February 2014 - Release-team - mailman3.cels.anl.gov

Re: [Release-team] Many errors on redeployment of IRIS
by Robert Olson 10 Feb '14

10 Feb '14

OK, then my guess was correct - they are not errors but rather lengthy backtraces from this warning: Class::MOP::load_class is deprecated at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Class/MOP.pm line 76. This bug is appropriate: https://rt.cpan.org/Public/Bug/Display.html?id=90983 and means that an update to the perl module Parse::Method::Signatures is needed. The reason it’s not picking up your deployment info is that it’s internally using the name InvocationService for locating the deployment information, so you will need to have a section [InvocationService] with the configuration. We will need to fix this service name / service directory confusion across the board going forward. It’ll require thinking through the desired policy & behavior for names. —bob On Feb 10, 2014, at 11:47 AM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: > Unfortunately, the way we're doing the release - it is a complete redeploy, or iris doesn't get any of the clients. > This was necessary because we also upgraded the operating system version. > > I'm having a hard time figuring out what dependency might be missing from the errors. > It is continuing to run with those errors though. One other thing, for some reason it isn't constructing the > auth/nonauth storage path properly from the deployment.cfg, even though we have KB_DEPLOYMENT_CONFIG set, and the following defined: > > > [invocation] > authenticated-storage-dir = /data/storage-auth > nonauthenticated-storage-dir = /data/storage-nonauth > authenticated-storage = /data/storage-auth > nonauthenticated-storage = /data/storage-nonauth > service-url = http://kbase.us/services/invocation > > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > > ________________________________________ > From: Olson, Robert D. > Sent: Monday, February 10, 2014 11:39 AM > To: Thomason, James; Murphy-Olson, Daniel E. > Cc: release-team(a)kbase.us > Subject: RE: Many errors on redeployment of IRIS > > Those errors look like it's trying to use a build of perl that is missing packages or something. > > ________________________________________ > From: Thomason, James [thomason(a)cshl.edu] > Sent: Monday, February 10, 2014 11:38 AM > To: Murphy-Olson, Daniel E. > Cc: Olson, Robert D.; release-team(a)kbase.us > Subject: Re: Many errors on redeployment of IRIS > > I’m unfamiliar with what the problems may be. I didn’t touch anything in invocation this time around, only twiddling a few javascript settings. This is deeper down - either in invocation or below that. > > Could you try just doing a deploy-iris instead of a full invocation build? I’d rather touch as little as possible, what with the demos and all. > -- > -Jim Thomason... > > Computational Science Developer @ The Ware Lab, > a USDA-ARS Laboratory at Cold Spring Harbor Laboratory > http://www.warelab.org/ > http://www.cshl.edu/ > > On Feb 10, 2014, at 9:20 AM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: > > I'm getting a lot of errors on startup of iris. Please see the attached log. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > <start.log> >

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Re: [Release-team] Many errors on redeployment of IRIS
by Murphy-Olson, Daniel E. 10 Feb '14

10 Feb '14

Unfortunately, the way we're doing the release - it is a complete redeploy, or iris doesn't get any of the clients. This was necessary because we also upgraded the operating system version. I'm having a hard time figuring out what dependency might be missing from the errors. It is continuing to run with those errors though. One other thing, for some reason it isn't constructing the auth/nonauth storage path properly from the deployment.cfg, even though we have KB_DEPLOYMENT_CONFIG set, and the following defined: [invocation] authenticated-storage-dir = /data/storage-auth nonauthenticated-storage-dir = /data/storage-nonauth authenticated-storage = /data/storage-auth nonauthenticated-storage = /data/storage-nonauth service-url = http://kbase.us/services/invocation ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: Olson, Robert D. Sent: Monday, February 10, 2014 11:39 AM To: Thomason, James; Murphy-Olson, Daniel E. Cc: release-team(a)kbase.us Subject: RE: Many errors on redeployment of IRIS Those errors look like it's trying to use a build of perl that is missing packages or something. ________________________________________ From: Thomason, James [thomason(a)cshl.edu] Sent: Monday, February 10, 2014 11:38 AM To: Murphy-Olson, Daniel E. Cc: Olson, Robert D.; release-team(a)kbase.us Subject: Re: Many errors on redeployment of IRIS I’m unfamiliar with what the problems may be. I didn’t touch anything in invocation this time around, only twiddling a few javascript settings. This is deeper down - either in invocation or below that. Could you try just doing a deploy-iris instead of a full invocation build? I’d rather touch as little as possible, what with the demos and all. -- -Jim Thomason... Computational Science Developer @ The Ware Lab, a USDA-ARS Laboratory at Cold Spring Harbor Laboratory http://www.warelab.org/ http://www.cshl.edu/ On Feb 10, 2014, at 9:20 AM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: I'm getting a lot of errors on startup of iris. Please see the attached log. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 <start.log>

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Re: [Release-team] Many errors on redeployment of IRIS
by Olson, Robert D. 10 Feb '14

10 Feb '14

Is the service actually not starting? What we might be seeing is a set of warnings Class::MOP::load_class is deprecated at /kbase/runtimes/20140109-prod/lib/perl5/site_perl/5.16.2/x86_64-linux/Class/MOP.pm line 76. which are triggering backtraces due to the plack settings. I've seen this elsewhere with plack-based apps where warnings induced backtraces. At the very bottom of the log it looks like the service went on to log the storage locations which makes it look like it kept running until closed down. Or did it shut down on its own? ________________________________________ From: release-team-bounces(a)lists.kbase.us [release-team-bounces(a)lists.kbase.us] on behalf of Olson, Robert D. [olson(a)mcs.anl.gov] Sent: Monday, February 10, 2014 11:39 AM To: Thomason, James; Murphy-Olson, Daniel E. Cc: release-team(a)kbase.us Subject: Re: [Release-team] Many errors on redeployment of IRIS Those errors look like it's trying to use a build of perl that is missing packages or something. ________________________________________ From: Thomason, James [thomason(a)cshl.edu] Sent: Monday, February 10, 2014 11:38 AM To: Murphy-Olson, Daniel E. Cc: Olson, Robert D.; release-team(a)kbase.us Subject: Re: Many errors on redeployment of IRIS I’m unfamiliar with what the problems may be. I didn’t touch anything in invocation this time around, only twiddling a few javascript settings. This is deeper down - either in invocation or below that. Could you try just doing a deploy-iris instead of a full invocation build? I’d rather touch as little as possible, what with the demos and all. -- -Jim Thomason... Computational Science Developer @ The Ware Lab, a USDA-ARS Laboratory at Cold Spring Harbor Laboratory http://www.warelab.org/ http://www.cshl.edu/ On Feb 10, 2014, at 9:20 AM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: I'm getting a lot of errors on startup of iris. Please see the attached log. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 <start.log> _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] Many errors on redeployment of IRIS
by Olson, Robert D. 10 Feb '14

10 Feb '14

Those errors look like it's trying to use a build of perl that is missing packages or something. ________________________________________ From: Thomason, James [thomason(a)cshl.edu] Sent: Monday, February 10, 2014 11:38 AM To: Murphy-Olson, Daniel E. Cc: Olson, Robert D.; release-team(a)kbase.us Subject: Re: Many errors on redeployment of IRIS I’m unfamiliar with what the problems may be. I didn’t touch anything in invocation this time around, only twiddling a few javascript settings. This is deeper down - either in invocation or below that. Could you try just doing a deploy-iris instead of a full invocation build? I’d rather touch as little as possible, what with the demos and all. -- -Jim Thomason... Computational Science Developer @ The Ware Lab, a USDA-ARS Laboratory at Cold Spring Harbor Laboratory http://www.warelab.org/ http://www.cshl.edu/ On Feb 10, 2014, at 9:20 AM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: I'm getting a lot of errors on startup of iris. Please see the attached log. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 <start.log>

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Re: [Release-team] Many errors on redeployment of IRIS
by Thomason, James 10 Feb '14

10 Feb '14

I’m unfamiliar with what the problems may be. I didn’t touch anything in invocation this time around, only twiddling a few javascript settings. This is deeper down - either in invocation or below that. Could you try just doing a deploy-iris instead of a full invocation build? I’d rather touch as little as possible, what with the demos and all. -- -Jim Thomason... Computational Science Developer @ The Ware Lab, a USDA-ARS Laboratory at Cold Spring Harbor Laboratory http://www.warelab.org/ http://www.cshl.edu/ On Feb 10, 2014, at 9:20 AM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov<mailto:[email protected]>> wrote: I'm getting a lot of errors on startup of iris. Please see the attached log. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 <start.log>

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Many errors on redeployment of IRIS
by Murphy-Olson, Daniel E. 10 Feb '14

10 Feb '14

I'm getting a lot of errors on startup of iris. Please see the attached log. ---- Daniel Murphy-Olson Sr. Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

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Re: [Release-team] Iris rev
by Nomi Harris 10 Feb '14

10 Feb '14

In addition to the tutorial bug that Jim fixed, here’s another reason to redeploy IRIS: there seems to be a problem with the fba commands. I thought the old command names would work in IRIS (even if they're deprecated)? IRIS seems to recognize kbfba-loadgenome (but it doesn’t work) but it doesn’t recognize fba-loadgenome. >/ fba-loadgenome -e "kb|g.0" fba-loadgenome: invalid command >/ kbfba-loadgenome -e "kb|g.0" Return code from kbfba-loadgenome: 255JSONRPC error: Authentication required for fbaModelServices but no authentication header was passed JSONRPC error code: JSONRPC error data: Trace begun at /kb/deployment/lib/Bio/KBase/fbaModelServices/Client.pm line 2392 Bio::KBase::fbaModelServices::Client::genome_to_workspace('Bio::KBase::fbaModelServices::Client=HASH(0x252b1c0)', 'HASH(0x25a60f0)') called at /kb/deployment/lib/Bio/KBase/fbaModelServices/Helpers.pm line 118 Bio::KBase::fbaModelServices::Helpers::runFBACommand('HASH(0x25a60f0)', 'genome_to_workspace', 'Getopt::Long::Descriptive::Opts::__OPT__::1=HASH(0x32c5828)') called at /kb/deployment/plbin/ kbfba-loadgenome.pl line 60 (Yes, I am logged into IRIS.) I tried loading other genome IDs and got the same error. Other kbfba commands (that I could try after kbfba-loadgenome failed—most of the fba commands require a genome or model) didn’t work either. >/ kbfba-exportmedia Carbon-D-Glucose readable -w KBaseMedia Media export failed! >/ kbfba-importpheno "kb|g.0" WT-phenotypes.txt --phenoid Ecoli.Phenos Phenotype import failed! Nomi On Feb 8, 2014, at 11:17 AM, Thomason, James <thomason(a)cshl.edu> wrote: > Could somebody kick out a new iris deploy, please? > > There’s no need to do a full invocation release unless one of those is scheduled anyway, just a new iris deploy will suffice. > > It fixed a glitch that was preventing tutorials from showing up. > > Many thanks, > > -- > -Jim Thomason... > > Computational Science Developer @ The Ware Lab, > a USDA-ARS Laboratory at Cold Spring Harbor Laboratory > http://www.warelab.org/ > http://www.cshl.edu/

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Iris rev
by Thomason, James 08 Feb '14

08 Feb '14

Could somebody kick out a new iris deploy, please? There’s no need to do a full invocation release unless one of those is scheduled anyway, just a new iris deploy will suffice. It fixed a glitch that was preventing tutorials from showing up. Many thanks, -- -Jim Thomason... Computational Science Developer @ The Ware Lab, a USDA-ARS Laboratory at Cold Spring Harbor Laboratory http://www.warelab.org/ http://www.cshl.edu/

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Re: [Release-team] Changes for deploy
by Michael Sneddon 07 Feb '14

07 Feb '14

Ran through most of the FBA functions called from the narrative, and things still seem to be working correctly.... On Fri, Feb 7, 2014 at 6:57 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > Cool! I tried one method against > https://kbase.us/services/KBaseFBAModeling, and it actually seemed to > work as expected. I'll start switching over other narrative functions and > see if we encounter any issues. > > > On Fri, Feb 7, 2014 at 6:50 PM, Shane Canon <scanon(a)lbl.gov> wrote: > >> >> I think this fell through the cracks with all the excitement. >> >> I've deployed in production. I'm worried there may be an issue. Can you >> check it out? >> >> --Shane >> >> On Feb 7, 2014, at 5:51 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: >> >> I know all the mongo problems got in the way, but any updates on >> deploying the FBA service to production? >> thanks, >> -michael >> >> >> On Fri, Feb 7, 2014 at 9:19 AM, Shane Canon <scanon(a)lbl.gov> wrote: >> >>> >>> I'll quickly pull the update and then we can start promoting things to >>> prod soon. Dan: Does this sound good? >>> >>> --Shane >>> >>> On Feb 7, 2014, at 9:08 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: >>> >>> > I think this can up because we have FBAModeling in limbo. >>> > >>> > Chris fixed command-line help on "ga-annotate-ws-genome" and >>> "fba-adjustmapcomplex" and checked them into master. >>> > >>> > WHAT is our next step? Are we going to >>> > >>> > 1. update the test VM with his latest changes or >>> > 2. promote the version in test to production? >>> > >>> > This is a critical module and we shouldn't postpone this decision any >>> further. The burden in on the deploy team so I would like to hear their >>> vote. >>> > >>> > Miriam >>> > >>> > >>> > From: Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> >>> > Date: Thursday, February 6, 2014 4:03 PM >>> > To: "release-team(a)kbase.us<mailto:[email protected]>" < >>> release-team(a)kbase.us<mailto:[email protected]>> >>> > Subject: [Release-team] Changes for deploy >>> > >>> > >>> > FYI. For some modules, I've had to make some changes to get things to >>> deploy. This makes pulling updates a bit of a pain. >>> > So I'm not trying to keep things in a branch, so that I can just do a >>> merge to get any updates. I've been calling this branch >>> > deploy-20140206. I'm _not_ pushing it to git.kbase.us. It is just >>> local to the t1 cluster. >>> > >>> > --Shane >>> > _______________________________________________ >>> > Release-team mailing list >>> > Release-team(a)lists.kbase.us<mailto:[email protected]> >>> > https://lists.kbase.us/mailman/listinfo/release-team >>> > >>> >>> _______________________________________________ >>> Release-team mailing list >>> Release-team(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/release-team >>> >> >> >> >

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Re: [Release-team] Changes for deploy
by Michael Sneddon 07 Feb '14

07 Feb '14

Cool! I tried one method against https://kbase.us/services/KBaseFBAModeling, and it actually seemed to work as expected. I'll start switching over other narrative functions and see if we encounter any issues. On Fri, Feb 7, 2014 at 6:50 PM, Shane Canon <scanon(a)lbl.gov> wrote: > > I think this fell through the cracks with all the excitement. > > I've deployed in production. I'm worried there may be an issue. Can you > check it out? > > --Shane > > On Feb 7, 2014, at 5:51 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > > I know all the mongo problems got in the way, but any updates on deploying > the FBA service to production? > thanks, > -michael > > > On Fri, Feb 7, 2014 at 9:19 AM, Shane Canon <scanon(a)lbl.gov> wrote: > >> >> I'll quickly pull the update and then we can start promoting things to >> prod soon. Dan: Does this sound good? >> >> --Shane >> >> On Feb 7, 2014, at 9:08 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: >> >> > I think this can up because we have FBAModeling in limbo. >> > >> > Chris fixed command-line help on "ga-annotate-ws-genome" and >> "fba-adjustmapcomplex" and checked them into master. >> > >> > WHAT is our next step? Are we going to >> > >> > 1. update the test VM with his latest changes or >> > 2. promote the version in test to production? >> > >> > This is a critical module and we shouldn't postpone this decision any >> further. The burden in on the deploy team so I would like to hear their >> vote. >> > >> > Miriam >> > >> > >> > From: Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> >> > Date: Thursday, February 6, 2014 4:03 PM >> > To: "release-team(a)kbase.us<mailto:[email protected]>" < >> release-team(a)kbase.us<mailto:[email protected]>> >> > Subject: [Release-team] Changes for deploy >> > >> > >> > FYI. For some modules, I've had to make some changes to get things to >> deploy. This makes pulling updates a bit of a pain. >> > So I'm not trying to keep things in a branch, so that I can just do a >> merge to get any updates. I've been calling this branch >> > deploy-20140206. I'm _not_ pushing it to git.kbase.us. It is just >> local to the t1 cluster. >> > >> > --Shane >> > _______________________________________________ >> > Release-team mailing list >> > Release-team(a)lists.kbase.us<mailto:[email protected]> >> > https://lists.kbase.us/mailman/listinfo/release-team >> > >> >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team >> > > >

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