[web] portal.biohpc.swmed.edu [email] biohpc-help ......apr 11, 2018  · cloud services - web based...

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  • Interactive Environments & Data Exploration

    1

    [web] portal.biohpc.swmed.edu

    [email] [email protected]

    Updated for 2018-04-11

  • Why Interactive Environments

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    • Debugging

    • Visualization

    • Scripts/command generator

    • Submit job directly to cluster without writing SLURM scripts

    • Dedicated node for web services

    • And more ..

  • Interactive sessions with BioHPC

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    Reserve Session with command• srun• remoteGPU/remoteGUI

    Cloud Services• Web based Visualization• Web Desktop

    BioHPC On-Demand• DIGITS• Jupyter• Rstudio• BisQue (coming soon)

  • Reserve Session with command - srun

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    srun --partition=super --pty --time=00:10:00 /bin/bash

    srun create a resource allocation --partition select interactive partition--pty run task zero in pseudo terminal mode--time setup time limit/bin/bash gives you a pseudo terminal that runs bash

  • Reserve Session with command - srun

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  • Reserve Session with command – remoteGPU/remoteGUI

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    @nucleus005(login node), TurboVNC Version 2.1.1Virtual Network Computing-is a remote display system that allows you to view and interact with a desktop environment running on a remote computer-provides high-speed solution for remotely displaying image-intensive applications over all types of networks

  • Reserve Session with command – remoteGPU/remoteGUI

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    First, setup your VNC password with the command:

    vncpasswd

    • Primary VNC Password• Optional view-only password

    • Password file saved at ~/.vnc/passwd• Password has to be longer than 5 characters

  • Reserve Session with command – remoteGPU/remoteGUI

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    How to request?

    • remoteGUI: super partition • remoteGPU: GPU partition• 20 hours time limit

    Need more time? Send extension request along with JobId to BioHPC-help

    How to access?

    VNC server: nucleus.biohpc.swmed.edu:30829

    Nucleus082

  • Cloud Services - Web based Visualization

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    Web based visualization access: https://portal.biohpc.swmed.edu/terminal/webgui/

    • WebGUI/WebGUI256reserve a CPU node

    • WebGPU/WebGPUv1reserve a GPU node, good for ImageJ, Amira, stand-alone paraview or compile your CUDA

    codestep 1: add visualization software as a modulestep 2: vglrun

    https://portal.biohpc.swmed.edu/terminal/webgui/

  • Cloud Services - Web based Visualization

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    • WebGUI 312 nodes available from partition super & 32GB, Minimum 32GB RAM

    • WebGUI256 126 nodes available from partition 256GB & 256GBv1, Minimum

    256GB RAM

    • WebGPU 20 nodes available from partition GPU, Minimum 1 GPU card, Tesla

    K20/K40 or 2 Tesla P100 cards

    • WebGPUv1 12 nodes available from partition GPUv1, 2 Tesla P100 GPU cards

    • WebWinDCV 20 nodes available from partition GPU, Virtual windows environment

    (32 cores, 192GB RAM) running on a GPU node

  • Cloud Services - Web based Visualization (webGUI - directly submitting job to cluster)

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    PEET used in conjunction with IMODeTomo is IMOD’s GUI interface

    Steps:

    Step 1: processchunks (broken up job into "chunks“, each for a single cpu.)Step 2: salloct -> return JobIDStep 3: srun with JobID queuechunks (from the initial processchunks command)Step 4: clean up allocation

    Required module version:peet/1.11.0-alpha(will load imod/4.8.50-beta as well)

    eTomoIMOD/PEET

  • Cloud Services - Web based Visualization (webGUI - directly submitting job to cluster)

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    Queue Max # CPUs #CPUs / NODE

    128 GB 16*16=256 16

    256 GB 24*16=256 24

    384 GB 16*2=32 16

    super 16*16=256 16

    GPU 16*2=32 16

    submit directly from eTomo GUI interface

  • Cloud Services - Web based Visualization (webGUI – 32 GB partition)

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    What if you’ve been assigned to a 32GB partition?

    How do I know?$ sinfo -p 32GBPARTITION AVAIL TIMELIMIT NODES STATE NODELIST32GB up infinite 1 drain NucleusA01332GB up infinite 9 alloc NucleusA[003,006-007,014,077-081]32GB up infinite 70 idle NucleusA[002,004-005,008-012,015-076]

    How to reduce memory reservation for applications (e.g: ImageJ)?ImageJ --mem 16g

  • Cloud Services - Web based Visualization (webGPU - 3D rendering)

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  • Cloud Services - Web based Visualization (webGPUv1 - processing with multiple GPUs)

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    @GUP nodemodule add relion/intel/openmpi/cuda80/2.0-betaexport VISIBLE_CUDA_DEVICES=“0,1”vglrun relion

    Specify GPU info

  • Cloud Services - Web Desktop

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    A Dedicate Compute Node + No time limt + reserved for certain group/lab

    https://portal.biohpc.swmed.edu/terminal/webdesktop/

    This service allows certain BioHPC groups to launch long-running interactive

    sessions on a dedicated GPU visualization server. There is no time limit for these sessions, but the server is shared among multiple users in the group.

    4 Tesla K80 GPU cards

    https://portal.biohpc.swmed.edu/terminal/webdesktop/

  • Cloud Services - BioHPC OnDemand

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    A Dedicate Compute Node + Service

  • 18

    DIGITS is a Python-based frontend for machine-learning tools Caffe, Tensorflow, and Torch

    Helps reduce the workload of building an artificial neural network

    Lots of computing power needed to do the training – uses dual P100 Tesla GPU cards

    Cloud Services - BioHPC On-Demand DIGITS

    example convolutional neural network

  • 19

    Radau P, Lu Y, Connelly K, Paul G, Dick AJ, Wright GA. "Evaluation Framework for

    Algorithms Segmenting Short Axis Cardiac MRI." The MIDAS Journal -Cardiac MR Left

    Ventricle Segmentation Challenge, http://hdl.handle.net/10380/3070

    Image segmentation example – Locate left ventricle of the heart within an MRI

    Cloud Services - BioHPC On-Demand DIGITS

    Tutorial: https://github.com/NVIDIA/DIGITS/blob/master/examples/medical-imaging/README.md

    https://github.com/NVIDIA/DIGITS/blob/master/examples/medical-imaging/README.md

  • 20

    1. Create a Dataset

    Cloud Services - BioHPC On-Demand DIGITS

  • 21

    2. Create and Train a Model

    Cloud Services - BioHPC On-Demand DIGITS

  • 22

    Cloud Services - BioHPC On-Demand DIGITS

    3. Test inference on validation data

  • Cloud Services - BioHPC On-Demand Jupyter

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  • 24

    What is a Jupyter Notebook?

    • Interactive document that contains both computer code and rich text elements

    • Python code snippets• Paragraph• Equations• Figures• Links

    • What is it for?

    • Writing code• Publication-quality figures• Class exercises• Reproducibility• Building webpages

    Source: https://plot.ly/python/ipython-notebook-tutorial/

    Cloud Services - BioHPC On-Demand Jupyter

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    Cloud Services - BioHPC On-Demand Jupyter

    Demo: Using Bokeh for Visualizing and Exploring Data in Jupyter

    https://github.com/bokeh/bokeh-notebooks/tree/master/quickstart

  • 26

    * You may also use https://rstudio.biohpc.swmed.edu for small tasks

    Use your BioHPC username and password to login

    Cloud Services - BioHPC On-Demand RStudio

    https://rstudio.biohpc.swmed.edu/

  • 27

  • Cloud Services - BioHPC On-Demand Bisque (Coming soon)

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  • Check status of all web-based interactive sessions

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