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Scipion is an image processing framework.

Homepage: http://scipion.i2pc.es/

Documentation: https://scipion-em.github.io/docs/

Loading the environment

Scipion can be used through environment modules:

module load scipion/2.0

CSSB Notes

How to start

The original script is called scipion but we have made a wrapper called scipion2 which uses a CSSB specific configuration file. So call somewhere:

scipion2

Maxwell Cluster Usage

When you started Scipion with the CSSB scipion2 command you get a special configured cluster submission user interface.

CPU Cluster Submission

The Queue parameters dialog window defines the CSSB/DESY cluster usage.

Notes:

  • The addition GUI appears when you set Use queue? to Yes and press the Execute button.
  • The Time (hours) is pre-set to 7 days which is the maximum in the all partition.
  • The Total cores setting from the Queue Parameters override the Parallel MPI entry from the original user interface.
  • The amount of total cores defines the amount of nodes used (8 nodes * 48 cores = 384 MPI with Threads = 1).
  • The CPUs per task must be the same as the Parallel Threads entry.
  • The free nodes and the corresponding Constraints can be seen by calling the alias sinfo_detailed on the command line.

GPU Cluster Submission

Notes:

  • The template is limited to use 1 node so just change the Constraints to P100 or V100.
  • If the node has 2 GPUs inside add to GPU IDs 0 1.

Known limitations

Unblur

  • cistem-unblur runs best if you use all cores of one node on the cluster with threads e.g. Threads = 48, Total cores: 48
  • grigoriefflab-unblur runs best if you use just a few threads on a local node, better use the newer CisTEM version

Xmipp

  • The Xmipp GPU programs need CUDA 8.0 which has problems on the new Volta V100 GPU cards. Use P100 cards instead.

Scipion 2.0 contains the following packages:

PluginVersion
3DFSC2.5
ascp3.7.4
Bsoft1.9.0
Chimera1.13.1
cisTEM1.0.0-beta
cryoEF1.1.0
ctfffind44.1.13
ctffind3.5
dogpicker0.2.1.1
EMAN22.3
frealign9.07
gautomatch0.56
gctf1.18
localrec1.2.0
locscale0.1
mag_distortion1.0.1
MotionCor21.3.0
nma2.0
Relion3.0
ResMap1.95
simple2.1
spider25.02
summovie1.0.2
topaz0.2.1
unblur1.0.2
xmipp3.19.04

Integration to other external software

SoftwareVersionNote
crYOLO1.5global model prediction with CSSB cryolo-1.5 conda environment successful
Phenix1.13-2998scipion provided tests passed
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