Mathematical Biophysics
Understanding living systems
Differences
This shows you the differences between two versions of the page.
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i:placenta:data [2020/04/30 10:54] Igor Chernyavsky [Mounting misc Remote file systems on Linux] |
i:placenta:data [2022/03/07 13:23] (current) Igor Chernyavsky [Running COMSOL] |
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| Line 105: | Line 105: | ||
| | c | cs3 | 8 | 3.3 GHz (Intel Xeon E5-2643) | 128 | | | | c | cs3 | 8 | 3.3 GHz (Intel Xeon E5-2643) | 128 | | | ||
| | d | cs4 | 8 | 3.3 GHz (Intel Xeon E5-2643) | 128 | | | | d | cs4 | 8 | 3.3 GHz (Intel Xeon E5-2643) | 128 | | | ||
| - | | e | cs5 | 12 | 2.5 GHz (Inter Xeon E5-2430v2) | 128 | | | + | | e | cs5 | 12 | 2.5 GHz (Inter Xeon E5-2430v2) | 128 | [offline] | |
| | f | cs6 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 128 | | | | f | cs6 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 128 | | | ||
| | g | cs7 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 128 | | | | g | cs7 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 128 | | | ||
| | h | cs8 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 128 | | | | h | cs8 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 128 | | | ||
| - | | i | cs9 | 16 | 3.0 GHz (Intel Xeon E5-2623v3) | 256 | | | + | | i | cs9 | 8 (x2) | 3.0 GHz (Intel Xeon E5-2623v3) | 256 | | |
| - | | j | cs10 | 16 | 3.0 GHz (Intel Xeon E5-2623v3) | 256 | | | + | | j | cs10 | 8 (x2) | 3.0 GHz (Intel Xeon E5-2623v3) | 256 | no COMSOL | |
| - | | k | cs11 | 32 | 3.0 GHz (AMD Opteron 6220) | 256 | CPU-intensive | | + | | k | cs11 | 12 (x2) | 3.4 GHz (Intel Xeon 6128) | 1280 | CPU- & Memory-intensive; no COMSOL | |
| - | | l | cs12 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 192 | | | + | | l | cs12 | 12 | 2.5 GHz (Intel Xeon E5-2430v2) | 192 | | |
| - | | | citadel | 8 (x2) | 3.4 GHz (Intel Xeon E5-1680v4) | 256 | GPU-intensive (Nvidia GTX1080 8GB 1.6GHz) | | + | | m | cs13 | 56 (x2) | 2.2 GHz (Intel Xeon 6238R) | 1024 | CPU- & Memory-intensive; 892GB SSD (/tmp) | |
| + | | n | cs14 | 56 (x2) | 2.2 GHz (Intel Xeon 6238R) | 1024 | CPU- & Memory-intensive; 892GB SSD (/tmp) | | ||
| + | | | minerva | 20 (x2) | 2.2 GHz (Intel Xeon 4114) | 1536 | Memory- & GPU-intensive (2x Nvidia P100 16GB); 2 TB HDD | | ||
| + | | | citadel | 8 (x2) | 3.4 GHz (Intel Xeon E5-1680v4) | 256 | Visualisation & GPU-intensive (Nvidia GTX1080 8GB); 8 TB HDD | | ||
| - | Note that all CS cores run in a single-thread mode (HT is switched off). | + | Note that cs1-cs8 cores run in a single-thread mode (HT is switched off). |
| Line 134: | Line 137: | ||
| <code> | <code> | ||
| - | $ module load comsol53 | + | $ module load COMSOL/5.6 #or COMSOL/6.0 |
| $ comsol & | $ comsol & | ||
| </code> | </code> | ||
| + | |||
| + | **Note 1**: If there are errors related to OpenGL, try | ||
| + | <code> | ||
| + | $ comsol -3drend sw & | ||
| + | </code> | ||
| + | |||
| + | **Note 2**: COMSOL is //not// available on compute servers ''cs10'' and ''cs11''. | ||
| + | |||
| + | **Note 3**: You could check available software versions by | ||
| + | <code> | ||
| + | $ module avail | ||
| + | </code> | ||
| + | |||
| + | To install COMSOL on a self-managed PC or laptop, download the [[https://livemanchesterac-my.sharepoint.com/:u:/g/personal/chris_paul_manchester_ac_uk/EUu_mH4g5TxOj2Zj02jPpdYBN5fD0RfE5BK9lPLB0RzF7Q?e=4%3aD1k4ox&at=9 | distributive [6 GB]]] (multi-platform ISO disk image, supporting Linux, MacOS and Windows) and use the following details during the setup: | ||
| + | <code>licence port@hostname: 15700@lfarm4.eps.manchester.ac.uk; licence number: 7076735</code> | ||
| ==== Running MATLAB ==== | ==== Running MATLAB ==== | ||
| Line 146: | Line 164: | ||
| + | ==== Other software ==== | ||
| + | |||
| + | [[https://manchester.saasiteu.com/Modules/SelfService/#knowledgeBase/view/AFC87036FF584A79ABFABA678D76FBA7 | ||
| + | | GraphPad Prism 8.0 Installer]] - see instructions. | ||
| + | |||
| + | [[http://www.itservices.manchester.ac.uk/software/ | UoM Research Software Repository]] | ||
| + | |||
| + | **Note**: When running your code at the University compute cluster (known as Computational Shared Facility, [[http://ri.itservices.manchester.ac.uk/csf3 | CSF]]), use the following to enable Internet access (e.g. to install necessary packages for Julia, Python, R, etc.): | ||
| + | <code> | ||
| + | module load tools/env/proxy | ||
| + | </code> | ||
| - | <div rightalign>--- //Igor Chernyavsky, 2019/07/15 18:00// ---</div> | + | <div rightalign>--- //Igor Chernyavsky, 2021/07/22 15:00// ---</div> |
| Line 178: | Line 207: | ||
| fusermount -u ~/Shared/Dropbox/ | fusermount -u ~/Shared/Dropbox/ | ||
| </code> | </code> | ||
| - | For uploading a large file (>~ 10GB) or multiple files, use [[https://github.com/andreafabrizi/Dropbox-Uploader|Dropbox-Uploader]] script: | + | For uploading a large file (>~ 10GB) or multiple files, use [[https://github.com/andreafabrizi/Dropbox-Uploader|dropbox_uploader]] script: |
| <code> | <code> | ||
| ./dropbox_uploader -s -p upload /LOCAL_FOLDER /REMOTE_FOLDER | ./dropbox_uploader -s -p upload /LOCAL_FOLDER /REMOTE_FOLDER | ||
