Wednesday, November 23, 2011

JAVA number formatter

import java.text.NumberFormat;

NumberFormat f = new DecimalFormat("#00.00000000");
String refinedNumber = f.format(arrT[i]);

Saturday, November 5, 2011

MATLAB cell array

Accessing cell array : {}-for getting array, () - for elem of this array

example : access cell array and string compare

for i=1:totSample % ID
    for j=1:totRepeat
        a =( promoter_ID{1}(i) ) ;  % check the first column cell array
        b = ( promoter_repeat{1}(j) ); % check the first column cell array
        if strcmp(a,b) % yes it overlaps with some repeat

Thursday, November 3, 2011

linux connect via ssh on cluster

ssh -t dsa // it will promt for password and name of key file

1. suppose file name is mykey. It will generate two file mykey and

2. it will also generate hidden folder .ssh. There will be a file named known_hosts in that folder.

3. copy this two file into .ssh folder

cd .ssh
cp  ../mykey ../ .

4. keep this folder with 3 files for future.

5. Once admin give u access to server, type


First time it will prompt password. But from next it will not.

For cluster 
1. cd user
2. cd DMF6
3. cd ../user/alamt
4. cp -rf DMF6 ../alamt/.
5. cp
6.  chmod a+x
7. ./ node25 CGI tanvir_01

scp Copy file from remote -->  local

open terminal in local machine

scp source destination

> scp*.rank    /home/tanviralam/tst

scp Copy from local --> remote

scp local remote

> scp /home/tanviralam/myfile.txt

sftp  Connect to remote pc using GUI
1. login using ssh
2. type following in location bar


3. So you can see and use gui of remote machine.

Cluster commands
1. see number of nodes in cluster:  bhosts

2. See the number of processor in nodes:

ssh node25 cat /proc/cpuinfo | grep -c processor

Or you can login and then see it

    First login into that node. for example login into node 25 .
    type> ssh node25
    type> ssh node25 cat /proc/cpuinfo | grep -c processor

3. see the running jobs

   type> top