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documents:101103imagej_cluster_short [2010/11/03 16:14] – created kotadocuments:101103imagej_cluster_short [2020/11/26 09:11] (current) – external edit 127.0.0.1
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 ====== Using Cluster (Quick Version) ====== ====== Using Cluster (Quick Version) ======
  
-===== Processing by ImageJ from Command Line =====+**Note: This page is outdated (June 1, 2016)**. I will prepare a newer version. 
  
-Command syntax is+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. 
  
-**/g/almf/software/ij/doIJ.sh <fullpath to macro file> <fullpath to image file>**+===== 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: For example:
-<sxh shell+<code
-/g/almf/software/ij/doIJ.sh /g/almf/software/ij/getArgumentMacro.ijm /g/almf/miura/blobs.tif +sh /g/almf/software/bin2/doIJ.sh /g/almf/software/ij/getArgumentMacro.ijm /g/almf/miura/blobs.tif 
-</sxh>+</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. 
  
-**Processing Single Image file by ImageJ, throw the job to cluster**+==== a bit more on customization ====
  
-Above commands should be pasted in another shell script as follows:+To customize arguments and so on, shell commands should be written in another shell script as follows:
 <sxh shell> <sxh shell>
 #!/bin/sh #!/bin/sh
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 /usr/pbs/bin/qsub -q clusterng /g/almf/software/ij/cl_doIJ.sh /usr/pbs/bin/qsub -q clusterng /g/almf/software/ij/cl_doIJ.sh
 </code> </code>
- 
  
 ===== Processing All Image Files in a Folder ===== ===== Processing All Image Files in a Folder =====
 +
 +**Script name: qsubIJbatch**
  
 Syntax is  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>
  
-**sh /g/almf/software/ij/clust5fullp.sh </full/path/to/dir> <File Name of Macro File>**+===== Example Commands for Bory and Christian =====
  
-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: +converting lif to tif stacks:\\ 
-<sxh shell+<del> 
-sh /g/almf/software/ij/clust5fullp.sh /g/almf/miura/testsmalls headlesstest3.ijm +sh /g/almf/software/ij/lifcon.sh /g/haering/Pombescreen/test.lif 
-</sxh>+</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
documents/101103imagej_cluster_short.1288800852.txt.gz · Last modified: 2016/05/24 12:46 (external edit)

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