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Sample job:
{{{#!highlight xml
<ActivityDescription xmlns="http://www.eu-emi.eu/es/2010/12/adl">
    <ActivityIdentification>
        <Name>test job</Name>
        <Description>A test job showing the features of EMI-ES</Description>
        <Type>single</Type>
        <Annotation>test</Annotation>
    </ActivityIdentification>
    <Application>
        <Executable><Path>cpi</Path></Executable>
        <Error>std.err</Error>
        <Output>std.out</Output>
    </Application>
    <Resources>
        <SlotRequirement>
            <NumberOfSlots>2</NumberOfSlots>
            <SlotsPerHost>2</SlotsPerHost>
            <ExclusiveExecution>true</ExclusiveExecution>
        </SlotRequirement>
        <ParallelEnvironment>
           <Type>OpenMPI</Type>
        </ParallelEnvironment>
    </Resources>
    <DataStaging>
        <InputFile> <Name>pre.sh</Name> <Source><URI>pre.sh</URI></Source> </InputFile>
        <InputFile> <Name>cpi.c</Name> <Source><URI>cpi.c</URI></Source> </InputFile>
    </DataStaging>
</ActivityDescription>
}}}

MPI-Start as EMI-ES ParallelEnvironment backend

Contents

  1. UNICORE
  2. ARC
    1. Explicit mpi-start
    2. mpi-start backend
  3. CREAM

1. UNICORE

The UNICORE EMI-ES ParallelEnvironment is a complete implementation of the specification. The configuration is done via xml files where the mapping from the job specification to the final executable is specified.

For each mpi-flavor that needs to be supported by mpi-start an entry in the idb must be included. For example for OpenMPI: 

   1 <ee:ExecutionEnvironment xmlns:ee="http://www.unicore.eu/unicore/jsdl-extensions">
   2     <ee:Name>OpenMPI</ee:Name>
   3     <ee:Version>1.5.4</ee:Version>
   4     <ee:Description>Runs OpenMPI job using mpi-start to start the job</ee:Description>
   5     <ee:ExecutableName>/usr/bin/mpi-start</ee:ExecutableName>
   6     <ee:CommandlineTemplate>#EXECUTABLE -t openmpi #ARGS #USERCOMMAND #USERARGS</ee:CommandlineTemplate>
   7     <ee:Argument>
   8       <ee:Name>Output</ee:Name>
   9       <ee:IncarnatedValue>-o </ee:IncarnatedValue>
  10       <ee:ArgumentMetadata>
  11         <ee:Type>string</ee:Type>
  12         <ee:Description>Write the job output to a FILE instead of to the standard output stream</ee:Description>
  13       </ee:ArgumentMetadata>
  14     </ee:Argument>
  15     <ee:Argument>
  16       <ee:Name>PostHook</ee:Name>
  17       <ee:IncarnatedValue>-post </ee:IncarnatedValue>
  18       <ee:ArgumentMetadata>
  19         <ee:Type>string</ee:Type>
  20         <ee:Description>Use the file as post hook</ee:Description>
  21       </ee:ArgumentMetadata>
  22     </ee:Argument>
  23     <ee:Argument>
  24       <ee:Name>PreHook</ee:Name>
  25       <ee:IncarnatedValue>-pre </ee:IncarnatedValue>
  26       <ee:ArgumentMetadata>
  27         <ee:Type>string</ee:Type>
  28         <ee:Description>Use the file as pre hook</ee:Description>
  29       </ee:ArgumentMetadata>
  30     </ee:Argument>
  31     <ee:Argument>
  32       <ee:Name>Error</ee:Name>
  33       <ee:IncarnatedValue>-e </ee:IncarnatedValue>
  34       <ee:ArgumentMetadata>
  35         <ee:Type>string</ee:Type>
  36         <ee:Description>Write the job error to a FILE instead of to the standard error stream</ee:Description>
  37       </ee:ArgumentMetadata>
  38     </ee:Argument>
  39     <ee:Option> 
  40       <ee:Name>Verbose</ee:Name> 
  41       <ee:IncarnatedValue>-v</ee:IncarnatedValue> 
  42       <ee:OptionMetadata> 
  43         <ee:Description>Enable verbose mode</ee:Description> 
  44       </ee:OptionMetadata> 
  45     </ee:Option> 
  46     <ee:Option> 
  47       <ee:Name>PerNode</ee:Name> 
  48       <ee:IncarnatedValue>-pnode</ee:IncarnatedValue> 
  49       <ee:OptionMetadata> 
  50         <ee:Description>Start one process per available node</ee:Description> 
  51       </ee:OptionMetadata> 
  52     </ee:Option> 
  53     <ee:Option> 
  54       <ee:Name>PerSocket</ee:Name> 
  55       <ee:IncarnatedValue>-psocket</ee:IncarnatedValue> 
  56       <ee:OptionMetadata> 
  57         <ee:Description>Start one process per available socket</ee:Description> 
  58       </ee:OptionMetadata> 
  59     </ee:Option> 
  60     <ee:Option> 
  61       <ee:Name>PerCore</ee:Name> 
  62       <ee:IncarnatedValue>-pcore</ee:IncarnatedValue> 
  63       <ee:OptionMetadata> 
  64         <ee:Description>Start one process per available core</ee:Description> 
  65       </ee:OptionMetadata> 
  66     </ee:Option> 
  67 </ee:ExecutionEnvironment>

Sample job: 

   1 <ActivityDescription xmlns="http://www.eu-emi.eu/es/2010/12/adl">
   2     <ActivityIdentification>
   3         <Name>test job</Name>
   4         <Description>A test job showing the features of EMI-ES</Description>
   5         <Type>single</Type>
   6         <Annotation>test</Annotation>
   7     </ActivityIdentification>
   8     <Application>
   9         <Executable><Path>cpi</Path></Executable>
  10         <Error>std.err</Error>
  11         <Output>std.out</Output>
  12     </Application>
  13     <Resources>
  14         <SlotRequirement>
  15             <NumberOfSlots>2</NumberOfSlots>
  16             <SlotsPerHost>2</SlotsPerHost>
  17             <ExclusiveExecution>true</ExclusiveExecution>
  18         </SlotRequirement>
  19         <ParallelEnvironment>
  20            <Type>OpenMPI</Type>
  21         </ParallelEnvironment>
  22     </Resources>
  23     <DataStaging>
  24         <InputFile> <Name>pre.sh</Name> <Source><URI>pre.sh</URI></Source> </InputFile>
  25         <InputFile> <Name>cpi.c</Name> <Source><URI>cpi.c</URI></Source> </InputFile>
  26     </DataStaging>
  27 </ActivityDescription>

2. ARC

ARC supports MPI jobs through the RunTimeEnvironments. There are two options for integrating them with mpi-start

  1. Explicit mpi-start usage by users.
  2. mpi-start as backend of parallel jobs

2.1. Explicit mpi-start

In this use case, the only requirements is that mpi-start is available at the nodes that will execute the job. There is no need for a RuntimeEnvironment and the user must set as executable for the jobs mpi-start. A minimal job description is shown below: 

   1 <ActivityDescription xmlns="http://www.eu-emi.eu/es/2010/12/adl">
   2     <ActivityIdentification>
   3         <Name>MPI Test job</Name>
   4         <Description>A test job showing the features of EMI-ES</Description>
   5         <Type>single</Type>
   6     </ActivityIdentification>
   7     <Application>
   8         <Executable>
   9             <Path>/usr/bin/mpi-start</Path>
  10             <Argument>-t</Argument>
  11             <Argument>openmpi</Argument>
  12             <Argument>-pre</Argument>
  13             <Argument>pre.sh</Argument>
  14             <Argument>cpi</Argument>
  15         </Executable>
  16         <Error>std.err</Error>
  17         <Output>std.out</Output>
  18     </Application>
  19     <Resources>
  20         <SlotRequirement>
  21             <NumberOfSlots>2</NumberOfSlots>
  22             <SlotsPerHost>2</SlotsPerHost>
  23             <ExclusiveExecution>true</ExclusiveExecution>
  24         </SlotRequirement>
  25     </Resources>
  26 
  27     <DataStaging>
  28         <InputFile><Name>pre.sh</Name><Source><URI>pre.sh</URI></Source></InputFile>
  29         <InputFile><Name>cpi.c</Name><Source><URI>cpi.c</URI></Source>
  30         </InputFile>
  31 </DataStaging>
  32 </ActivityDescription>

Note that the -t openmpi option is passed explicitly to indicate to mpi-start which implementation to use.

2.2. mpi-start backend

In this case, a RuntimeEnvironment prepares the execution with mpi-start, hiding from the user the details of the implementation. Any additional arguments to mpi-start must be passed as environment variables.

A sample runtime environment for running !OpenMPI applications would be: 

   1 #!/bin/sh
   2 
   3 export I2G_MPI_TYPE=openmpi
   4 
   5 case "$1" in
   6 0)
   7         joboption_args="mpi-start -- $joboption_args"
   8 ;;
   9 1)
  10 ;;
  11 2)
  12 ;;
  13 *)
  14         return 1
  15 ;;
  16 esac

The job description would look as follows: 

   1 <ActivityDescription xmlns="http://www.eu-emi.eu/es/2010/12/adl">
   2     <ActivityIdentification>
   3         <Name>test job</Name>
   4         <Description>A test job showing the features of EMI-ES</Description>
   5         <Type>single</Type>
   6         <Annotation>test</Annotation>
   7     </ActivityIdentification>
   8     <Application>
   9         <Executable><Path>cpi</Path></Executable>
  10         <Error>std.err</Error>
  11         <Output>std.out</Output>
  12         <Environment><Name>I2G_MPI_PRE_RUN_HOOK</Name><Value>pre.sh</Value></Environment>
  13     </Application>
  14     <Resources>
  15         <SlotRequirement>
  16             <NumberOfSlots>2</NumberOfSlots>
  17             <SlotsPerHost>2</SlotsPerHost>
  18             <ExclusiveExecution>true</ExclusiveExecution>
  19         </SlotRequirement>
  20         <RuntimeEnvironment><Name>OPENMPI</Name></RuntimeEnvironment>
  21     </Resources>
  22     <DataStaging>
  23         <InputFile> <Name>pre.sh</Name> <Source><URI>pre.sh</URI></Source> </InputFile>
  24         <InputFile> <Name>cpi.c</Name> <Source><URI>cpi.c</URI></Source> </InputFile>
  25         <!-- Fake input file -->
  26         <InputFile> <Name>cpi</Name> <Source><URI>cpi</URI></Source> </InputFile>
  27     </DataStaging>
  28 </ActivityDescription>

3. CREAM

Cream does not support the ParallelEnvironment. Jobs may be sumbmitted using /usr/bin/mpi-start as executable. See the previous ARC example for details.

eciencia: Middleware/MpiStart/ParallelEnvironment (last edited 2013-03-11 16:19:19 by enol)