User Guide - CSI PC² Biometric Computing
Contents
1. The MPI EXEC COMMANDS depend on the used platform Reading the metadata For getting the information which is created during the clustering process centroids etc the tool read_clusteringmetadata can be used Usage read_clusteringmetadata f PATHTO clustering_metadata dat a c cc 3 2 Clustering Arguments a shows 6 shows cc shows the count t array count i the clust ter centroids the center of the bins of each cluster nr of elements in cluster 1 10 3 Cluster Tools 4 Frontend 4 1 Installation The frontend contains the graphic user interface GUI the scanner modules for iris and fingerprint and the feature extraction modules With this setup the GUI which controls all the modules on fron tend side and manages the connection to the cluster control deamon CCD will be installed To use the sensors the drivers for the iris and the fingerprint scanner must be installed The drivers are provided by IrisGuard and TST We are not allowed to make them available on our product With the installation of the TST driver a service is started To use the fingerprint sensor this service must be disabled To do this call systemcontrol administration services A list of services will be displayed You have to search for TST CoreService and TST DeviceManager Select one of it and click on the right mouse button Select properties A window will be opened Select starttype2. Checkout the latest sourcecode with svn co https csipc2 svn sourceforge net svnroot csipc2 trunk csipc2 Anony mous logins just have read access to this subversion repository At continued reading we will define path_before_csipc2 csipc2as the directory to the source code If you are interested in supporting this project by submitting bugreports or bugfixes in form of patches please ask at our mailinglist csipc2 devel lists sourceforge net and you might get write ac cess to the repository After getting the sourcecode please continue with one of the following sections concerning the in stallation of the Cluster Control Daemon CCD section 2 and or the Frontend section 4 1 Download 2 Cluster Control Daemon CCD 2 1 Prerequisites The Cluster Control Daemon CCD is part of CSI PC task force Before you start compiling the CCD you should consider the following prerequisites Cause the CCD is designed for performant parallel matching of large databases with millions of biometrical information by now fingerprints and or iriscodes we require high performance state of the art servers as clusters or supercomputers Considering a database with two million templates of each supported matching method the minimal hardware which would be required is shown in table 2 1 Component Required Architecture Intel compatible 64bit preferred architecture Cluster nodes 4 8 CPU cores per node minimum of 2 with 2 0 GHz RAM per
3. The parameters path and path2 contains the path to the finger feature extraction module The standard module is installed with the GUI Additionaly the parameters of the feature extraction are saved in this string For that reason there are two strings The iris feature extraction generates a preview image first With a second call the extraction is done The block mf stands for maching finger There are 4 different matching modes for the fingerprint matching minutiae cluster filterbank and mixed If mode contains a 0 the default is selected This is setup on cluster side Use the 1 for minutiae the 2 for cluster the 3 for filterbank and the 4 for the mix of minutiae and clustering matching The block irissensor determines which type of iriscamera is used Set a 0 to use the Irisguard camera and the 1 for all other kinds The block fingersensor contains the path to the scanner module for fingerprints The TST module for the bird3 sensor is installed with the GUI To use an other scanner replace this path 4 3 Execution To start the GUI execute the gui exe file The application starts in a window The window is just for testing By clicking the maximization button of the window the window becomes a full screen application The GUI is optimized for public use with a touchscreen The full screen application can t be closed by the user To close the application disable the help and press ESC Source Good picture Click he
4. disabled and close the window with ok Then click on the right button again and choose stop Repeat the same for the other service To install the GUI just click on the install_csi exe This self extracting file will install all neces sary files for the gui After that copy the IFA_APIX ocxand IFA_API exeto the Windows system32 folder and run the command regsvr32 IFA_APIX ocx The fingerprint scanner and the feature extractions for iris and fingerprint can be called independently 4 2 Configuration Usually you do not need to configure the frontend system If it is necessary to reconfigure make your changes in the config ini In this section the single parameters of the ini file will be explained The first block server contains the parameters name and port These two parameters represent the server name and the connection port You should use a secure connection In this case the server name is the localhost 127 0 0 1 To build a tunnel for a secure connection use a ssh client available for free on www ssh com The second block extraction determines if the extraction runs on the frontend or on the cluster To run the extraction on the frontend set on frontend 1 otherwise on_frontend 0 The block fef stands for feature extraction finger The parameter path contains the path to the finger feature extraction module The standard module is installed with the GUI 12 4 Frontend The block fei stands for feature extraction iris
5. node gt 2 GBytes Network Gbit Ethernet Infiniband SCI for MPI Storage 4Gbyte for database e g NAS SAN GPFS Table 2 1 CCD hardware requirements The table 2 2 shows what software packages are required for successfull compiling and running Component Required Operating system Unix Linux 2 6 x Compiler GCC gt 3 4 Intel Compiler 9 10 x MPI interconnect FPGA image processing MPICH MVAPICH or SCAMPI installed libs and headers e g admxrc2 for Xilinx 2 2 Compilation ImageMagick Version 6 3 3 Table 2 2 CCD software requirements For compiling the sourcecode the following directory structure will be used in our software path_before_csipc2 t dist t csipc2 t build t dist t usr doc path to where you unpacked the source sourcecode directory compilation directory prefix install directory documentation directory 4 2 Cluster Control Daemon CCD In csipc2 exists a configuration script config sh which does the following tasks automatically for you e create build and install directories if necessary e generate configure and Makefile scripts with autotools e execute csipc2 configure options You may pass configure options to config sh Specific configure options are listed in table 2 3 Option Description with wand config FILE FILE points to Wand config of the ImageMagick library with mpicc FILE FILE points to the comp
6. not be held responsible for any physical or psychological damage caused by this document All text pictures tables or other included materials are property of the Computer Engineering Group or the Project Group CSI PC Any used material of third partys are included with permission and identified in place You are allowed to copy or distribute this document Modifications are prohibited Published by the Project Group CSI PC http csipc2 sourceforge net Contents 1 Download 1 2 Cluster Control Daemon CCD 3 2 Kereteguisiles sunt e E A E a EP E ESE wea Siig 3 222 CoMpldton A ESIMEES AE ee A R E ra 3 2 37 Installation coo 2 Geb a ea een ii Sede ia ts 4 24 Execution rn a Sui ts a s ee eS 5 2 5 Known Problems e ecra oug dene ht eee a ee ee 5 3 Cluster Tools 7 31 Cs1 dbt oolt 2 28 2 nr en ee ee 7 3 2 CELIS NE a ale SR RDA E AA AA ete seek anes ans 8 4 Frontend 11 41 Installation 2 Ai ws eo bbe we hind Ee tate ae Shp wie ae eae AE 11 24 E svt Aye e x RR EA 11 4 3 Execution ens Ce E GAS ta eee SR we tis UE a Pa 12 4 4 Known Problems 0 0 mn 13 Copyright 15 iv Contents 1 Download To do biometrical identification with the software of the CSI PC project group you can get the source code in several ways e Get a tarball or zipfile of a release version Go to the download section of http www csipc2 de and get the latest software release package e Get the cutting edge version via subversion
7. parallel version called clustering_mpi They are used the following way Clustering To start a sequential clustering the following informations have to be given to the programme 1 Database directory 2 Nr of database files in the directory 3 Nr of clusters 4 Nr of bins If for example the database which is located in fingerprintdata fp cluster and includes to db files has to be divided into 45 clusters with each 10 bins following command has to be used clustering fingerprintdata fp cluster 2 45 10 The number of clusters and bins can be freely chosen but for efficency the number of clusters should be the square root of the number of templates in the whole database The number of bins should be between 8 to 10 Parallel clustering Because clustering can be very time intensive a version based on MPI exists Following arguments have to be set c CONFIG FILE The path to the database and the number of headnodes are the used options from that file can be the same as used for the CCD nc NR OF CLUSTERS The number ot na NR OF ARD BINS The number ot clusters bins After a clustering process is successfully done a new file clustering_metadata dat exists at the database path There all important information for the matching is saved Using the data from the above example the parallel clustering would be started with MPI EXEC COMMANDS clustering_mpi c parameters cfg nc 45 na 10
8. been installed on every node in the same di rectory ideally it is installed on a shared directory we choose shared here The CCD should be started with mpirun of the corresponding MPI interconnect opt mpich gec bin mpirun for example The supported CCD options are listed in table 2 4 Option Description c FILE points to the configuration FILE default etc csipc2 ccd cfg 1 FILE points to the logging FILE default dev null d PATH PATH where the database is stored default db b PATH PATH to the FPGA bytecode images H number of headnodes to use B enable benchmark mode h print help Table 2 4 CCD options CLI options have higher priority than configfile options Use absolute pathnames only Sample execution t opt mpich gcc bin mpicc np 8 shared csipc2 bin ccd c shared csipc2 etc ccd cfg d shared db 1 tmp ccd log H 4 N In the given example ccd is executed on eight nodes The configfile is shared csipc2 etc ccd cfg logging will go to tmp ccd log and benchmarking will be enabled The database ist stored at shared db and number of four H 4 headnodes will work on it 2 5 Known Problems The following problems are known in Version 1 0 CCD breaks using ScaliMPI or MVAPICH After doing some MPI communication some nodes stop working and receiving messages We are currently working on a solution As a workaround you might use MPICH or send us a patch solving thi
9. d start the tool with n 1 ranks Please make sure that all paths can be accessed on all nodes through the same path on a network filesystem for example Overview over the commandline arguments i input dir Database or picture collection input directory o output dir Database output directory c lt CREATE gt lt CONVERT gt lt EXT _FINGER gt The tool can x a database n headnodes Number of headnodes t lt ir gt lt fp gt lt db gt Database mode for creating ir Iris fp fingerprint db triple _dp combined database for iris and fingerprints help printout a help message Operation Modes CREATE Create a new and empty database o n and t option must be given csi_dbtool c CREATE o mnt test n 5 t db CONVERT Converts an existing database to an equivalent database with a diverent number of headnodes i o and n option must be given csi_dbtool c CONVERT i mnt test o mnt test2 n 3 EXT_FINGER Extracts an picture collection from the input directory to an database If there is no database in the target directory it creates one mpiexec n 5 csi_dbtool c EXT _FINGER i mnt picture o mnt picture db 8 3 Cluster Tools 3 2 Clustering Before the clustering matching can be used the database has to be prepared the so called clustering Therefore two tools exist The clustering is the sequential programme the other is the
10. dl UNIVERSITAT PADERBORN Die Universit t der Informationsgesellschaft User Guide PG CSI PC Supervising Tutors Prof Dr Marco Platzner Dr Jens Simon Dipl Inf Tobias Schumacher Members Samir Brulic Samira Brulic Pascal Deppe Dominic Eschweiler Rosbeh Etemadi Klaus Herbold Christoph Konersmann Robert Meiche Christoph Scholz Nils Timm Andre Uckermann Elmar Weber Ren C Zorn PADERBORN CENTER FOR PARALLEL COMPUTING Paderborn Center for Parallel Computing PC An institution of the University of Paderborn Paderborn on May 20 2008 Project Group CSI PC University of Paderborn Samir Brulic Samira Brulic Pascal Deppe Dominic Eschweiler Rosbeh Etemadi Klaus Herbold Christoph Konersmann Robert Meiche Christoph Scholz Nils Timm Andre Uckermann Elmar Weber Ren C Zorn AUTHORS samir brulic csipc2 de samira brulic csipc2 de pascal deppe csipc2 de dominic eschweiler csipc2 de rosbeh etemadi csipc2 de klaus herbold csipc2 de christoph konersmann csipc2 de robert meiche csipc2 de christoph scholz csipc2 de nils timm csipc2 de andre ueckermann csipc2 de elmar weber csipc2 de rene zorn csipc2 de Copyright 2007 2008 Computer Engineering Group All Rights Reserved P1 7 01 6 University of Paderborn Warburger Str 100 33098 Paderborn Germany http www cs uni paderborn de fachgebiete computer engineering group html This document is distributed without any warranty The authors may
11. iler of the specific MPI interconnect you want to use with admxrc2 header PATH PATH to Xilinx headers with admxrc2 lib PATH PATH to Xilinx libs enable fpga enable support for FPGA s enable debug enable debugging mode definitely more verbose enable gtk2 build utilities using the gtk2 library enable sse enable SSE optimizations enable sse2 enable SSE2 optimizations enable sse3 enable SSE3 optimizations Table 2 3 Configure options We assume in the following examples that ImageMagick is installed in opt ImageMagick and MPICH using GCC is installed in opt mpich gcc and further more that those will be used for compilation If you want debugging enabled and want to have it installed in opt csi a sample compilation could be cd path_before_csipc2 csipc2 config sh with wand config opt ImageMagick bin Wand config with mpicc opt mpich gcc bin mpicc N nable debug enable ss nable sse2 enable gtk2 prefix opt csi cd build make To build the source within an SRPM Package not available yet just type rpmbuild rebuild csipc2_ccd srpm 2 3 Installation After compiling the sourcecode just type the following to install the CCD cd path_before_csipc2 build make install If available you also could install binaries from RPM Packages with rpm ivh csipc2_ccd x86_64 rpm 2 4 Execution 5 2 4 Execution To execute the CCD we assume that the software has
12. ns to this docu ment are allowed except with an identifier to the modifications that those are written by you You are not allowed to copy redistribute or modify any content identified as front cover back cover or any design pattern used in this document or the document itself as a whole without a written notice of the Project Group CSI PC Disclaimer For documents and software published by the Project Group CSI PC they do not war ranty or assume any responsibility for accuracy completeness or usefullness The Project Group CSI PC may not be held responsible for any damage caused by their publications
13. re to stant feature extraction Cancel Rescan x Bad picture Pross here nation and look in the camera again Dest The checkbox Help disables or enables the help function of the GUI If the box is checked tooltips will appear on the active buttons These tooltips tell what to do If the activation of a button makes no sense in the actual state the buttons are disabled So only the clickable buttons have tooltips No more than 3 buttons are active at the same time The usability of the application is given 4 4 Known Problems 13 In first case you have to decide if you want to scan an iris or a fingerprint Click the button iris to scan an iris or the button finger to scan a finger These buttons start the corresponding sensor After clicking iris look in the camera One eye should be visible in the mirror If you are too close or too far away the camera will tell you If you do not use the IrisGuard camera the photo is not shot automatically You have to click in the preview window to shoot the picture After clicking finger press your finger on the sensor The sensor starts blinking After scanning the scanned picture will appear in the GUI In the second case you can decide between 3 buttons Click cancel to return to the first state After clicking cancel you can select again if you want to scan a finger or an iris If the quality of the pic ture is bad click on rescan After clicking rescan use the sensor again If the pict
14. s issue Missing Wand Magick h You got the wrong ImageMagick version Please use version 6 3 3 or above CCD uses 100 CPU time This problem relates to the MPI interconnect waiting for MPI messages By now there is no workaround planed 2 Cluster Control Daemon CCD 3 Cluster Tools 3 1 Csi_dbtool The first task that should be done with this tool is to convert an existing database to an equivalent database with a different size of headnodes Headnodes are the nodes which are fetching the Data from the cluster filesystem and distribute them over the MPI Interface The number of headnodes should be equivalent to the number of ethernet links or whatever the filesystem cluster has The second task which could be done with this tool is to extract very large collections of fingerprint pictures to the template database To absolve this the tool knows two different modes which would be detected automatically The first mode applies if the tool is started in a non MPI Environment or if the number of ranks is smaller then two In this case the tool acts in a non parallel manner because the extraction process would not profit from a parallel processing If the tool is started in a MPI Environment with a rank size greater than two the tool would act in parallel where rank zero is the node for task management and template storing All other ranks are used for computing the extraction If you wish to compute on n ranks for example you shoul
15. ure is good press OK After clicking OK the feature extraction will start if extraction on frontend is set up Otherwise the click is just a confirmation of the picture If you extract an iris on frontend side you have to click the OK button twice After the first click a preview image is shown The boundaries of the eyelids the white area of the eye sclera and the black area of the eye pupil should be correct If they are not rescan the eye To close the preview click on the screen The second click will extract the rest of the eye Now you can save or match the template which the GUI has created in the last step Click on save to send the template to the database A message with the template number will be returned To match the template against all other templates in the database click on mat ch The return message will contain the result of the matching Click on reset to clear the textfield and start a new job 4 4 Known Problems The GUI does not start Copy the IFA_API exe and the IFA_APIX ocx to the Windows system32 folder and run the command regsvr32 IFA_APIX ocx to solve the problem 14 4 Frontend Copyright Author All text and other materials included in this document are property of the Computer Engi neering Group or the Project Group CSI PC Content You are allowed to copy and redistribute any included textual information in parts or as a whole only with reference to this document and the CSI PC No modificatio
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