February 2006 - cddlm-wg

FW: Example jsdl document for a BLAST submission (was Re: [ogsa-wg] Teleconference minutes - 1 February 2006)
by Milojicic, Dejan S (HP Labs) 10 Feb '06

10 Feb '06

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(a)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(a)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>

1 0

Example jsdl document for a BLAST submission (was Re: [ogsa-wg] Teleconference minutes - 1 February 2006)
by Andreas Savva 10 Feb '06

10 Feb '06

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

1 0

import namespace tests
by Steve Loughran 09 Feb '06

09 Feb '06

I've set up a new package for <import namespace /> tests, set_09_import_namespace, and moved the one existing test in there, correcting it on the way (I think it was broken). None of these tests work on my implementation, and I dont expect to have it fixed by monday. Indeed, there are some implications of the import-into-namespace process that only become clear when I think about implementing it, that we can discuss next week. How many of the tests work on other systems? -steve (p.s.I've also moved the lazy reference test 2005_02_18) to the lazy references package. That's just to make it easier to group things that are passing by feature.

1 0

Notes from 2/8 2006
by Milojicic, Dejan S (HP Labs) 08 Feb '06

08 Feb '06

Attendees: Flavio, Guilherme, Ayla, Jun, Stuart, Rakesh, Steve, and Dejan. Ayla: working on making several changes on parser against test repository. Changed architecture to work better (for parallelization). They also start preparing applications for the demo. Steve: the resolution process was broken since he was doing it too early, during import. He will have a functional demo by next week. Stuart: they have running with a new tester, a new parser, have a few questions. They have one test that fails with another parser, another test fails, so there are some problems, they can not have everything that pass. Steve suggests that tests should not be taken for granted at this time, until he fixes due to earlier problems. Stuart will come up with a list of questions so that he can have the parser address all the test cases that exist. Jun: now integrating new CDL parser to implement API and component model environment. Jun will show two demos, one is deployment and component model and the Web application deployment. The other one is the CDL test case. Will answer Steve's question later. Dejan: quick reminder on the sessions, we need to be there on Mon 3:30-5pm and on Mon-Tue-Wed at 5:30-7pm. The sessions will respectively be on: Demos of CDDLM reference implementations CDDLM and relationship to other technologies Planning interoperability demonstrations at GGF17 BoF on Interoperability Fests at GGF16 (hosted by others) Thanks, Dejan. PS Reminder to Jun and the rest of the team, we need to come up with very simple examples of CDL that corresponds to JSDL), we will be provided equivalents in JSDL.

1 0

Reference resolution and attributes
by Steve Loughran 02 Feb '06

02 Feb '06

This is a query related to the reference resolution tests 02-0019 to 02-0022, that are about to appear in the repository, and the resolution algorithm on p19-21 it matters to me, as I'm using some attributes to add dynamic type information for run time binding, and I want to be sure that I have understood the details. cddlm-cdl-2005-02-0019 ================ When you resolve a reference, the attributes of the source node are copied into the new destination node, That is, this CDL <cdl:cdl> <cdl:system> <source attribute="value" cdl:ref="/dest" /> <dest>dest</dest> </cdl:system> </cdl:cdl> </ct:resolve> resolves to this <cdl:system> <source attribute="value" >dest</source> <dest>dest</dest> </cdl:system> </ct:resolved> this is good, as it lets me declare type on a source that a reference does not need to redefine cddlm-cdl-2005-02-0020 ================ You do not merge in the attributes of the destination node. In <cdl:cdl> <cdl:system> <source cdl:ref="/dest" /> <dest attribute="value">dest</dest> </cdl:system> </cdl:cdl> out <cdl:system> <source >dest</source> <dest attribute="value">dest</dest> </cdl:system> If this is correct, I'm not so sure it meets my needs. I'd expect a reference destination to have the right to be fussier about its attributes. cddlm-cdl-2005-02-0021 ================ When you "copy all child nodes" (step 4.2), that includes attributes <cdl:cdl> <cdl:configuration> <dest> <nested1 attr="value">nested1</nested1> <nested2 attr="value2">nested2</nested2> </dest> </cdl:configuration> <cdl:system> <source attribute="value" cdl:ref="/" cdl:refroot="dest" /> </cdl:system> </cdl:cdl> <cdl:system> <source> <nested1 attr="value">nested1</nested1> <nested2 attr="value2">nested2</nested2> </source> </cdl:system> </ct:resolved> cddlm-cdl-2005-02-0022 ================ When you "copy all child nodes" (step 4.2), that includes text and comments. <cdl:cdl> <cdl:configuration> <dest> Text1 <nested1 attr="value">nested1</nested1> Text2 <nested2 attr="value2">nested2</nested2> Text3 </dest> </cdl:configuration> <cdl:system> <source attribute="value" cdl:ref="/" cdl:refroot="dest"/> </cdl:system> </cdl:cdl> resolves to <cdl:system> <source> Text1 <nested1 attr="value">nested1</nested1> Text2 <nested2 attr="value2">nested2</nested2> Text3 </source> </cdl:system> I've added all these tests; I hope we are at least consistent. Looking at test #0020, I would argue that merging attributes would be consistent with the sematics of cdl:extends ... -steve

1 0

Do we have a blast CDL or a SmartFrog spcification for Blast which we can use to convert to CDL
by Milojicic, Dejan S (HP Labs) 01 Feb '06

01 Feb '06

Hi Team, I am at the OGSA-CDDLM session, and I was asked to provide a CDL for the BLAST. Does anyone have an existing example of CDL (or a SmartFrog language deployment configuration) that we can use for continued discussion on CDDLM and OGSA and in particular for the comparison between CDDLM and JSDL. Thanks, Dejan. PS Andreas and Hiro, when you obtain the JSDL, can you please pass it to us so that we can match the two?

1 0

CDDLM CDL examples
by Jun Tatemura 01 Feb '06

01 Feb '06

Dear All, Please find the attached PowerPoint slides for today's discussion on CDDLM CDL examples. Best Regards, Jun Tatemura NEC Laboratories America

1 0

Notes from the Regular CDDM Meeting, Wednesday February 1st
by Milojicic, Dejan S (HP Labs) 01 Feb '06

01 Feb '06

Attending: Flavio, Guilherme, Ayla, Jun, Steve, and Dejan. > 1. Update on reference implementations UFCG: looked at Jun's comments, will make some adjustments. Were busy doing research in the past week. Will also provide a presentation to Dejan before next GGF. HPL Bristol: also make things consistent with Jun's updates. Trying to get instantiation, not yet there, but confident that he will have them by GGF. NEC: Continues with the CDL implementation based on the discussion, separately they are developing the deployment API demo. Have not integrated new version of the CDL, but will do so by GGF. > 2. Planning GGF16 in Athens No specific change wrt past status. > 3. Planning OGSA meeting later on the same day Jun will send two examples by noon today. > 4. Various Steve: the name space policy implements the policy we agreed upon. Tests are more correct this week than last week. This has been fixed based on Jun's comments. Discussion about the compatibility with WSRF/WSDM, etc. Dejan stated that so many things are already in flux now, so this may not be an issue by the time we are demonstrating interoperability. Steve thinks that we are in good shape with demonstrating interoperability of CDL by the means of existing tests. Dejan adds that we should only document them and provide some experience in using them across 2 or more reference implementations and this should hopefully be enough. We will discuss this further at GGF. Thanks, Dejan. PS Steve wishes everyone "Happy February". Thanks Steve!

1 0

FW: [ogsa-wg] Proposed agenda for Feb. 1st call
by Milojicic, Dejan S (HP Labs) 01 Feb '06

01 Feb '06

HI CDDLM members, The OGSA meeting is today, please plan to join if possible. Jun will post two CDLs before the noon PST today. Thanks, Dejan. -----Original Message----- From: owner-ogsa-wg(a)ggf.org [mailto:owner-ogsa-wg@ggf.org] On Behalf Of Andreas Savva Sent: Tuesday, January 31, 2006 7:45 PM To: ogsa-wg(a)ggf.org Subject: Re: [ogsa-wg] Proposed agenda for Feb. 1st call > Telecon minutes approval (if available) See https://forge.gridforum.org/projects/ogsa-wg/document/minutes-20060125/e n/1 https://forge.gridforum.org/projects/ogsa-wg/document/minutes-20060130/e n/1 Hiro Kishimoto wrote: > Hi all, > > The following is a proposed agenda for OGSA-WG telecon on Feb. 1st > Wednesday from 4pm to 6pm (CST). > > Dial-in numbers for Wednesday: > Free: +1-888-452-0308 > Intl/Toll: +1-484-644-0505 > PIN: 71815 > > Screen share service will be provided. > URL: http://ogsa.glance.net > Session key: 0201 > See more explanation: > http://www-unix.gridforum.org/mail_archive/ogsa-wg/2004/06/msg00077.ht > ml > > 1) Early discussion (20 min) > Note taker assignment > Roll call > Byte IO WG F2F minutes approval (Jan. 19am) > https://forge.gridforum.org/projects/ogsa-wg/document/ogsa-f2f-minutes > -20060119-am > > Telecon minutes approval (if available) > OGSA Basic Security Profile final call status (Takuya) > OGSA WSRF BP 1.0 final call status (Tom) > IBM RSM academic/SDOs license program update (Jay) > Agenda bashing > > 2) CDDLM-WG joint call (40 min) > > From F2F meeting minutes: >> * Summary of CDDLM/ACS joint session >> - Discussed the role of CDL and JSDL, and where they overlap (data >> staging). - Agreed that more information is needed on how to >> use CDL. Some >> examples (simple to complex) would help. >> - Proposed action for Dejan: Take a real use case (e.g., gaussian) >> and walk through it, highlighting CDL usage. >> >> - No major change to the overall EMS picture. An initial proposal to >> make the BES container responsible for driving the deployment of >> new capabilities on itself was rejected. >> - JM still orchestrates the deployment (defined by CDL) and >> startup of a job (defined by JSDL). >> >> - More work is needed on Discovery, what properties are advertised >> by BES and how those are used by RSS. >> - In particular how are already deployed capabilities discovered, >> how they are updated after deployment, their lifetime and how >> that affects how or when they are advertised. >> - Tentative agreement on Jay's statement: >> - Deployment is driven by Job management >> - Provisioning is driven by policy > https://forge.gridforum.org/projects/ogsa-wg/document/ogsa-f2f-minutes > -20060117-am/en/2 > > > See also Andrew's notes on gridforge: > https://forge.gridforum.org/projects/ogsa-wg/document/cddlm-acs-joint- > session-notes/en/1 > > > 3) EMS discussion (30 min) > Continuing discussion on EMS composite roadmap document. > Darren has uploaded updated composite roadmap draft (v0.7) > https://forge.gridforum.org/projects/ogsa-wg/document/proposed-ems-roa > dmap/en/7 > > > 4) GGF16, GGF17, April F2F meeting plan (30 min) > OGSA-WG is planning to have F2F meetings back-to-back with GGF16 > (Athens) and GGF17 (Tokyo). We are also planning to have interim > F2F meeting in April (venue TBD). > > Please answer the following on-line survey. > http://www.zoomerang.com/survey.zgi?p=WEB224YEN4D5Z3 > > Prep for GGF16 outreach session > >> - OGSA outreach session; lower attendance last time; considering >> options like - Town hall (asked not to call it that) >> - Presentation from projects on what they'd like to see in OGSA >> - Or other groups on how their spec combines or not with ogsa >> - A panel <CHOICE FORMAT> >> - applications? >> - ogsa adoption >> - working with ogsa <CHOSEN TOPIC> >> - JSDL, EGEE, DAIS as initial candidates >> - Or ask people to come and ask questions. >> >> - Need to also have updated presentation material (and keep them up >> to date) > > > 5) Wrap up > AOB > > <NEXT CALL> > > Feb. 6 (Mon): Arch 1.5 final text review, GGF16 prep Feb. 8 (Wed): > Info model, EMS design team > GGF16 prep > > GGF16 (Athens): Feb. 13-16 > OGSA-WG F2F meeting (NTUA @ Athens): Feb. 17 -- Andreas Savva Fujitsu Laboratories Ltd

1 0

Reminder: Regular CDDM Meeting, Wednesday February 1st
by Milojicic, Dejan S (HP Labs) 01 Feb '06

01 Feb '06

Hi, We shall have a regular meeting tomorrow/today, Wed 2/1/06, at 6am PST. We will use our usual numbers: +1 866-639-4732 (toll free while in US) Code 2362906 (followed by a '#' sign) +1 574-948-0379 (toll & international) Agenda: 1. Update on reference implementations 2. Planning GGF16 in Athens 3. Planning OGSA meeting later on the same day 4. Various Thanks, Dejan.

1 0