D4science

Sep 26, 2018

06:33 PM D4Science Infrastructure Support #12249 (Feedback): Need installed KNIME 3.6 and R 3.4 including the listed plugins

Matthias Filter wrote:
> Unfortunately this does not work as our IT does not allow communication via ssh.
> In add... Andrea Dell'Amico

04:57 PM D4Science Infrastructure Task #12443 (Feedback): Enable TLS/SSL on the mongodb development cluster

I changed the playbook so that it builds the CAfile adding both the root CA and the intermediate one. To ensure that ... Andrea Dell'Amico

Sep 25, 2018

08:08 PM D4Science Infrastructure Task #12443: Enable TLS/SSL on the mongodb development cluster

Well, if it's what they want... I just changed the playbook so that by default it uses the `DST_Root_CA_X3` CA file, ... Andrea Dell'Amico

07:32 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

I run both the workflows, they still fail and there's always the message related to the lock file.
We are stalled,... Andrea Dell'Amico

07:05 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

The only `lock` files I see are the ones listed (3.6.0 is from our installation, 3.6.1 is your tar file):
~~~
./k... Andrea Dell'Amico

Sep 24, 2018

01:03 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

The workflow still fails. I've found the following thread, that can maybe give some hints? https://forum.knime.com/t/... Andrea Dell'Amico

Sep 19, 2018

07:26 PM D4Science Infrastructure Task #12516 (Feedback): PF-KPIs VRE: new PostgreSQL database is needed

Done, passwords sent privately. Andrea Dell'Amico

07:19 PM D4Science Infrastructure Task #12516 (In Progress): PF-KPIs VRE: new PostgreSQL database is needed

Andrea Dell'Amico

Sep 18, 2018

06:45 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

I reinstalled all the de.bund.* plugins, then I run the dummy workflow again. The result is attached.
Andrea Dell'Amico

05:57 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

The deployment variables for the plugins are the following:
~~~
knime_plugin_uninstall: []
#- de.bund.bfr.kni... Andrea Dell'Amico

04:16 PM D4Science Infrastructure Task #12364 (Closed): Move the data directory of the new geonetwork installations outside the webapp directory

All the other tasks, the ones that create the data directory with the correct permissions, are already present.
Andrea Dell'Amico

04:15 PM D4Science Infrastructure Task #12364 (In Progress): Move the data directory of the new geonetwork installations outside the webapp directory

Set for the preproduction geonetwork, adding
~~~
tomcat_m_other_java_opts: '-Dgeonetwork.dir={{ geonetwork_data_... Andrea Dell'Amico

02:42 PM D4Science Infrastructure Support #12508: Access logs for SDILab geonetwork

The logs are already available at https://geonetwork-sdi-lab.d4science.org/gcube-logs/ Andrea Dell'Amico

12:57 PM D4Science Infrastructure Support #12505 (Closed): Restart SDI_Lab Geonetwork

Done. Andrea Dell'Amico

12:56 PM D4Science Infrastructure Support #12505 (In Progress): Restart SDI_Lab Geonetwork

Andrea Dell'Amico

Sep 14, 2018

05:27 PM D4Science Infrastructure Task #12490 (Closed): Ask for a wildcard certificate for open-science.it

The certificate is in place. Andrea Dell'Amico

04:58 PM D4Science Infrastructure Task #12490 (In Progress): Ask for a wildcard certificate for open-science.it

The domain registration has been changed. I created the DNS records for open-science.it and www.open-science.it, when... Andrea Dell'Amico

04:56 PM D4Science Infrastructure Task #12490 (Closed): Ask for a wildcard certificate for open-science.it

And configure the DNS records to point to the infra load balancer.
Andrea Dell'Amico

04:59 PM D4Science Infrastructure Task #12241: Setup New gateway open-science.it

I opened a subtask for the certificate. Andrea Dell'Amico

04:52 PM D4Science Infrastructure Task #12241 (In Progress): Setup New gateway open-science.it

The domain registration has been changed. I created the DNS records for `open-science.it` and `www.open-science.it`, ... Andrea Dell'Amico

01:20 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

I'm out of office today, I'll elaborate in the next days.
Andrea Dell'Amico

12:39 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

Sorry, I forgot the attachment. It's there now. We are installing KNIME 4.6.0, FYI.
Andrea Dell'Amico

Sep 13, 2018

11:08 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

Lars Valentin wrote:
> On one of our servers I can connect via ssh and -X window and start the KNIME in the GUI.
... Andrea Dell'Amico

06:17 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

There's no GUI available on the servers, so the command line is the only possible way to run knime. On which nodes di... Andrea Dell'Amico

11:56 AM D4Science Infrastructure Task #12449 (Closed): Add Nagios checks on couchbase cluster

The change worked, it seems. I'm closing the ditcket. Andrea Dell'Amico

Sep 12, 2018

06:27 PM D4Science Infrastructure Task #12449 (Feedback): Add Nagios checks on couchbase cluster

I just configured a timeout in the couchbase check code:
~~~
r = requests.get(url, auth=(options.username, option... Andrea Dell'Amico

11:47 AM D4Science Infrastructure Task #12449: Add Nagios checks on couchbase cluster

We do not collect metrics in nagios, and the checks are failing because the service is so slow to answer that the tim... Andrea Dell'Amico

06:21 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

@lars.valentin@bfr.bund.de any news? did you run your workflows? Andrea Dell'Amico

12:34 PM D4Science Infrastructure Task #12461 (Closed): Cleanup the mongodb ansible roles and the playbooks under d4science-gcube

Done.
Andrea Dell'Amico

12:23 PM D4Science Infrastructure Task #12461 (In Progress): Cleanup the mongodb ansible roles and the playbooks under d4science-gcube

Andrea Dell'Amico

12:20 PM D4Science Infrastructure Task #12461 (Closed): Cleanup the mongodb ansible roles and the playbooks under d4science-gcube

* The correct role is mongodb-org-3.2.yml, all the other ones must be removed and that one renamed
* The used play... Andrea Dell'Amico

Sep 11, 2018

05:42 PM D4Science Infrastructure Task #12448 (Feedback): Add a letsencrypt hook script to the mongodb-org-3.2 ansible role

The hook script has been added to the role.
I also added the two variables to the `mongo_dev/all.yml` file:
~... Andrea Dell'Amico

05:19 PM D4Science Infrastructure Task #12448 (In Progress): Add a letsencrypt hook script to the mongodb-org-3.2 ansible role

Andrea Dell'Amico

05:13 PM D4Science Infrastructure Task #12450: Manage SSL in the mongodb configuration template

We do not have a completely managed cluster, so I didn't touch the configuration that provides x509 authentication be... Andrea Dell'Amico

05:12 PM D4Science Infrastructure Task #12450 (Closed): Manage SSL in the mongodb configuration template

Andrea Dell'Amico

04:56 PM D4Science Infrastructure Task #12450 (In Progress): Manage SSL in the mongodb configuration template

I added some variables to the mongodb-org-3.2 role:
~~~
mongodb_ssl_enabled: False
mongodb_ssl_letsencrypt_manag... Andrea Dell'Amico

12:03 PM D4Science Infrastructure Task #12413 (Closed): Nagios check: Provide a functional check for checking the IS-Collector instances

Andrea Dell'Amico

Sep 10, 2018

07:53 PM D4Science Infrastructure Task #12413: Nagios check: Provide a functional check for checking the IS-Collector instances

The checks have been added. They fail when the string `Profile` is not found.
I'm also adding the https checks.
Andrea Dell'Amico

07:35 PM D4Science Infrastructure Task #12446: Remove accounting_service bucket

Luca Frosini wrote:
> Before removing the bucket, the Nagios checks have to be removed. @tommaso.piccioli@isti.cnr.i... Andrea Dell'Amico

07:32 PM D4Science Infrastructure Task #12449: Add Nagios checks on couchbase cluster

Can you list the buckets that need monitoring?
Andrea Dell'Amico

04:22 PM D4Science Infrastructure Task #12450 (Closed): Manage SSL in the mongodb configuration template

Links to the documentation: https://docs.mongodb.com/v3.2/tutorial/configure-ssl/
Also the membership between cl... Andrea Dell'Amico

04:10 PM D4Science Infrastructure Task #12448 (Closed): Add a letsencrypt hook script to the mongodb-org-3.2 ansible role

Add a script that restarts the mongodb server when the certificate is renewed. Andrea Dell'Amico

Sep 07, 2018

05:29 PM D4Science Infrastructure Task #12425 (Closed): Enable TLS/SSL on the mongodb clusters

It's supported since 3.0 and the configuration seems straightforward.
The documentation: https://docs.mongodb.com/... Andrea Dell'Amico

12:14 PM D4Science Infrastructure Task #12413: Nagios check: Provide a functional check for checking the IS-Collector instances

It's fine by me. Andrea Dell'Amico

Sep 06, 2018

06:50 PM D4Science Infrastructure Task #12397: re-provision manuele resource-registry and database

Luca Frosini wrote:
> Sorry, this error is different from the errors fo tickets #12396 and #12406.
>
> can you p... Andrea Dell'Amico

04:23 PM D4Science Infrastructure Task #12396: re-provision dev resource-registry and database

Add a `ignore_errors: True` to the nagios related tasks. Take the geoserver-smartgears.yml playbook as an example. Andrea Dell'Amico

12:16 PM D4Science Infrastructure Task #12227 (Closed): Encoding issue on Dataminer proto 5

Andrea Dell'Amico

Sep 05, 2018

05:03 PM D4Science Infrastructure Task #12393 (Closed): Do not setup /etc/hosts on the OpenStack VMs

`/etc/hosts` will be now modified on our pure xen hypervisors only. Andrea Dell'Amico

04:58 PM D4Science Infrastructure Task #12393 (Closed): Do not setup /etc/hosts on the OpenStack VMs

The private IP address can change between reboots. Andrea Dell'Amico

11:29 AM D4Science Infrastructure Task #12352: Add new VO scope D4OS to all the dataminer instances

It's running. Andrea Dell'Amico

11:00 AM D4Science Infrastructure Task #12352: Add new VO scope D4OS to all the dataminer instances

Done. I also added a task to force the removal of the `state` directory from inside the main playbook so there's no n... Andrea Dell'Amico

Sep 04, 2018

05:48 PM D4Science Infrastructure Task #12387 (Closed): Increment the prometheus data retention, right now it's too limited.

How much? 6 months? One year? Last solar year plus the current one? Andrea Dell'Amico

05:37 PM D4Science Infrastructure Task #12227 (Feedback): Encoding issue on Dataminer proto 5

Done. As the problem was impacting dataminer5-proto.d4science.org only, the new version of Rprofile.site will be prov... Andrea Dell'Amico

05:26 PM D4Science Infrastructure Task #12227: Encoding issue on Dataminer proto 5

Gianpaolo Coro wrote:
> the problem does not occur anymore. Why this operation had to be forced?
You lamented a l... Andrea Dell'Amico

05:07 PM D4Science Infrastructure Task #12384: Provide a cronjob for restarting VREModeler service

I confirm that node22 is part of the production nodes also in the ansible inventory. If it can be moved into the pre ... Andrea Dell'Amico

01:52 PM D4Science Infrastructure VM Creation #11771: Please create a VM having access to prod authorization service

Luca Frosini wrote:
> Please note the plugin will be released as uber-jar
Does that means that the VM should be d... Andrea Dell'Amico

01:51 PM D4Science Infrastructure Task #10368 (Closed): DM Pool Manager not working (improvement on the notification mechanism)

Andrea Dell'Amico

01:49 PM D4Science Infrastructure Incident #12380: node22.p.d4science.research-infrastructures.eu is not responding

I assumed that it was production, from the hostname (it's still a Ubuntu 12.04 FYI).
About the restart, a cron job... Andrea Dell'Amico

09:55 AM D4Science Infrastructure Incident #12380 (Closed): node22.p.d4science.research-infrastructures.eu is not responding

From the nohup.out file:
~~~
Exception in thread "Thread-11647282" java.lang.OutOfMemoryError: Java heap space
... Andrea Dell'Amico

Sep 03, 2018

08:28 PM D4Science Infrastructure Task #176: Configure DSS to support EUDAT-D4Science integration

Can we close this one? Andrea Dell'Amico

08:25 PM D4Science Infrastructure Task #12227: Encoding issue on Dataminer proto 5

Can we restart this activity? Andrea Dell'Amico

08:24 PM D4Science Infrastructure Task #12018 (Closed): Please update OrientDB ansible script

Andrea Dell'Amico