User contributions for Adk44

13 May 2019

• 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
• 12:3212:32, 13 May 2019 diff hist +6,504‎ N Tardis scheduling policy ‎ Created page with "We appear to need to take another look at tardis's scheduling policy. Greg and Catherine would like everyone to agree on a policy and then give it a reasonable trial before st..." current
• 12:3212:32, 13 May 2019 diff hist +313‎ N See unpacked nodes ‎ Created page with "To do this, type: diagnose -n | grep 'Running' | awk '{print $1, $3}' I'm curious as to why this is useful, can you explain? --Catherine 13:41, 27 August 2..." current
• 12:3112:31, 13 May 2019 diff hist +3,763‎ N Remastering Knoppix ‎ Created page with "Quick notes on how I made a remastered Knoppix for David Wales. Closely based on an article by Robert Bernier at linuxdevcenter.com but updated for a newer Knoppix. This ass..." current
• 12:3112:31, 13 May 2019 diff hist +1,135‎ N Rama upgrade ‎ Created page with "Rama needs upgrading to a supported operating system. SLES10 looks like a good choice as it will last for the rest of the machine's natural life. Things that will change: *..." current
• 12:3012:30, 13 May 2019 diff hist +3,179‎ N Proposed changes to backup and archiving ‎ Created page with "==Current systems== We need more backup space as workstation disks are getting larger and we have acquired several more clusters. We currently have about 3Tb split over t..." current
• 12:3012:30, 13 May 2019 diff hist +2,197‎ N Porfuncs Documentation ‎ Created page with "Various system functions are included in the porfuncs module, generated from porfuncs.sh. They are documented here as a reference for developers. Please use these subroutines,..." current
• 12:2912:29, 13 May 2019 diff hist +392‎ N Other IT stuff ‎ Created page with "Made this page so I can provide links to older IT pages and not clutter up the 'headlines' on the front page. * New mek-quake * Backup strategy * Proposed changes..." current
• 12:2912:29, 13 May 2019 diff hist +2,756‎ N Optimization tricks ‎ Created page with "== Profiling == * Compile your code with pgf90 and the following flags: FFLAGS= -Mextend -g -traceback -pg * Run GMIN on your input. Note that gmon.out is produced. * Run..." current
• 12:2812:28, 13 May 2019 diff hist +4,577‎ N NECI Parallelization ‎ Created page with "It seems that there are two main aims of NECI Parallelization * To Reduce Integral Cache storage needs (and also to therefore compute the stored integrals in parallel) * To Su..." current
• 12:2812:28, 13 May 2019 diff hist +1,532‎ N Migrating to the new SVN server ‎ Created page with "All of these steps assume you put the repository in ~/svn so modify as needed! * update your local copy (important! If this doesn't work, it means the old server has been tak..." current
• 12:2812:28, 13 May 2019 diff hist +3,996‎ N Mercurial ‎ Created page with "== General introduction == Mercurial is what you call a distributed version management system. That means, you have a local copy of the repository (including the full history)..." current
• 12:2712:27, 13 May 2019 diff hist +891‎ N Torque and Maui ‎ Created page with "Notes on local use of Torque and Maui. Probably not much in here for end users, unless you're very curious. == Environment passing == Weirdism: qsub -v PATH does not work o..." current
• 12:2712:27, 13 May 2019 diff hist +698‎ N Maui compilation ‎ Created page with "It's 7/6/06 at time of writing On new mek-quake torque-2.1 does not work with current Maui because they have chnaged the libraries from libpbs.a to libtorque.a . Found a patc..." current
• 12:2612:26, 13 May 2019 diff hist +195‎ N New mek-quake ‎ Created page with "This is a large cluster system to be used by the Wales and Vendruscolo groups. Differences from Clust Mek-quake initial setup notes Maui compilation Mek-qua..." current
• 12:2612:26, 13 May 2019 diff hist +1,052‎ N Mek-quake initial setup notes ‎ Created page with "So far: * PBS set up with Maui (see Maui compilation) * Modules mainly there although probably a few bugs left * Prologue and epilogue working OK (and safe for concurrenc..." current
• 12:2612:26, 13 May 2019 diff hist +3,235‎ N Mek-quake Queueing system ‎ Created page with "Please write your thoughts about the mek-quake queueing system here. And please sign your posts! --Catherine 16:26, 21 June 2006 (BST) My thoughts are that w..." current
• 12:2512:25, 13 May 2019 diff hist +2,842‎ N Lapack compilation ‎ Created page with "I had some problems using the atlas modules, which seem to be not applicable to all machines (e.g. 64-bit P4s). I compiled my own lapack routines (available from [http://www...." current
• 12:2512:25, 13 May 2019 diff hist +825‎ N LDAP plans ‎ Created page with "== LDAP Plans == None of this is set in stone, although it is now looking like it will actually happen. why? * authentication of users (initially so they can share passwor..." current
• 12:2412:24, 13 May 2019 diff hist +1,225‎ N Intel Trace Analyzer and Collector ‎ Created page with "This is a thing that came as part of the Intel cluster toolkit on zero but I am still figuring out how to use it, sp these are rough notes. module add itac mpicc -trace -o..." current
• 12:2412:24, 13 May 2019 diff hist +464‎ N Fixing thunderbird links ‎ Created page with "Under suse 10.2 on steelhorn clicking on URL's in emails ceased to open the link in firefox. To fix this you need to add the following lines to your ~/.thunderbird/<xxxxxxxx>...." current
• 12:2312:23, 13 May 2019 diff hist −29‎ Comprehensive Contents Page ‎ →‎Miscellaneous
• 12:2212:22, 13 May 2019 diff hist +265‎ N Differences from Clust ‎ Created page with "* Scheduling done by the core rather than the node, so you can run single-core jobs. * Queue names consequently different * node scratch filesystems available under /nodescrat..." current
• 12:2212:22, 13 May 2019 diff hist +1,734‎ N Decoding heat capacity curves ‎ Created page with "This is a short introduction on how to analyse and decode heat capacity curve features (D.J. Wales ''Phys. Rev. E'' '''95''', 030105(R), 2017). After creating your data base..."
• 12:2212:22, 13 May 2019 diff hist +2,756‎ N Computing values only once ‎ Created page with "== Profiling == * Compile your code with pgf90 and the following flags: FFLAGS= -Mextend -g -traceback -pg * Run GMIN on your input. Note that gmon.out is produced. * Run..." current
• 12:2112:21, 13 May 2019 diff hist +346‎ N Computer Office services ‎ Created page with "This has moved to [http://hogthrob.ch.cam.ac.uk/mediawiki/index.php?title=Computer_Officer_Services the COs' wiki]. COs only! And even more recently, this has gone public on..." current
• 12:2112:21, 13 May 2019 diff hist 0‎ N File:Chain crossing.png ‎No edit summary current
• 12:2012:20, 13 May 2019 diff hist +124‎ N Chain crossing ‎ Created page with "File:chain_crossing.png Example of a path containing two chain-crossings. Coarse-grained C-alpha model with SB keyword." current
• 12:2012:20, 13 May 2019 diff hist +3,990‎ N Backup strategy ‎ Created page with "Thoughts about our backup strategy. We currently back up via home grown scripts to JBODs and that works very well. We have no central fileserver and there is no political sup..." current
• 12:1912:19, 13 May 2019 diff hist +1,659‎ N Parameter-scanning script ‎ Created page with "<pre> #!/bin/csh # need data.template, qsub.template and input.*.crd in the top level directory (from which this script is run) # as well as all the other necessary files fo..." current
• 12:1812:18, 13 May 2019 diff hist +17,962‎ N Computing CHARMM FF energy using GMIN, MMTSB and CHARMM ‎ Created page with "Below script (compare.sh) computes the Charmm FF energy of the same structure. Useful for cross-validating force field settings in GMIN data file, CHARMM input file and MMTSB..." current