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institute_lorentz:xmaris [2022/06/10 08:40] – [Web access] lenocil | institute_lorentz:xmaris [2022/06/10 13:59] – [Installing extra software] lenocil | ||
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Xmaris services, that is terminal, scheduler/ | Xmaris services, that is terminal, scheduler/ | ||
- | {{ : | + | {{ : |
- | Similarly to a traditional shell access, Xmaris OpenOnDemand is available only for connections within the __IL intranet__. IL users who wish to access OpenOnDemand from their remote home locations could for example instruct their browsers to SOCKS-proxy their connections via our SSH server. | + | Similarly to a traditional shell access, Xmaris OpenOnDemand is available only for connections within the __IL intranet__. IL users who wish to access OpenOnDemand from their remote home locations could for example |
- | Open a local terminal and type | + | Open a local terminal and type (substitute username with your IL username) |
<code bash> | <code bash> | ||
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* Submit batch jobs to the slurm scheduler/ | * Submit batch jobs to the slurm scheduler/ | ||
* Open a terminal. | * Open a terminal. | ||
- | * Launch interactive jupyter notebooks. | + | * Launch interactive |
* Monitor cluster usage. | * Monitor cluster usage. | ||
* Create and launch your very own OnDemand application (read [[https:// | * Create and launch your very own OnDemand application (read [[https:// | ||
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|maris075 |gpuIntel|2 x Nvidia Tesla P100 16GB | 6.0| | |maris075 |gpuIntel|2 x Nvidia Tesla P100 16GB | 6.0| | ||
- | Use the '' | + | Xmaris GPUs must be allocated using slurm' |
+ | <code bash> | ||
+ | srun -p gpuIntel --gres=gpu: | ||
+ | </ | ||
===== Xmaris scientific software ===== | ===== Xmaris scientific software ===== | ||
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Any pre-installed software can be made available in your environment via the '' | Any pre-installed software can be made available in your environment via the '' | ||
- | It is possible to save a list of modules you use often in a //module collection// | + | It is possible to save a list of modules you use often in a //module collection// |
<code bash> | <code bash> | ||
module load mod1 mod2 mod3 mod4 mod5 mod6 | module load mod1 mod2 mod3 mod4 mod5 mod6 | ||
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|TensorFlow-1.15.0-Miniconda3/ | |TensorFlow-1.15.0-Miniconda3/ | ||
- | To create | + | The following example shows how you can create a tensorflow-aware jupyter |
<code bash> | <code bash> | ||
- | # only on maris075 (GPU node) | + | # We use maris075 (GPU node) and load the optimised tf module |
ml load TensorFlow/ | ml load TensorFlow/ | ||
- | pip install --user | + | |
- | pip install --user jupyter-client==5.3.1 | + | # We install ipykernel, because necessary to run py notebooks |
- | ipython kernel install | + | python -m pip install |
+ | |||
+ | # We create a kernel called TFQuantum based on python from TensorFlow/ | ||
+ | python -m ipykernel | ||
+ | |||
+ | # We edit the kernel such that it does not execute python directly | ||
+ | # but via a custom wrapper script | ||
+ | cat $HOME/ | ||
+ | |||
+ | { | ||
+ | " | ||
+ | "/ | ||
+ | "-m", | ||
+ | " | ||
+ | " | ||
+ | " | ||
+ | ], | ||
+ | " | ||
+ | " | ||
+ | " | ||
+ | " | ||
+ | } | ||
+ | } | ||
+ | |||
+ | # The wrapper script will call python but only after loading any | ||
+ | # appropriate module | ||
+ | cat / | ||
+ | |||
+ | #!/bin/env bash | ||
+ | ml load TensorFlow/ | ||
+ | |||
+ | exec python $@ | ||
+ | |||
+ | # DONE. tfquantum will appear in the dropdown list of kernels | ||
+ | # upon creating a new notebook | ||
</ | </ | ||
- | When launching a jupyter notebook remember to specify '' | + | |
=== TensorFlow with Graphviz === | === TensorFlow with Graphviz === | ||
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* via a traditional // | * via a traditional // | ||
- | Whatever installation method you might choose, please note that you do not have administrative rights to the cluster. | + | Whatever installation method you might choose, please note that you **do not have** administrative rights to the cluster. |
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</ | </ | ||
- | :!: The environment variable '' | + | |:!: The environment variable '' |
- | ml|here]]. | + | ml|here]].| |
- | :!: When compiling OpenBLAS it is not sufficient to define '' | + | |:!: When compiling OpenBLAS it is not sufficient to define '' |
Then execute | Then execute | ||
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to make available to the '' | to make available to the '' | ||
- | :!: '' | + | |:!: '' |
Should you want to customise the building process of a given software please read how to implement [[https:// | Should you want to customise the building process of a given software please read how to implement [[https:// |