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MLalign2D on the Grid

MLalign2D on the Grid. MLalign2D on the Grid. Germán Carrera, Alfredo Solano (CNB/CSIC) EMBRACE COURSE Monday 19th of February to Friday 23th. CNB-CSIC Madrid. MLalign2D on the Grid. What we have to do to run MLalign2D on the EGGE Grid?

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MLalign2D on the Grid

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  1. MLalign2D on the Grid MLalign2D on the Grid Germán Carrera, Alfredo Solano (CNB/CSIC) EMBRACE COURSE Monday 19th of February to Friday 23th. CNB-CSIC Madrid

  2. MLalign2D on the Grid • What we have to do to run MLalign2D on the EGGE Grid? • We have ported MLalign2D and an early version of MLrefine3D to the Grid: • This software uses the DIANE framework to launch the jobs to the Gird and a program called GANGA for the jobs management.

  3. MLalign2D on the Grid • This presentation pretends to be an explanation of how to run this application on the EGEE Grid. • 1 Previous steps • 1.1 Accessing to the UI (User Interface) • (eg:)ssh -X user@machine • user is the username • machine is the name of the UI

  4. MLalign2D on the Grid • 1.2 Openning a Grid proxy • (eg:)voms-proxy-init --voms biomed --valid 50:0 • biomed is the virtual organization (vo) • --valid 50:0 is an optional flag that shows the expiration time of the proxy (50 hours in this case) • (eg:)voms-proxy-destroy (To close the current proxy) • (eg:)voms-proxy-info --all (To consult diverse information about your opened proxy)

  5. MLalign2D on the Grid • 1.3 Uploading your images to the UI (User Interface) • (eg:) scp -r directory user@machine:directory • directory is the name of the directory that contains your images • user is the username • machine is the name of the UI • directory(2) is the name of the directory that will be created on the user interface

  6. MLalign2D on the Grid • 2 Configuring DIANE for xmipp_MLalign2D and xmipp_MLrefine3D • 2.1 Adding the paths of GANGA/DIANE and xmipp_MLalign2D/xmipp_MLrefine3D binary files • The path of GANGA binaries in villon machine is /opt/ganga/install/slc3_gcc323/4.2.1/bin • The path of DIANE binaries in villon machine is /opt/diane/specific/slc3_gcc323/HEAD/DIANE/dev/commands • The path of the MLalign2D and MLrefine3D binary files is /opt/xmipp • (eg:) export PATH=/opt/ganga/install/slc3_gcc323/4.2.1/bin:$PATH • (eg:) export PATH=/opt/diane/specific/slc3_gcc323/HEAD/DIANE/dev/commands:$PATH • (eg:) export PATH=/opt/xmipp:$PATH • You can add the previous lines to the .bashrc file (is placed in your home directory) and run (eg:) source .bashrc - to fix the changes

  7. MLalign2D on the Grid • 2.2 DIANE/xmipp_MLalign2D xmipp_MLrefine3D ".job" configuration files • 2.2.1 Coping a ".job" file to our home directory • (eg:) cp /opt/diane/specific/slc3_gcc323/HEAD/DIANE/dev/workspace/xmipp_test.job $HOME

  8. MLalign2D on the Grid • 2.2.2 Description of the ".job" file tags • Directory With this variable we indicate the directory in which we have the ".sel" file and the images that it references • (eg:) dir = '/home/user/imagesdir/' Application With this variable we indicate that we want to use the xmipp_MLalign2D application • (eg:) Application = 'xmipp' Data (MLalign2D) Data var contains different tags, the description of each one is: • Program we can choose between xmipp_MLalign2D and xmipp_MLrefine3D • Niter contains the number of iteractions • imgselfile contains the path to the ".sel" file • inirefsel contains the path to the reference images • add_params to add more params to the execution • MLroot Rootname for all output files • noise • offset • Nsplit split the full set of images in different subsets • iter Number of iteractions of each subset of images (allways at 1)

  9. MLalign2D on the Grid Data = {'Niter' : 2, 'Program' : 'MLalign2D' 'imgselfile' : dir+'selfile.sel', 'inirefsel' : dir+'refselfile.sel', # CREATE THE REFERENCE IMAGES FIRST! 'add_params' : '', 'MLroot' : 'output', 'noise' : 0, 'offset' : 0, 'Nsplit' : 3, # SPLIT ALL IMAGES IN A NUMBER OF GROUPS 'iter' : 1 }

  10. MLalign2D on the Grid JobChain It references the Data var (eg:) JobChain = [Data] JobInitData Init data for the execution of DIANE/xmipp_MLalign2D jobs (eg:) JobInitData = None (eg: MLalign2D case) InputFiles = [Data['imgselfile'],Data['inirefsel'],'/opt/xmipp/xmipp_MLalign2D'] (eg: MLalign3D case) InputFiles = [Data['imgselfile'],Data['inirefsel'],'/opt/xmipp/xmipp_MLrefine3D'] InputFiles Input files needed for the execution of DIANE/xmipp_MLalign2D jobs (eg:) InputFiles = [Data['imgselfile'],Data['inirefsel'],'/opt/xmipp/xmipp_MLrefine3D'] * '/opt/xmipp/ is the path of some xmipp programs in our user interface

  11. MLalign2D on the Grid • 2.3 Running DIANE with xmipp_MLalign2D and xmipp_MLrefine3D • tcsh • source /opt/diane/specific/slc3_gcc323/HEAD/DIANE/etc/environment.csh • diane.startjob -j $PWD/xmipp_test.job -w5@LCG --ganga Where xmipp_test.job is the file we have defined before • -w5@ (eg: 5) is the number of workers (CPU's on the Grid), LCG is the backend • --ganga is the management and job submission tool • If all goes well you have to obtain something like that: DIANE: 11:43:40: job output in: /home/gcarrera/diane.workspace/jobs/ • You can see the status of your jobs usign the “ganga” utilit • You can add new workers with the command (eg:) diane.ganga.submitworkers –job=xmipp_test_gem.job –nw=10 –bk=lcg • When DIANE execution has finished you can consult diverse information accessing to the MonALISA Repository at http://lcgui003.cern.ch:8080/

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