Scipion 3.0.12-foss-2021a-CUDA-11.3.1

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.

Accessing Scipion 3.0.12-foss-2021a-CUDA-11.3.1

To load the module for Scipion 3.0.12-foss-2021a-CUDA-11.3.1 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load Scipion/3.0.12-foss-2021a-CUDA-11.3.1

BEAR Apps Version

2021a

Architectures

EL8-haswell (GPUs: NVIDIA P100) — EL8-icelake (GPUs: NVIDIA A100, NVIDIA A30)

The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

Extensions

  • biopython 1.76
  • configparser 5.0.2
  • emtable 0.0.14
  • littleutils 0.2.2
  • outdated 0.2.2
  • peppercorn 0.6
  • plotter 1.3.19
  • PyWavelets 1.4.1
  • scipion-app-3.0.12
  • scipion-em-3.0.23
  • scipion-em-gctf-3.1.1
  • scipion-em-xmipp-22.7.0
  • scipion-pyworkflow-3.0.27
  • tifffile 2022.10.10
  • tikzplotlib 0.10.1
  • tkcolorpicker 2.1.3
  • webcolors 1.12

More Information

For more information visit the Scipion website.

Dependencies

This version of Scipion has a direct dependency on: bibtexparser/1.4.0-GCCcore-10.3.0 ctffind/4.1.14-foss-2021a-CUDA-11.3.1 CUDA/11.3.1 foss/2021a freetype/2.10.4-GCCcore-10.3.0 GSL/2.7-GCC-10.3.0 HDF5/1.10.7-gompi-2021a Java/11 libjpeg-turbo/2.0.6-GCCcore-10.3.0 libpng/1.6.37-GCCcore-10.3.0 libreadline/8.1-GCCcore-10.3.0 LibTIFF/4.2.0-GCCcore-10.3.0 libxml2/2.9.10-GCCcore-10.3.0 libxslt/1.1.34-GCCcore-10.3.0 matplotlib/3.4.2-foss-2021a MotionCor2/1.4.7-GCCcore-10.3.0-CUDA-11.3.1 OpenCV/4.5.3-foss-2021a-CUDA-11.3.1-contrib Pillow/8.2.0-GCCcore-10.3.0 Python/3.9.5-GCCcore-10.3.0 RELION/3.1.3-foss-2021a-CUDA-11.3.1 scikit-learn/0.24.2-foss-2021a SQLite/3.35.4-GCCcore-10.3.0 Tcl/8.6.11-GCCcore-10.3.0 Tk/8.6.11-GCCcore-10.3.0 Xmipp/3.22.07-Helios-foss-2021a-CUDA-11.3.1 zlib/1.2.11-GCCcore-10.3.0

Last modified on 1st December 2022