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IMOD on Helix & Biowulf
IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the Boulder Laboratory for 3-D Electron Microscopy of Cells. [IMOD home page]

Running IMOD on Helix

Sample session:

[susanc@helix ~]$ module load imod

[susanc@helix ~]$ module list
Currently Loaded Modulefiles:
  1) imod/4.7.5

[susanc@helix ~]$ tif2mrc cell*.tif cellmrc

Running a single IMOD batch job on Biowulf

Set up a batch script along the following lines:


cd /data/$USER/myimagedir

module load imod

tif2mrc cell*.tif cell.mrc
newstack cell*.mrc 

Submit this job with:

qsub -l nodes=1 myjob.bat

If your IMOD job is likely to need more than the default 1 GB of memory, submit with

qsub -l nodes=1:g24:c24 myjob.bat

Submit a swarm of IMOD jobs

Set up a swarm command file along the following lines:

cd /data/$USER/myimagedir; tif2mrc cell*.tif cell.mrc
cd /data/$USER/myimagedir2; tif2mrc cell*.tif cell.mrc
Submit this swarm with:
swarm -g 2 -f swarm.cmd --module imod/4.7.5
where '-g 2' tells swarm that each command (a single line in the swarm command file) requires 2 GB of memory. This value should be predetermined by you. If you have no idea how much memory a single command requires, submit a swarm with a single line. The standard output file from that job will report the amount of memory used.

Running IMOD interactively

If you plan to use the GUI 3dmod, it's best to allocate an interactive node and run it on there. You need to set up an Xwindows connection to Biowulf for any graphics programs to work. Sample session:

biowulf% qsub -I -l nodes=1:g24:c24 -V
qsub: waiting for job 6525954.biobos to start
qsub: job 6525954.biobos ready

[susanc@p2286 ~]$ module load imod

[susanc@p2286 ~]$ module list
Currently Loaded Modulefiles:
  1) imod/4.7.5

[susanc@p2286 ~]$ 3dmod