Use of "find" command in Linux

http://www.cyberciti.biz/tips/linux-findinglocating-files-with-find-command-part-2.html

In the first part we talked about find command basic usage.

Now let us see how to use find command
(a) To gain lots of useful information about users and their files

(b) Monitor and enhance the security of system using find command

Finding all set user id files

setuid ("suid") and setgid are access right flags that can be assigned to files and directories on a Unix based operating system. They are mostly used to allow users on a computer system to execute binary executables with temporarily elevated privileges in order to perform a specific task.
# find / -perm +u=s
OR
# find / -perm +4000

See also, shell script to find all programs and scripts with setuid set on.

Finding all set group id files

# find / -perm +g=s
OR
# find / -perm +2000

See also, shell script to find all programs and scripts with setgid bit set on.

Finding all large directories

To find all directories taking 50k (kilobytes) blocks of space. This is useful to find out which directories on system taking lot of space.
# find / -type d -size +50k
Output:

/var/lib/dpkg/info
/var/log/ksymoops
/usr/share/doc/HOWTO/en-html
/usr/share/man/man3

Finding all large files on a Linux / UNIX

# find / -type f -size +20000k
Output:

var/log/kern.log
/sys/devices/pci0000:00/0000:00:02.0/resource0
/sys/devices/pci0000:00/0000:00:00.0/resource0
/opt/03Jun05/firefox-1.0.4-source.tar.bz2

However my favorite hack to above command is as follows:
# find / -type f -size +20000k -exec ls -lh {} \; | awk '{ print $8 ": " $5 }'

/var/log/kern.log: 22M
/sys/devices/pci0000:00/0000:00:02.0/resource0: 128M
/sys/devices/pci0000:00/0000:00:00.0/resource0: 256M
/opt/03Jun05/firefox-1.0.4-source.tar.bz2: 32M

Above command will find all files block size greater than 20000k and print filename followed by the file size. Output is more informative as compare to normal find command output

Short LaTex Math Guide

A short LaTex Math Guide can be found here.

Click the link to download a pdf file.

Archive command summary (ar)

How to use "ar" command to generate library is here.

Some examples are:

1. To create a library, enter:

   ar -v -q lib.a strlen.o strcpy.o
   

   If the lib.a library does not exist, this command creates it and enters into it copies of the files strlen.o and strcpy.o. If the lib.a library does exist, then this command adds the new members to the end without checking for duplicate members. The v flag sets verbose mode, in which the ar command displays progress reports as it proceeds.

2. To list the table of contents of a library, enter:

   ar -v -t lib.a
   

   This command lists the table of contents of the lib.a library, displaying a long listing similar to the output of the ls -l command. To list only the member file names, omit the -v flag.

3. To replace or add new members to a library, enter:

   ar -v -r lib.a strlen.o strcat.o
   

   This command replaces the members strlen.o and strcat.o. If lib.a was created as shown in example 1, then the strlen.o member is replaced. A member named strcat.o does not already exist, so it is added to the end of the library.

4. To specify where to insert a new member, enter:

   ar -v -r -b strlen.o lib.a strcmp.o
   

   This command adds the strcmp.o file, placing the new member before the strlen.o member.

5. To update a member if it has been changed, enter:

   ar -v -r -u lib.a strcpy.o
   

   This command replaces the existing strcpy.o member, but only if the file strcpy.o has been modified since it was last added to the library.

6. To change the order of the library members, enter:

   ar -v -m -a strcmp.o lib.a strcat.o strcpy.o
   

   This command moves the members strcat.o and strcpy.o to positions immediately after the strcmp.o member. The relative order of the strcat.o and strcpy.o members is preserved. In other words, if the strcpy.o member preceded the strcat.o member before the move, it still does.

7. To extract library members, enter:

   ar -v -x lib.a strcat.o strcpy.o
   

   This command copies the members strcat.o and strcpy.o into individual files named strcat.o and strcpy.o, respectively.

8. To extract and rename a member, enter:

   ar -p lib.a strcpy.o >stringcopy.o
   

   This command copies the member strcpy.o to a file named stringcopy.o.

9. To delete a member, enter:

   ar -v -d lib.a strlen.o
   

   This command deletes the member strlen.o from the lib.a library.

10. To create an archive library from multiple shared modules created with the ld command, enter:

    ar -r -v libshr.a shrsub.o shrsub2.o shrsub3.o ...
    

    This command creates an archive library named libshr.a from the shared modules named shrsub.o, shrsub2.o, shrsub3.o, and so on. To compile and link the main program using the libshr.a archive library, use the following command:

    cc -o main main.c -L/u/sharedlib -lshr
    

    The main program is now executable. Any symbols referenced by the main program that are contained by the libshr.a archive library have been marked for deferred resolution. The -l flag specifies that the libshr.a library be searched for the symbols.

11. To list the contents of lib.a, ignoring any 32-bit object file, enter:

    ar -X64 -t -v lib.a
    

12. To extract all 32-bit object files from lib.a, enter:

    ar -X32 -x lib.a
    

13. To list all files in lib.a, whether 32-bit, 64-bit, or non-objects, enter:

    ar -X32_64 -t -v lib.a
    

LSF user's quick reference guide

LSF User's Quick Reference can be found here.

Thanks.

Intel Compiler Options

Options -ip (Linux and Mac OS X) and /Qip (Windows) enable additional interprocedural optimizations  for  single-file compilation.

Option -fma enables the combining  of  floating-point  multiplies  and add/subtract operations. However, if you specify -mp  (Linux)  or -fp-model  strict  (Linux)  but do not explicitly specify -fma, the default  is -no-fma.

Environment Variables for Intel Compilers

export CC=icc
export CFLAGS='-O3 -mp -ip'
export CXX=icpc
export CXXFLAGS='-O3 -mp -ip'
export F77=ifort
export FFLAGS='-O3 -mp -ip'

Ubuntu

From DHCP to Static IP: Convert DHCP network configuration to static IP configuration

Minimum X11 installation for Ubuntu server:  apt-get install xdm xfce4

Set Up Ubuntu-Server 6.10 As A Firewall/Gateway For Your Small Business Environment

Page: 1, 2, 3, 4, 5, 6, 7, and 8

How to install firefox in Ubuntu: sudo apt-get install firefox

MPI reference site

http://www.hku.hk/cc/sp2/workshop/html/samples/exercises.html

Happy Face in LaTex

$\ddot\smile$

Try!

How to setup remote subversion server through ssh

This site provides an excellent tutorial.

http://subversion.tigris.org/faq.html#ssh-svnserve-location

Mounting remote file system using SSH

Using svn with iDisk is very disappointing although I am a real Mac fan. However, this solution of using sshfs (Secure Shell File System) give me a new solution of setting up SVN server.

Cheers!

http://www.pqrs.org/tekezo/macosx/sshfs/document.html

SVN works perfect in Mac

See this site:

http://developer.apple.com/tools/subversionxcode.html

http://www.wishingline.com/notebook/2008/10/macsvnsshserver/

changing paper size in LaTex

Sometimes a certain specific class file does not support options of paper size.  Default is usually A4.  The following line in the very front of your LaTex file, just below, will allow you to generate letter-sized pdf file as an outcome.

\usepackage[letterpaper]{geometry}

ssh session alive

It is very frequently happening that a terminal with ssh session dies after a certain period of time by any reason.  It looks like a server setting should be modified, which cannot be done by an end-user.  But, there is one thing can be done by each user.

1. Go to your .ssh directory:

      cd ~/.ssh

2. Check whether you have "config" file.  Anyway, open/create it: 

      vi config

3. Put the following line in the file:

      KeepAlive yes

Bibtex capital letters

Edit your bibtex file and use {} for words that you want to keep the style.

@article{greenwade93,        

   author  = "George D. Greenwade",        

   title   = "The {C}omprehensive {T}ex {A}rchive {N}etwork ({CTAN})",        

   year    = "1993",        

   journal = "TUGBoat",        

   volume  = "14",     

   number  = "3",     

   pages   = "342--351" 

}

source: http://www.andy-roberts.net/misc/latex/latextutorial3.html

The underscore symbol between C and FORTRAN

When a C function is called from FORTRAN routine, the C function should end with '_'.  In other words, a C function 'myfun_' should be called as 'myfun' in a FORTRAN code.  Actually this is an old paradigm between GNU C and FORTRAN compilers. Current GNU FORTRAN compiler, gfortran, does not follow this rule, and so does Intel compilers.   This is actually a serious problem in compiling BLACS and SCALAPACK libraries.

In compiling BLACS, Bmake.inc file should have an option:

INTFACE = -DAdd_

and in compiling SCALAPACK, SLmake.inc should have:

CDEFS     = -DAdd_

This option depends on compliers.

BLACS 64bit compiling

It is theoretically impossible to compile BLACS to make it work in 64 bit computing environment.  BLACS package downloadable from www.netlib.org works only on 32 bit OSs. Otherwise, all the libraries including BLAS, LAPACK, and SCALAPACK should be recomiled with 32 bit option.  A possible way to go around this bottleneck is to use Intel MKL library, specifically,

   -lmkl_blacs_openmpi_lp64 

The latest version of openmpi-1.2.8 works well with Intel-BLACS and scalapack compiled using Intel FORTRAN compiler, ifort.

Private network setup guide

http://www.linuxjunkies.org/articles/linux_networking_part1.html

Compile openmpi-1.2.8 using Intel Compilers

./configure --prefix=/opt/openmpi-1.2.8/intel   CC=icc   CXX=icpc   F77=ifort   FC=ifort

Lapack compile script to save messages

./xlintstd <> dtest.out 2>&1

Kerberos configuration file

When I install Kerberos to connect MHPCC machine, krb5 configuration needs to be edited. The location of krb5.conf is by default /usr/local/krb5. However, I got an error message like:

kinit(v5): Configuration file does not specify default realm when parsing name ........

This error has been resolved by copying

/usr/local/krb5/krb5.conf

to

/etc/krb5.conf

or
/etc/kerberosV/krb5.conf

Symbolic link did not work.

Not to show URLs in LaTex generated papers

When I prepare a manuscript using LaTex with Elsevier package, two reference styles are provided, elsart-num.bst and elsart-harv.bst, which generate reference lists ordered by citation number and author's name, respectively.  It often shows long URLs, which is absolutely not necessary for any purposes. 

Not to show URLs in my final manuscript, I did as follows:

1. Open .bst file.

2. Search "write.url" and replace it by "% write.url" within

• FUNCTION {article}
• FUNCTION {book}
• FUNCTION {booklet}
• FUNCTION {inbook}
• FUNCTION {incollection}
• FUNCTION {inproceedings}
• FUNCTION {manual}
• FUNCTION {masterthesis}
• FUNCTION {misc}
• FUNCTION {phdthesis}
• FUNCTION {proceedings}
• FUNCTION {techreport}
• FUNCTION {unpublished}

But, do not make any changes where "write.url" is defined in FUNCTION {write.url}.

3. Another way is to redefine FUNCTION {write.url}, but I did not figure out how to yet.

Add a user in a sudoer list

In most Unix/Linux system, the suoder file is /etc/sudoers.

1. Login as a normal user.

2. Type/enter "su" followed by a root password.

3. Open /etc/sudoers using vi or any editor and include a line

freeman ALL=(ALL) ALL

which will provide all the administration authority of the system to the user, "freeman".

How to setup xhost file

1. Create or edit the file "/etc/Xn.hosts" where 'n' is the display number of the server on the local host, normally 0, as in "/etc/X0.hosts".
   
   To deny all X access to your system, the file /etc/X0.hosts will contain a single character, "-".
   
   To grant access to hosts "host1.com" and "host2.com" and no other hosts the file /etc/X0.hosts will consist of:
   
   -
   +host1.com
   +host2.com
2. Search through all files in the directory /usr/lib/X11/xdm for occurances of the command "xhost +" or "/usr/bin/X11/xhost +". Remove or comment out all such lines.
3. Inform users that any xhost commands should be removed or commented out of user startup scripts, such as .cshrc, .login, .profile, etc.

Source: http://www.pseriestech.org/forum/rs6000/configure-xhost-files-109.html

Manual configuration of DNS in Ubuntu

(1) Open /etc/resolv.conf file:
vi /etc/resolv.conf

(2) Add your ISP nameserver as follows:

search isp.com
nameserver 202.30.38.101
nameserver 163.180.16.53.1

Note Max. three nameserver can be used/defined at a time.

How to make landscape documents or pages using LaTex

http://texblog.wordpress.com/2007/11/10/landscape-in-latex/

Adjusting space between items

\begin{itemize}\setlength{\itemsep}{-2mm}
\item
\end{itemize}

Inline figure in LaTex

\usepackage{wrapfig }

\begin{wrapfigure}{r}{0.4\textwidth}
\centering
\includegraphics[width=0.4\textwidth]{leadfield.eps}
\caption{Text wrap around figure}
\noindent
%\hrulefill
\label{test}
\end{wrapfigure}

Highest Impact Factor Journals in the category of Environmental Engineering

Mark	Rank	Abbreviated Journal Title (linked to journal information)	ISSN	Total Cites	Impact Factor	Immediacy Index	Articles	Cited Half-life
	1	APPL CATAL B-ENVIRON	0926-3373	10376	4.651	0.666	356	4.9
	2	ENVIRON SCI TECHNOL	0013-936X	51326	4.363	0.615	1202	6.2
	3	WATER RES	0043-1354	23992	3.427	0.353	485	6.9
	4	INDOOR AIR	0905-6947	1272	2.887	0.524	42	4.7
	5	J HAZARD MATER	0304-3894	6521	2.337	0.277	1039	3.6
	6	ECOL ENG	0925-8574	1786	2.175	0.384	112	5.8
	7	ENVIRON MODELL SOFTW	1364-8152	1748	2.099	0.976	165	3.4
	8	INT J LIFE CYCLE ASS	0948-3349	772	1.607	0.712	66	4.6
	9	J AIR WASTE MANAGE	1047-3289	3197	1.523	0.200	135	7.3
	10	OZONE-SCI ENG	0191-9512	784	1.515	0.109	55	8.1

Highest Impact Factor Journals in the category of Fluid & Plasma Physics

Mark	Rank	Abbreviated Journal Title (linked to journal information)	ISSN	Total Cites	Impact Factor	Immediacy Index	Articles	Cited Half-life
	1	ANNU REV FLUID MECH	0066-4189	4329	9.471	2.471	17	>10.0
	2	NUCL FUSION	0029-5515	6687	3.278	0.731	234	6.5
	3	PLASMA PHYS CONTR F	0741-3335	5479	3.070	0.346	234	5.4
	4	PHYS REV E	1539-3755	57936	2.483	0.504	2255	5.6
	5	PHYS PLASMAS	1070-664X	14648	2.325	0.534	794	5.3
	6	MICROFLUID NANOFLUID	1613-4982	299	2.241	0.586	70	2.2
	7	PLASMA PROCESS POLYM	1612-8850	441	2.132	0.494	83	2.3
	8	PLASMA SOURCES SCI T	0963-0252	2429	2.120	0.522	113	6.1
	9	J FLUID MECH	0022-1120	27263	2.026	0.413	501	>10.0
	10	PHYS FLUIDS	1070-6631	15514	1.780	0.217	567	>10.0

Highest Impact Factor Journals in the category of Applied Physics

Mark	Rank	Abbreviated Journal Title (linked to journal information)	ISSN	Total Cites	Impact Factor	Immediacy Index	Articles	Cited Half-life
	1	NAT MATER	1476-1122	13606	19.782	5.278	133	3.2
	2	MAT SCI ENG R	0927-796X	3114	14.400	0.167	6	6.2
	3	ADV FUNCT MATER	1616-301X	8320	7.496	0.683	461	2.9
	4	SMALL	1613-6810	2696	6.408	1.033	272	2.0
	5	MRS BULL	0883-7694	3836	5.168	1.468	79	6.0
	6	LASER PART BEAMS	0263-0346	1422	4.696	1.278	72	2.8
	7	ORG ELECTRON	1566-1199	924	3.879	0.386	101	3.1
	8	APPL PHYS LETT	0003-6951	157868	3.596	0.627	5818	5.4
	9	PROG ELECTROMAGN RES	1559-8985	1433	3.320	0.739	249	1.9
	10	NANOTECHNOLOGY	0957-4484	10839	3.310	0.461	1259	2.7

Highest Impact Factor Journals in the category of Chemical Engineering

Mark	Rank	Abbreviated Journal Title (linked to journal information)	ISSN	Total Cites	Impact Factor	Immediacy Index	Articles	Cited Half-life
	1	PROG ENERG COMBUST	0360-1285	1983	5.269	1.250	16	9.6
	2	J CATAL	0021-9517	27254	4.737	0.800	330	8.4
	3	APPL CATAL B-ENVIRON	0926-3373	10376	4.651	0.666	356	4.9
	4	DYES PIGMENTS	0143-7208	3024	2.796	0.501	349	4.6
	5	CATAL TODAY	0920-5861	15484	2.764	0.490	502	6.3
	6	P COMBUST INST	1540-7489	4714	2.647	0.593	383	7.8
	7	J MEMBRANE SCI	0376-7388	15786	2.432	0.346	537	6.6
	8	PROCESS BIOCHEM	1359-5113	6114	2.336	0.198	243	4.6
	9	J SUPERCRIT FLUID	0896-8446	2629	2.189	0.434	221	5.1
	10	COMBUST FLAME	0010-2180	7089	2.184	0.183	131	9.2

Several symbols in LaTex expression

underscore = \_
percent sign = \%

Editor Tutorials

vi Editor: http://www.eng.hawaii.edu/Tutor/vi.html

nano Editor: http://mintaka.sdsu.edu/reu/nano.html

LaTex new commands

\newcommand{\degrees}{$\!\!$\char23$\!$}
\newcommand{\pageseparate}{\clearpage}
\newcommand{\refhere}{\textcolor{red}{(Refs.) }}
\newcommand{\tcol}[1]{\textcolor{red}{#1}}
\newcommand{\vspaceOne}{\vspace{1in}}
\newcommand{\vspaceTwo}{\vspace{2in}}

CEE696 (618) Scientific Parallel Computing for Engineers

Classroom and time change

Tuesday 3:00 pm - 4:50 pm, Holmes 244

Tuesday 5:00 pm - 5:50 pm, POST 214 (Don Kim Lab.)

LaTex Useful Packages

\usepackage{amsmath}
\usepackage{color} % To make texts and math colored
\usepackage{geometry}\geometry{letterpaper} % To change size of paper
\usepackage{graphics,graphicx,epstopdf,psfig} % Graphic packages frequently used
\usepackage{nomencl} % To generate nomenclature
\usepackage{setspace}\doublespacing %To set doublespacing and singlespacing
\usepackage{revnum} % To reverse enumerate, 4,3,2, and 1.
\usepackage{wrapfig } % To have inline figures
\usepackage{hyperref} % To have hypertext protocol references
\usepackage{soul} % To highlight texts
\usepackage{ulem} %To strike words

Three values

Vision, Discipline, and Passion

The 7 habits of Highly Effective People (by Stephen R. Covey)

1. Be Proactive
2. Begin with the End in Mind
3. Put First Things First
4. Think Win/Win
5. Seek First to Understand, Then To Be Understood
6. Synergize
7. Sharpen the Saw
8. Find your voice and inspire others to find theirs

How to change the background image of beamer

It is possible to use a different background template, e.g. an empty
Powerpoint file that is converted to PNG, JPG, EPS or PDF.

\usebackgroundtemplate{
\includegraphics[width=\paperwidth,
height=\paperheight]{LaQuSo}
}

My New iPhone Today

Cluster Expansion: 2007 version

2007 version

Computing Hardware:

• 16 nodes, each node with 2 Xeon (2.3 GHz) processors, and 2 GB memory per processors
  
• 3 new nodes, each new node with 2 quad core 2.33 GHz processors, and 2 GB memory per processors
• Total: 56 processors (> 2.3 GHz) with 112 GB memory

Disk Space

• 200 GB for working space
  
• 2.0 TB for backup and data storage

Software:

• Queueing system: Platform LSF (Load Sharing Facility) pro 6.2
  
• Compilers: Intel FORTRAN 90 and Intel C/C++
• Library: BLAS, BLACS, ATALAS, LAPACK, ScaLAPACK, OPENMPI

how to install openvpn in Ubuntu

login as a root, type and enter:

aptitude update

aptitude install openvpn

Life Motto

The motto of my life is "Beautiful Challenge".

-- Sumi Jo --

FEW

Food

Energy

Water

(by Prof. Jaechun Choe)

Vision

"Vision is foresight with insight based on hindsight"
--Dr. Myles Munroe --

Laminar Flow

American Physical Society Meeting

During my stay at Rice University in the middle of my first sabbatical, it was a great time to attend 2008 March meeting of American Physical Society. Here are some pictures of New Orleans.

Click here

Maui High Performance Computing Center

Jaws at MHPCC was ranked 25th and 17th among supercomoputers in the world and the United State, respectively, as of Nov. 2007.

System Name: Jaws

Site: Maui High-Performance Computing Center (MHPCC)

System Family: Dell PowerEdge ClusterSystem 

Model: PowerEdge 1955Computer PowerEdge 1955, 3.0 GHz, Infiniband

Vendor: Dell

Application area: Research

Main Memory: 5200 GB

Installation Year: 2006

Operating System: RedHat Enterprise 4

Memory 5200 GB

Interconnect: Infiniband

Processor: Intel EM64T Xeon 51xx (Woodcrest) 3000 MHz (12 GFlops)

Introductory MPI tutorial

Examples from Using MPI, 2nd Ed.

WYDIWIG

What You Design is What You Get

latex strike

latex strike

\usepackage{ulem}

\sout{Bill Clinton}G.W. Bush is the pres.

from here

My place at Rice for my sabbatical research, Weiss Hall 117

Getting started with SSH

A Good Tutorial by Kimmo Suominen

Notes on using Job Arrays (MPI), job dependencies, and processor reservation

Click Here

By Mehdi Bozzo-Ray from Platform Computing Inc.

ssh-keygen

A good tutorial for ssh-keygen and how to connect a remote host without using a password can be found HERE.

How to use a three-button mouse as in Linux environment

Here are some possible solutions.

Excellent SSH tunneling tutorial

Mike Chirico (mchirico@users.sourceforge.net) or (mchirico@comcast.net)
Copyright (c) 2005 (GNU Free Documentation License)
Last Updated: Fri Nov 11 15:49:44 EST 2005 
http://souptonuts.sourceforge.net/sshtips.htm

Beamer

Original Site

• The LaTeX Beamer Class Homepage

Tutorials

• http://www.win.tue.nl/latex/documentation/tuebeamer/tueslides.pdf
  
• http://www.math.utah.edu/~smith/AmberSmith_GSAC_Beamer.pdf
  
• http://www.ctan.org/tex-archive/macros/latex/contrib/beamer/doc/beameruserguide.pdf
  

Examples  site 1

One Day Oahu City Tour

1. Punch Bowl Cemetery

  

2. Iolani Place + Kamehameha Statue

 

3. Aloha Tower (go up to the top for photo + lunch)

 

4. Pali Mountain look out

  

5. Korean President S. M. Lee's statue and Korean Christian Church

One Day Oahu East Tour

Depart at 8:00 am

1. Kapiolani Community College: use student parking, take photo with tall cactus

2. Diamond head: go around or climb up, when exit temporarily park at the scenic point at the right hand side and watch Hanauma Bay

3. Optional: Kahala Mandalin Hotel for beach and dolphin shows

4. Koko Marina Center: lunch at McDonal or Zippy (bento order for group tour)

5. Hanauma Bay

6. Sandy Beach - watch surfing

7. Sea Life Park

8. Return to and enjoy Hanuma Bay until sunset

M.I.T.-Walter Lewin- Complete Breakdown of Intuition

Free Useful Mac Software

• Mac-Tex
• TexShop
• LaTexiT
• LaTeX Equation Editor
  
• SvnX

My mother land in winter, Pyung-Chang, S. Korea