[cddlm] FW: Example jsdl document for a BLAST submission (was Re: [ogsa-wg] Teleconference minutes - 1 February 2006)

10 Feb 2006

      Hi Team,

Below is the JSDL for which we need to provide an equivalent CDL. We
need to have it before the F2F. If not earlier, I hope that we can work
on it during GGF at Athens. Looking forward to seeing you tehre.

Thanks,

Dejan. 

-----Original Message-----
From: owner-ogsa-wg@ggf.org [mailto:owner-ogsa-wg@ggf.org] On Behalf Of
Andreas Savva
Sent: Thursday, February 09, 2006 6:29 PM
To: 'ogsa-wg'; cddlm-wg@ggf.org
Subject: Example jsdl document for a BLAST submission (was Re: [ogsa-wg]
Teleconference minutes - 1 February 2006)

I've uploaded a jsdl document describing a BLAST submission:
https://forge.gridforum.org/projects/ogsa-wg/document/jsdl_blast_instanc
e/en/1

Thanks to Chris Smith for contributing this example.
Andreas

 From the minutes of Feb 1:
...
Action:
   - Dejan(CDDLM) to provide a CDL for deploying and configuring
BLAST
   - Steve/Andreas(JSDL) to provide a JSDL document for submitting a
     BLAST job
@@jsdl_blast_instance 
Open Grid Services Architecture : Document Manager : Design Teams :
Execution Management Services : Input Materials : @@jsdl_blast_instance 

 jsdl_blast_instance  [MAIL]  [PRINT]
Example JSDL BLAST document
Last Edited On: 2006-02-09 by Andreas Savva
Type: XML File
Size: 7.15 KB
Current version: 1, Active version: 1, All: *1 * 

------------------------------------------------------------------------
--------

<?xml version="1.0" encoding="UTF-8"?>
<jsdl:JobDefinition 
xmlns:jsdl="http://schemas.ggf.org/jsdl/2005/11/jsdl"
xmlns:jsdl-posix="http://schemas.ggf.org/jsdl/2005/11/jsdl-posix"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
  xsi:schemaLocation="http://schemas.ggf.org/jsdl/2005/11/jsdl jsdl.xsd
http://schemas.ggf.org/jsdl/2005/11/jsdl-posix jsdl-posix.xsd">
  <jsdl:JobDescription>
    <jsdl:JobIdentification>
      <jsdl:JobName>Blast1</jsdl:JobName>
      <jsdl:Description>Blast query number 1</jsdl:Description>
      <jsdl:JobAnnotation>Blast1Annotation</jsdl:JobAnnotation>
      <jsdl:JobProject>BlastProject</jsdl:JobProject>
    </jsdl:JobIdentification>
    <jsdl:Application>
      <jsdl:ApplicationName>BlastN</jsdl:ApplicationName>
      <jsdl:ApplicationVersion>NCBI BLAST
2.2.13</jsdl:ApplicationVersion>
      <jsdl:Description>BlastN performs nucleotide similarity
searching</jsdl:Description>
      <jsdl-posix:POSIXApplication>

<jsdl-posix:Executable>/usr/local/bin/blastall</jsdl-posix:Executable>
        <jsdl-posix:Argument>-p</jsdl-posix:Argument>
        <jsdl-posix:Argument>blastn</jsdl-posix:Argument>
        <jsdl-posix:Argument>-d</jsdl-posix:Argument>
        <jsdl-posix:Argument>est</jsdl-posix:Argument>
        <jsdl-posix:Argument>-T</jsdl-posix:Argument>
        <jsdl-posix:Argument>T</jsdl-posix:Argument>
        <jsdl-posix:Input
filesystemName="HOME">sequences1.txt</jsdl-posix:Input>
        <jsdl-posix:Output
filesystemName="HOME">sequences1.html</jsdl-posix:Output>
        <jsdl-posix:Error
filesystemName="HOME">sequences1.err</jsdl-posix:Error>
        <jsdl-posix:WorkingDirectory
filesystemName="HOME">blastqueries</jsdl-posix:WorkingDirectory>
        <jsdl-posix:Environment
name="PATH">/usr/bin:/usr/local/bin:/usr/local/bio/bin</jsdl-posix:Envir
onment>
        <jsdl-posix:Environment name="TMPDIR" filesystemName="TMP"/>
        <jsdl-posix:WallTimeLimit>60</jsdl-posix:WallTimeLimit>
        <jsdl-posix:FileSizeLimit>1073741824</jsdl-posix:FileSizeLimit>
        <jsdl-posix:CoreDumpLimit>0</jsdl-posix:CoreDumpLimit>
        <jsdl-posix:DataSegmentLimit>32768</jsdl-posix:DataSegmentLimit>

<jsdl-posix:LockedMemoryLimit>8388608</jsdl-posix:LockedMemoryLimit>
        <jsdl-posix:MemoryLimit>67108864</jsdl-posix:MemoryLimit>

<jsdl-posix:OpenDescriptorsLimit>16</jsdl-posix:OpenDescriptorsLimit>
        <jsdl-posix:PipeSizeLimit>512</jsdl-posix:PipeSizeLimit>
        <jsdl-posix:StackSizeLimit>1048576</jsdl-posix:StackSizeLimit>
        <jsdl-posix:CPUTimeLimit>30</jsdl-posix:CPUTimeLimit>
        <jsdl-posix:ProcessCountLimit>8</jsdl-posix:ProcessCountLimit>

<jsdl-posix:VirtualMemoryLimit>134217728</jsdl-posix:VirtualMemoryLimit>
        <jsdl-posix:ThreadCountLimit>8</jsdl-posix:ThreadCountLimit>
        <jsdl-posix:UserName>csmith</jsdl-posix:UserName>
        <jsdl-posix:GroupName>bio</jsdl-posix:GroupName>
      </jsdl-posix:POSIXApplication>
    </jsdl:Application>
    <jsdl:Resources>
      <jsdl:CandidateHosts>
        <jsdl:HostName>cluster1</jsdl:HostName>
        <jsdl:HostName>cluster2</jsdl:HostName>
      </jsdl:CandidateHosts>
      <jsdl:FileSystem name="TMP">
        <jsdl:FileSystemType>temporary</jsdl:FileSystemType>
        <jsdl:Description>
          Temporary space that does not necessarily persist after the
job
          terminates and which might not be shared between resources,
but 
          which will be fast.
        </jsdl:Description>
        <jsdl:DiskSpace>
          <jsdl:LowerBoundedRange>10737418240.0</jsdl:LowerBoundedRange>
        </jsdl:DiskSpace>
      </jsdl:FileSystem>
      <jsdl:FileSystem name="HOME">
        <jsdl:FileSystemType>normal</jsdl:FileSystemType>
        <jsdl:Description>Chris's home directory</jsdl:Description>
        <jsdl:MountPoint>/home/csmith</jsdl:MountPoint>
      </jsdl:FileSystem>
      <jsdl:ExclusiveExecution>true</jsdl:ExclusiveExecution>
      <jsdl:OperatingSystem>
        <jsdl:OperatingSystemType>
          <jsdl:OperatingSystemName>MACOS</jsdl:OperatingSystemName>
        </jsdl:OperatingSystemType>

<jsdl:OperatingSystemVersion>10.4.4</jsdl:OperatingSystemVersion>
        <jsdl:Description>Mac OS version 10.4.x</jsdl:Description>
      </jsdl:OperatingSystem>
      <jsdl:CPUArchitecture>
        <jsdl:CPUArchitectureName>powerpc</jsdl:CPUArchitectureName>
      </jsdl:CPUArchitecture>
      <jsdl:IndividualCPUSpeed>
        <jsdl:LowerBoundedRange>2147483648.0</jsdl:LowerBoundedRange>
      </jsdl:IndividualCPUSpeed>
      <jsdl:IndividualCPUTime>
        <jsdl:UpperBoundedRange>60.0</jsdl:UpperBoundedRange>
      </jsdl:IndividualCPUTime>
      <jsdl:IndividualCPUCount>
        <jsdl:Exact>2.0</jsdl:Exact>
      </jsdl:IndividualCPUCount>
      <jsdl:IndividualNetworkBandwidth>
        <jsdl:LowerBoundedRange>104857600.0</jsdl:LowerBoundedRange>
      </jsdl:IndividualNetworkBandwidth>
      <jsdl:IndividualPhysicalMemory>
        <jsdl:LowerBoundedRange>1073741824.0</jsdl:LowerBoundedRange>
      </jsdl:IndividualPhysicalMemory>
      <jsdl:IndividualVirtualMemory>
        <jsdl:LowerBoundedRange>1073741824.0</jsdl:LowerBoundedRange>
      </jsdl:IndividualVirtualMemory>
      <jsdl:IndividualDiskSpace>
        <jsdl:LowerBoundedRange>1073741824.0</jsdl:LowerBoundedRange>
      </jsdl:IndividualDiskSpace>
      <jsdl:TotalCPUTime>
        <jsdl:UpperBoundedRange>600.0</jsdl:UpperBoundedRange>
      </jsdl:TotalCPUTime>
      <jsdl:TotalCPUCount>
        <jsdl:Exact>10.0</jsdl:Exact>
      </jsdl:TotalCPUCount>
      <jsdl:TotalPhysicalMemory>
        <jsdl:LowerBoundedRange>10737418240.0</jsdl:LowerBoundedRange>
      </jsdl:TotalPhysicalMemory>
      <jsdl:TotalVirtualMemory>
        <jsdl:LowerBoundedRange>10737418240.0</jsdl:LowerBoundedRange>
      </jsdl:TotalVirtualMemory>
      <jsdl:TotalDiskSpace>
        <jsdl:LowerBoundedRange>10737418240.0</jsdl:LowerBoundedRange>
      </jsdl:TotalDiskSpace>
      <jsdl:TotalResourceCount>
        <jsdl:Exact>5.0</jsdl:Exact>
      </jsdl:TotalResourceCount>
    </jsdl:Resources>
    <jsdl:DataStaging>
      <jsdl:FileName>blastqueries/sequences1.txt</jsdl:FileName>
      <jsdl:FilesystemName>HOME</jsdl:FilesystemName>
      <jsdl:CreationFlag>overwrite</jsdl:CreationFlag>
      <jsdl:Source>

<jsdl:URI>file:/Users/csmith/blastqueries/sequences1.txt</jsdl:URI>
      </jsdl:Source>
    </jsdl:DataStaging>
    <jsdl:DataStaging>
      <jsdl:FileName>blastqueries/sequences1.html</jsdl:FileName>
      <jsdl:FilesystemName>HOME</jsdl:FilesystemName>
      <jsdl:CreationFlag>overwrite</jsdl:CreationFlag>
      <jsdl:Target>

<jsdl:URI>file:/Users/csmith/blastqueries/sequences1.html</jsdl:URI>
      </jsdl:Target>
    </jsdl:DataStaging>
    <jsdl:DataStaging>
      <jsdl:FileName>blastqueries/sequences1.err</jsdl:FileName>
      <jsdl:FilesystemName>HOME</jsdl:FilesystemName>
      <jsdl:CreationFlag>append</jsdl:CreationFlag>
      <jsdl:Target>

<jsdl:URI>file:/Users/csmith/blastqueries/sequences1.err</jsdl:URI>
      </jsdl:Target>
    </jsdl:DataStaging>
  </jsdl:JobDescription>
</jsdl:JobDefinition>

[cddlm] FW: Example jsdl document for a BLAST submission (was Re: [ogsa-wg] Teleconference minutes - 1 February 2006)

Milojicic, Dejan S (HP Labs)