mpi4py should be installed now. -Shane On Jan 20, 2014, at 7:26 AM, "Mundy, Michael B. (Mike)" <[email protected]> wrote:

Shane,

Thanks for adding cogent. I forgot that cogent has a dependency on mpi4py (it throws annoying error messages if it is not found).

I was running on t1. I'm confused by the new test environment for this build. Are all of the servers supposed to be running on t1? Or on the instances specified in /root/services? For example, the services file says that workspace_deluxe should be running on t49 at port 7058. But when I checked on t49 this morning there was nothing listening on port 7058.

I'll be at Argonne Tuesday and Wednesday. Who would be the best person to work with there?

Mike Mundy | Senior Analyst Programmer | Bioinformatics Systems Unit | 507-266-7232 | [email protected] Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org

From: Shane Canon <[email protected]> Date: Friday, January 17, 2014 2:39 PM To: Michael Mundy <[email protected]> Cc: "[email protected]" <[email protected]>, Christopher Henry <[email protected]>, Stephen Chan <[email protected]>, Matthew Benedict <[email protected]>, "Chia, Nicholas, Ph.D." <[email protected]>, "N.L. Harris" <[email protected]> Subject: Re: [Release-team] Python servers non-functional in January build

1. I'm not sure about this. Is this on t1 or production? It could be the client tools aren't matched. ws is the new workspace which isn't "public" yet.

2. I'm seeing this too and I think it is related to going through the nginx proxy. There have been some discussions about this.

3. I added cogent on the 2014 runtime on t1. Let me know if you need more.

--Shane

On Jan 17, 2014, at 10:45 AM, "Mundy, Michael B. (Mike)" <[email protected]> wrote:

...

Shane,

Here's what I found in my testing: I used https://kbase.us/services/ws/ as the URL for the new workspace service but I'm getting a "HTTPError: HTTP Error 502: Bad Gateway" error when accessing it. I'm getting a "client-tests/1_V2.fasta: error: Error creating node: request error: 411 Length Required" error when trying to upload a file to shock. The shock team had already looked at this and said it was a problem with the old shock server. The shock-client.cfg file for the ubuntu user has the server URL set to url=http://kbase.us/services/shock-api. Is that URL going to the server in the new deployment. The cogent Python package isn't installed in the kbase Python installation (cogent is installed in the system Python installation). Mike Mundy | Senior Analyst Programmer | Bioinformatics Systems Unit | 507-266-7232 | [email protected] Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org

From: Shane Canon <[email protected]> Date: Friday, January 17, 2014 11:01 AM To: Michael Mundy <[email protected]> Cc: "[email protected]" <[email protected]>, Christopher Henry <[email protected]>, Stephen Chan <[email protected]>, Matthew Benedict <[email protected]>, "Chia, Nicholas, Ph.D." <[email protected]>, "N.L. Harris" <[email protected]> Subject: Re: [Release-team] Python servers non-functional in January build

Mike,

When I originally built the runtime and deployment, I inadvertently used 2013 instead of 2014 in the path. I've created a new runtime and deployment with the correct date (/kbase/deployments/20140109-prod/ and /kbase/runtimes/20140109-prod/). That version should have Steve's changes. Can you test that out? I still need to restart a few services that were originally started with the 2013 tree. I will do that now.

--Shane

On Jan 17, 2014, at 8:43 AM, "Mundy, Michael B. (Mike)" <[email protected]> wrote:

...

Authenticated Python servers are currently non-functional in the January build. Steve Chan has fixed the problem with changes to the auth module with the following commits:

commit 12f346a4ed8e2d30a580d85e7e7987c78568b9bb Merge: 1d98332 0eca1d4 Author: Steve Chan <[email protected]> Date: Mon Jan 13 15:46:37 2014 -0800

Merge branch 'master' into dev_requests-1.x

Conflicts: Bio-KBase-Auth/lib/Bio/KBase/Auth.pm python-libs/biokbase/nexus/__init__.py

commit 0eca1d43361b8955b0d9ce391778cd5a86561150 Author: Steve Chan <[email protected]> Date: Mon Jan 13 15:41:46 2014 -0800

Part of cleanup for the Nexus/requests library API drift

Can we get these two commits in the build and installed on the t1 system. The Probabilistic Annotation and Compression Based Distance services cannot complete the build until this is done.

Mike Mundy | Senior Analyst Programmer | Bioinformatics Systems Unit | 507-266-7232 | [email protected] Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org _______________________________________________ Release-team mailing list [email protected] https://lists.kbase.us/mailman/listinfo/release-team