To run the whole volume reconstruction

On GANYMEDES PC workstation:

Open an other xterm window (right button click and click on 'Xterm')

ganymedes:~ % ssh -X mdxxx@rnice

rnicexx% cd id19                                              

Submit the reconstruction file in executing:

rnicexx% mqueue sample_name

or

rnicexx% mqueue sample_name1 sample_name2

...

or

rnicexx% mqueue sample_name[1-5]

 

 

For Paganin reconstruction:

rnicexx% mqueue_PAG sample_name

 

 

or

rnicexx% mqueue_PAG sample_name1 sample_name2

...

rnice55:/data/visitor/in679/id19 % mqueue_PAG 0.6*mush*
...Use the following command to put your (array) job into the OAR batch queue:
oarsub -S ./0.6_mushroom_01_bottom_1000_0.2_u17.6_25_xc10_withontoppag.oar
[ADMISSION RULE] Modify resource description with type constraints
OAR_JOB_ID=2192771
OAR_JOB_ID=2192772
OAR_JOB_ID=2192773
OAR_JOB_ID=2192774
OAR_ARRAY_ID=2192771

To see information about job submission:
oarinfo 2192771

oarstat -u

oardel_myjobs

 

Your reconstructed volume can be huge.

A 2048x2048x2048 volume in float (4 bytes) format gives 8 files of 4 Gb each!!!

We so usually propose to reduce it in 1 byte (256 grey levels): mrecad procedure or in 2 bytes (16 bits): VOL_recad_OAR('prefix') in Matlab