User contributions for Adk44

13 May 2019

• 13:0513:05, 13 May 2019 diff hist 0‎ N File:Group compare.png ‎No edit summary current
• 13:0513:05, 13 May 2019 diff hist 0‎ N File:Hbond group6.png ‎No edit summary current
• 13:0413:04, 13 May 2019 diff hist 0‎ N File:Naotvside18.png ‎No edit summary current
• 13:0313:03, 13 May 2019 diff hist 0‎ N File:Naotvtop18.png ‎No edit summary current
• 13:0213:02, 13 May 2019 diff hist 0‎ N File:Tzwithoutgr.png ‎No edit summary current
• 13:0113:01, 13 May 2019 diff hist 0‎ N File:Tzwithgr.png ‎No edit summary current
• 13:0013:00, 13 May 2019 diff hist 0‎ N File:Chriscleanroom1.jpg ‎No edit summary current
• 12:5812:58, 13 May 2019 diff hist +1,762‎ N Victor Ruehle ‎ Created page with "Here is a collection of wiki pages I find usefule or am working on: == General == * Mercurial * Wales Group Fortran conventions for group software == Crystal struc..." current
• 12:5712:57, 13 May 2019 diff hist 0‎ N File:Km591 twz3.jpg ‎No edit summary current
• 12:5612:56, 13 May 2019 diff hist 0‎ N File:Km591 twz1.png ‎No edit summary current
• 12:5612:56, 13 May 2019 diff hist 0‎ N File:Km591 twz2.jpg ‎No edit summary current
• 12:5412:54, 13 May 2019 diff hist +2,539‎ N User:Ab2111 ‎ Created page with "== Current projects == === Torsional movesets for biomolecules: Biased Gaussian Sampling === Favrin et. al have developed a movecass for MC simulations of biomolecules: [htt..." current
• 12:5312:53, 13 May 2019 diff hist −2‎ Main Page ‎ →‎Comprehensive Contents Page
• 12:5312:53, 13 May 2019 diff hist −2‎ Main Page ‎ →‎Group Members Only
• 12:5212:52, 13 May 2019 diff hist +230‎ N SuSE 11.1 ‎ Created page with "== Notes on SuSE 11.1 for workstations == === compilers === * pgi - even 8.0 only supports suse 10.3 (and sles 11 which is based on opensuse 11.1) * intel * pathscale - sles..." current
• 12:5212:52, 13 May 2019 diff hist +5,291‎ N SuSE 10.3 workstation image ‎ Created page with "It is time to produce a spec for the next generation of the workstation image. This is to be based on SuSE 10.3 as 11.0 is too new for compiler support. We also considered Ubu..." current
• 12:5112:51, 13 May 2019 diff hist +2,396‎ N SuSE 10.2 workstation image ‎ Created page with "The SuSE 10.1 workstation image is rolled out and working; it's time to start worrying about 10.2 == Improvements in 10.2 == * LDAP support: your password will be your L..." current
• 12:5012:50, 13 May 2019 diff hist +3,466‎ N SuSE 10.1 workstation image ‎ Created page with "We need a new workstation image as SuSE 9.3 won't be supported for very much longer (ends Easter 2007). In order that I don't have to do this this again in six months I'm goin..." current
• 12:5012:50, 13 May 2019 diff hist +1,451‎ N Upgrading sword ‎ Created page with "This happened, so I leave this page here only for reference. Sword needs an upgrade. I'd like to move it to SuSE 9.3. The destiny upgrade went OK, whic..." current
• 12:5012:50, 13 May 2019 diff hist +898‎ N Upgrading destiny ‎ Created page with "Destiny is to be upgraded to SuSE and at the same time have a new disk installed to give a bigger /scratch and /usr/local. I will be withdrawing CRYSTAL98 and Portland versio..." current
• 12:4912:49, 13 May 2019 diff hist +4,126‎ N Blacklisting Compilers ‎ Created page with "Some compiler versions just don't work with our code. This might be due to a bug in the compiler, or maybe the compiler version is too old and doesn't include the features we..." current
• 12:4912:49, 13 May 2019 diff hist +7,696‎ N Compiler Flags ‎ Created page with "This page serves as documentation for the mysterious compiler flags: please keep it up to date. It includes a description of what each flag does and a list of flags in use for..." current
• 12:4812:48, 13 May 2019 diff hist −29‎ Comprehensive Contents Page ‎ →‎Miscellaneous/uncategorised
• 12:4812:48, 13 May 2019 diff hist −1,512‎ Comprehensive Contents Page ‎ →‎Group practice
• 12:4612:46, 13 May 2019 diff hist +2,417‎ N Uploading non image files to the wiki ‎ Created page with "For security reasons, the 'Upload file' functionality of the wiki only lets you upload images with .png, .gif, .jpg and .jpeg extensions. This can be a bit of a pain when you..." current
• 12:4612:46, 13 May 2019 diff hist +2,086‎ N Printing files from the command line using 'lpr' ‎ Created page with "You cannot print files directly from one of the clusters so the first thing you need to do is transfer the file to your workstation. This can be done using the ''scp'' command..." current
• 12:4612:46, 13 May 2019 diff hist +436‎ N Finding bugs in latex documents that will not compile ‎ Created page with "When you try to compile a latex document that contains an error - the compilation will halt with an (often cryptic) error message and a '''?''' prompt. At this point, you can..." current
• 12:4512:45, 13 May 2019 diff hist +77‎ N Running programs in the background ‎ Created page with "To run a job in the background, type & after your command, i.e. [command] &" current
• 12:4512:45, 13 May 2019 diff hist +320‎ N Installing packages on your managed CUC3 workstation ‎ Created page with "Although we don't have access to apt-get, or the package management application in Ubuntu, it appears you are able to access the 'aptitude' package manager still using sudo: <..." current
• 12:4412:44, 13 May 2019 diff hist +5,661‎ N A guide to using SLURM to run GPU jobs on pat ‎ Created page with "We now have a queueing system set up for use with some of our GPU machines. The head node is pat.ch.private.cam.ac.uk and all jobs should be submitted to the queue from there...." current
• 12:4412:44, 13 May 2019 diff hist +2,209‎ N A guide to using SLURM to run PATHSAMPLE ‎ Created page with "Below are two example submission scripts for running PATHSAMPLE jobs on clusters using the SLURM queueing system, e.g. volkhan and sinister. Keyword SLURM can be used to launc..." current
• 12:4312:43, 13 May 2019 diff hist +1,164‎ N Identifying job on a node ‎ Created page with "Sometimes it may happen that on some node you have more than one job running and only one among them you need to kill. How find which one it is? If you only know which output..." current
• 12:4312:43, 13 May 2019 diff hist +4,493‎ N Submitting jobs, interactively or to a cluster queue system ‎ Created page with "This is a brief summary for those who haven't found/read the [http://www-co.ch.cam.ac.uk/facilities/compute-servers/theory/maui/maui-pbs-introduction.html documentation] provi..." current
• 12:4212:42, 13 May 2019 diff hist +1,222‎ N Removing an excessive number of files from a directory - when 'rm' just isn't enough ‎ Created page with "If you have say 10000 files, all named ''output.[number]'', trying to get rid of them all with the usual ''rm output.*'' command won't work as when you expand the * to produce..." current
• 12:4212:42, 13 May 2019 diff hist +1,157‎ N Conversion between different image file formats ‎ Created page with "The ''convert'' command is an extremely powerful way of changing an image into a different format, or modifying it in ways you never thought possible! It is only available on..." current
• 12:4212:42, 13 May 2019 diff hist +1,056‎ N Conversion between different data file formats ‎ Created page with "==== For AMBER ==== xyz -> inpcrd awk '{printf("%12.7f %11.7f %11.7f "), $1, $2, $3} {getline} {printf("%11.7f %11.7f %11.7f\n"), $1, $2, $3}' input.xyz > input.inpcr..." current
• 12:4112:41, 13 May 2019 diff hist +162‎ N Using tar and gzip to compress/uncompress files ‎ Created page with "Compress with bzip2 directory temp tar cvfj temp.tar.bz temp Uncompress with bzip2 directory temp tar xvfj temp.tar.bz Cat compressed file bzcat temp.bz" current
• 12:4012:40, 13 May 2019 diff hist +1,244‎ N Sorting a file by multiple columns ‎ Created page with "If you have a file you want to sort using multiple columns of numbers, the ''sort'' command is your new best friend! For example, here is a section from a file I'm trying to..." current
• 12:4012:40, 13 May 2019 diff hist +10,094‎ N Short 'awk' examples ‎ Created page with "The examples below were prepared by Eric Pement and taken from this [http://www.student.northpark.edu/pemente/awk/awk1line.txt web page]. As the ''awk'' syntax is so....random..." current
• 12:3912:39, 13 May 2019 diff hist +4,095‎ N Quick guide to awk ‎ Created page with "== Introduction == awk is useful for combining regular expressions with editing and other functions so that you can easily modify text files with conditional flow control. T..." current
• 12:3912:39, 13 May 2019 diff hist +18,380‎ N Short 'sed' examples ‎ Created page with "The examples below were prepared by Eric Pement and taken from this [http://sed.sourceforge.net/sed1line.txt web page]. A detailed description can be found [http://www.gnu.org..." current
• 12:3812:38, 13 May 2019 diff hist +1,094‎ N Mounting sharedscratch locally ‎ Created page with "Thanks to Phil in Computer Support for this: 1) If you're not on a computer within the theory sector, first you'll need to set up the VPN client as instructed [http://www-co...." current
• 12:3812:38, 13 May 2019 diff hist +720‎ N Using 'ssh-keygen' to automatically log you into clusters from your workstation ‎ Created page with "== Using ssh-copy-id == Just run the command ssh-copy-id [user@]machine for example, to ssh and scp to clust from your workstation, just issue the command ssh-copy-id clu..." current
• 12:3712:37, 13 May 2019 diff hist +1,341‎ N Transfering files to and from your workstation ‎ Created page with "First off you should only be using programs that use the ssh libraries for transferring files. Furthermore you should not be using a system that allows rcp or rlogin because t..." current
• 12:3712:37, 13 May 2019 diff hist +1,811‎ N Setting up aliases to quickly log you in to a different machine ‎ Created page with "== Using ssh config == Create the file ''~/.ssh/config'' if it does not exists. Set up the config file. There are lots of guides around. Say you want to log into sinister unde..." current
• 12:3612:36, 13 May 2019 diff hist +427‎ N Bash history searching ‎ Created page with "I learned these commands from looking over David's shoulder and have found them very useful. ===Search bash history=== A very useful way to quickly repeat a previous command,..." current
• 12:3612:36, 13 May 2019 diff hist +115‎ N Bash loop tricks ‎ Created page with "===Simple counter loop=== <pre> for ((i=1; i <= $max ; i++)) do echo $i done </pre> $max can be a number also." current
• 12:3612:36, 13 May 2019 diff hist +950‎ N Piping and redirecting output from one command or file to another ‎ Created page with "Piping entails sending standard output to the standard input of a linux command. Pipes are the primary power of using the command line. They can be used with sed, awk, perl,..." current
• 12:3512:35, 13 May 2019 diff hist +3,796‎ N Basic linux commands everyone should know! ‎ Created page with "Here are a few simple linux commands that should make life a bit easier for you. Please everyone, add anything you think would be useful! You may want to read the computer of..." current
• 12:3312:33, 13 May 2019 diff hist +831‎ N Zippo Sicortex machine ‎ Created page with "Please record useful notes about the new SiCortex machine here. == Specifying nodes == A node specific hello world program: <pre> $ cat hosthello.c #include <unistd.h> #inc..." current