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Hands-On Training for XMIPP MLalign2D on Grid at CNB-CSIC Madrid

Join us for an intensive Hands-On course on XMIPP MLalign2D on Grid, led by Germán Carrera and Alfredo Solano from CNB/CSIC. This training takes place from Monday, February 19th to Friday, February 23rd, 2024, at the CNB-CSIC in Madrid. Participants will learn how to align 2D images effectively using XMIPP on a grid computing environment. The course covers setup procedures, proxy management, data downloading and preparation, and job submission techniques with DIANE and GANGA. Enhance your skills in computational biology with practical exercises and expert guidance.

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Hands-On Training for XMIPP MLalign2D on Grid at CNB-CSIC Madrid

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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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