Wednesday, November 23, 2011

JAVA number formatter


import java.text.NumberFormat;

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

Saturday, November 5, 2011

MATLAB cell array


Accessing cell array : {}-for getting array, () - for elem of this array
=============================================
carray{i}
carray{i}(elemIndex)


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
          display('yes')    
        else
          display('no')
        end    
 
    end
end

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 mykey.pub

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 ../mykey.pub .

4. keep this folder with 3 files for future.

5. Once admin give u access to server, type

ssh alamt@cluster.cbrc.kaust.edu.sa

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 run_job_vlad.sh run_job_tanvir.sh
6.  chmod a+x run_job_tanvir.sh
7. ./run_job_tanvir.sh node25 CGI tanvir_01
8.


scp Copy file from remote -->  local
======================

open terminal in local machine

scp source destination


> scp   alamt@cluster.cbrc.kaust.edu.sa:/home/alamt/DMF6/CGI.tanvir_01.results/*.rank    /home/tanviralam/tst


scp Copy from local --> remote
======================

scp local remote

> scp /home/tanviralam/myfile.txt alamt@cluster.cbrc.kaust.edu.sa:/home/alamt/store/myfile.txt


sftp  Connect to remote pc using GUI
======================
1. login using ssh alamt@cluster.cbrc.kaust.edu.sa
2. type following in location bar

  sftp://alamt@cluster.cbrc.kaust.edu.sa

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