[cddlm] FW: Example jsdl document for a BLAST submission (was Re: [ogsa-wg] Teleconference minutes - 1 February 2006)
Milojicic, Dejan S (HP Labs)
dejan.milojicic at hp.com
Thu Feb 9 21:35:23 CST 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 at ggf.org [mailto:owner-ogsa-wg at ggf.org] On Behalf Of
Andreas Savva
Sent: Thursday, February 09, 2006 6:29 PM
To: 'ogsa-wg'; cddlm-wg at 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>
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