institute_lorentz:xmaris
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| institute_lorentz:xmaris [2022/06/10 07:56] – [Compute nodes data disks] lenocil | institute_lorentz:xmaris [2022/06/10 12:47] – [Installing extra software] lenocil | ||
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| xmaris users are strongly advised they delete (or at least move to the shared data disk), if any, their data from the compute nodes scratch disks upon completion of their calculations. All data on the scratch disks __might be cancelled without prior notice__. | xmaris users are strongly advised they delete (or at least move to the shared data disk), if any, their data from the compute nodes scratch disks upon completion of their calculations. All data on the scratch disks __might be cancelled without prior notice__. | ||
| - | The home disk ''/ | + | Note that **disk policies might change at any time at the discretion of the cluster owners**. |
| ---- | ---- | ||
| + | Please also note the following | ||
| + | * xmaris' | ||
| + | * The **OLD** (as in the old maris) ''/ | ||
| - | :!: **All data** on the scratch partitions is assumed to be temporary and will be **deleted** upon a node re-installation. | ||
| - | :!: When usisng xmaris please note that the home partition | ||
| - | |||
| - | :!: The **OLD** (as in the old maris) ''/ | ||
| ==== Xmaris usage policies ==== | ==== Xmaris usage policies ==== | ||
| - | Usage policies are updated regularly in accordance with the needs of the cluster owners and **may change at any time without notice**. At the moment there is an __enforced usage limit of 128 CPUs per user__ that does not apply to the owners. Job execution priorities are defined via a complex [[https:// | + | Usage policies are updated regularly in accordance with the needs of the cluster owners and **may change at any time without notice**. At the moment there is an __enforced usage limit of 128 CPUs per user__ that does not apply to the owners. Job execution priorities are defined via a complex [[https:// |
| <code bash> | <code bash> | ||
| scontrol show config | grep -i priority | scontrol show config | grep -i priority | ||
| Line 80: | Line 79: | ||
| * execute slurm' | * execute slurm' | ||
| - | * visit https:// | + | * browse to https:// |
| - | :!: The link above is accessible only within the IL workstations network. | ||
| ===== How to access Xmaris ===== | ===== How to access Xmaris ===== | ||
| Access to Xmaris is not granted automatically to all Lorentz Institute members. Instead, a preliminary approval must be granted to you by the cluster owners (read [[|here]]). | Access to Xmaris is not granted automatically to all Lorentz Institute members. Instead, a preliminary approval must be granted to you by the cluster owners (read [[|here]]). | ||
| Line 88: | Line 87: | ||
| Once you have been authorised to use Xmaris, there are two ways to access its services: | Once you have been authorised to use Xmaris, there are two ways to access its services: | ||
| - | - using an ssh client | + | - using a web browser |
| - | - using a web browser | + | - using an SSH client |
| + | |||
| - | Both methods can provide terminal access, but connections via web browsers offer you extra services such as sftp (drag-and-drop file transfers) | + | Both methods can provide terminal access, but connections via web browsers offer you extra services such as sftp (drag-and-drop file transfers), jupyter interactive notebooks, virtual desktops and more at the click of your mouse. **We advise** all users either |
| ==== Access via an ssh client ==== | ==== Access via an ssh client ==== | ||
| Line 97: | Line 97: | ||
| The procedure differs on whether you try to connect with a client connected to the IL intranet or not. | The procedure differs on whether you try to connect with a client connected to the IL intranet or not. | ||
| - | * When within the IL network, for instance if you are using a Lorentz Institute workstation, | + | * When within the IL network, for instance if you are using a Lorentz Institute workstation, |
| <code bash> | <code bash> | ||
| Line 110: | Line 110: | ||
| - | :!: If you were a maris user prior to the configuration switch to xmaris, you might find out that many terminal functions and programs could not be working as expected. This is due to the presence in your xmaris home directory of old shell initialisation scripts still tied to the STRW sfinx environment. You can override them (preferably after making a backup copy) by replacing their contents with the default CentOS shell initialisation scripts, for instance for bash these are located in ''/ | + | |:!: If you were a maris user prior to the configuration switch to xmaris, you might find out that many terminal functions and programs could not be working as expected. This is due to the presence in your xmaris home directory of old shell initialisation scripts still tied to the STRW sfinx environment. You can override them (preferably after making a backup copy) by replacing their contents with the default CentOS shell initialisation scripts, for instance for bash these are located in ''/ |
| ==== Web access ==== | ==== Web access ==== | ||
| 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> | ||
| Line 132: | Line 132: | ||
| * 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:// | ||
| Line 153: | Line 153: | ||
| |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 ===== | ||
| Line 190: | Line 193: | ||
| 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 | ||
| Line 206: | Line 209: | ||
| |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 === | ||
| Line 235: | Line 273: | ||
| * 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. |
| Line 263: | Line 301: | ||
| </ | </ | ||
| - | :!: 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 | ||
institute_lorentz/xmaris.txt · Last modified: 2024/02/29 14:16 by jansen
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