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Visitor policy - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Visitor_policy6 Jan 2021: This information is used to set up UCS computer accounts in advance and is needed for any new member of staff. -
Maui compilation - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Maui_compilationMaui compilation. From Docswiki. 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 -
Maui compilation - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Maui_compilation6 Jan 2021: Maui compilation. From CUC3. 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 -
Dijkstra test.py - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Dijkstra_test.pyPATHSAMPLE then attempts to connect A and B and will repeat this until it finds a new minimum that reconnects A and B (this is however very unlikely to happen). -
Computer Office services - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Computer_Office_services6 Jan 2021: Computer Office services. From CUC3. This has moved to the COs' wiki. COs only! And even more recently, this has gone public on (Raven password needed, but if you got here then you already have one). Retrieved from "". Navigation menu. Personal tools -
DMACRYS interface - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/DMACRYS_interfaceThese have to be renamed in DMACRYS! UPDATE: the new PGI is slightly better, but as Davids recommends, don't use PGI! ... Moves via XML. This idea has been cancelled, use new Python interface instead I'm thinking of implementing a move protocol using an -
General queueing problems - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/General_queueing_problems6 Jan 2021: General queueing problems. From CUC3. This page is for general queueing discussion. There are specific pages for discussing mek-quake and tardis. I have moved the paragraph from the page for me-quake as it is more appropriate here. --Catherine 09:55, -
GMIN TESTS module - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/GMIN_TESTS_moduleIt will contain tests of routines such as those in the new GMIN MOVES module. -
GPU processing - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/GPU_processing6 Jan 2021: I need a new version of the image without those SuSE libs to use on these machines. ... The auto-patching script doesn't do kernels on 10.2 so it will always need a computer officer's intervention to do a new kernel anyway. -
PYGMIN & DMACRYS - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/PYGMIN_%26_DMACRYSIt has a strong focus on an object oriented & modular design which makes it very powerful to try new functionality. -
SVN setup - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/SVN_setup6 Jan 2021: These variables will now be automatically set when you open a new shell, but for now, we need to load them manually. ... Whenever you introduce a new keyword or feature, it should be documented. -
Jenkins CI - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Jenkins_CIPlease feel free to contribute new tests and to improve the old ones! ... If you are absolutely certain that your changes have made the code better, you should replace the expected_output folder with your new output files and commit the changes. -
CamCASP/ToDo/diskIO - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/ToDo/diskIO6 Jan 2021: I should find a concrete example that compares the old and new, but till I do that, here are some numbers for a calculation done on the new quad-core machine -
Backup strategy - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Backup_strategyRunning out of space on existing JBODs. Workstations tend to contain archives of old user accounts because new users need old users' data (or PI wants to hang onto it) but ... So we need a gigantic new JBOD to accomodate the growing data. -
Other useful scripts - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Other_useful_scripts6 Jan 2021: a symbolic link to the file's new location and leaving all other files untouched. -
Remastering Knoppix - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Remastering_KnoppixKNOPPIX_remastered | nice -5. /create_compressed_fs - 65536 > masterISO/KNOPPIX/KNOPPIX. Then boot up SuSE and copy the new compressed file over your old /KNOPPIX/KNOPPIX. ... Boot the knoppix system to test the new KNOPPIX file. Keep going round and -
OS X and Linux tips - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/OS_X_and_Linux_tips6 Jan 2021: perl -pi -e 's/old string/new string/' list_of_files. is equivalent to. for file in list_of_files; do sed -e 's/old string/new string/' $file > tmp mv -
Zippo Sicortex machine - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Zippo_Sicortex_machineZippo Sicortex machine. From Docswiki. Please record useful notes about the new SiCortex machine here. -
Backup strategy - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Backup_strategy6 Jan 2021: Running out of space on existing JBODs. Workstations tend to contain archives of old user accounts because new users need old users' data (or PI wants to hang onto it) but ... So we need a gigantic new JBOD to accomodate the growing data. -
Computer Office services - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Computer_Office_servicesComputer Office services. From Docswiki. This has moved to the COs' wiki. COs only! And even more recently, this has gone public on (Raven password needed, but if you got here then you already have one). Retrieved from "". Navigation menu. Personal -
Remastering Knoppix - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Remastering_Knoppix6 Jan 2021: KNOPPIX_remastered | nice -5. /create_compressed_fs - 65536 > masterISO/KNOPPIX/KNOPPIX. Then boot up SuSE and copy the new compressed file over your old /KNOPPIX/KNOPPIX. ... Boot the knoppix system to test the new KNOPPIX file. Keep going round and -
Porfuncs Documentation - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Porfuncs_DocumentationIt should be omitted from new code. IARGC. subroutine iargc_subr(n) integer, intent(out) :: n. -
CamCASP/Programming/6 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Programming/66 Jan 2021: filestatus = character(3): OLD/old or NEW/new or OVR/ovr or ADD/add! NEW: This is a new file to be opened! ... NEW). In the latter case, any existing file by the same name is over-written! -
Git Workflow - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Git_WorkflowCheckout the new repository and start writing the paper in the blank directory. ... else. All development should occur on branches. To create a new branch, run. -
Optimising a path - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Optimising_a_path6 Jan 2021: Eventually additions of new connections to the database will no longer reduce the rate constant. -
GMIN MOVES module - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/GMIN_MOVES_moduleIn short, a new parser is being developed by Kyle to allow the construction of a highly flexible move set. ... csw34> Temporary calls to new step taking routines for testing IF (NEWMOVEST) THEN! -
Useful PBS scripts - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Useful_PBS_scripts6 Jan 2021: This causes many "interesting" issues when I attempted to use the RESTART files for new calculations. -
CamCASP/ToDo/diskIO - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/CamCASP/ToDo/diskIOI should find a concrete example that compares the old and new, but till I do that, here are some numbers for a calculation done on the new quad-core machine -
Git-NECI - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Git-NECI6 Jan 2021: git checkout branchname' will allow you to swap branches, and 'git checkout -b newbranchname' will allow you to create a new branch. ... If you are in the middle of something, then want to work on something else, you can either create a new branch, or -
Blacklisting Compilers - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Blacklisting_CompilersWe also issue a waring reminding users they need to reconfigure if they have module loaded a new compiler. # ... To add a new ban, find the list for the appropriate compiler in CMakeLists.txt, then copy the above example, changing the condition and -
Adding a model to GMIN - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Adding_a_model_to_GMIN6 Jan 2021: Adding a model to GMIN. From CUC3. This is rough outline of the subrounties that need to be changed to add a new model to GMIN. -
Adding a model to GMIN - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Adding_a_model_to_GMINAdding a model to GMIN. From Docswiki. This is rough outline of the subrounties that need to be changed to add a new model to GMIN. -
Adding a model for PATHSAMPLE - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Adding_a_model_for_PATHSAMPLE6 Jan 2021: Adding a model for PATHSAMPLE. From CUC3. Under Construction. This is rough outline of the subrounties that need to be changed to add a new model to GMIN. ... connectodata.f -- print out new output structures start.<n>, finish.<n>,. --mp466 00:24, 8 July -
Branching and Merging - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Branching_and_Mergingtrunk) as follows:. svn copy url-old url-new. where, for example, url-old is $SVN/trunk and url-new is $SVN/branches/your-new-branch-name. ... 5 then new functionality exists to help you (see the SVN manual for more information). -
Environment modules - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Environment_modules6 Jan 2021: If you do module avail after loading the use.own module, you'll see there's a new section: /home/${USER}/privatemodules. -
SuSE 10.2 workstation image - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/SuSE_10.2_workstation_imageAdd stuff you'd like in the new image here. gaim (chat client). ... OpenOffice.org (Office suite). OpenSSH (SSH client). Pan (news client). Pine (mail/news client). -
CamCASP/Programming/9 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Programming/96 Jan 2021: New code: make_T_AO_mono 1 6.58 Old code: make_T_AO_mono 1 65.06. This speed-up occurs for all systems I've looked at. -
OPTIM/Q-Chem Tutorial - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/OPTIM/Q-Chem_Tutorialajwt3/code/qchem/qcsetup.bash. H. 2. O test. create a new directory with the following files h2o.inp. -
NECI-testcode - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/NECI-testcode6 Jan 2021: NECI-testcode. From CUC3. This is a new page to post info on how to migrate the test code between machines, as was done between discovery and scepter recently. ... Note that new benchmarks need to be produced if the number of cores changes as certain -
Optimising a path - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Optimising_a_pathEventually additions of new connections to the database will no longer reduce the rate constant. -
Talk:Catherine Pitt - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Talk:Catherine_Pitt6 Jan 2021: The ACML on tardis was already fixed (this is where I found the note) and I've done the new FFTW module on tardis (won't go live until I unleash -
Adding a model for PATHSAMPLE - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Adding_a_model_for_PATHSAMPLEAdding a model for PATHSAMPLE. From Docswiki. Under Construction. This is rough outline of the subrounties that need to be changed to add a new model to PATHSAMPLE. ... connectodata.f -- print out new output structures start.<n>, finish.<n>,. --mp466 -
Mek-quake Queueing system - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Mek-quake_Queueing_system6 Jan 2021: Mek-quake Queueing system. From CUC3. 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 what works best on most of the other clusters to keep -
Wales Group - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Wales_GroupIf you add a new page to this wiki, please provide a link to it in the Comprehensive Contents Page under the section you think most appropriate. ... Can be very useful for visualizing your system and for rapidly implementing and testing new ideas. -
Wales Group Version control - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Wales_Group_Version_control6 Jan 2021: Note that Google Reader has a delay in updating the feeds, so you won't see new logs up to an hour after they are created and are visible with Firefox. -
Pathsampling short paths - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Pathsampling_short_pathsHowever, when you have the path.info file(s) from OPTIM you may not want to use them to start a new database -- instead, you can add them (one at a ... Systematically increasing the number of connections per minimum. Starting from an existing KTN, with -
Useful Python Scripts - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Useful_Python_Scripts6 Jan 2021: This is especially helpful when trying to reorder code for a cleaner flow, trying to remove issues leading to circular dependencies, or for becoming familiar with the structure of a new -
SuSE 10.1 workstation image - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/SuSE_10.1_workstation_imageOpenSSH (SSH client) DONE. Pan (news client) DONE. Pine (mail/news client) DONE. ... rasmol (molecular visualisation) DONE. TeX/LaTeX (document preparation system) DONE. Thunderbird (mail/news client) DONE. -
NECI Re-write - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/NECI_Re-write6 Jan 2021: Sets of defaults that can be called via a date. New memory book-keeping scheme in place. ... Currently the old routines just call the new ones with some of the options set to a default value. -
Using GMIN to generate endpoints - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Using_GMIN_to_generate_endpointsCopy the coords.prmtop and coords.inpcrd files you just made into a new directory, and add the following file:. ... For vacuum, use igb=0 and delete "saltcon" keyword. min_md.in - the AMBER (SANDER) settings for molecular dynamics (used to generate new
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