JP's Help and FAQ page !

LSF
SSH Login without password
Libraries
Image Editing
Video Editing
Pdf/PS Editing

Many people come to me to fix this or that problem in computation. Mostly those problems are related to installing or running a software package. I have found that in most cases the problems arise due to poor understanding of some basic things. In what follows, I will discuss a few things which if you understand clearly can make your life easy.

LSF

For LSF healp see this .

SSH Login without password

There are many situations in which you want to login a machine B (Linux) from machine A (Linux) using ssh without giving password. This may be necessary also for program like Mesaage Passing Intercae (MPI). You can achive this in three simple steps:

Generate ssh keys in machine A

jayanti@machineA$ ssh-keygen

which will create a file 'id_rsa.pub' inside the directory '.ssh'. In second step you have to copy the id_rsa.pub file from machine A to .ssh/authorized_keys of machine B

scp ~/.ssh/id_rsa.pub  jayanti@machineB:~/.ssh/authorized_keys

In the last step you can login to machine B from A without password.

jayanti@machineA$ ssh jayanti@machineB

Static and Dynamic libraries (On a Linux System)

On a Linux system most software packages are installed in the form of libraries which are either dynamic (.so files or "shared objects") or static libraries (.a files). Here I do not want to discuss about what static and dynamic libraries are, I just want to answer the following questions:

Why to create libraries ?
How to create libraries ?
How to use libraries ?
What are header files and how to use them ?

1. Why to create libraries ?

In every software package, which is distributed in the form of a source code (FORTRAN or C files), there are a large number of files which contain programs for doing many things. In most cases there are programs in a code which can be used in some other codes also and it makes sense to pack them into a single library file which can be easily used by other codes. By creating a library we can pack a large number of program files in a single library file .

2. How to create libraries ?

For example, we have two files named sum.c and diff.c in which we have programs to compute sum and difference of numbers, we can pack these in a single library file in the following way.

gcc -c sum.c 
gcc -c diff.c

This will create two files named sum.o and diff.o from which we can create a static library file named libmymath.a in the following way:

ar rc  libmymath.a sum.o diff.o

This will create a library file named libmymath.a

Shared/dynamic libraries can be created in the following way

gcc -Wall -g  -shared -Wl,-soname,libtest.so.0 -o libtest.so.0 sum.o diff.o

For example download this .tar.gz file.

3. How to use libraries ?

We can write the following main program main.c which uses the function sum and diff which are packed in the library libmymath.a .

#include
#include
#include
int sum (int, int);
int diff(int, int);

int main(int argc, char *argv[]){
    int a, b, c, d;
    printf("give two number \n");
    scanf("%d %d",&a,&b);

    c=sum(a,b);
    d=diff(a,b);

    printf("sum=%d. diff=%d\n",c,d);

   return(0);
}

Now there are the following two way to use the library. In the first case we use:

gcc main.c libmymath.a -lm

This is not the common way by which libraries are used. In general we use the PATH of the directory where the library file is and then use -lnameoflib . For example, in the present case we can use:

gcc main.c -L/PATH  -lmymath

Note that in the present case the name of the library is libmymath.a so we use -lmymath . We add a - sign and replace lib by l and do not use .a.

I have my GSL library named libgsl.a in the directory /data/software/gsl/lib/ so I should use

gcc main.c -L/data/software/gsl/lib -lgsl

to use the gsl library. Note that you may be having your own compilation options do not forget them.

Another most standard way to use library is to put the path of your library in your .bashrc file. For example in the case of my GSL, I can put the following two lines in my .bashrc file:

LD_LIBRRAY_PATH=$LD_LIBRRAY_PATH:/data/software/gsl/lib
export LD_LIBRRAY_PATH

and after that I must do:

source .bashrc

After doing all this now I do not have to give the full path of the library and I can use

gcc main.c  -lgsl

Note that sometime it may happen that the name of the library you want to use does not start from lib . In that situation you must give the full name of the library at the time of compiling/running the program. For example if you have a library like lapack_LINUX.a you can use that in the following way:

gfortran test.f90 PATH/lapack_LINUX.a

where path may be like /data1/software/lapack/lapack-3.3.1

In order to know all the libraries installed on your Linux computer and their version run:

/sbin/ldconfig -p

In order to know which of the libraries are used by a binary executable use the command ldd . For example the following command tells us which of the libraries are used by the command ls

ldd /bin/ls

A very good introduction of libraries is given here .

4. What are header files and how to use them ?

In general with every software package there are header files or .h which contains the values of parameters, variable definition and specification for functions and we must give the path of these files using the -I files. In the case of my GSL I must use:

gcc main.c -L/data/software/gsl/lib -lgsl  -I/data/software/gsl/include

After knowing all this, there is no reason for you not being able to use a library, if you know where your library files ( .a) and header files (.h ) are.

I will add more about libraries later on, however, in case you have any problem, mail me at [prasad.jayanti@gmail.com]

How to create banners using Image Magic

In order to create a simple banner do the following :

convert -size 650x100 -background  transparent -fill blue \
 -pointsize 64 -gravity center 'label:JP Media & Art Work' logo.png

Note the following things :

'\' is for line break
'-size 650x100' is used to set the size of the banner
'-background transparent' is used to set the background
'-pointsize 64' for setting the font size
'-gravity center' is used to position the text

If you want to write a full paragraph with line breaks, do the following:

convert -size 600x180 -background  transparent -fill blue \
 -pointsize 32 -gravity center  caption:'Sometime sky becomes
   so dark\n  I cannot see  stars and lose track \n  when you
     recognize me \n I know I have not gone too far' poem1.png

here '\n' is used for line break. If you want to change the color of background and text you can do that using:

convert -size 650x100 -background  gray  -fill blue  -pointsize \
   64 -gravity center 'label:JP Media & Art Work'  logo.png

For my image-magic notes click here .

Video editing with mencoder

Deleting section from a video

mencoder video3.avi -ofps 25 -o clip1.avi -oac lavc -ovc lavc -vf scale=320:240 -ss 59 -endpos 15

Joining clips together

mencoder clip1.avi clip2.avi clip3.avi -o result.avi -oac lavc -ovc lavc

Extracing audio from video

ffmpeg -i uttarakhand...Paradise_on_Earth.mp4 -f mp3 -ab 192000 -vn music.mp3

Adding audio to video

Joining multiple pdf files

In order to do that you will need ghost view (gv) which is avaliable from gnu (most probably it will be already there on your linux system). Now we want to join pdf files file1.pdf file2.pdf and want to make combined file joined.pdf. This can be done using the following command:

gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=joined.pdf file1.pdf file2.pdf

There is no limitation on the number of files.

Remove pages from PDF files on Linux

The following command will remove pages from 10-25.

pdftk old.pdf cat 1-9 26-end output new.pdf

Another command is :

 gs -sDEVICE=pdfwrite -dNOPAUSE -dQUIET -dBATCH -dFirstPage=m -dLastPage=n -sOutputFile=output.pdf input.pdf