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=== Data analysis tools === |
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Computer simulations involve the use of a set of analysis tools. Here, we share notes and ideas on programs commonly used in the CSML. |
Computer simulations involve the use of a set of analysis tools. Here, we share notes and ideas on programs commonly used in the CSML. |
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* [[Autocorrelation]] |
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* [[Generic Analyzer]] |
* [[Generic Analyzer]] |
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* [[Gnuplot]] |
* [[Gnuplot]] |
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* [[Compressed data files]] |
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=== Programming === |
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* [[Compiler notes]] |
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* [[Debugging]] |
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* [[Programming notes]] |
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Ideally, we prepare manuscripts in [http://en.wikipedia.org/wiki/LaTeX LaTeX]. Occasionally, especially when collaborating with other research groups, it may be necessary to work in Microsoft Word. |
Ideally, we prepare manuscripts in [http://en.wikipedia.org/wiki/LaTeX LaTeX]. Occasionally, especially when collaborating with other research groups, it may be necessary to work in Microsoft Word. |
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* [[Notes on |
* [[Notes on using LaTeX for manuscripts]] |
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* [[Notes on Microsoft Word |
* [[Notes on using Microsoft Word for manuscripts]] |
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=== Job submission and scheduling === |
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* [[Notes on Torque]] |
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* [[Notes on Maui]] |
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=== UNIX === |
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* [http://www.linuxproblem.org/art_9.html Password-less login via ssh] |
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* Short version of password-less login: (1) go to your home folder (e.g. ariadne:~/ ). (2) type "ssh-keygen" and press the enter key a few times to leave all answers blank (unless you are prompted to override the existing key in which case you should type "yes"). (3) type "ssh-copy-id XX" , where "XX" is the server name or IP address you wish to ssh into and enter the password. You can repeat this step and add multiple addresses. (4) On servers running Open-SUSE (ariadne, minotaur, hydra) you should also copy the generated key to: "cp ~/.ssh/authorized_keys ~/.ssh/authorized_keys2 ". Re-login and voilà, no more password needed. The same procedure also works on a macOS. However, ssh-copy-id needs to be installed (e.g. via brew install ssh-copy-id) and step (4) should be skipped. |
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* [[Command-line interface on Linux/UNIX]] |
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=== Data visualization tools === |
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In order to communicate our research effectively, it is often useful to visualize the data from simulations. Here are a set of tools for creating/editing images and videos. |
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===== Visualizing Dump Files ===== |
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* [[VMD]] |
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* [[pymol]] |
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===== Handling image/video files ===== |
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* [[FFmpeg]] |
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=== Miscellaneous === |
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* [[Dropbox]] |
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* [[Clonezilla]] |
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Latest revision as of 10:28, 9 October 2019
Data analysis tools
Computer simulations involve the use of a set of analysis tools. Here, we share notes and ideas on programs commonly used in the CSML.
Programming
Document processing
Ideally, we prepare manuscripts in LaTeX. Occasionally, especially when collaborating with other research groups, it may be necessary to work in Microsoft Word.
Job submission and scheduling
UNIX
- Password-less login via ssh
- Short version of password-less login: (1) go to your home folder (e.g. ariadne:~/ ). (2) type "ssh-keygen" and press the enter key a few times to leave all answers blank (unless you are prompted to override the existing key in which case you should type "yes"). (3) type "ssh-copy-id XX" , where "XX" is the server name or IP address you wish to ssh into and enter the password. You can repeat this step and add multiple addresses. (4) On servers running Open-SUSE (ariadne, minotaur, hydra) you should also copy the generated key to: "cp ~/.ssh/authorized_keys ~/.ssh/authorized_keys2 ". Re-login and voilà, no more password needed. The same procedure also works on a macOS. However, ssh-copy-id needs to be installed (e.g. via brew install ssh-copy-id) and step (4) should be skipped.
- Command-line interface on Linux/UNIX
Data visualization tools
In order to communicate our research effectively, it is often useful to visualize the data from simulations. Here are a set of tools for creating/editing images and videos.