1. www.eu-eela.eu E-science grid facility for Europe and Latin America GRIP - Grid Image Processing for Biomedical Diagnosis SECOND EELA-2 GRID SCHOOL Querétaro, México. Leandro Ciuffo (INFN - Italia) Tutor Alejandro Llanos Fuentes (UFRO – Chile) Diego Vicencio Morales (UTFSM – Chile)

2. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 2 Aplicación Resultados 71% de cancerígenos Búsqueda de candidatos a núcleos Eliminación de fondo Lectura de la imagen

3. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 3 Agenda Objetivos Gridificación OurGrid Conclusión Trabajos Futuros

4. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 4 Objetivos Implementar paralelización Explorar posibilidades de manejo y almacenamiento grid

5. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 5 Gridificación Múltiples Jobs: [ Type = "collection"; InputSandbox = {"carcinoma.o"}; nodes = { [ JobType = "Normal"; NodeName = "node1"; Executable = "/bin/sh"; Arguments = "ejecucion1.sh"; InputSandbox = {"ejecucion1.sh",root.InputSandbox[0], "image6.png"}; StdOutput = "myoutput1.out"; StdError = "myerror1.err"; OutputSandbox = {"myoutput1.out","myerror1.err"}; ShallowRetryCount = 3; ], [ JobType = "Normal"; NodeName = "node2"; (...)‏ Múltiples imágenes

6. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 6 Gridificación Múltiples Jobs: [ Type = "dag"; InputSandbox = {"carcinoma.o","cotejador.o","inicializador.o"}; nodes =[ father =[ description =[ JobType = "Normal"; Executable = "/bin/sh"; Arguments = "padre.sh"; InputSandbox = {"padre.sh",root.InputSandbox[2]}; StdOutput = "father_output"; StdError = "father_error"; OutputSandbox = {"father_output","father_error","1parametros.txt","2parametros.txt","3parametros.txt"}; ShallowRetryCount = 1;];]; son1 = (...)‏ dependencies = { {father,{son1,son2,son3}}, {son1,final}, {son2,final} {son3,final} }; Dependencias Nodo de trabajo

7. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 7 Gridificación UI WMS CE WN AMGA SE init.sh carcinoma.sh ${date}_car_${PARAM}.jdl

8. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 8 Gridificación init.sh (Múltiples Jobs) #!/bin/sh Dir=`pwd`/inputfile NOW=$(date +%Y-%m-%d-%H_%M_%S) echo $NOW > $Dir/temporalFileName rm -rf `pwd`/JDLParameters/* for (( i=7 ; i<17 ; i=i+1 )) do let entero=$i/10 let decimal=$i%10 numero="${entero}.${decimal}" echo $numero sed 's(VAR('$numero'(g s(DIR('$Dir'(g' job-carcinoma.jdl >./JDLParameters/${NOW}_PAR_${numero}.jdl done glite-wms-job-submit -d alejandro -o carId2 --collection./JDLParameters Editar Jobs

9. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 9 Gridificación carcinoma.jdl [ Type = "Job"; JobType = "Normal"; Executable = "carcinomaSH.sh"; StdOutput = "carcinoma.out"; StdError = "carcinoma.err"; Requirements = other.GlueCEInfoHostName=="kuragua.uniandes.edu.co" || other.GlueCEInfoHostName=="ce.labmc.inf.utfsm.cl" || other.GlueCEInfoHostName=="ce01.eela.if.ufrj.br" || other.GlueCEInfoHostName=="ce01.macc.unican.es"; InputSandbox = {"DIR/temporalFileName","DIR/mdclient.config","DIR/carcinomaSH.sh","DIR/carcinoma", "DIR/image.png"}; OutputSandbox = {"carcinoma.err","carcinoma.out"}; Arguments = "VAR image.png"; ShallowRetryCount = 3; ]

10. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 10 Gridificación carcinoma.sh (WN) #!/bin/bash export LFC_HOST=lfc.eela.ufrj.br export LCG_GFAL_INFOSYS=bdii.eela.ufrj.br:2170 chmod +x carcinoma export LD_LIBRARY_PATH=$VO_PROD_VO_EU_EELA_EU_SW_DIR/librerias/:$LD_LIBRARY_PATH NOW=`cat temporalFileName` url=$(hostname)./carcinoma $1 $2 lcg-cr --vo $PROD -l lfn:/grid/$PROD/carcinoma/${NOW}_PAR_$1 -d lnx105.eela.if.ufrj.br file://$PWD/carcinoma.out mdcli addentry /schooldir/grip/${NOW}_PAR_$1 imageFile $2 parameter $1 hostname $url mdcli setattr /schooldir/grip/${NOW}_PAR_$1 outputlfn lfn:/grid/prod.vo.eu-eela.eu/carcinoma/${NOW}_PAR_$1 AMGA SE Directorio compartido: CE

11. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 11 Gridificación AMGA Entries imageFile (varchar 255) paramenter (float) hostname (varchar 255) outputlfn (varchar 255) 2009-10-08-18_57_22_PAR_1.2 Image.png1.2ce01.eela….lfn:/grid/pr… 2009-10-08-18_57_22_PAR_1.0 Image.png1.0kuragua.un...lfn:/grid/pr..

12. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 12 OurGrid job: label: carcinomaJob requirements: (os=linux) task: init: put carcinoma carcinoma put image6.png image6.png put CarcinomaSH.sh CarcinomaSH.sh put lib.tar lib.tar remote: sh CarcinomaSH.sh 0.11 image6.png final: get salida.txt salida1.txt task: init: put carcinoma carcinoma put fragmento_re1.png fragmento_re1.png put CarcinomaSH.sh CarcinomaSH.sh put lib.tar lib.tar remote: sh CarcinomaSH.sh 0.11 fragmento_re1.png final: get salida.txt salida2.txt 71.79 porciento son cancerígenos 96.29 porciento son cancerígenos

13. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 13 Conclusión Paralelización: –Implentenación de diferentes instancias Utilización de componentes grid: –SE –AMGA –LFC Middleware: –OurGrid

14. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 14 Trabajos Futuros Aplicación WEB (GENIUS) SecureStorage Middleware DIRAC Verificación de paralelización MPI

15. www.eu-eela.eu Querétaro, Second EELA-2 Grid School, 09-10-2009 15 ¿Preguntas?