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Computational Chemistry (F14CCH)

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Computational Chemistry (F14CCH) Computational Chemistry (F14CCH) Connecting to Remote Machines Using CCP1GUI CONDOR is a queuing system that can be accessed from the Linux machines of the Left Mouse Button: Turn theoretical research groups and distributes the submitted jobs to free compute nodes. Hold right + up or down: Zoom Since the machines are protected by firewalls you have to connect to a specific node, Hold wheel + move: Move PARIS , on which you were given an account on. Click Atom => Select Fragment => Add Use PuTTY to connect to remote machines, PARIS in this case. Open putty.exe , Assign all elements, also the hydrogens, before creating the GAMESS input file enter the hostname as paris.chem.nott.ac.uk . The login is your university (click on “All X => H” in the tool panel). If you cannot see one of the windows of username and the default password is ChangeMeSoon . When you first log in on CCP1GUI, it might be hiding outside the desktop area. Right click on the taskbar CONDOR you must change your password using kpasswd ! It must be strong, icon => Move => hold cursor keys to the left until the window appears. including mixed case letters and numbers. Creating a GAMESS Input File / Running a Local Job Compute => GAMESS-UK Copying Files from/to PARIS Molecule: Options => Title To exchange files with PARIS in order to submit files to CONDOR for calculation or Task => select requested task copy results back, you first have to copy them from the Windows machine to PARIS Theory: Select SCF Method (and post SCF Method, if required) via the SSHClient. It cannot be installed in the CAL but can be accessed at NAL Optimisation: Runtype => Opt. Coords => Cartesian => Accessing the Internet => SSH FTP Client Job: Job Group => Job Name (no blanks!) Select “Quick connect”: Host name: paris.chem.nott.ac.uk To write an input file for submisstion to CONDOR : User name: your IS user name (pcyz...) Calc => Write Inputfile (to C:\ccp1gui\jobname.in) To run the job on the local machine (for short jobs): If you do not see a split window with your local machine left and the remote Calc => Run machine to the right, click on “Window => New File Transfer ”. Job Crashes With ^M Characters in the Output file When logged in on PARIS with the SSHClient, drag-and-drop all your files from the Explorer or the left window to your directory on PARIS (right) and vice versa. If this happens, then the input file was saved in DOS-format. To change that it should be sufficient if you do: Caution: The SSHClient also offers a small terminal but due to problems with vim it is strongly recommended to use PuTTY instead. PuTTY makes life a great deal vi file.in easier with e.g. text colours. Do not use the FTP client terminal. :set ff=unix :wq To log off properly click on “ Disconnect ” in the tool bar or File => Disconnect . If you additionally see the “^M” characters in the .in file, you might also need :%s/^M//g (to create “^M” type “Ctrl+v m”, not simply ^M!) Computational Chemistry (F14CCH) Important Unix Commands Using vim cd d change to directory d Vim has two modes: insertion mode, and command mode. You start in command cd change back to home directory mode, where almost every key and combination of keys is assigned an operation (e.g. „delete a line“). Insertion mode begins upon entering an insertion or change mkdir d create new directory d command ( i, a, c, o). [ Esc ] returns to command mode (where you can quit). Most cp f1 [f2…] d copy files fx to directory d commands execute as soon as you type them except for “colon” commands which mv f1 [f2…] d move files fx to directory d execute when you press the enter key. mv f1 f2 move (rename) file f1 to f2 vi [f] start vim (and edit the file f if given), vim works as weel rm f delete file f vimdiff f1 f2 view the differences between files f1 f2 rmdir d delete directory f (must be empty) vimtutor basic tutorial for handling vim (very helpful, essential!) rm -r d delete non-empty directory d (be extremely careful!!!) ls list files in directory In Command Mode ls -l or l list detailed output of directory :w file save to file (or simply save, if file is omitted) pwd print working (current) directory :q quit (use :q! to quit without saving) exit quit the current shell (or return to where you came from) i enter the input mode (to enter text) Esc leave the input mode (enter command mode) <tab> use to auto-complete filenames in the shell u undo last change Ctrl-r redo last undo cat f list contents of file f Shift-v select lines (use Ctrl-v to select a text block) more f list file f by screen (scroll with space, quit with q) dd delete current line less f list file f by screen (PgUp/Down, Cursorkeys, quit with q) y copy selected lines grep „ptn“ f lists all lines of file f which contain the pattern ptn P or p paste the deleted text before or after current position diff f1 f2 list differences between files f1 and f2 (see also vimdiff!) /string search for string N or n search forward or backward for next match man command displays the manual page of the given command go to beginning of file gg go to end of file condor_submit f submit file f to the condor queuing system G this that replace this with that (the % means in the whole file) condor_q view the condor queue (which jobs are being processed) :%s/ / /g remove the job with number id (shown by ) condor_rm id condor_q condor_status check the status of all available condor nodes and CPUs Cut and Paste a Block of Text (e.g. New Atom Coordinates) ssh [email protected] Ctrl–v begin block selection connect to PARIS via a Mac OS or Linux terminal (replacing Putty) cursor keys to select the text block scp –r [email protected]:~/charmm . y to copy the selection copy the folder charmm from PARIS to the current directory :e file to open an existing or create a new file (if needed) scp file [email protected]:~/charmm p to paste the copied text copy the file file from the current directory to the folder charmm on PARIS :w save the file Computational Chemistry (F14CCH) Using CONDOR The CONDOR Submission Script Only for the CHARMM water tutorial you are going to execute CHARMM directly To submit a job to the CONDOR queuing system, you need the input files for on PARIS . For the other calculations you have to use a submission script (see CHARMM or GAMESS and the submission script with the instructions for CONDOR . further down), which sends the job to one of the compute nodes. If the larger A submission script, e.g. for CHARMM in this case, looks like this: calculations were run on PARIS , the whole queuing system may crash! universe = vanilla executable = /opt/condor/software/bin/charmm Using CHARMM with CONDOR input = build.inp output = build.out The folder contains six input files for the MD simulation ( ) and charmm md_*.inp error = build.e the run script for them ( charmm.sub , in which you have to adapt some settings to log = build.log your job). Edit md_build.inp and change the amino acid to the one which is to be calculated. The file name prot.pdb cannot be changed, since all following should_transfer_files = YES scripts will use it. To run the simulation submit the job with when_to_transfer_output = ON_EXIT transfer_input_files = build.inp,file1,file2 condor_submit charmm.sub queue Check the output files, whether all calculations ran successfully (a skull at the end of the file is usually a bad sign). If everything looks OK, copy it with the SSHClient For each job you have to configure the submission script appropriately. This to your local machine to analyse it using CCP1GUI for example. includes the sections input , output , error and log as well as the line transfer_input_files . The latter has to list all files (separated by commas), which have to be submitted to the machine that calculates the job. Using GAMESS with CONDOR You can name the submission script however you like and can simply copy the template file to a new name, which fits the current job. Keeping the submission Copy the .in file created by CCP1GUI to the folder gamess on PARIS (or create a new folder for it and copy the submission script into it as well). The folder contains script instead of always using the same makes it easier later to rerun the job in case something went wrong. the run script gamess.sub , in which you have to adapt some settings to your job (see the following section for that). After this submit the job with condor_submit gamess.sub The Text File Format Differs Under Windows and Unix The most important information is at the very end of the output file. Use the “G” Unix uses a different text format than Windows does. Notepad for example will not command in vim to get there fast (rather than pressing 200 times PageDown…). recognize line feeds in a Unix text file. You can change the file format in vim using :set ff=dos and :set ff=unix , respectively. Under Windows you should not Usually it is useful to run a “rough” optimization at first using a smaller basis set use Notepad but a decent editor, e.g.
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