User contributions for Adk44
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13 May 2019
- 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
- 12:1812:18, 13 May 2019 diff hist +587 N David's .inputrc file Created page with "This will reduce your typing. It sets up ESC then . as the last item on the previous line and ESC then , and backward search in history matching the start of what you have alr..." current
- 12:1712:17, 13 May 2019 diff hist +1,116 N Recommended bash aliases Created page with "~wales/.bashalias Copying ~wales/.inputrc to your home directory will also reduce your typing. It sets up ESC then . as the last item on the previous line and ESC then , and..." current
- 12:1712:17, 13 May 2019 diff hist +1,658 N Pdb to movie.py Created page with " #! /usr/bin/env python """ Calculates the movieseg or a OPTIM coord file from a given PDB file arguments: 50 format('CA: ',3(f8.3,1x),'CB: ',3(f8..." current
- 12:1612:16, 13 May 2019 diff hist +996 N Colourdiscon.py Created page with "Script useful for DISCONNECTIVITY users To do this save the code in ''colourdiscon.py'' file, change privileges of this file: chmod 755 colourdiscon.py and type: ./Colou..." current
- 11:1611:16, 13 May 2019 diff hist +4,201 N Local rigid body in OPTIM Created page with "Here we describe our implementation of local rigid body in OPTIM. ---- POTENTIAL ---- Currently I have only done this for CHARMM and NAB only. ---- MAKEIMAGE ---- Currently..." current
- 11:1611:16, 13 May 2019 diff hist +3,260 N Local Rigid Body Framework Created page with "== Introduction == In this framework you can group arbitrary sets of atoms into rigid bodies. It currently works only in GMIN, but I will soon implement this in OPTIM too. You..." current
- 11:1611:16, 13 May 2019 diff hist +20,574 N Rigid body input files for proteins using genrigid-input.py Created page with "== Overview == The use of rigid bodies requires two files: the rbodyconfig file (definition of rigid bodies) and the coordsinirigid file. The genrigid-input.py creates those f..." current
- 11:1511:15, 13 May 2019 diff hist +1,682 N Automatic Rigid Body Grouping Created page with "== Introduction == For large systems, grouping the rigid bodies can be tedious and painful. I intend to automate this with a pdb file as an input. Unfortunately depending on f..." current
- 11:1511:15, 13 May 2019 diff hist +3,152 N Computing normal modes in angle-axis Created page with "On this page I will describe how you can compute normal modes in angle-axis framework. It is likely that you may have to implement your own potential (until rigid body sandbox..." current
- 11:1411:14, 13 May 2019 diff hist +1,040 N Angle-axis framework Created page with "= Introduction = In the angle-axis framework, rotations are described by a vector of rotation, while its magnitude is the angle of rotation. A good review on rotations in gene..." current
- 11:1411:14, 13 May 2019 diff hist +5,958 N GenCoords Models Created page with "The following parametric models are defined for use with the GenCoords program. The parameters listed here are specified at run time as param1, param2, ..., paramNp in an..." current
- 11:1311:13, 13 May 2019 diff hist +2,149 N GenCoords Created page with "GenCoords is a Fortran program to generate arbitrary arrangements of ellipsoids interacting with the paramonov-yaliraki potential. A series of user defined parametric mode..." current
- 11:1311:13, 13 May 2019 diff hist +1,853 N Gencoords Created page with "GenCoords is a Fortran program to generate arbitrary arrangements of ellipsoids interacting with the paramonov-yaliraki potential. A series of user defined parametric mode..." current
- 11:1311:13, 13 May 2019 diff hist +1,544 N Ellipsoid.xyz Created page with "The ellipsoid.xyz file is the output of GMIN when using the PY keyword. The file defines the positions and orientations of the set of ''repulsive'' ellipsoids for each [..." current
- 11:1211:12, 13 May 2019 diff hist +37 N Ellipsoid.model.xyz Created page with "Same as the ellipsoid.xyz format." current
- 11:1111:11, 13 May 2019 diff hist +899 N Ellipsoid.model Created page with "The ellipsoid.model file is used to specify the parametric model that GenCoords uses to arrange a set of ellipsoids in a starting pattern. The file has the following forma..." current
- 11:1111:11, 13 May 2019 diff hist +2,664 N Density of states and thermodynamics from energy distributions at different temperatures Created page with "This is a tutorial for a set of MATLAB scripts which takes as input potential energy values observed for different replicas in a temperature Replica Exchange (REX) simulation..." current
- 11:1011:10, 13 May 2019 diff hist +710 N Xmgrace Created page with "The below command will read in a saved session file, read some data in column format (blank space delimited). Use the index and the second column as the X and Y axises. A pos..." current
- 11:1011:10, 13 May 2019 diff hist +638 N Xmakemol Created page with "A program for visualizing atomic and molecular systems. It is fast and flexible enough to view clusters, and bioploymers The input format has one atom per line with an atom i..." current
- 11:0911:09, 13 May 2019 diff hist +2,147 N Xfig Created page with "<h2>LaTeX fonts in Xfig figures</h2> Xfig supports LaTex fonts. Fig files are thus a convenient intermediate file format when generating figures for LaTeX documents. <h3>Man..." current
