October 2013 - Release-team - mailman3.cels.anl.gov

Re: [Release-team] Runtime size
by Thomas Brettin 15 Oct '13

15 Oct '13

This is very helpful. I'll bring this up with Folker tomorrow. On Oct 14, 2013, at 8:58 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > Since the size of the mac dmg came up the other day I decided to figure out where some of that growth came from. Attached is a chart of the installed size of the various modules that get installed into the runtime; this is linux build data but the mac build should be roughly analogous (though it doesn't include R). > > Units of size is MB. > > the python and perl runtime_1 components are the core interpreters; the runtime_2 components are the module collections that are installed. > > --bob > > <kb-runtime.png>_______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Runtime size
by Robert Olson 14 Oct '13

14 Oct '13

Since the size of the mac dmg came up the other day I decided to figure out where some of that growth came from. Attached is a chart of the installed size of the various modules that get installed into the runtime; this is linux build data but the mac build should be roughly analogous (though it doesn't include R). Units of size is MB. the python and perl runtime_1 components are the core interpreters; the runtime_2 components are the module collections that are installed. --bob

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Re: [Release-team] 2nd test mac dmg
by Robert Olson 11 Oct '13

11 Oct '13

The runtime has grown quite a bit. It also may be larger due to building on mountain lion instead of snow leopard; I suspect there may be more 64-bit built stuff which may increase the size of the executables. If I can get a snow leopard build machine again I'll be doing builds there (I'd like to have a copy I can use ...) Thank you for poking at it. --bob On Oct 11, 2013, at 1:02 AM, Nomi Harris wrote: > The previous dmg was 257M; this one is 1.04G. Why is it so much bigger? (And the installed image is 2.8G! Whoa!) > > I did a very basic sanity check--I was able to download, install, and launch it (all of those took a while, since it's so huge), and it brought up a terminal window as expected, and it responded appropriately to the few kbase commands I typed. > > Nomi > > On Oct 10, 2013, at 9:41 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > >> is at http://bioseed.mcs.anl.gov/~olson/20131010-prod-dmg-2.dmg >> >> This is cut from the following tags: >> >> KBaseFBAModeling 20131010-prod >> assembly 20131010-prod >> auth 20131010-prod >> cbd 20131010-prod >> communities_api 20131010-prod >> functional_ortholog_predictor 20131010-prod >> genome_annotation 20131010-prod >> genotype_phenotype_api 20131010-prod >> idserver 20131010-prod >> invocation 20131010-prod >> jnomics 20131010-prod >> kb_seed 20131010-prod >> kbapi_common 20131010-prod >> kbrest_common HEAD >> m5nr 20131010-prod >> networks 20131010-prod >> ontology_service 20131010-prod >> phispy 20131010-prod >> plant_expression_service 20131010-prod >> probabilistic_annotation 20131010-prod >> sim_service 20131010-prod >> translation 20131010-prod >> trees 20131010-prod >> typecomp 20130926-test >> workspace_service 20131010-prod >> dev_container_tools HEAD >> kb_model_seed 20131010-prod >> jars HEAD >> strep_repeats HEAD >> erdb_service 20131010-prod >> >> I have not been able to test since the build machine is running mountain lion; the runtime as compiled there will not run on my snow leopard machine. >> >> --bob >> _______________________________________________ >> 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] 2nd test mac dmg
by Nomi Harris 11 Oct '13

11 Oct '13

The previous dmg was 257M; this one is 1.04G. Why is it so much bigger? (And the installed image is 2.8G! Whoa!) I did a very basic sanity check--I was able to download, install, and launch it (all of those took a while, since it's so huge), and it brought up a terminal window as expected, and it responded appropriately to the few kbase commands I typed. Nomi On Oct 10, 2013, at 9:41 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > is at http://bioseed.mcs.anl.gov/~olson/20131010-prod-dmg-2.dmg > > This is cut from the following tags: > > KBaseFBAModeling 20131010-prod > assembly 20131010-prod > auth 20131010-prod > cbd 20131010-prod > communities_api 20131010-prod > functional_ortholog_predictor 20131010-prod > genome_annotation 20131010-prod > genotype_phenotype_api 20131010-prod > idserver 20131010-prod > invocation 20131010-prod > jnomics 20131010-prod > kb_seed 20131010-prod > kbapi_common 20131010-prod > kbrest_common HEAD > m5nr 20131010-prod > networks 20131010-prod > ontology_service 20131010-prod > phispy 20131010-prod > plant_expression_service 20131010-prod > probabilistic_annotation 20131010-prod > sim_service 20131010-prod > translation 20131010-prod > trees 20131010-prod > typecomp 20130926-test > workspace_service 20131010-prod > dev_container_tools HEAD > kb_model_seed 20131010-prod > jars HEAD > strep_repeats HEAD > erdb_service 20131010-prod > > I have not been able to test since the build machine is running mountain lion; the runtime as compiled there will not run on my snow leopard machine. > > --bob > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Ubuntu VM for testing
by Dan Olson 11 Oct '13

11 Oct '13

The 20131010-prod VM is available for testing at: http://bioseed.mcs.anl.gov/~dolson/kbase-20131010.vdi.gz ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

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2nd test mac dmg
by Robert Olson 10 Oct '13

10 Oct '13

is at http://bioseed.mcs.anl.gov/~olson/20131010-prod-dmg-2.dmg This is cut from the following tags: KBaseFBAModeling 20131010-prod assembly 20131010-prod auth 20131010-prod cbd 20131010-prod communities_api 20131010-prod functional_ortholog_predictor 20131010-prod genome_annotation 20131010-prod genotype_phenotype_api 20131010-prod idserver 20131010-prod invocation 20131010-prod jnomics 20131010-prod kb_seed 20131010-prod kbapi_common 20131010-prod kbrest_common HEAD m5nr 20131010-prod networks 20131010-prod ontology_service 20131010-prod phispy 20131010-prod plant_expression_service 20131010-prod probabilistic_annotation 20131010-prod sim_service 20131010-prod translation 20131010-prod trees 20131010-prod typecomp 20130926-test workspace_service 20131010-prod dev_container_tools HEAD kb_model_seed 20131010-prod jars HEAD strep_repeats HEAD erdb_service 20131010-prod I have not been able to test since the build machine is running mountain lion; the runtime as compiled there will not run on my snow leopard machine. --bob

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Services deployed production
by Dan Olson 10 Oct '13

10 Oct '13

The following services were successfully deployed in production: invocation (Iris) KBaseFBAModeling workspace_service kmer_annotation_figfam probabalistic_annotation ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

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Script testing
by Shane Canon 09 Oct '13

09 Oct '13

Miriam, What is your process for testing the scripts? --Shane

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assembly service ready for testing
by Fangfang Xia 09 Oct '13

09 Oct '13

Hi Tom and Dan, We got the local instance of Iris to work, and the assembly service is ready for testing. The test scripts in the repo have been updated for a couple new commands. Here's a basic workflow in IRIS: (on the client machine): wget http://www.mcs.anl.gov/~fangfang/test/smg.fa (upload smg.fa to Iris) ar-run -f smg.fa (note job_id returned) ar-stat ar-get -j job_id -a --stdout > contigs.fa (more detailed reports will show up in a directory: AR$job_id) The contigs.fa can be imported to the workspace for annotation and modeling. Thanks, Fangfang On Oct 7, 2013, at 10:10 AM, Fangfang Xia <fangfang.xia(a)gmail.com> wrote: > Hi Tom, > > Could you put assembly service on the list? We will add Iris integration. We hope that part will be ready for testing by Tuesday noon. > > Thanks, > > Fangfang > > > On Oct 7, 2013, at 9:35 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> Hi again, >> >> We are starting our final deployment push today. I haven't heard from many of the module owners. Please let us know. This week we will try to follow a tight schedule. The schedule is documented in the minor release punch list document (https://docs.google.com/document/d/1QxZtbKUtAp_7Dj6ArEEaQvUcyl92xn80PzIVm_K…) >> >> Because of the lack of any variance on the deadline, we're going to try to wrap testing up COB Wednesday and start the construction of the dmg, ubuntu image, and IRIS on Thursday. >> >> Also happing this week, starting today is the cut-over of the central store release candidate to production. >> >> Every attempt will be made to accommodate everyone, but our deadline is firm. >> >> I will open up a Google hangout today around noon for folks to connect to. >> >> Finally, you should not assume that your module is on the deploy list (though it probably is). Please email me, cc the release-team(a)lists.kbase.us. >> >> Tom >> >> >> On Oct 5, 2013, at 6:47 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> >>> Hi Everyone, >>> >>> Please let me know if you want your service module deployed next week. We will have to follow a rigid schedule. Deployments will take place. Testing will have to be concluded by COB wednesday. On thursday, we'll start the last Iris deployment, start on the ubuntu image and the dmg. >>> >>> Thanks >>> Tom >> >> _______________________________________________ >> Kbase-devel mailing list >> Kbase-devel(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-devel >

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Re: [Release-team] IRIS test deploy number 1
by Dan Olson 08 Oct '13

08 Oct '13

I do get a 500 in the debugger, however that path exists on the server: Request URL: http://kbase.us/services/invocation Request Method: POST Status Code: HTTP/1.1 500 Internal Server Error Request Headers 21:29:27.000 User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:24.0) Gecko/20100101 Firefox/24.0 Referer: http://www.kbase.us/services/docs/invocation/Iris/iris.html Pragma: no-cache Origin: http://www.kbase.us Host: kbase.us DNT: 1 Content-Type: application/x-www-form-urlencoded; charset=UTF-8 Content-Length: 105 Connection: keep-alive Cache-Control: no-cache Accept-Language: en-US,en;q=0.5 Accept-Encoding: gzip, deflate Accept: text/plain, */*; q=0.01 Request Body {"params":[null,"/","/"],"method":"InvocationService.list_files","version":"1.1","id":"7416387966598615"} Response Headers Δ89ms Server: nginx/1.1.19 Date: Wed, 09 Oct 2013 02:28:50 GMT Content-Type: application/json Content-Length: 457 Connection: keep-alive Access-Control-Allow-Origin: http://www.kbase.us Response Body Δ0ms {"version":"1.1","error":{"name":"JSONRPCError","code":-32603,"message":"The JSONRPC server invocation of the method \"list_files\" failed with the following error:\n>\tInvalid path '/tmp/InvocationService/nonauthenticated-storage' (cwd='/' base='/tmp/InvocationService/nonauthenticated-storage/' dir='/tmp/InvocationService/nonauthenticated-storage//') at /kb/deployment/lib/Bio/KBase/InvocationService/UserSession.pm line 159.\n"},"id":"7416387966598615"} ----- Original Message ----- > From: "Thomas Brettin" <brettin(a)mcs.anl.gov> > To: "Shane Canon" <scanon(a)lbl.gov> > Cc: "Dan Olson" <dolson(a)mcs.anl.gov>, release-team(a)kbase.us > Sent: Tuesday, October 8, 2013 9:23:30 PM > Subject: Re: [Release-team] IRIS test deploy number 1 > > yup, see previous screen shot > > that command ain't available in prod, it's a new release > > > On Oct 8, 2013, at 9:22 PM, Shane Canon <scanon(a)lbl.gov> wrote: > > > > > Tom or Dan, > > > > Do you know if there is a command I could run to easily confirm > > that I'm on the test node? > > > > --Shane > > > > On Oct 8, 2013, at 7:20 PM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > > > >> Still not working for me. Same result. > >> > >> What happens when you try different browsers? > >> > >> ----- Original Message ----- > >>> From: "Thomas Brettin" <brettin(a)mcs.anl.gov> > >>> To: "Dan Olson" <dolson(a)mcs.anl.gov> > >>> Cc: release-team(a)kbase.us > >>> Sent: Tuesday, October 8, 2013 9:16:10 PM > >>> Subject: IRIS test deploy number 1 > >>> > >>> I ROCK! > >>> > >>> well, maybe not, but in any case check out IRIS > >>> > >>> remember that you have to change your /etc/hosts file > >>> > >>> here is the entries in my /etc/hosts > >>> > >>> 140.221.84.191 kbase.us www.kbase.us > >>> > >>> I haven't tested any of the commands, that's another whole can of > >>> worms :-) > >>> > >>> > >>> > >> _______________________________________________ > >> Release-team mailing list > >> Release-team(a)lists.kbase.us > >> https://lists.kbase.us/mailman/listinfo/release-team > > > >

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