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SDSC Gordon Info

Everyone who applied for SDSC Gordon compute time for the map challenge will receive an initial allocation of 22,000 service units per proposed target. Altogether 14 users plan to perform a total of 45 reconstructions. Some useful links:

Other things to be aware of:

  • Our shared 20TB storage space area is /oasis/projects/nsf/ddp235.  All of the benchmark data (~13TB) for the challenge has been copied from EMPIAR to the subfolder /oasis/projects/nsf/ddp235/benchmarks and should be accessible to you. Please avoid making additional copies!
  • Each user can control the permissions on their subdirectories using the chmod commands.  You may want to create areas to be shared with the group (e.g. for sharing compiled software) and private areas.
  • Keep in mind that any publications that arise from this work should acknowledge that the research was supported by a Director's Discretionary Award on the  Gordon supercomputer at the  San Diego Supercomputer Center, University of California, San Diego


Dec 18: Users who have been allocated time on Gordon can also request time on the Comet system (GPU hardware).

Feb 17: Inquiry was made regarding increasing the 48 hour wall-time for jobs on Gordon, but it is difficult to break this policy. For Relion users should make use of the restart option.

Feb 29:  SDSC has installed Relion, Frealign and EMAN2 on Comet and Gordon. Users can add the software to their paths using the following commands:

module load relion
module load frealign
module load eman2


EMDataBank Validation Challenges are supported by NIH National Institute of General Medical Sciences

Please send your challenge questions, comments and feedback to

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