Quick tutorial how to use PLGrid Infrastructure at ACC Cyfronet AGH.
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Training is going to be conducted at Zoom platform. Link to training on Wed 25th Nov at 10:00: https://cyfronet.zoom.us/j/5511864266?pwd=TzZIZWc4aitvRG1OTVI1azJQQ0hiQT09 |
Setup
Accounts
Each trainee is going to use his or her PLGrid account on Prometheus cluster. To obtain such account trainee has to register at Portal PLGrid webpage. Deails of procedure is described in PLGRID - accounts and affiliation.
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Usually PLGrid user has to create (or be added to) computational grant at PLGrid Portal - Grants, but during training all participants is going to use training grants.
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For training purpose participant can obtain short term affiliation with trainer (Klemens Noga) as supervisor. Necessary information are listed below:
To be activated affiliation has to be approved by supervisor (Klemens Noga in this case). After approval the confirmation e-mail will be sent. |
Software
Prometheus cluster runs on Linux and could be accessed trough CLI or GUI. Additional software has to be installed on participants' computers to be able to connect to Prometheus.
- To access CLI at Promehteus trough shell account SSL user has to have SSH client installed on his or her computer:
- To access GUI at Promehteus TurboVNC software should be installed. Detailed installation procedure is available (in polish) at Obliczenia w trybie graficznym: pro-viz.
Survey
Link to short survey about participants. It will help to establish
Contact
In case of any questions do not hesitate to contact me through e-mail Klemens Noga
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-mail: klemens.noga@cyfronet.pl
Materials and resources
SLURM scripts - slurm.tar.gz
Presentation - 2020-11-18-MCB-hpc-intro.pdf
Relion tutorial - relion31_tutorial.pdf
Relion documentation at BIOwulf - https://hpc.nih.gov/apps/RELION/
Questions and issues
- So where we can find scripts from relion to use in sbatch ?
- Klemens Noga prepare scripts and put it below.
- Describe in details workload with RELION
- using pro-viz
- using sbatch
- How to setup and use users python module
- How to open pdf files in pro-viz
- Feature request: Chimera in pro-viz
- How to solve memory or time limit problems in cryosparc
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