DataGRID at the ZMAW User Manual
Contents
1. qmon 3 Queue submit host 12. figure 1 4 Applications In this section we describe the implementation of more complex applications on the grid There are a few examples collected in the grid repository The purpose of these examples is to demonstrate some features of the grid engine Once you feel confident concerning the functionality and use of the grid engine you can wrap your own applications in a job script and submit it to the grid 4 1 Examples In the repository opt gridware sge applications there are samples of grid appli cations as tar balls To test and perform one of the applications you need to 1 log into a submit host 2 copy the corresponding taarball to your working directory and unpack it 3 carefully read the README file and follow the instructions E g for the application gCCDAS cp opt gridware applications gCCDAS tgz tar zxpf gCCDAS tgz cd gCCDAS more README o ole 4 1 1 gCCDAS Second derivatives This example is taken from the project CCDAS for details see http CCDAS org Sec ond derivatives of the cost function J x w r t the optimal model parameters x are used to approximate the parameter uncertainties The corresponding matrix Ons N DET aa he WEL 1 is called Hessian and has n entries where n denotes the number of entries As discussed in the computations of the individual columns of the Hessian are independent of each other although there are saving when computing multiple colu
3. individual postprocessing and as a demonstration how the performance of typical postprocesing workflows can be improved 1 Gridenable your own application Having shown how the grid can be used to improve workflows and processes of scientists you probably wonder how you can make cabable your applications for the grid The general answer is that you analise your application for parts which can be fractionalised in parts which can be performed in parallel Furthermore there are information needed which specify the considered worflow with the used data models and executables These so called meta data has to be provided by the user and can be used to wrap your application in a grid script 1 1 Wrapperscript We provide a template gTemplate to simplify to wrap your application in a gridscript 1 2 Meta data Following meta data has to be provided by the users e application name of the appl e executable this is the executable that performs a sub task e input data e output For the application examples above we get Application CCDAS A Submit hosts We list here the current submit hosts at the ZMAW kurs0Ol zmaw de urs02 zmaw de urs04 zmaw de urs05 zmaw de urs06 zmaw de urs07 zmaw de urs08 zmaw de urs09 zmaw de kursl0 zmaw de nN nN AN AA linde mpi zmaw de mccoy cis zmaw de pappel mpi zmaw de tanne mpi zmaw de Index grid user 1 Job 1
4. is in the above example simple sh and the jobid is 721 more SHOME simple sh e721 If it exists and is empty or just contains some timing or scheduling informations all is fine Then you should find the standard output of the respective job in more simple sh o721 Wed Jul 27 11 38 26 CEST 2005 Wed Jul 27 11 38 46 CEST 2005 Congratulations your grid job did as it should write date and time sleep for 20 seconds and again display date and time Otherwise if e your job stays in the state q and or w for more than some minutes e itis in error state E e the error output SHOME lt jobname gt e lt jobid gt shows some error messages e or you get in any other trouble and you can t get rid of these problems on your own don t hesitate to contact the grid adminis trator at CIS iei E OMON FEMA control i File Task 59 9 5 Figure 1 QMON Main control window 3 2 2 Use the graphical user interface QMON Above we described how you to submit a job by entering shell commands on a terminal Some people prefer to work with a graphical user interface GUI The GUI for the Sun Grid Engine is called gmon Note Unfortunately qmon does not work on all plattforms at the moment If you encounter problems on your machine please contact the grid administrator If you call qmon according to qmon amp the QMON Main Control window will pop up with a lot of buttons see
5. DataGRID at the ZMAW User Manual Max Planck Institute for Meteorology April 24 2006 Docu Version 0 2 Contents 1 What s a grid 2 The grid system at the ZMAW 3 Getting started 3 1 Before you can use the grid 3 2 Submit your first job ZZL Wee the command ne sas a eGo 2 a ta gil a Rev ae ee Be el 3 2 2 Use the graphical user interface QMON 2 222 4 Applications 4 1 Examples 4 1 1 gCCDAS Second derivatives 4 2 2 2 2 aa See x 4 1 2 gBETHY Domain decomposition 0 4 1 3 gECHAM post Postprocessing of model output l Gridenable your own application 2 2 2 2 Come 1 1 Wrapperscript 12 Metadata A Submit hosts ii un RP BB BH W DDr N 1 What s a grid There is a quite simple answer A grid is a collection of computing resources providing a transparent single point access There is a quite complex and sophisticated answer as well see e g http en wikipedia org wiki Furthermore there are different kinds and implementations of grid systems depending on what it should be good for 2 The grid system at the ZMAW The Sun Grid Engine SGE N1GE6 is installed and configured as a test configuration at the MPI for Meteorology and administrated by CIS The SGE is a Distributed Resource Manage ment DRM tool which accepts jobs users requests for computer resources This jobs are put in a holding area socalled queu
6. NetCDF SERVICE or EXTRA format 3 Further postprocessing is done by CDOs Climate Data Operators or the so called PIN GOS E g extracting mean values from time series or selecting pressure level from the athmospheric data Unfortunately the meaning of the term grid is ambivalent here In earth system models a grid denotes the segmentation of the globe surface in gridcells whereas in IT technologies a grid is refered to as a service for sharing computer power and data storage To distinguish the different meanings we allways refer to former as model grid ECHAM is an atmospheric general circulation model for more details see http www mpimet mpg de en extra models echam 4 Finally the data has to be stored in a data base or in an archive The corresponding subtasks are assigned to the following four scripts which are packed in the tar ball gECHAM post tgz 1 gFTP sh This is not ECHAM specific but executes just several ftp transfers on several execution nodes 2 gAFTER sh The afterburner is called In the current form just one code is selected from the given monthly RAW file 3 gCDO sh The CDOs or one of the PINGO programs are called to select specific codes and levels 4 gFILL sh Should fill the data in the database This is not implemented so far Remark These post processing test scripts are by no way comprehensive and their only purpose is to give a base for your
7. e and send to appropriate worker nodes as soon as they can be executed They are managed during execution and records are logged when they are finished More detailed descriptions and manuals of the grid engine N1GE6 itself are provided on the Sun websites e g http docs sun com app docs coll1 1017 3 More informations about the cooperative project DataGrids in Earth System Sciences can be found onhttp www cis zmaw de inAbout Us Projects DataGrid 3 Getting started After you are registered and have done a few settings it is very easy to use the grid by submitting jobs 3 1 Before you can use the grid Some prerequisites must be fulfilled before you can submit jobs to the grid 1 Become a grid user You must be registered as a grid user In principle all users that have an account at the DKRZ can be registered If you are not sure whether you are already registered or you want to apply for registration please fill out the form on the project website above or contact your grid administrator gridadmin dkrz de 2 Log on a submit host After registration you must log in to a so called submit host a computer which allows for submitting and controlling batch jobs You can find a list of all current submit hosts in the appendix If you want your own workstation to be a submit host please mark the corresponding field in the registration form 3 Set the SGE environment variables The grid engine environment var
8. iables are set by the commands source opt gridware sge zmaw common settings csh for C shell users rsp amp opt gridware sge zmaw common settings sh for Bourne shell users 4 Test your grid environment Check your settings by entering the command je qconf ss All submit hosts should be listed Now you are ready for grid computing 3 2 Submit your first job 3 2 1 Use the command line To test whether your grid environment is working submit a simple test job from shell and check the execution status e g qsub opt gridware sge examples jobs simple sh Your job 721 simple sh has been submitted gqstat job ID prior name user state submit start at queue 721 0 55500 simple sh m216015 r 07 26 2005 18 35 25 The job with job id 721 is running now state r When the job is finished it will no longer be listed by qst at and the output is written to a file There are several other job states e g e q the job is queued i e put in an appropriate job container the queue e w the job is waiting for execution e F an error occurred Especially in the case of errors you probably want to know what happened to your submitted job To get more detailed information enter qstat f j 721 and check the messages there By default the output directory of the grid jobs is your home directory Please check first the error output file lt jobname gt e lt jobid gt whereby jobname
9. mns in a simple job But by parallelising the computations into several independant jobs the CPU time can be reduced significantly Once you have copied and unpacked the application package gCCDAS tgz please read the README file and follow the instructions 4 1 2 gBETHY Domain decomposition The Biosphere Energy Transfer and Hydrology model BETHY simulates exchange fluxes be tween the biosphere and the atmosphere for grid cells of a global grid For more details about the model see The grid cells of this model grid are treated entirely independent of each others so we can seperate the global grid into tails i e groups of grid cells Sometimes this is called domain decomposition The gBETHY application is an example of a very simple domain decomposition of BETHY whereby the different tails are executed on different execu tion hosts Once you have copied and unpacked the application package gBETHY tgz please read the README file and follow the instructions 4 1 3 gECHAM post Postprocessing of model output We consider here a typical post processing workflow of ECHAM data at the ZMAW which consists in four steps 1 Get the raw data from the output stream of a model run an archive or out of a data base 2 The standard post processor for ECHAM output data is the afterburner providing sev eral operations as selecting codes transform model grid spectral to Gaussian and write data in GRIB
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