documents:101103imagej_cluster_short
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documents:101103imagej_cluster_short [2010/11/24 23:08] – kota | documents:101103imagej_cluster_short [2011/08/18 14:42] – kota | ||
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====== Using Cluster (Quick Version) ====== | ====== Using Cluster (Quick Version) ====== | ||
- | ===== Processing by ImageJ from Command Line ===== | + | 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 / | ||
+ | </ | ||
+ | Otherwise, please add the path above in front of script name. | ||
- | Command syntax is | + | ===== Interactive Usage of Cluster CPU ===== |
- | **/ | + | Before submitting huge data with your script, you might want to test run the script interactively |
+ | - 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, | ||
+ | |||
+ | |||
+ | ===== Processing by ImageJ from Command Line ===== | ||
+ | |||
+ | **Script name: doIJ** | ||
+ | |||
+ | Syntax | ||
+ | < | ||
+ | sh doIJ < | ||
+ | </ | ||
For example: | For example: | ||
- | < | + | < |
- | sh / | + | sh / |
</ | </ | ||
+ | |||
+ | 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 ===== | ===== Processing Single Image file by ImageJ, throw the job to cluster ===== | ||
- | Above commands should be pasted | + | **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 | ||
+ | < | ||
+ | **sh qsubIJ /d/e/f.ijm / | ||
+ | </ | ||
+ | |||
+ | 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: | ||
+ | **/ | ||
+ | " | ||
+ | |||
+ | ==== a bit more on customization ==== | ||
+ | |||
+ | To customize arguments and so on, shell commands should be written | ||
<sxh shell> | <sxh shell> | ||
#!/bin/sh | #!/bin/sh | ||
Line 35: | Line 68: | ||
/ | / | ||
</ | </ | ||
- | |||
===== Processing All Image Files in a Folder ===== | ===== Processing All Image Files in a Folder ===== | ||
- | Syntax is | + | **Script name: qsubIJbatch** |
- | + | ||
- | **sh / | + | |
+ | Syntax is | ||
+ | < | ||
+ | sh qsubIJbatch </ | ||
+ | </ | ||
For example, if you want to process all images under /// | For example, if you want to process all images under /// | ||
<code bash> | <code bash> | ||
- | sh / | + | sh qsubIJbatch |
</ | </ | ||
Line 54: | Line 88: | ||
sh / | sh / | ||
</ | </ | ||
- | **/ | + | **sh / |
actual processing: | actual processing: | ||
- | **sh /g/almf/softwae/ij/clust5fullp.sh** / | + | **sh /g/almf/software/bin2/qsubIJbatch** / |
documents/101103imagej_cluster_short.txt · Last modified: 2020/11/26 09:11 by 127.0.0.1