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<!DOCTYPE html>
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<title>Starting up on Satori — MIT Satori User Documentation documentation</title>
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<li class="toctree-l2"><a class="reference internal" href="satori-basics.html#what-is-satori">What is Satori?</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Starting up on Satori</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#getting-your-account">Getting Your Account</a></li>
<li class="toctree-l2"><a class="reference internal" href="#shared-hpc-clusters">Shared HPC Clusters</a></li>
<li class="toctree-l2"><a class="reference internal" href="#logging-in-to-satori">Logging in to Satori</a></li>
<li class="toctree-l2"><a class="reference internal" href="#the-satori-portal">The Satori Portal</a></li>
<li class="toctree-l2"><a class="reference internal" href="#setting-up-your-environment">Setting up Your Environment</a></li>
<li class="toctree-l2"><a class="reference internal" href="#transferring-files">Transferring Files</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#using-scp-or-rysnc">Using scp or rysnc</a></li>
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<li class="toctree-l2"><a class="reference internal" href="satori-workload-manager-using-slurm.html#a-note-on-exclusivity">A Note on Exclusivity</a></li>
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<li class="toctree-l3"><a class="reference internal" href="satori-workload-manager-using-slurm.html#note-on-pytorch-1-4">Note on Pytorch 1.4</a></li>
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<li class="toctree-l1"><a class="reference internal" href="satori-troubleshooting.html">Troubleshooting</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-ai-frameworks.html">IBM Watson Machine Learning Community Edition (WML-CE) and Open Cognitive Environment (Open-CE)</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#install-anaconda">[1] Install Anaconda</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#wml-ce-and-open-ce-setting-up-the-software-repository">[2] WML-CE and Open-CE: Setting up the software repository</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#wml-ce-and-open-ce-creating-and-activate-conda-environments-recommended">[3] WML-CE and Open-CE: Creating and activate conda environments (recommended)</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#wml-ce-installing-all-frameworks-at-the-same-time">[4] WML-CE: Installing all frameworks at the same time</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#wml-ce-testing-ml-dl-frameworks-pytorch-tensorflow-etc-installation">[5] WML-CE: Testing ML/DL frameworks (Pytorch, TensorFlow etc) installation</a><ul>
<li class="toctree-l3"><a class="reference internal" href="satori-ai-frameworks.html#controlling-wml-ce-release-packages">Controlling WML-CE release packages</a></li>
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<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#the-wml-ce-supplementary-channel-is-available-at-https-anaconda-org-powerai">The WML CE Supplementary channel is available at: https://anaconda.org/powerai/.</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-ai-frameworks.html#the-wml-ce-early-access-channel-is-available-at-https-public-dhe-ibm-com-ibmdl-export-pub-software-server-ibm-ai-conda-early-access">The WML-CE Early Access channel is available at: https://public.dhe.ibm.com/ibmdl/export/pub/software/server/ibm-ai/conda-early-access/.</a></li>
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<li class="toctree-l1"><a class="reference internal" href="satori-distributed-deeplearning.html">Distributed Deep Learning</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-large-model-support.html">IBM Large Model Support (LMS)</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-julia.html">Julia on Satori</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#getting-started">Getting started</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#getting-help">Getting help?</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#a-simple-batch-script-example">A simple batch script example</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#recipe-for-running-single-gpu-single-threaded-interactive-session-with-cuda-aware-mpi">Recipe for running single GPU, single threaded interactive session with CUDA aware MPI</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#running-a-multi-process-julia-program-somewhat-interactively">Running a multi-process julia program somewhat interactively</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-julia.html#an-example-of-installing-https-github-com-clima-climatemachine-jl-on-satori">An example of installing https://github.com/clima/climatemachine.jl on Satori</a></li>
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<li class="toctree-l1"><a class="reference internal" href="satori-R.html">R on Satori</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-R.html#getting-started-with-r">Getting Started with R</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-R.html#installing-packages">Installing Packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-R.html#a-simple-batch-script-example">A Simple Batch Script Example</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-R.html#r-and-python">R and Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-R.html#running-r-in-a-container">Running R in a container</a></li>
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<li class="toctree-l1"><a class="reference internal" href="satori-cuda-aware-mpi.html">Using MPI and CUDA on Satori</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#getting-started">Getting started</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#compiling">Compiling</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#submiting-a-batch-script">Submiting a batch script</a><ul>
<li class="toctree-l3"><a class="reference internal" href="satori-cuda-aware-mpi.html#batch-script-header">Batch script header</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-cuda-aware-mpi.html#assigning-gpus-to-mpi-ranks">Assigning GPUs to MPI ranks</a></li>
<li class="toctree-l3"><a class="reference internal" href="satori-cuda-aware-mpi.html#running-the-mpi-program-within-the-batch-script">Running the MPI program within the batch script</a></li>
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<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#a-complete-example-slurm-batch-script">A complete example SLURM batch script</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#using-alternate-mpi-builds">Using alternate MPI builds</a></li>
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<li class="toctree-l1"><a class="reference internal" href="lsf-templates/satori-lsf-ml-examples.html">Example machine learning LSF jobs</a><ul>
<li class="toctree-l2"><a class="reference internal" href="lsf-templates/satori-lsf-ml-examples.html#a-single-node-4-gpu-keras-example">A single node, 4 GPU Keras example</a></li>
<li class="toctree-l2"><a class="reference internal" href="lsf-templates/satori-lsf-ml-examples.html#a-single-node-4-gpu-caffe-example">A single node, 4 GPU Caffe example</a></li>
<li class="toctree-l2"><a class="reference internal" href="lsf-templates/satori-lsf-ml-examples.html#a-multi-node-pytorch-example">A multi-node, pytorch example</a></li>
<li class="toctree-l2"><a class="reference internal" href="lsf-templates/satori-lsf-ml-examples.html#a-multi-node-pytorch-example-with-the-horovod-conda-environment">A multi-node, pytorch example with the horovod conda environment</a></li>
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<li class="toctree-l1"><a class="reference internal" href="satori-howto-videos.html">Satori Howto Video Sessions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-howto-videos.html#installing-wmcle-on-satori">Installing WMCLE on Satori</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-howto-videos.html#pytorch-with-ddl-on-satori">Pytorch with DDL on Satori</a></li>
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<li class="toctree-l2"><a class="reference internal" href="satori-howto-videos.html#jupyterlab-with-ssh-tunnel-on-satori">Jupyterlab with SSH Tunnel on Satori</a></li>
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<li class="toctree-l1"><a class="reference internal" href="satori-public-datasets.html">Satori Public Datasets</a></li>
<li class="toctree-l1"><a class="reference internal" href="singularity.html">Singularity for Satorians</a><ul>
<li class="toctree-l2"><a class="reference internal" href="singularity.html#fast-start">Fast start</a></li>
<li class="toctree-l2"><a class="reference internal" href="singularity.html#other-notes">Other notes</a></li>
<li class="toctree-l2"><a class="reference internal" href="singularity.html#interactive-allocation">Interactive Allocation:</a></li>
<li class="toctree-l2"><a class="reference internal" href="singularity.html#non-interactive-batch-mode">Non interactive / batch mode</a></li>
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<li class="toctree-l1"><a class="reference internal" href="satori-relion-cryoem.html">Relion Cryoem for Satorians</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-relion-cryoem.html#prerequisites">Prerequisites</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-relion-cryoem.html#quick-start">Quick start</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-relion-cryoem.html#other-notes">Other notes</a></li>
</ul>
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<li class="toctree-l1"><a class="reference internal" href="satori-copy-large-filesets.html">Copying larger files and large file sets</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-copy-large-filesets.html#using-mrsync">Using mrsync</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-copy-large-filesets.html#using-aspera-for-remote-file-transfer-to-satori-cluster">Using Aspera for remote file transfer to Satori cluster</a></li>
<li class="toctree-l1"><a class="reference internal" href="satori-doc-examples-contributing.html">FAQ</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-doc-examples-contributing.html#tips-tricks-and-questions">Tips, tricks and questions</a><ul>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/storage/index.html">How can I see disk usage?</a></li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/storage/index.html#where-should-i-put-world-or-project-shared-datasets">Where should I put world or project shared datasets?</a></li>
<li class="toctree-l3"><a class="reference internal" href="portal-howto/customization.html">How can I create custom Jupyter kernels for the Satori web portal?</a><ul>
<li class="toctree-l4"><a class="reference internal" href="portal-howto/customization.html#steps-to-create-a-kernel">Steps to create a kernel</a></li>
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<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/carlos-quick-start-commands/index.html">How do I set up a basic conda environment?</a></li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html">System software queries</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-linux-distribution-version-am-i-running">What Linux distribution version am I running?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-linux-kernel-level-am-i-running">What Linux kernel level am I running?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-software-levels-are-installed-on-the-system">What software levels are installed on the system?</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#system-hardware-queries">System hardware queries</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-is-my-cpu-configuration">What is my CPU configuration?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-much-ram-is-there-on-my-nodes">How much RAM is there on my nodes?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-smt-mode-are-my-nodes-in">What SMT mode are my nodes in?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-cpu-governor-is-in-effect-on-my-nodes">What CPU governor is in effect on my nodes?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-are-the-logical-ids-and-uuids-for-the-gpus-on-my-nodes">What are the logical IDs and UUIDs for the GPUs on my nodes?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-is-the-ibm-model-of-my-system">What is the IBM model of my system?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#which-logical-cpus-belong-to-which-socket">Which logical CPUs belong to which socket?</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#questions-about-my-jobs">Questions about my jobs</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-can-i-establish-which-logical-cpu-ids-my-process-is-bound-to">How can I establish which logical CPU IDs my process is bound to?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#can-i-see-the-output-of-my-job-before-it-completes">Can I see the output of my job before it completes?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#i-have-a-job-waiting-in-the-queue-and-i-want-to-modify-the-options-i-had-selected">I have a job waiting in the queue, and I want to modify the options I had selected</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#i-have-submitted-my-job-several-times-but-i-get-no-output">I have submitted my job several times, but I get no output</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-do-i-set-a-time-limit-on-my-job">How do I set a time limit on my job?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#can-i-make-a-jobs-startup-depend-on-the-completion-of-a-previous-one">Can I make a job’s startup depend on the completion of a previous one?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-do-i-select-a-specific-set-of-hosts-for-my-job">How do I select a specific set of hosts for my job?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#how-do-i-deselect-specific-nodes-for-my-job">How do I deselect specific nodes for my job?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#my-jobs-runtime-environment-is-different-from-what-i-expected">My job’s runtime environment is different from what I expected</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#i-want-to-know-precisely-what-my-jobs-runtime-environment-is">I want to know precisely what my job’s runtime environment is</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/ondemand_portal_queries/index.html">Portal queries</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/ondemand_portal_queries/index.html#i-see-no-active-sessions-in-my-interactive-sessions">I see no active sessions in My Interactive Sessions?</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html">How do I build a Singularity image from scratch?</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#set-up-to-run-docker-in-ppc64le-mode-on-an-x86-machine">Set up to run Docker in ppc64le mode on an x86 machine</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#run-docker-in-ppc64le-mode-on-an-x86-machine-to-generate-an-image-for-satori">Run Docker in ppc64le mode on an x86 machine to generate an image for Satori</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#import-new-docker-hub-image-into-singularity-on-satori">Import new Docker hub image into Singularity on Satori</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#using-singularity-instead-of-docker">Using Singularity instead of Docker</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-tutorial-examples.html">Green Up Hackathon IAP 2020</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial-examples/index.html">Tutorial Examples</a><ul>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/pytorch-style-transfer/index.html">Pytorch Style Transfer</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/pytorch-style-transfer/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/pytorch-style-transfer/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/pytorch-style-transfer/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/pytorch-style-transfer/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/neural-network-dna-demo/index.html">Neural network DNA</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/neural-network-dna-demo/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/neural-network-dna-demo/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/neural-network-dna-demo/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/neural-network-dna-demo/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/transfer-learning-pathology/index.html">Pathology Image Classification Transfer Learning</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/transfer-learning-pathology/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/transfer-learning-pathology/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/transfer-learning-pathology/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/transfer-learning-pathology/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html">Multi Node Multi GPU TensorFlow 2.0 Distributed Training Example</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#prerequisites-if-you-are-not-yet-running-tensorflow-2-0">Prerequisites if you are not yet running TensorFlow 2.0</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#what-s-going-on-here">What’s going on here?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/tensorflow-2.x-multi-gpu-multi-node/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/eric-fiala-wmlce-notebooks-master/index.html">WMLCE demonstration notebooks</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/eric-fiala-wmlce-notebooks-master/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/eric-fiala-wmlce-notebooks-master/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/eric-fiala-wmlce-notebooks-master/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/eric-fiala-wmlce-notebooks-master/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html">Finding clusters in high-dimensional data using tSNE and DB-SCAN</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html">BigGAN-PyTorch</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html#useful-references">Useful references</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="tutorial-examples/index.html#measuring-resource-use">Measuring Resource Use</a><ul>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/energy-profiling/index.html">Intergrated energy use profiling</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/energy-profiling/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/energy-profiling/index.html#commands-to-run-this-example">Commands to run this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/energy-profiling/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/energy-profiling/index.html#useful-references">Useful references</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/nvprof-profiling/index.html">Profiling code with nvprof</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/nvprof-profiling/index.html#description">Description</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/nvprof-profiling/index.html#commands-to-run-the-examples">Commands to run the examples</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/nvprof-profiling/index.html#useful-references">Useful references</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="satori-getting-help.html">Getting help on Satori</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-help.html#email-help">Email help</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-help.html#slack">Slack</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-help.html#slack-or-satori-support-techsquare-com">Slack or satori-support@techsquare.com</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-help.html#satori-office-hours">Satori Office Hours</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-getting-help.html#tips-and-tricks">Tips and Tricks</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="ause-coc.html">Acceptable Use and Code of Conduct</a><ul>
<li class="toctree-l2"><a class="reference internal" href="ause-coc.html#acceptable-use-guidelines">Acceptable Use Guidelines</a></li>
<li class="toctree-l2"><a class="reference internal" href="ause-coc.html#code-of-conduct">Code of Conduct</a></li>
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<div class="section" id="starting-up-on-satori">
<h1>Starting up on Satori<a class="headerlink" href="#starting-up-on-satori" title="Permalink to this headline">¶</a></h1>
<div class="section" id="getting-your-account">
<h2>Getting Your Account<a class="headerlink" href="#getting-your-account" title="Permalink to this headline">¶</a></h2>
<p>Satori is available to all MIT students and staff with an active Kerberos ID. The first step to using Satori
is to activate your account. To do that, go to the portal page (<a class="reference external" href="https://satori-portal.mit.edu/" target="_blank">https://satori-portal.mit.edu/</a>). Click the
“Authenticate with Globus” button, and you’ll be asked to select an organization. Select
“Massachusetts Institute of Technology” and click “Continue”. You’ll be taken to your MIT Kerberos login
page, where you should log in. Follow the prompts (you’ll be asked if you want to associate with an existing
Globus login, if you don’t use Globus you can ignore this and press left button) and follow the instructions
on the screen. Your account should be activated at this point.</p>
</div>
<div class="section" id="shared-hpc-clusters">
<h2>Shared HPC Clusters<a class="headerlink" href="#shared-hpc-clusters" title="Permalink to this headline">¶</a></h2>
<p>Satori is an HPC-style shared cluster. You are sharing this resources with a number of other researchers,
staff, and students so it is important that you read this page and use the system as intended.</p>
<p>Being a cluster, there are several machines connected together with a network. We refer to these as <strong>nodes</strong>.
Most nodes in the cluster are referred to as <strong>compute nodes</strong>, this is where the computation is done on the
system (where you will run your code). When you log into the system at the command line you are on a special
purpose node called the <strong>login node</strong>, or the <strong>head node</strong>. The login node, as its name suggests, is where
you log in and is for editing code and files, installing packages and software, downloading data, and starting
jobs to run your code on one of the compute nodes.</p>
<p>Each job is started using a piece of software called the scheduler, which is a resource manager for the system.
You let it know what resources you need and what you want to run, and the scheduler will find those resources and
start your job on them. When your job completes those resources are relinquished. The scheduler is what ensures
that no two jobs are using the same resources, so it is very important not to run anything unless it is submitted
properly through the scheduler. You should not run anything on the login/head node.</p>
</div>
<div class="section" id="logging-in-to-satori">
<h2>Logging in to Satori<a class="headerlink" href="#logging-in-to-satori" title="Permalink to this headline">¶</a></h2>
<p>There are two ways to log into and use Satori. The first is through the portal, where you can view the files
in your home directory, start a shell, and use Jupyter Lab. The second is through ssh. Take a look at the
<a class="reference external" href="https://mit-satori.github.io/satori-ssh.html" target="_blank">Satori Login</a> page for more information.</p>
</div>
<div class="section" id="the-satori-portal">
<h2>The Satori Portal<a class="headerlink" href="#the-satori-portal" title="Permalink to this headline">¶</a></h2>
<p>Once you’ve logged into the portal, you’ll see a few tabs at the top of the page. You can:</p>
<ul class="simple">
<li><strong>View the Files in your Home Directory:</strong> Click on Files -> Home Directory. From here you can download and upload files. Also can also drag and drop files from your computer into this window to transfer them to the system.</li>
<li><strong>View your Active Jobs:</strong> Click on Jobs -> Active Jobs. Here you can see a list of all of your currently running jobs. You can click on the arrow to the left of each line to see more information about the job.</li>
<li><strong>Start a Shell:</strong> Click on Clusters -> Satori Shell Access. This will open a shell in a new browser tab that will be on the login node. From here you can submit a batch job or start an interactive session to run your code.</li>
<li><strong>Start a Jupyter Notebook:</strong> Click on Interactive Apps -> Jupyter Notebook. From here you can create a new Jupyter Lab instance. The <a class="reference external" href="https://mit-satori.github.io/satori-ssh.html" target="_blank">Satori Login</a> page describes which options you should choose when starting Jupyter Lab.</li>
</ul>
<p>If you haven’t used an HPC system before, you may want to start by using Jupyter Lab in the portal. If you select
the options described on the <a class="reference external" href="https://mit-satori.github.io/satori-ssh.html" target="_blank">Satori Login</a> page your environment
should be set up to run many of the popular machine learning frameworks in the Jupyter Notebooks.</p>
</div>
<div class="section" id="setting-up-your-environment">
<h2>Setting up Your Environment<a class="headerlink" href="#setting-up-your-environment" title="Permalink to this headline">¶</a></h2>
<p>There are two ways we manage software and environemnts in Satori. The first is conda, which is the general package
manager for the second. The second are environment modules.</p>
<ol class="arabic simple">
<li><strong>Environment Modules</strong>: Environment modules are pre-packaged environments for software, tools, and libraries. It allows you to load and unload these as you go. It’s always good to check to see if a module exists for a tool before installing it yourself. To see the full set of modules available, first load the spack module (<cite>module load spack</cite>), then run the <cite>module avail</cite> command. A few common module commands are:</li>
</ol>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>module avail <span class="c1"># Shows the available modules</span>
module load MODULENAME <span class="c1"># Load the module MODULENAME</span>
module list <span class="c1"># List the modules that you have loaded</span>
module rm MODULENAME <span class="c1"># Unload the module MODULENAME</span>
module unload MODULENAME <span class="c1"># Unload the module MODULENAME</span>
module switch MODULE1 MODULE2 <span class="c1"># Unload MODULE1 and load MODULE2</span>
</pre></div>
</div>
<ol class="arabic simple" start="2">
<li><strong>Conda</strong>: Conda is the package manager for the system. The thing to know when you create your conda environment is that you want to make sure you are getting your packages from the right channel. We have in depth instructions on how to properly set up a conda environment on the <a class="reference external" href="https://mit-satori.github.io/satori-ai-frameworks.html" target="_blank">WMLCE</a> page. Steps 1-3 will show you how to create and properly set up a conda environment, Step 4 will set up the machine learning frameworks.</li>
</ol>
</div>
<div class="section" id="transferring-files">
<h2>Transferring Files<a class="headerlink" href="#transferring-files" title="Permalink to this headline">¶</a></h2>
<p>There are multiple ways to transfer files:</p>
<ul class="simple">
<li>At the command line using scp or rsync</li>
<li>On the Satori Portal using the File explorer</li>
<li>Using other tools like <a class="reference external" href="https://winscp.net/eng/download.php" target="_blank">WinSCP</a>, <a class="reference external" href="https://cyberduck.io/download/" target="_blank">Cyberduck</a>, etc</li>
</ul>
<div class="section" id="using-scp-or-rysnc">
<h3>Using scp or rysnc<a class="headerlink" href="#using-scp-or-rysnc" title="Permalink to this headline">¶</a></h3>
<p>Both scp and rsync are command line tools that you can use to transfer files to and from remote systems
like Satori. They both work like cp, but you have to specify the hostname of the remote system. You’ll
need to know the path to the file or directory that you want to transfer and the path to the location where
you want to transfer the file or directory. To transfer a file from your computer to Satori, for example:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp <local-file.py> [email protected]:/path/to/location/
</pre></div>
</div>
<p>To transfer a file from Satori you’d do a similar thing, but swap the arguments. For example, to transfer
to the current directory:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp [email protected]:/path/to/file/<remote-file.py> .
</pre></div>
</div>
<p>To transfer a directory use the -r (recursive) flag as you would with cp and other Linux commands.</p>
<p>The rysnc command works similarly, but has more options. For example, you can run it with the -u (update)
option, which will only transfer files that have not already been transferred.</p>
</div>
<div class="section" id="satori-portal-file-explorer">
<h3>Satori Portal File Explorer<a class="headerlink" href="#satori-portal-file-explorer" title="Permalink to this headline">¶</a></h3>
<p>Using the File Explorer on the Satori Portal you can navigate, view, and transfer files. To get to the File
Explorer, log into the Satori Portal and click Files -> Home Directory. From here you can click use the
Upload and Download buttons to move your files. You can also drag and drop files from your computer into
the File Explorer window to transfer them to the system.</p>
</div>
</div>
<div class="section" id="types-of-jobs">
<h2>Types of Jobs<a class="headerlink" href="#types-of-jobs" title="Permalink to this headline">¶</a></h2>
<p>There a couple of different ways you can run on Satori. We’ve already mentioned that you can start up
Jupyter Lab from the Satori Portal and run Jupyter Notebooks there. You can also open a terminal in Jupyter
and run at the command line there. This is a great place to start if you are more familiar with Jupyter.
Outisde of Jupyter, there are two other main ways to run your code, the first are <strong>interactive jobs</strong>, the second
are <strong>batch jobs</strong>.</p>
<div class="section" id="running-interactive-jobs">
<h3>Running Interactive Jobs<a class="headerlink" href="#running-interactive-jobs" title="Permalink to this headline">¶</a></h3>
<p>In an interactive job you are running at the command line on a compute node. You can start up a Julia or Python
shell and run interactively there, or you can run scripts or programs at the command line. Interactive sessions
won’t end until you exit them or you come to the end of your time limit. Interactive jobs are very good for
testing, debugging, figuring out your workflow, or interactive data exploration. When you first port your code
to Satori, it can be helpful to first run it in an interactive session, so you can iteratively make edits and
rerun your code, without waiting for new resources each time. However, once you have a script that you are fairly
confident will run without need for intervention, it’s time to move on to a batch job.</p>
<p>Visit the <a class="reference external" href="https://mit-satori.github.io/satori-workload-manager-using-lsf.html#interactive-jobs" target="_blank">Interactive Jobs</a>
section to see how to start an interactive session using the exisitng LSF workload manager.</p>
<p><strong>Note</strong> Satori is in the process of being migrated to the SLURM Workload manager. Visit the <a class="reference external" href="https://mit-satori.github.io/satori-workload-manager-using-slurm.html#interactive-jobs" target="_blank">Interactive Jobs</a>
section to see how to start an interactive session using the new SLURM workload manager.
<strong>Note:</strong> More recent CUDA Drivers are only available on Slurm.</p>
</div>
<div class="section" id="running-batch-jobs">
<h3>Running Batch Jobs<a class="headerlink" href="#running-batch-jobs" title="Permalink to this headline">¶</a></h3>
<p>Batch jobs are the most common type of job on HPC clusters. You have a script or executable you’d like to run and
you submit that to the scheduler using a submission or batch script. From there, the scheduler will decide when
and where to run your script, and when your script comes to completion or runs into an error the job will end.</p>
<p>Visit the <a class="reference external" href="https://mit-satori.github.io/satori-workload-manager.html#batch-scripts" target="_blank">Batch Jobs</a>
section to see how to submit a batch job using the existing LSF workload manager , as well as some sample submission scripts and other information on monitoring batch jobs.</p>
<p><strong>Note</strong> Satori is in the process of being migrated to the SLURM Workload manager. Visit the <a class="reference external" href="https://mit-satori.github.io/satori-workload-manager-using-slurm.html#batch-scripts" target="_blank">Batch Jobs</a>
section to see how to submit a batch job using the new SLURM workload manager , as well as some sample submission scripts and other information on monitoring batch jobs.</p>
<p>One of the most common questions on batch jobs is how to know what is going on with them, how does the user
know if there is an error or monitor the output of the job. In your submission script you specify where you
want the errors and output for your job. Print statements in your code can be very useful for debugging or
for quickly checking the progress of a job. One handy command for watching these files is “tail” with the “-f”
option. This command will print the last few lines of a file, and with “-f” will wait and print new lines as
they are written to the file. For example:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>tail -f my_job.log-12345
</pre></div>
</div>
<p>Will print the output of the log file my_job.log-12345, where 12345 is the Job ID for this particular job. To
exit the “following” mode, press Ctrl+C.</p>
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