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xmipp_MLalign2D on Grid Hands On

xmipp_MLalign2D on Grid Hands On. xmipp_MLalign2D on Grid Hands On. Germán Carrera, Alfredo Solano (CNB/CSIC) EMBRACE COURSE Monday 19th of February to Friday 23th. CNB-CSIC Madrid. xmipp_MLalign2D on Grid Hands On. Open two consoles to the UI $ ssh villon

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xmipp_MLalign2D on Grid Hands On

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  1. xmipp_MLalign2D on Grid Hands On xmipp_MLalign2D on Grid Hands On Germán Carrera, Alfredo Solano (CNB/CSIC) EMBRACE COURSE Monday 19th of February to Friday 23th. CNB-CSIC Madrid

  2. xmipp_MLalign2D on Grid Hands On • Open two consoles to the UI $ ssh villon • Check the proxy is open. If not, open it (100 hours): $ voms-proxy-info $ voms-proxu-init -voms biomed -valid 100: • If there's few time left, destroy the current one and create a new one. $ voms-proxy-destroy

  3. xmipp_MLalign2D on Grid Hands On • List the contents of the 'xmipp' subdir in the LFC catalog: $ lfc-ls /grid/biomed/xmipp • Download to the exercise data: $ lcg-cp --vo biomed lfn:/grid/biomed/xmipp/demo_heterogen.tar.gz file:$PWD/demo.tar.gz • Uncompress the data $ tar zxf demo.tar.gz $ ls Tag $ cd Tag

  4. xmipp_MLalign2D on Grid Hands On • Create a selfile with all the images $ xmipp_do_selfile "images/*" > tag.sel • Create a selfile for all the references $ xmipp_do_selfile "ML*" > ref.sel

  5. xmipp_MLalign2D on Grid Hands On • Prepare DIANE session, open a tcsh shell $ tcsh • Load DIANE environment $ source /opt/diane/specific/slc3_gcc323/1.4.8/DIANE/etc/environment.csh • OPTIONAL: Add a blacklist file to the .gangarc file • (eg: ExcludedCEs = ic\.ac\.uk ce1-egee\.fesb\.hr heplnx206\.pp\.rl\.ac\.uk .lip\.pt datagrid\.cea\.fr lcg002\.ihep\.ac\.cn polgrid1\.in2p3\.fr lcfgng\.cs\.tau\.ac\.il ce02\.esc\.qmul\.ac\.uk)

  6. xmipp_MLalign2D on Grid Hands On • Create the DIANE job definition file $ cp /opt/diane/specific/slc3_gcc323/1.4.8/DIANE/dev/workspace/xmipp_test.job tag.job • Edit the file $ vi tag.job $ emacs -nw tag.job $ $MY_FAV_EDITOR tag.job (if is available)

  7. xmipp_MLalign2D on Grid Hands On • Change directory ('dir') IMPORTANT: last slash must be present • Number of iterations ('Niter') • Module to use (2D), 'Program' : 'Mlalign2D' • Output root name ('output') • Number of subsets ('Nsplit') • Absolut path to executable, 'InputFiles' • Launch job, prepare monitoring $ diane.startjob -j tag.job -w50@LCG --ganga

  8. xmipp_MLalign2D on Grid Hands On • Start GANGA in terminal #2 $ ganga $ ganga --gui • And Pray! ;-) (to Santa Catalina)

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