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GRID superscalar User`s Manual Version 1.5.0 - People

1. rm f REN GS_file tasks chk destGen And now the worker side delete rm f REN destGen So you can make delete anytime you want to clean all those files You will seldom need to do this but it could be useful if you find a bug in your master code or even in GRID superscalar although we hope you don t 32 5 Frequently Asked Questions FAQ Here there are some typical questions that may arise when working with GRID superscalar We recommend you to look in the table of contents of this manual to find faster what you are looking for 5 1 Globus 5 1 1 What is Globus Why do I need it Can you give me some useful commands Globus provides services for running your jobs remotely transferring files and more It is needed to access other machines outside your administration domain There are some useful commands that you can test grid proxy info to see the status of your proxy grid proxy init to start your proxy grid proxy destroy to end your proxy globus job run to run remote jobs globus ur copy to copy files between machines 5 1 2 have several log files In my workers home directory They are named gram_job_mgr_ lt number gt log Usually when a Globus job fails it leaves information in a log called gram_job_mgr_ lt number gt log If you don t need the information inside you can erase them safely Depending on your Globus installation they can appear always when errors rise or neve
2. I see some temporary files remaining How can I manage to erase them correctly You can erase all subdirectories that are named gram_scratch_ lt random_name gt Some input files can remain also their names will be familiar for you The rest of temporary files are described in section 4 4 5 5 Other questions 5 5 1 love GRID superscalar It has saved me lots of work hours We will appreciate comments and suggestions about our tool You can reach the authors at grid superscalar ac upc es 34 5 5 2 hate your run time It s giving me lots of problems Don t give up If you really think you are in a situation that you cannot solve we can try to see what could be happening in your particular case Contact us at GRID superscalar mailing list grid superscalar ac upc es 38
3. Perl Binding Also three files are generated for the Perl binding app stubs c app worker pl and app i You must call gsstubgen with flags s p in order to generate these files File app stubs c is exactly the same file as the generated for the C C case see Figure 2 1 File app worker pl is the main program of the code executed in the servers similar to app worker c for the C C case Figure 2 2 but in Perl The file app i is an interface file that will be used by SWIG SWIG is a software development tool that connects programs written in C and C with a variety of high level programming languages primarily common scripting languages such as Perl Python Tcl Tk and Ruby Basically the app i file it is a translation from the IDL syntax to the interface syntax required by SWIG of the application functions interface From file app i SWIG generates two files app wrap c and app pm File app wrap c is linked with file app stubs c and with the GRID superscalar library and a dynamic library is generated app so File app pm indicates the Perl interpret to dynamically load the library app so when the application functions specified by the IDL file are called from the client program These all files are required at the master side 11 2 5 Writing the Master The main program that the user writes for a GRID superscalar application is basically identical to the one that would be written for a sequential version of the application Maybe
4. app functions c at the workers When working with Perl involved files are app pl app so and app pm at the master and app worker pl app functions pm at the workers section 3 2 Compile when needed e Consider modifying environment variables to change their default values You can set the run time to write debug information leave logs at workers pass messages with sockets instead of files define which port uses your gsiftp servers length of your parameters length of paths and URL s length of messages and length of the RSL string that describes each job If you change a value do the same at the worker side if this variable applies also at the worker side Also define LD_LIBRARY_PATH when needed section 3 3 e Define broker cfg that describes the machines involved in the computation section 3 4 diskmaps cfg that specifies shared disks and working directories section 3 5 and finally estimations cfg with the expected duration time for each function in each machine section 3 6 e Start your Globus proxy with grid proxy init if it wasn t already started e Check that no file named tasks chk exists if you want to start the computation from the beginning The final step is running your application by simply executing the binary that contains your main code 3 2 Copying and compiling your code It s essential to know that some files are going to be at the master side and some files are going to be at the worker side But
5. can approximate this value by adding 40 characters to the maximum length of a machine name in your system Default value is 255 GS_MAXMSGSIZE Size of the messages that will be sent between the master and the worker This could grow if you use lots of output files or output scalars Default value is 1000 it s the lower limit GS_MAXRSL This variable is related to Globus In order to run a Globus job a string that describes it must be constructed This is done with a language called Resource Specification Language In addition you can receive a message from the master recommending you to raise this value or telling that the value is not big enough Default value is 5000 the lower limit is set to 1000 GS_ENVIRONMENT This variable is considered an advanced feature Some extra environment variables could be needed to be passed when executing your jobs with Globus i e when your jobs are parallel These variables can be passed with this parameter Your GS_ENVIRONMENT string can be as long as pointed by GS_MAXPATH Each variable must be in parentheses VARIABLEI valuel VARIABLE2 value2 Take into account that the content of GS_ENVIRONMENT will be sent to each worker machine Note that you can use setenv or export as the command to define an environment variable This can change depending on the shell your system has Your main program is going to load the GRID superscalar shared library so you have to put its path into
6. for environment variables at both sides to have all code compiled and ready to run in all machines and to define correctly all the cfg files at the master side Check also that your workerGS sh files have execute permission You can check also if have all GRID superscalar environment variables defined at the master side Take a look at LD_LIBRARY_PATH and confirm that the GS master library path is defined there if needed And just run your main code app 3 8 Recovering from a checkpoint file GRID superscalar has a feature that automatically checkpoints your tasks This means that previously executed tasks won t have to be repeated when we detect an error in a task When restarting from a checkpoint file GRID superscalar will warn you with this message at the master FOUND CHECKPOINT FILE 27 This file is named tasks chk and is in you master s working directory Sometimes you won t desire that GRID superscalar restarts from this checkpoint If this is the case you can simply delete this file from your file system and GRID superscalar will start execution from the beginning Do not try to build your own checkpoint file because it can be really dangerous This file is not the only one that stores information in order to recover your previous executed tasks 28 4 Debugging your GRID superscalar program 4 1 Monitoring your execution GRID superscalar run time doesn t have by now a specific monitorin
7. its lifetime has expired Try the Globus command grid proxy info to see if you have started it If you have not remember to use grid proxy init If it has expired you can run grid proxy destroy and grid proxy init again 5 3 4 The master ends with this message or similar app error while loading shared libraries libGS master so 0 cannot open shared object file No such file or directory You have to add to your environment variable LD_LIBRARY_PATH your GRID superscalar library location 5 3 5 WhenIset GS_ SHORTCUTS to 1 I get this message ERROR Check environment variables values Why That is because you haven t read this manual We said that you won t be able to turn this to 1 because file forwarding mechanism is no more supported We don t discard to recover this feature in the future so that s the reason because this variable still remains 5 3 6 I get this message ERROR Check environment variables values But I have all variables defined and GS_SHORTCUTS is set to 0 Your environment variables are wrong or too small You cannot set GS_SOCKETS to a value different from 0 or 1 for example We have set some lower limits in order to run your master correctly See chapter 3 3 Defining environment variables 5 3 7 When working with GS_SOCKETS set to 1 I get a segmentation fault at the master More precisely this happens when a previous execution ends prematurely or not and I try to launch
8. makes you to loose potential parallelism So we recommend that you don t use this call unless there is no other option The last thing you can consider is to turn GS_SOCKETS to 1 in order to allow communications by sockets In current prototype this is only allowed when working with the C C bindings in Perl is not supported GRID superscalar works with files to achieve communication between the master and the workers But when all involved machines have external connectivity you can set this communication to be done by sockets This way of sending messages is faster because no information is written to disk and it is sent directly to the destination We recommend that you take benefit from this advanced feature if your machines accomplish the requirements 2 8 Known restrictions You have to remember always that GRID superscalar run time considers files as the main operands of each function they define the data dependencies and they have the main information required to execute a task and to store results In order to achieve better performance when executing your application GRID superscalar uses 16 renaming techniques in your files This way more parallelism can be extracted from your algorithm But that feature has several implications regarding file names when programming with GRID superscalar Here is the list of restrictions e You have to use GRID superscalar special primitives to open and close files section 2 5 1 in th
9. of the code according to the ones defined in the IDL file You can find and copy generated headers for your functions at app h file In Perl case you have to write your app functions pm file also copying your functions and you should look at the IDL file and shift the parameters into variables in the same order Remember to use GSWorker module Again you must remember that renaming techniques could have been applied to files so you cannot refer to a file with the name you think it has You have to use the input output parameters defined in the function header By the way you are allowed to create a temporary file with the name you prefer but ALWAYS referring to current working directory and do whatever is required So you can t create temporary files with absolute or relative paths All temporary files will be destroyed at the end of the task As an example Figure 2 3 shows the code for the matrix multiply function include lt time h gt include lt stdio h gt include lt errno h gt include block cc include GS_worker h include matmul h define BSIZE 2 Blocks size in elements 14 block lt double gt GetBlock char file int rows int cols 3 void PutBlock block lt double gt A char file void matmul char f1 char f 2 char f3 block lt double gt A block lt double gt B block lt double gt C GetBlock f1 BSIZE BSIZE GetBlock f2 BSIZE BSIZE GetBlock f
10. order to determine potential problems When set to 10 you will receive less information than before but enough to follow the execution of your tasks If you set this variable to 0 it means that we don t want debug information Default value is 0 e GS_LOGS Set to 1 tells the master to leave execution logs of all tasks executed in all server machines These logs will be named OutTaskXX log and ErrTaskXX log according to the standard output and standard error messages given at that task where XX is the number of the task Each time you call to a function defined in the IDL file a new task number is generated This way you can know to which call corresponds the log file If set to 0 this logs won t be left at workers Default value is 0 e GS_SOCKETS Currently GRID superscalar allows two ways of master and worker communication in the C C binding sockets or files The former means that the worker machine has external connectivity and can talk to the master with a direct connection The latter means that the worker doesn t have direct external connectivity i e a node of a cluster and has to communicate with the master through files To choose socket communication we have to set this variable to 1 Otherwise if we want to use file communication we must set it to 0 Default value is 0 Note that in Perl version you cannot set it to 1 This is also explained in section 2 7 e GS_MIN_PORT This variable only applies when working with GS
11. so the new process will replace the current one Don t do this because if someone kills your worker you won t get any information about that 3 4 How broker cfg works This will be the description of the first configuration file needed by your program developed with GRID superscalar In this file we have to tell what machines will be our workers what machine will be the master and some characteristics of this machines To understand the syntax we can see a generic example Machine LimitOfJobs Queue WorkingDirectory Master doesn t have LimitOfJobs or Queue workerl limitl queuel pathl worker2 limit2 queue2 path2 master path The first line acts as a help to define all your machines Then you have to specify the name of the worker the limit of jobs that can be running in that machine at the same time 1 is the minimum value the queue that has to be used when submitting to that machine none if you don t have to use a queue system and the working directory for this machine this means that you can find there the workerGS sh file and the app worker file Concerning the master you just have to write the master hostname that s because the operating system doesn t have always the right information and the path where the master executable file is We can see an example of our matrix multiplication case Machine LimitOfJobs Queue WorkingDirectory Master doesn t have LimitOfJobs or Queue khafre cepba upc es 4 none home
12. the GRID superscalar distribution This automatically generated code is mainly two files the function stubs and the skeleton for the code that will be run on the servers If you are not familiar with this two terms stubs and skeleton we can say as a summary that stubs are wrappers on the client or master side and skeletons are wrappers on the server or worker side Some specifications are needed in order to communicate a client and a server and this wrappers are the key point to do it they can code or decode parameters pass some information between them From the user s point of view he just has to call in C C case gsstubgen app idl Or in Perl case gsstubgen s p app idl You can also execute gsstubgen without any parameters to see a list of possible modifiers to choose an option At current version of GRID superscalar we have bindings for C C and Perl We are going to see in more detail what happens in each case These bindings have in common that the name chosen for the IDL file will determine the name of the generated files 2 4 1 C C Binding For C and C the files generated by gsstubgen are app stubs c app worker c and app h We can see now how will be this files in our matrix example Figure 2 1 shows the stubs file that will be generated for the IDL file defined in previous section 2 3 when the C C interface is used For each function in the IDL file a wrapper function is defined In the wrapper
13. the master immediately 34 The problem is that some previous jobmanagers stay running at worker machines because socket verision of the run time doesn t wait for them to finish to be faster than file version Before executing again be sure that no gobus process remains in the workers or simply wait 30 seconds the higher time the running jobmanagers will stay when the worker ends 5 3 8 I get this message ERROR AT TASK 0 8 8 4 veka MACHINE khafre cepba upc es the job manager could not stage in a file The cause can be that your gsiftp service is not reachable or is not started in your master Be sure to have an opened port for it You can telnet to that port default is 2811 localhost gt telnet localhost 2811 Trying 127 0101 Connected to localhost Escape character is 220 localhost GridFTP Server 1 5 GSSAPI type Globus GSI wu 2 6 2 gec32dbg 1032298778 28 ready If you don t get this output or a similar one contact your system administrator and tell him that the gsiftp service is not working 5 3 9 I get this message ERROR Submitting a job to hostname Globus error the connection to the server failed check host and port One of your workers cannot run Globus jobs because the service called gatekeeper is not started or its port is closed by a firewall You can do this to check it localhost gt telnet hostname 2119 Trying 147 83 42 31 Connected to hostn
14. your program with GRID superscalar e Define an IDL file named lt myapplication gt idl that contains the headers of the functions that are going to be run on the Grid Write as parameters all files and scalars involved in the computation trying to avoid out and inout scalars e Generate stubs and skeletons with gsstubgen lt idl_file gt in C C case and gsstubgen s p lt idl_file gt in Perl case e Write change your master code to call this new defined functions Use GS_On at the beginning GS_Off 0 when the program ends correctly GS_Off 1 when you detect an error in the master and the file management primitives when working with files in the master don t expect that the files have their original names Avoid using GS_Barrier e Create a file at the workers named lt myapplication gt functions c pm that contains the body of the functions defined in the IDL file Use passed parameters instead of the expected names of the files Call external binaries with GS_System and leave a possible error code at gs_result In next sections you will get more detailed information about each step However you can go to section 3 1 to see a quick guide about how to run your program 2 2 Identifying functions that will be run on the GRID In application programming there are some options available in structuring the code One really useful way is to program functions instead of programming everything in a big main function This he
15. 0 0 A 0 0 B 0 0 C 0 0 C 0 0 Figure 4 3 Another hint of how many jobs are being executed in a worker machine at the same time is in the file system You can see several sub directories named gram_scratch_ lt random_name gt Each of this directory is created to let the user work with it s own temporary files So the directory where the worker is really being executed is the weirdly named one You can see also other files in master and worker named RENXX where XX is an integer number Do not mess with these files because they are the result of applying renaming techniques to your main code They will be correctly removed during the execution and at the end of the main master program If your master seems stopped and no process owned by your username is in any of the worker machines you may have a problem because the execution won t go on In order to solve this situation you have to see all information first as the master debug information 4 2 Master debug information In previous section 3 3 Defining environment variables we have seen that we can set GS_DEBUG to 10 or 20 so the master is going to give us more information on how the execution is going It is useful to redirect all this standard output to a file so you can examine it with more patience The most important information you have to consider is the one that is given about the queues that are defined inside the GRID superscalar run time You can see prints about ru
16. 10720 0 0017 1310720 So just one operation that is really fast executed in server machines 3 7 Am I ready to run Not yet Before you run something that uses Globus and GRID superscalar does you have to start a user proxy This proxy will authenticate the current user in all the machines that are going to be the workers so you don t have to type your password every time you access to a machine The command is grid proxy init There is a useful flag valid that allows you to make it last more than 12 hours You can see this and more flags with help You can also use grid proxy info to see if your proxy is already running or grid proxy destroy to stop your proxy If you don t have this command in the path you better ask your system administrator about how to initialize your Globus environment Another important thing to consider is at the worker side You can copy all the code in the worker side in whatever machines that are going to be workers from our execution But you must remember to change in workerGS sh the line that points to the LD_LIBRARY_PATH it must contain the right path regarding that machine And also remember to change GRID superscalar library location from Makefile if needed Yes You are now ready If you want to be really sure about this you can do again some checks Be sure to have all files mentioned in previous sections in the master side and in the worker machines Remember to have the same values
17. 3 BSIZE BSIZE A B Cc Ne Ne Ne A gt mul A B C PutBlock C 3 A and B are sources delete A delete B delete C Figure 2 3 We can see that our matmul functions c file needs to include the definition of the block block cc and define the size of the block Also PutBlock and GetBlock functions are required to get the blocks from disk to memory and then proceed with the multiplication These functions could have been also defined in a separated file and then included in matmul functions c There are some special variables and primitives that must be called when creating the worker code We will give more details in the following subsection 2 6 1 Special primitives e GS_System command_line When you need to call an external executable file i e a simulator you have to use GS_System passing as a parameter the command line to be executed You can suppose that your current working directory is the one that you have defined for that machine in broker cfg file its working directory see section 3 4 How broker cfg works so you can use an absolute path or a relative path to call that program e gs result This is not a primitive This is a special variable that can be used to pass an error code to the master so the master can stop the execution If you don t use it gs_result defaults to 0 that means no error is detected in the task If you detect an error you can put an error cod
18. 5 4 6 I receive this message at the master ERROR Submitting a job to hostname Globus error the cache file could not be opened in order to relocate the user PION eeren rieo EE ei Malavasi eee ea a 37 5 4 7 I receive this message at the master ERROR Submitting a job to hostname Globus error the job manager failed to create the temporary SIG OUE filename aussen een ordain teased Ea 37 5 4 8 I get this message ERROR Submitting a job to hostname Globus error data transfer to the server failed u uceeeenneeeenenneeeeneneneeeeeennen en 37 5 4 9 After having a quota problem in a worker I see some temporary files remaining How can I manage to erase them correctly ccssccccccsesseceeeeees 37 5 5 OTHER QUESTIONS 2023535505555 ara eis E E aN 37 5 5 1 Ilove GRID superscalar It has saved me lots of work hours 37 5 5 2 I hate your run time It s giving me lots of problems 38 1 Introduction The aim of GRID superscalar is to reduce the development complexity of Grid applications to the minimum in such a way that writing an application for a computational Grid may be as easy as writing a sequential application Our assumption is that Grid applications would be in a lot of cases composed of tasks most of them repetitive The granularity of these tasks will be of the level of simulations or programs and the data objects will be files GRID superscalar allows application developers to write their
19. GRID superscalar User s Manual Version 1 5 0 CEPBA IBM Research Institute March 24 2004 1 INTRODUCTION a 22a 5 2 DEVELOPING YOUR PROGRAM WITH GRID SUPERSCALAR 7 I WICKS TAR EEE 7 2 2 IDENTIFYING FUNCTIONS THAT WILL BE RUN ON THE GRID 7 2 3 DEFNINGTHE IDG FILE 2 02 8 2 4 GENERATING STUBS AND SKELETONS 0 cccccssssececsessececeesseeeeeesesaeeeenes 9 2 4 1 C Ct BIMNdIN Goliad tae aplasia cap E E ek 10 24 2 SPEIL Binding Sasse ni 11 2 5 WRITING THE MASTER 2 428882 Seesen 12 23A Special DRUIDEN oncidii ei Os 12 2 6 WRITING THE WORKERS cceeesssssseennnssseennnnsnennnnnnnsnnnnsnennnnsnennnnnsnennnnnnn 14 2 6 1 Special DAMIT VeS nee ileus Dee le Td coasted ant sea ge 15 2 7 HINTS TO ACHIEVE A GOOD PERFORMANCE ccccsssscccesssscceessssceseeeess 16 2 8 KNOWN RESTRICTIONS ccccccccssscccccsssccccesssccsesssccseesssccsseseccsseuecesseess 16 2 9 THE GSBUIED TOOL a seen esse E a eiS 17 3 RUNNING THE DEVELOPED PROGRAM seseesseccessssccssssceceesscoceessese 19 Bele gt QUICKSTART EAEE EERST 19 3 2 COPYING AND COMPILING YOUR CODE ccccsssscecsssseeeeessneceesesaeeees 19 3 3 DEFINING ENVIRONMENT VARIABLES c sccccssssececessseeeeeesesseeeenssaeeees 22 3 4 HOW BROKER CFG WORKS h aissis oina ea a AE T OTa 24 3 5 HOW DISKMAPS CFG WORKS sssscccecececcesessseseeceseceseeusesseeceseseseausnsnes 25 3 6 HOW ESTIMATIONS CFG WORKS cccccccesesccccesssscccusssceseess
20. INE hostname HAS FAILED Globus error error from system Checkpoint file erased for safety reasons What happened wu sea ersten 35 5 3 11 I get an error like this when trying to run the master License Manager Error Your license expired on 23 02 2004 Please contact Rosa M Badia rosab ac upc es What is all this stuff about licenses I haven t OC QUIF CO ON r Aue nee lines te 36 5 4 THE WORKERS inni eoor e E E E E EE EER 36 5 4 1 The first task executing returns an error of this kind ERROR AT TASK 0 xx x When I see log files at the worker side I find this at the ErrTask0 log app worker error while loading shared libraries libGS worker so 0 cannot open shared object file No such file or Directory Aa se A Somme aiid 36 5 4 2 I get this message when I try to execute a remote task ERROR AT TASK 0 Akk kxk kkk MACHINE hostname the executable file permissions do not allow execution ccccccccessseceseenteceeeenteeees 36 5 4 3 The firs task ends with an error but now when I look into the worker I find in ErrTask0 log workerGS sh app worker No such file or direcion ee ee ee 36 5 4 4 Once more my first task fails but my log files are empty That s COAG 1 A ae aaa a aaa a a a a taut 36 5 4 5 Ialways get errors when trying to run a task into a worker Is it Globus fault Is it GRID superscalar fault Is it my fAUIt 0 cece e ste eeeeenteeees 37
21. _SOCKETS set to 1 Some machines have constraints in connectivity regarding to opened ports For this reason you have to tell to GRID superscalar an available range of ports to be used to open a reply port when working with the sockets version Default value is 20340 e GS_MAX PORT The upper threshold It is considered only when GS_SOCKETS is set to 1 22 GS_SHORTCUTS Allow or not 1 or 0 shortcut mechanism between workers This mechanism allows you to resolve faster more data dependencies between tasks Currently this feature is not supported so you won t be able to change its value to 1 GS_FTPORT This integer tells us where the gsiftp port is located for transferring files If you don t know which port is the gsiftp using you can ask your system administrator Default port is 2811 GS_NAMELENGTH Maximum length of the names of the files involved in the computation This means the files used when calling your new GRID superscalar functions defined with our IDL Default value is 255 GS_GENLENGTH Maximum length of scalar variables nvolved in the computation i e maximum digits of a number This value doesn t determine the precision when representing the scalar in the computer arquitecture Default value is 255 GS_MAXPATH Maximum length of a given path in your application Must be 10 or more characters Default value is 255 GS_MAXURL Maximum URL size from your program i e machine name plus invoked service and port You
22. achine all owned by your username The most common is globus jobmanager started by globus job manager script pl so you can see sometimes both Figure 4 2 This process globus jobmanager will handle the execution of your remote job copy files start the binary When files are being copied to that machine you can see the corresponding globus url copy process running Figure 4 2 And when the worker binary is running you can see a workerGS sh and a matmul worker processes Figure 4 3 When the worker binary ends you can see still the remaining globus jobmanager The most typical case is to have as many globus jobmanager processes as the limit of jobs defined in that machine in broker cfg file If there is a queue system in that machine some more processes can be there depending on your queue system but the basic ones described before will also appear username 7312 22 0 0 1 5356 3956 S 12 06 0 00 usr bin perl aplic GLOBUS 2 2 libexec globus job manager script pl username 7235 2 7 0 1 5208 3244 S 12 06 0 00 globus job manager conf aplic GLOBUS 2 2 etc globus job manager con username 7319 0 0 0 0 5216 2376 S 12 06 0 00 aplic GLOBUS 2 2 bin globus url copy gsiftp kandake cepba upc es 2 Figure 4 2 And when the transfers end username 8035 1 0 0 0 2152 1016 S 12 06 0 00 bin sh home at khafre MatMul workerGS sh 0 0 A 0 0 B 0 0 C 0 0 C 0 0 29 username 8036 1 0 0 0 1804 580 S 12 06 0 00 matmul worker
23. ame Escape character is Where hostname is the worker that we suspect is failing The connection has to remain till you write quit If you get a Connection refused message tell your system administrator that Globus is not working properly because the gatekeeper is not started or is unreachable 5 3 10 When the master is going to end I get this message ERROR REMOTE DELETION OF FILES IN MACHINE hostname HAS FAILED Globus error error from system Checkpoint file erased for safety reasons What happened When the master ends it recovers all result files and erases temporary files in all the workers involved in the computation If this final process fails the master reaches anon consistent state In this situation it cannot recover from the checkpoint file You 35 can get your results by hand and erase temporary files or start your execution again from the beginning The main reason that makes this error appear is when you don t have enough quota in the master to receive the result files but check the Globus error sentence to know this more precisely 5 3 11 I get an error like this when trying to run the master License Manager Error Your license expired on 23 02 2004 Please contact Rosa M Badia rosab ac upc es What is all this stuff about licenses I haven t acquired any We use to generate GRID superscalar distributions with expiration date so you can take benefit from our new versio
24. an environment variable called LD_LIBRARY_PATH You have to avoid erasing other previous defined library paths when defining the new one check it with env command An example follows setenv LD_LIBRARY_PATH GS_HOME 1ib LD_LIBRARY_PATH 23 Don t do this if the variable doesn t exist previously This step is not needed when GRID superscalar libraries are installed in a standard location You may ask your system administrator about this At the worker side there is a file named workerGS sh If there is not you must create one This file MUST have execute permission because the master will invoke it It s content must be similar to this bin sh export GS_MIN_PORT 20341 export GS_MAX_PORT 20459 export LD_LIBRARY_PATH GS_HOME lib app worker S Take into account now that we used export to define the environment variables because we are now using a shell that supports this command This file will set the environment variables in the worker side You can suppose that no previous environment variables are defined and set them here if needed i e when running an external simulator GS_MIN_PORT and GS_MAX_PORT are only required when working with GS_SOCKETS set to 1 and when we want to modify the default values Also LD_LIBRARY_PATH must be set if needed considering the local machine not the master If you are familiar with scripting languages you could think that you can add an exec before last line
25. application in a sequential fashion The requirements to run that sequential application in a computational Grid are the specification of the interface of the tasks that should be run in the Grid and at some points calls to the GRID superscalar interface functions and link with the run time library The rest of the code already written for your application doesn t have to change because GRID superscalar has bindings to several programming languages Our tool provides an underlying run time that is able to detect the inherent parallelism of the sequential application and performs concurrent task submission In addition to a data dependence analysis based on those input output task parameters that are files techniques such as file renaming and file locality are applied to increase the application performance Current GRID superscalar prototype is based on Globus Toolkit 2 x GRID superscalar is a new programming paradigm for GRID enabling applications composed of an interface and a run time With GRID superscalar a sequential application composed of tasks of a certain granularity is automatically converted into a parallel application where the tasks are executed in different servers of a computational GRID The behavior of the application when run with GRID superscalar is the following for each task candidate to be run in the GRID the GRID superscalar run time inserts a node in a task graph Then the GRID superscalar run time system seeks fo
26. at khafre MatMul 24 kadesh cepba upc es 16 short home at kadesh MatMul kadesh8 cepba upc es 8 mbench home at kadesh8 MatMul kandake cepba upc es home at kandake MatMul In this example kandake is going to be the master and khafre kadesh and kadesh8 are going to be the workers We can submit 4 16 and 8 jobs to each machine at the same time and kadesh jobs will go to a queue named short and kadesh8 jobs will go to a queue named mbench Each machine has also defined its working directory 3 5 How diskmaps cfg works In current working systems it s usual to have disks shared between various machines With this configuration file we can tell the master when a shared disk exists so there is no need of transferring the file between these machines because both can reach the file Let s have a look at a generic example to understand the syntax Machine NameOfSharedDisk PathnameInTheMachine workerl diskO pathl worker2 diskO path2 master diskO path3 workerl disklocall path4 worker2 disklocal2 path5 master disklocal3 path6 This file is divided in two parts The first part describes the shared disks between machines You can name the disk as you want but remember to use the same name for the same physical disk You can read the information like this workerl can see diskO using path1l worker2 can see diskO using path2 and so on This means that workerl and worker2 can access to diskO but it has a different path i
27. der to compile correctly At the worker we could have this Makefile CC g t CFLAGS g Wall I GS_HOME include all matmul worker matmul worker matmul worker o matmul functions o g Wall matmul worker o matmul functions o o matmul worker L GS_HOME lib 1GS worker clean 21 rm f core o matmul worker Note that we are compiling with C because the block type included in matmul functions c is defined in C Here we have to link matmul worker with matmul functions object and with GS worker library The resulting executable will be named matmul worker Remember that each part must be compiled in the machine where it is going to be run in the C C case so we can avoid architecture incompatibilities and GRID superscalar library location differences 3 3 Defining environment variables Some environment variables are required to get your program running These environment variables allow you to change some behavior of the GRID superscalar run time without having to recompile neither your program nor the GRID superscalar library You don t have to define them if you don t want because they have a default value but we recommend you to check if the default value satisfies your requirements This part is concerning the master or client e GS_DEBUG You can set this variable to receive more or less debug information When it s 20 the master will write at its standard output lots of useful information in
28. e in this variable This code must be higher than 0 because 0 is used to say that everything is ok and negative values are reserved for the GRID superscalar run time You can even build your own error code mapping to detect what is happening in the worker by giving each number a meaning And now we have all the programming work done so we are ready for running our application 15 2 7 Hints to achieve a good performance When programming your application you can take into account several indications in order to achieve a better performance than if you don t This is not a mandatory thing to do because you can have already your code programmed and you don t want to severely modify the sources So you can run your application without knowing anything about this section but we recommend you to follow reading because maybe with some little changes you can really increase the performance of your application The first restriction we find when trying to run some tasks in parallel is when a true data dependence is found This happens when a task wants to read a file input File that is generated at a previous task output File If the input file is not really necessary i e it could be some debug information not needed data we recommend that you do not include this file as an input file in the task definition at the IDL file You could also think about other data dependencies when a task needs to write in the same file that a previous o
29. e and its callbacks mechanism you can find this also as printed information If you are not familiar the information is 30 really self explaining Remember that all this parameters refer to the worker where the job is going to be run There is also another important thing to remember about returning values of tasks You can see at some point this debug information TASK 11 JUST EXTRACTED and some lines later ERROR Code 0 In this case the returning value of the task is 0 so everything is ok But if something different from 0 is returned a worker has detected an error so the master is going to stop its execution An error code different from 0 will be shown in the master even when you have GS_DEBUG set to 0 As described in section 2 6 Writing the Workers you can detect errors by setting gs_result to a value different from 0 So here we will know at the master when a worker fails If you receive a negative error code this means that there is an operating system problem your code can have an invalid memory reference someone could have killed your process Probably you want to see what happens into the worker and look at the worker log files 4 3 Worker log files As shown in section 3 3 we can tell GRID superscalar run time to leave standard output and standard error information in the worker that has executed a task This information can be really useful when trying to determine why our program does
30. e master And you must use the file descriptors returned by this functions to work with the files You can never suppose that a file has its original name e You cannot rename files at the master side in your program If this renaming is unavoidable you have to copy the file to a new one with the new name but remember to use GRID superscalar special primitives to handle files while doing this copy e You cannot remove files that are used as input or output parameters in your IDL defined functions before calling to GS_Off because you cannot do it in a safe way e In the worker side you cannot call an external application in your functions code by calling system provided by the C library You must use GS_System section 2 6 1 But you can use a relative or absolute path when calling to this external application e Inside worker functions it is not allowed to refer to a file by its original name when this file is passed as a parameter from the function You must use the parameters defined in the function However you can create a temporary file in current working directory and refer to it by its name e You cannot define the same working directory between a master and a worker at broker cfg section 3 4 e It is not available to define output files that belong to a shared disk This feature is provided to share source files section 3 5 e Perl binding doesn t allow you to set GS_SOCKETS to 1 You can see that not all this res
31. e used for renaming techniques They are different versions of a file during the original file lifetime They can appear at the master and at the workers e GS_fileXX Some extra information must be saved when checkpointing local tasks in your main program This information is stored in those files They are created at the master side e tasks chk This file is only in the master It allows you to restart from a task your execution without having to repeat previously done computations If you delete it the master will restart all the computations from the beginning e OutTaskXX log ErrTaskXX log Standard output and standard error from the task with number XX at the worker side They won t be generated when GS_LOGS is set to 0 e destGen XX They appear at the master and at the workers This name identifies the files that are messages from a task between the master and the workers When GS_SOCKETS is set to 1 these files don t have to appear If the master is stopped you can delete them without any danger Some files transferred as sources to tasks can remain in the working directory of the workers You can also delete them with no danger if everything is stopped However remember that if you are planning to execute your program again you don t have to worry because these files will also be overwritten In addition you can add to your Makefile some basic rules to erase all this files So we have at the master side delete
32. edTime and MasterBandwidth N workerl_linkspeed time_opl time_op2 time_opN worker2_linkspeed time_opl time_op2 time_opN master_linkspeed N has to be the number of operations defined at app idl Then the workers have its own link speed in bytes per second and for each operation defined at appl idl file a measure of the time in seconds hat the operation is supposed to last in that machine The end of the file contains the master link speed also specified in bytes per second Let s see all this in a real case We are going to suppose a different example from matmul to add a little more size to the file NumberOfOperations new line BandwidthBytesPerSecond OpId0SimulatedTime OpId1lSimulatedTime and MasterBandwidth 4 1310720 0 1 1310720 0 2 1310720 0 1 1310720 7 02 8 0 3 0 001 17 5 6 0 25 0 001 This file will be for an IDL with 4 defined functions When executed in the first worker defined at broker cfg first operation is expected to last 0 1 seconds Second operation 3 7 and so on We can see that the first worker is the fastest and the second is the slowest one The more accurate these values are the better our scheduling policy will apply avoiding file transfers We can also see our configuration file in our matrix multiplication example 26 NumberOfOperations new line BandwidthBytesPerSecond OpId0SimulatedTime OpIdlSimulatedTime and BandwidthSpeed 1 1310720 0 001 1310720 0 002 13
33. figuration environment is ready you just have to call configure configure with gs prefix GS_HOME Here GS_HOME means the path were you have installed GRID superscalar You can see other available options using the help modifier but the typical option is the one used in the given example 18 3 Running the developed program In order to run our developed application we have to prepare the binary files in every machine that will be used for running our program other configuration files and environment variables This constraint applies in current version of GRID superscalar Nevertheless we are already working in a deployment environment which will automate all this steps Anyway it s always good to know how the internals work so we encourage you to follow reading This section will explain how to copy and compile your code how to define environment variables how to make your configuration files and finally some basic Globus commands needed to run your program We will suppose from now that you have an installation of GRID superscalar under GS_HOME directory 3 1 Quickstart These are the main steps that you have to follow when running you GRID superscalar enabled application e Install Globus 2 2 or 2 4 not 2 0 or 3 x and GRID superscalar libraries e Copy in the corresponding machines the files that each of them needs In C C case you need app h app stubs c and app c at the master and app h app worker c and
34. first of all we can talk about installation 19 requirements Current version of GRID superscalar uses Globus Toolkit 2 2 or 2 4 2 0 is not compatible You need at least a client installation in the master machine and a server installation in each machine that is going to be a worker You also need to have the gsiftp service running in every machine involved in the computation included in Globus Toolkit distribution so transfer of files between machines can be done From GRID superscalar you will need the GS master library at master machine and the GS worker library at worker machines You will need also the gsstubgen tool at the master side and the library includes GS master h at the master GS worker h at the workers and gs_base64 h at every machine All these files are included in the GRID superscalar distribution The GRID superscalar also includes a tool called moved libtool sh This tool repairs the library files if you decide to move them to a new directory You have to use it like this moved libtool sh new_path_for_the_libraries GS_HOME 1lib la Regarding developed files location where each file must be placed will be clearer with a graphical description There are differences between C C binding and Perl binding As Figure 3 1 shows at the master we need app c hat contains the main application app h with previously defined function headers and app stubs c generated with gsstubgen In the case of Perl Fi
35. function the parameters of the function that are strings and filenames are encoded using base64 format Then the Execute function is called The Execute function is the main primitive of the GRID superscalar interface It s the entrance point to the run time include lt stdio h gt include lt stdlib h gt include lt limits h gt include lt string h gt include lt gs_base64 h gt include lt GS_master h gt include matmul h int gs_result void matmul file fl file 2 file f3 Marshalling Demarshalling buffers Allocate buffers Parameter marshalling Execute matmulOp 3 0 1 0 f1 2 3 3 Deallocate buffers Figure 2 1 The other file automatically generated by gsstubgen is shown in Figure 2 2 This is the main program of the code executed in the servers Inside this program 10 calls to the original user functions are performed Before calling the user functions the parameters are decoded include lt stdio h gt include lt stdlib h gt include lt limits h gt include lt string h gt include lt gs_base64 h gt include lt GS_worker h gt include matmul h int main int argc char argv enum operationCode opCod enum operationCode atoi argv 2 IniWorker argc argv switch opCod case matmulOp matmul argv 3 argv 4 argv 6 break EndWorker gs_result argc argv return 0 Figure 2 2 2 4 2
36. g system This means that if you want to see how your jobs are going you have to use standard operating system methods of monitoring processes These commonly are ps and top This section is not intended to be an operating systems tutorial but we can give you some hints and examples of what you can and cannot see So when you run your master program you can see several threads belonging to it in particular you can see 3 for example in Linux see Figure 4 1 This is normal because the master creates a thread to listen to messages and this thread needs a thread master in Linux So don t be worried if the name of your master process appears more than once PID USER PRI NI SIZE RSS SHARE STAT CPU MEM TIME COMMAND 25273 username 19 10 3012 3012 2384 SN 94 8 2 3 0 00 in ftpd 25272 username 19 10 3012 3012 2384 S N 88 7 2 3 0 01 in ftpd 25266 username 9 0 6172 6172 2656 S 0 0 4 8 0 00 matmul 25267 username 9 0 6172 6172 2656 S 0 0 4 8 0 00 matmul 25268 username 9 0 6172 6172 2656 S 0 0 4 8 0 00 matmul Figure 4 1 At the master side you can also see a process called in ftpd and owned by root consuming CPU Figure 4 1 This means that a file is being transferred so the gsiftp service is being used If you want to see what processes are running in a worker you don t have any other way by now than to log into that machine and see it for yourself You can see several processes that can tell you what is happening in that m
37. gure 3 2 we need app pl with the main application app so dynamic library generated to call GRID superscalar run time and app pm the Perl module that will be called from app pl app idl I j client i l server I I l 1 app stubs c l C apn gt I app functions c I l Figure 3 1 In the worker side we need app h app worker c generated automatically and app functions c where we wrote all our functions Looking at Perl again we see that we need app worker pl the generated skeleton and app functions pm with the functionality In both versions we need an additional file called workerGS sh that will define all environment variables at the worker side We will talk about this in the next section 20 Figure 3 2 Final step in C C binding is to compile all parts You can take our example as the base to make your own Makefile CC gcc CFLAGS g Wall I GS_HOME include CXX gt CXXFLAGS g Wall I GS_HOME include all matmul matmul stubs c matmul h matmul idl gsstubgen matmul idl matmul o matmul cc matmul h matmul matmul o matmul stubs o g Wall g matmul o matmul stubs o L GS_HOME lib o matmul 1GS master clean rm f matmul o core As this master Makefile rules describe our matmul o must be linked with matmul stubs object and the GS master library Remember that your app c code must include GS_master h given with GRID superscalar distribution and app h in or
38. in broker cfg and that nobody has deleted last line from workerGS sh It has to contain this app worker 36 5 4 5 L always get errors when trying to run a task into a worker Is it Globus fault Is it GRID superscalar fault Is it my fault The first thing you can do when the remote executions fail is to run a single test to check that Globus can run jobs You can do globus job run workerl bin date And see if this returns the current date and time If this fails you can contact your system administrator and tell him that you cannot use Globus for running your jobs 5 4 6 I receive this message at the master ERROR Submitting a job to hostname Globus error the cache file could not be opened in order to relocate the user proxy Check if you have available disk space in that worker machine This error can leave some gram_scratch_ lt random_name gt subdirectories in the involved worker 5 4 7 I receive this message at the master ERROR Submitting a job to hostname Globus error the job manager failed to create the temporary stdout filename This can be also a problem with quota in hostname 5 4 8 I get this message ERROR Submitting a job to hostname Globus error data transfer to the server failed The reason could be that you don t have enough quota on the worker machine to transfer your input files Check this with the quota command 5 4 9 After having a quota problem in a worker
39. ived Several signals can be received so this could tell you that your program has an invalid memory reference typically a 11 error code been terminated almost always a 15 error code aborted 6 Signal number 9 kill cannot be reprogrammed so you will never receive a 9 error code You will have to look at the worker logs to see if a worker has been killed Not all signal numbers are standard so if you are not familiar with this operating system features you can ask your system administrator about this 31 4 4 Cleaning temporary files There are several hidden files that you can find in your master and in your workers when running your application developed with GRID superscalar These files that are needed to implement techniques as renaming to improve parallelism and so performance of your application or checkpointing to avoid repeating computation that has been already done are automatically erased during the execution of your program and when the application finishes For some strange reasons the application cannot finish correctly i e when the master crashes and some of these files can remain in their locations There is no real need to deal with these files because they will be overwritten if you execute again your application However we can see what are their names and which is their purpose so if you find yourself in trouble you can decide if you want to delete them or not e RENXX These files ar
40. lication programmer when executing the program Application code initialization for i 0 i lt N i T1 filel txt file2 txt T2 file4 txt file5 txt T3 file2 txt file5 txt file6 txt T4 file7 txt file8 txt T5 file6 txt file8 txt file9 txt Figure 1 1 2 Developing your program with GRID superscalar To develop an application in the GRID superscalar paradigm a programmer must go through the following three stages 1 Task definition identify those subroutines programs in the application that are going to be executed in the computational Grid 2 Task parameters definition identify which parameters are input output files and which are input output generic scalars 3 Write the sequential program main program and task code In the current prototype stages 1 and 2 task definition and task parameters definition are performed by writing an interface definition file IDL file This interface definition file is based in the CORBA IDL language which allows an elegant and easy way to write and understand syntax We selected that language simply because it was the one that best fitted our needs although GRID superscalar does not have any relation wth CORBA We are going to see all this in more detail into this chapter 2 2 1 Quickstart This section is intended to be as a reference of the steps that you have to follow when developing
41. lps in two ways it makes your code easier to understand and allows you to repeat the same functionality in other stages of your application This basic programming technique will be the key to gridify your application Your code may have some computation that you may want to be performed on the grid This computation can be already in a function called from the main program If this is not the case we recommend you to put your code into a local function in order to ease even more the use of GRID superscalar Another important step is to define the header of the function properly You have to put in this header the files needed input files output files or input output files and scalar parameters needed input or output i e you could need a scalar value to start a simulation If you need to return a file or a scalar write it in the header parameters as an output parameter This way you can return more than one value or file Current prototype doesn t allow the functions to have a return value so you have to return this value in the header This whole process will be seen really clear in our matrix multiplication example One typical operation done between matrixes is the multiplication When the matrixes grow in size it grows also the complexity of the algorithm Then we search a way to speed up this computation trying to parallelize our code A first step is to divide matrixes in blocks so we get several advantages from a version withou
42. n t run You can print information from inside your app functions c pm file to standard output and standard error that can give you a hint of what is happening there Each call to an IDL function from your master main program generates a new task so a new number to name it is also generated First task will be named task 0 next will be 1 and so on This will help you to determine which IDL call has generated a log file Some default information is printed from the run time at OutTaskXX log Task 0 SCode 0 Getting stats of TMP O cfg We are sending this 1 0 78 194940442219376564 3121 0 MasterName is kandake cepba upc es ReplyPort is 20342 This log is for Task 0 so it must be named OutTaskO log The SCode refers to the shortcut mechanism but we don t have to worry about that as explained when defining GS_SHORTCUTS environment variable When the worker gets stats of a file this means that this file is an output of this task Beyond the We are sending this sentence we have a message that is going to be sent to the master First integer refers again to shortcut stuff so we don t worry next we have the task number all its output scalars all the size of output files and the last integer refers to the value of gs_result This can be 0 positive or negative A 0 value would mean that there is no error a positive value would mean an error detected by the programmer and a negative value would mean that a signal has been rece
43. n all machines have access p matrix files stored into scratch at kandake mat_files from the master point of view Workers have to access this matrix files using another path So these files won t be transferred between machines In this real case DiskO is not the same physical disk in all these machines but a replica The working directories of each machine are also defined but we can see that kadesh and kadesh8 use the same working directory they belong to a cluster This means that files will be just transferred one time to that zone and both machines will be able to use them Note that this diskmaps cfg doesn t match with the one provided in GRID superscalar distribution into the matrix multiplication example That cfg file doesn t have any shared disks 3 6 How estimations cfg works With the objective of doing a better scheduling when giving tasks to the workers a file with the estimations of the execution of the functions must be provided This can be done by running an isolated execution of the function on the required machine or with a simulator Also the bandwidth of each machine specified in bytes per second must be given This will help the runtime in deciding where is the best place to execute our task depending on transfers of files needed and computation power of that worker The syntax can be extracted from this generic example NumberOfOperations new line BandwidthBytesPerSecond OpId0SimulatedTime OpId1lSimulat
44. n each machine it can be mounted in a different way The important thing is that when we pass as a parameter of a function a file beginning with path3 the GRID superscalar run time will detect that is placed in diskO and will avoid the transfer when possible This is also useful when we have mirrors of a database in several machines If we are going to use this database as inputs we can tell also where are this copies located in the server machines and in the client machine The second part specifies the name of the disk where the working directory is placed the working directory is defined in broker cfg Usually each machine will have its own disk name and the same path given into broker cfg file But sometimes you can be interested in some workers sharing a working directory i e into a cluster So some workers can have the same disk name to warn GRID superscalar about this sharing An example will clarify things achine NameOfSharedDisk PathnameInTheMachine kandake cepba upc es Disk0 scratch at kandake mat_files khafre cepba upc es Disk0 scratch at khafre mat_files kadesh cepba upc es DiskO scratch at kadesh mat_files kadesh8 cepba upc es Disk0 scratch at kadesh8 mat_files kandake cepba upc es DiskLocal0 home at kandake MatMul khafre cepba upc es DiskLocall home at khafre MatMul 25 kadesh cepba upc es DiskLocal2 home at kadesh MatMul kadesh8 cepba upc es DiskLocal2 home at kadesh8 MatMul With this configuratio
45. name GS_Close file_des and GS_FClose file_des You have to call this primitives to close the file you opened before The previous file descriptor explained as the return of the GS_Open and GS_FOpen primitives must be used here as a parameter You cannot forget this step or your GRID superscalar execution will never end Working with Perl you have to call close file_handle You just have to replace your calls for opening and closing files by GRID superscalar primitives to do this There is no need to change your read write calls Another important point is that you can t rename a file in your main code because this can disturb GRID superscalar run time If this renaming is unavoidable you can copy that file giving to the new copy the name you desire but always using the GRID superscalar file primitives The current set of specific GRID superscalar primitives is relatively small and we do not discard the possibility that more primitives could be included in future versions However what is more probable is that these functions will be hidden to the programmer by writing wrapper functions that will replace the system functions In the matrix multiply example our master will be include lt time h gt include lt stdio h gt include lt errno h gt include GS_master h include matmul h int main int argc char argv long int t time NULL char f1 15 2 15 f 3 15 file 15 FILE fp GS_On f
46. nction structure in your main code this step will be really simple You just have to write your function headers in our IDL form into a file called lt myapplication gt idl we will assume from now that is named app idl In order to learn how the syntax works we present a generic example interface MYAPPL void myfunctionl in File filel in scalar_type scalarl out File file2 void myfunction2 in File filel in File file2 out scalar_type scalarl void myfunction3 inout scalar_type scalarl inout File filel As you can see there is one requirement needed in this interface all functions must begin with void If you have to return a parameter you have to specify it as an output parameter Files are a special type of parameters since they define the tasks data dependences For that reason a special type File has been defined This type is also needed to differ a file from a string that could be needed in your function as an input i e when passing modifiers to a simulator call v f Let s detail what combinations are possible for each parameter in File out File inout File in scalar_type out scalar_type inout scalar_type The scalar_type can be one of these char wchar string wstring short int long float double and boolean Another important thing to have in consideration is that we do not recommend the use of output scalar parameters because they will have a little influence in the parallelism extrac
47. ne and when a task needs to write into a file that has first to be read by another task You don t have to worry about these dependencies because GRID superscalar will eliminate them The next indication is about out scalars In section 2 3 we have described that you can define a parameter as an output scalar but we also point that when you define this kind of parameter the performance could be worst than if you don t That is because you can be using this parameter immediately after calling to this IDL defined function Then the GRID superscalar runtime doesn t have any other possibility than to wait for this task to complete so this output scalar will be available This wait can be hidden if GRID superscalar has enough tasks available to be run in parallel and when the task with the output scalar is early scheduled for execution If we don t meet this conditions performance will diminish Another thing to avoid when trying to get a better performance is the call to GS_Barrier We have presented it as an advanced feature in section 2 5 1 because in most of cases you will never use this call In other cases you may need it When you call to GS_Barrier you tell the GRID superscalar run time to continue to run previous generated tasks but wait for all of them to finish This waiting means that no new tasks are going to be generated from this point main code is not going to continue till all previous tasks are done This synchronism point
48. nning waiting pending and ready tasks Waiting means that they are stopped waiting for a file to be transferred but this transfer has been started from another task Pending means that the task still has data dependencies to be resolved and ready means that it can be submitted at any time You can see also the decision that GRID superscalar takes when choosing which is going to be the next running task When the sentence ESTIMATION BEGINS appears this means that the run time is deciding where to run the job There is an estimation of transfer files and execution time for each task in the ready queue against each worker Estimation comes like this ESTIMATION 0 200000 Task 14 Machine 0 Size 0 000000 ESTIMATION 0 203664 Task 14 Machine 1 Size 4802 000000 ESTIMATION 0 203664 Task 14 Machine 2 Size 4802 000000 You can see here that the task 14 is going to last 0 2 seconds in worker 0 and more than 0 20 in worker and worker 2 That is because the files needed are not in these two workers in contrast with worker 0 that already has the files as pointed by the Size value that means how many file bytes do we have to transfer to that machine So worker 0 will be chosen as shown in sentence lt MARKED MACHINE 0 gt lt aS SS E SUBMITTED 1 gt This also tells us how many jobs are submitted to that worker at the same time If you are familiar with Globus RSL languag
49. nning with app your_function with all parameters of course Another change would be necessary on those parts of the main program where files are read or written Since the files are the objects that define the data dependences the run time needs to be aware of any operation performed on a file Let s see all those primitives We have detailed Perl syntax in parentheses Remember to put the name of the module before the call GSMaster 2 5 1 Special primitives e GS_On onO Tells the GRID superscalar run time that the program is beginning The best place of putting this is at the beginning of your main code but you can put it later always considering that you cannot call any GRID superscalar primitive or function if you have not called first GS_On e GS_Off code off code This call will wait for all remote tasks to end and will tell to the GRID superscalar run time to stop In order to indicate an error situation i e when your program has to end prematurely because you detect an error you have to set code to 1 Take into account that this GS_Off 1 will exit your main program You can put this also at the end of your code with GS_Off 0 indicating that there has been no error GS_Off 0 won t exit your main program but remember that you won t be able to call any GRID superscalar primitive or function from this point and till the end of your program e GS_Barrier barrier In some special cases you may need thi
50. ns of GRID superscalar with new features and fixed bugs It is not good that you remain with the same old and possibly not bug free version forever 5 4 The Workers 5 4 1 The first task executing returns an error of this kind ERROR AT TASK 0 849 When I see log files at the worker side I find this at the ErrTask0 log app worker error while loading shared libraries libGS worker so 0 cannot open shared object file No such file or directory You probably with good intentions deleted at workerGS sh a line that defines the LD_LIBRARY_PATH environment variable to load the GS worker library You cannot remove it if your GRID superscalar library is not installed into a standard location Just put it back 5 4 2 I get this message when I try to execute a remote task ERROR AT TASK 0 Hr rer MACHINE hostname 8 the executable file permissions do not allow execution You must check that the workerGS sh file in the worker named hostname has execute permission To change permissions you can run chmod ugo x workerGS sh 5 4 3 The firs task ends with an error but now when I look into the worker I find in ErrTask0 log workerGS sh app worker No such file or directory You have not compiled the worker in this machine 5 4 4 Once more my first task fails but my log files are empty That s crazy Be sure that your paths for finding the worker executable are correctly defined
51. or int i 0 i lt MSIZE i 13 for int j 0 j lt MSIZE j for int k 0 k lt MSTZE k sprintf fl A d 3d i k sprintf f2 B d d k 4 sprintf f3 C d d i 4 3 3 f1 2 matmul fl 2 3 GS_Off 0 printf Total time n t time NULL t printf d Hours d Minutes d Seconds n t 3600 t 3600 60 t 3600 60 return 0 In this particular case we just have to add GS_On and GS_Off because matmul is defined exactly with the same parameters that in our sequential version We have decided to remove all the local functions that we don t need and leave them in another file 2 6 Writing the Workers Additionally the user provides the code of the functions that have been selected to run on the GRID The code of those functions does not differ from the code of the functions for a sequential application The only current requirement is that they should be provided in a separate file from the main program This file must be called app functions c pm remember that app is the name we gave to the IDL file Moreover there are some basic rules to build it you have to include GS_worker h file given with GRID superscalar distribution and app h generated by gsstubgen This file will have as many functions as defined in your IDL file so you have to copy the code of your functions here or if your code was not structured in functions the parts
52. r You can contact your system administrator to know that 5 2 GRID superscalar tools 5 2 1 When I use gsstubgen I get this output Warning renaming file app stubs c to app stubs c Warning renaming file app worker c to app worker c Warning renaming file app h to app h What is this for In this case gsstubgen has done backups for your old generated files from your IDL definition This backups end with the character You can remove them by hand Next time if you don t want to generate backups use n flag 5 3 The master 5 3 1 When I set GS_DEBUG to 10 or 20 the output of my main program seems to appear in really weird places What is happening If you print something to the standard output the system has a buffer to print more information from one call So it s normal that sometimes appears in weird places 33 5 32 When I redirect all output given from the master to a file sometimes at the end some information is missing Why Again buffering of the operating system is cheating you You can also see that the order of some prints also change when printing by screen or when printing to the file But that s normal You can repeat the execution and see how it ends printing by screen 5 3 3 I get a message like this when trying to run the master ERROR activating Globus modules Check that you have started your user proxy with grid proxy info You forgot to start your Globus proxy or
53. r data dependences between the different tasks of the graph These data dependences are defined by the input output of the tasks that are files If a task does not have any dependence with previous tasks that have not been finished or which are still running i e the task is not waiting for any data that has not been already generated it can be submitted for execution to the GRID If that occurs the GRID superscalar run time requests a GRID server to the broker and if a server is provided it submits the task Those tasks that do not have any data dependence between them can be run on parallel on the grid This process is automatically controlled by the GRID superscalar run time without any additional effort for the user Figure 1 1 shows an overview of the behavior that we have described above The reason for only considering data dependences defined by parameter files is because we assume that the tasks of the applications which will take advantage of GRID superscalar will be simulations finite element solvers biology applications In all such cases the main parameters of these tasks are passed through files In any case we do not discard that future versions of the GRID superscalar will take into account all data dependencies GRID superscalar applications will be composed of a client binary run on client host and one server binary for each server host available in the computational GRID However this structure will be hidden to the app
54. s advanced feature Sometimes you might need all the submitted tasks to finish in order to take a decision and start working again GS_Barrier allows you to do that kind of synchronization as GS_Off does but it allows you to call more GRID superscalar functions later Don t use this 12 function unless you don t have any other choice because it can severely slow the parallelization of your code GS_Open filename mode and GS_FOpen filename mode As explained in previous section 2 5 GRID superscalar needs to have full control over the files These primitives will allow you to work with files while keeping GRID superscalar in control They both return a descriptor that MUST be used in order to work with these files i e to call read write functions These descriptors correspond to the ones returned by your C library when using open and fopen so you won t have to change following C library calls that work with these file descriptors Modes currently supported are R reading W writing and A append Perl case is special because several functions are defined open_r file_handle file_name open_w file_handle file_name open_a file_handle file_name Because some file renaming techniques are used to avoid data dependencies in your code and so achieve more parallelism you have to use this file descriptor returned in order to work with the file There is no guarantee that the files will be available with the expected
55. seseeeeesseseenesss 26 3 7 AM I READY TO RUN renaren cece AA A RATA TAA RA ARAE 27 3 8 RECOVERING FROM A CHECKPOINT FILE cccsssscceeesssseeeeeseseeeeseseeees 27 4 DEBUGGING YOUR GRID SUPERSCALAR PROGRAM 29 4 1 MONITORING YOUR EXECUTION cccccccsscccccesssccceesssceceessccceeesesseseeneess 29 4 2 MASTER DEBUG INFORMATION 0cssccecesssececsessececeeseseececsssaeeeenssneees 30 4 3 WORKER L OG FIEBS 42 2822 ies hs E iti a aoe tase vasa evi 8s 31 4 4 CLEANING TEMPORARY FILES cccccssscecesssscecsesseeeceesscaeeeessnaeeeenssneees 32 5 FREQUENTLY ASKED QUESTIONS FAQ eseesseseessssecssssocecssoceesscse 33 Sd GLOBUS emailen 33 5 1 1 What is Globus Why do I need it Can you give me some useful CoMmands Sans sense i 33 5 1 2 Ihave several log files In my workers home directory They are named grain JOD mer lt number gt lO au aka 33 5 2 GRID SUPERSCALAR TOOLS ccscscsceccccceccesssssceccessesessessseeccessessuneneess 33 5 2 1 When I use gsstubgen I get this output Warning renaming file app stubs c to app stubs c Warning renaming file app worker c to app worker c Warning renaming file app h to app h What is this for 33 5 3 TE MASTER 2 2 a A a a hE eS 33 5 3 1 When I set GS_DEBUG to 10 or 20 the output of my main program seems to appear in really weird places What is happening 33 5 3 2 When I redirect all output given from the ma
56. ster to a file sometimes at the end some information is missing Why cccccccssccceesssseceeeeees 34 5 3 3 I get a message like this when trying to run the master ERROR activating Globus modules Check that you have started your user proxy with DIA LOKS NO este art 34 5 3 4 The master ends with this message or similar app error while loading shared libraries libGS master so 0 cannot open shared object file NO such file or directory nenne rennen 34 5 3 5 When I set GS_SHORTCUTS to 1 I get this message ERROR Check environment variables values Why ccccccccsssscccessssececessssceeesssaeeesnsseeees 34 5 3 6 I get this message ERROR Check environment variables values But I have all variables defined and GS_SHORTCUTS is set to 0 34 5 3 7 When working with GS_SOCKETS set to 1 I get a segmentation fault at the master More precisely this happens when a previous execution ends prematurely or not and I try to launch the master immediatel 34 5 3 8 I get this message ERROR AT TASK 0 8 eR EERE MACHINE khafre cepba upc es the job manager could n t stage ima Near ise A E A uate ner AEE 35 5 3 9 I get this message ERROR Submitting a job to hostname Globus error the connection to the server failed check host and port 35 5 3 10 When the master is going to end I get this message ERROR REMOTE DELETION OF FILES IN MACH
57. t doing this division We don t need a full row or column to do some calculation because we can operate between blocks Another advantage is that you don t need to have all matrixes in memory because we just need the blocks that are going to be operated This is known as an out of core implementation This example is included in the GRID superscalar distribution so you can follow this explanation while looking at the source code We see that in our main code matmul cc there are three local functions PutBlock GetBlock and matmul The file named block cc contains the definition of a block and some useful operations We want to put the matrix multiplication running on the Grid so we must pay attention to matmul function We see that the definition is right because it has an input block named f1 another input block named f2 and an input output block named f3 void matmul char fl char f2 char f3 Each block is stored into a different file We can suppose a less favorable situation like this one double matmul char fl char f2 char f3 Imagine that you have a returning double which has the mean value between all the elements of the block We recommend you to add this double to the header and remove it from the return value so next steps will be even easier 2 3 Defining the IDL file The IDL file describes the headers of the functions that will be executed on the GRID If you have this functions already defined with a fu
58. ted from your code it can be reduced This only happens with output or inout scalar parameters not with input scalars So if you don t really need a scalar value to go on with your algorithm i e when you need this value to take a decision don t put it as an out scalar_type We can see all this now in the matrix example We are going to create a file named matmul idl This file is going to have this content interface MATMUL void matmul in File fl in File f2 inout File f3 So we have two input files and an input output file where the multiplication is going to be stored Remember that we don t have to add GetBlock and PutBlock functions to this IDL file because they are just functions to support our implementation they don t have any computation If you don t have your code structured in functions this and next steps will be not so easy but won t be difficult at all You have to think what parts of your code are needed to be run on the GRID and write a line in your IDL file for each of these parts There is also mandatory to see what files and parameters will be needed as inputs of this part of the code and what files and parameters are considered as results or outputs You just have to write it following the syntax described above 2 4 Generating stubs and skeletons From the interface definition that we have done in the previous step some code is automatically generated by gsstubgen a tool provided with
59. trictions are because of the file renaming done by GRID superscalar But you must consider them all 2 9 The gsbuild tool Since version 1 5 0 GRID superscalar distribution contains a tool named gsbuild that automates the steps needed to obtain from the sources the files you need in order to run you developed application If you execute it without parameters the help will appear Usage gsbuild lt action gt lt component gt lt appname gt Available actions copy Setup a compilation environment for the component for customization build Build the selected component clean Remove generated binaries Available components master Build or copy the master part worker Build or copy the worker part all Build or copy the master and workers parts 17 lt appname gt corresponds to the name of the application used for source files and IDL files The files needed to run this tool are lt appname gt c lt appname gt idl and lt appname gt functions c You also need to have previously installed in your system the tools automake autoconf and the library named libxml2 version 2 6 x There are some things to take into account before using the gsbuild tool You just can choose the build option when your code is done in C not C If your main code is done in C and named lt appname gt cc or other you will have to use the copy option that will create an environment to configure your compilation options When this con
60. you will have to modify a little your functions that is the header because you have to call now the functions described in your IDL file If your program was not written in functions you will have to extract the code you have identified to be run into the GRID from your main program and call the primitives that you have described in your IDL each primitive corresponds to a part of your code This is like putting the code from a part of your program into a function but the functions won t be written here You can save the code into another file or leave it here by now outside the main source of your program Other differences would be that at some points of the code some primitives of the GRID superscalar must be called For example GS_On and GS_Off are called at the beginning and at the end of the application respectively even if this end is caused by a premature exit As these functions are defined in the GS_master h file given with the GRID superscalar distribution it is necessary to include this file Also you have to include app h file generated with gsstubgen because it contains the headers of your new GRID superscalar functions defined in app idl In Perl case you must include the GSMaster module and the app module remember that the syntax is use GSMaster The On and Off functions are called as GSMaster on and GSMaster off And now your local functions are in an external module so you must call them begi

GRID superscalar User`s Manual Version 1.5.0 - People

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