====== Using Cluster (Quick Version) ======

**Note: This page is outdated (June 1, 2016)**. I will prepare a newer version. 

Since most of the scripts for cluster use is located under a specific directory in the ALMF server, I recommend you to add the path to your .tcshrc as below. 
<code shell>
set path=($path /g/almf/software/bin2)
</code>
Otherwise, please add the path above in front of script name. 

===== Interactive Usage of Cluster CPU =====

Before submitting huge data with your script, you might want to test run the script interactively to see if it is indeed working. To do so, you could access cluster in interactive mode. 

  - Log in to sub-master
  - then "qsub -I"
    - wait for some seconds, you will be assigned to a specific node where you could test around. 
    - To enable multi-threaded computation, do "qsub -I -l select=ncpus=2:mem=3gb" (in this case, uses 2 CPUs and 3Gb of memory).
 

===== Processing by ImageJ from Command Line =====

**Script name: doIJ**

Syntax
<code>
sh doIJ <fullpath to macro file> <fullpath to image file>
</code>
For example:
<code>
sh /g/almf/software/bin2/doIJ.sh /g/almf/software/ij/getArgumentMacro.ijm /g/almf/miura/blobs.tif
</code>

Use this script only for small tasks. Heavy calculation consumes the server resource where others are also using. 

===== Processing Single Image file by ImageJ, throw the job to cluster =====

**Script name: qsubIJ**

To process image file /a/b/c.tif with an ImageJ macro file /d/e/f.ijm, like above, but with cluster 
<blockquote>
 **sh qsubIJ /d/e/f.ijm /a/b/c.tif**
</blockquote>

Job will be submitted to the cluster, and what should be the output from ImageJ will be saved as a text file in your ALMF home directory:\\ 
**/g/almf/<Your Unix Username>/CLlogyyyymmdd_hhmm.txt**. \\
"yyyymmdd_hhmm" should be the time of execution. 

==== a bit more on customization ====

To customize arguments and so on, shell commands should be written in another shell script as follows:
<sxh shell>
#!/bin/sh
#PBS -N ImageJProcess
#PBS -l walltime=1:00:00
#
# *** Script for single image file procesing by ImageJ ***
#
#   two arguments for full paths to (2) an image file and (1) a macro file is required
#   assuming that macro file takes the fisrt argument as the 
#   Kota Miura (cmci.embl.de)
#   20101103
#   ****************************************************
#
sh /g/almf/software/ij/doIJ.sh /g/almf/software/ij/getArgumentMacro.ijm /g/almf/miura/blobs.tif
</sxh>

and then save the script as something like "cl_doIJ.sh". Execute the job by following command in terminal
<code>
/usr/pbs/bin/qsub -q clusterng /g/almf/software/ij/cl_doIJ.sh
</code>

===== Processing All Image Files in a Folder =====

**Script name: qsubIJbatch**

Syntax is 
<code>
sh qsubIJbatch </full/path/to/dir> <File Name of Macro File>
</code>
For example, if you want to process all images under ///g/almf/miura/testsmalls// using an ImageJ macro file //headlesstest3.ijm//, then your command would be:
<code bash>
sh qsubIJbatch /g/almf/miura/testsmalls headlesstest3.ijm
</code>

===== Example Commands for Bory and Christian =====

converting lif to tif stacks:\\
<del>
sh /g/almf/software/ij/lifcon.sh /g/haering/Pombescreen/test.lif
</del>\\
**sh /g/almf/software/bin2/lifconvert** /g/haering/Pombescreen/pb2/100927ExpNo2.lif

actual processing:\\
**sh /g/almf/software/bin2/qsubIJbatch** /g/haering/Pombescreen/test.lif_tifStack headlesstest3.ijm