rhel-5-x86_64" -u

Of course, contents in " " is specified for a given repository name. Option "-u" indicates update.

4. Select "next" in most sequential cases in repoman. Click the name of rpm that you want to install. And, finally enjoy using it.

Restarting LSF deamon after electric outage

2010-02-06T11:42:00.010-10:00

When I got a notice of a total electric outage of my building, yesterday I shutdown all the nodes of my cluster, being managed by LSF. Those nodes include 18 worker and 1 master nodes.

By advises from Platform Inc., I did the followings:

1. Login as a root:
  sudo bash

2. Login as a lsfadmin:
  su - lsfadmin

3. type and enter the following:
  lmgrd -c /opt/lsf/conf/license.dat

4. Log out lsfadmin to be root again, and start lsf deamon:
  /etc/init.d/lsf_daemons start

(to stop, one can use the following command. But, I did not.)
  /etc/init.d/lsf_daemons stop

No need to be a root but lsfadmin to do the followings.

A few of my nodes has two quad-cores, open lsf.conf file

  vi /opt/lsf/conf/lsf.conf

and at the end of the file put a line:

  LSF_ENABLE_DUALCORE=Y

Then, reconfigure LSF:

  lsadmin reconfig
  badmin mbdrestart

Locations of MacTex files and how to texhash

2010-01-08T17:27:00.009-10:00

Class files: /usr/local/texlive/2009/texmf-dist/tex/latex/
BST files: /usr/local/texlive/2009/texmf-dist/bibtex/bst/
STY files: /usr/local/texlive/2009/texmf-dist/tex/latex/

To update ls-R database, type and enter in Mac Terminal

>>sudo /usr/texbin/texhash

Email Links in LaTeX-Generated PDFs

2009-11-28T10:00:00.002-10:00

\usepackage{url,hyperref}

\href{mailto:albertsk@gmail.com}{albertsk@gmail.com}

from http://markelikalderon.com/2007/10/16/email-links-in-latex-generated-pdfs/

How to update Ubuntu.

2009-11-28T09:26:00.002-10:00

sudo apt-get update; sudo apt-get upgrade

That's it!

How to use Crontab on Mac OS X

2009-11-19T13:51:00.000-10:00

http://www.bradrice.com/wposx/archives/51

Add a user from the command line

2009-09-26T15:47:00.002-10:00

* To specify the password using the passwd command:

# adduser

# passwd

# cfmsync -f

Carl Friedrich Gauss

2009-05-21T13:11:00.001-10:00

Mathematics is the queen of sciences and number theory the queen of mathematics.
She often condescends to render service to astronomy and other natural of sciences, but in all relations she is entitled to the first rank.

-Carl Friedrich Gauss(1777~1855): German mathematician, astronomer and physicisist -

Automatically Bcc an Address on Every Message in Mac OS X Mail

2009-02-23T10:30:00.002-10:00

My Apple Mail seems to leak its memory or at least performs less. If I keep it on, then it uses more than one GB of memory, slowing down overall speed. Mail is doing something, which I cannot figure out. I initially thought it would be because of IMAP protocol, but even if I use only POP3, nothing changes.

So, I decided to use less of Mail. Whichever mails sent to my hawaii.edu account are automatically forwarded to my gmail account. I automatically download all emails arrtived at my Google account using POP. Make certain actions based on mail contents. Then, all of my replied emails should be bcc'd to a separate account other than hawaii.edu or gmail. edu. I choose my me.com account.

The followings explain how to ask Apple Mail to sent a bcc to my me.com account, implicitly. During I send any mail, I wouldn't notice that bcc'd one is sent.

To auto-Bcc a copy of every message you send from Mac OS X Mail to a particular email address.
* Open Terminal.
* Type "defaults read com.apple.mail UserHeaders".
* Press Enter.
* If that command returns "The domain/default pair of (com.apple.mail, UserHeaders) does not exist", then, type "defaults write com.apple.mail UserHeaders '{"Bcc" = "bcc@address"; }'" (excluding the outermost quotation marks) and replace bcc@address with the address you want to be used for the automatic copy.

`\citet{jon90}`	-->	Jones et al. (1990)
`\citet[chap. 2]{jon90}`	-->	Jones et al. (1990, chap. 2)
`\citep{jon90}`	-->	(Jones et al., 1990)
`\citep[chap. 2]{jon90}`	-->	(Jones et al., 1990, chap. 2)
`\citep[see][]{jon90}`	-->	(see Jones et al., 1990)
`\citep[see][chap. 2]{jon90}`	-->	(see Jones et al., 1990, chap. 2)
`\citet*{jon90}`	-->	Jones, Baker, and Williams (1990)
`\citep*{jon90}`	-->	(Jones, Baker, and Williams, 1990)