D4science

Oct 30, 2018

12:31 PM D4Science Infrastructure Task #12799: Memory problems on ckan-d4s1.d4science.org

There's no other way right now, and it's the reason why the two main CKAN instances have so much RAM.
Andrea Dell'Amico

12:29 PM D4Science Infrastructure Incident #12756 (Closed): ShareLatex on VRE CollabResearch crashes very often

The problem disappeared. Andrea Dell'Amico

12:17 PM ISTI Open Access Feature #12721: Beautify the object identifiers

I tried different combinations of URL rewriting, but nothing works: the rule that removes the `index.php?` part of th... Andrea Dell'Amico

11:38 AM D4Science Infrastructure Task #12798 (Closed): Upgrade the oVirt cluster

All the hypervisors have been upgraded. Andrea Dell'Amico

Oct 29, 2018

07:16 PM D4Science Infrastructure Task #12798: Upgrade the oVirt cluster

dlib15x has been upgraded. Andrea Dell'Amico

06:38 PM D4Science Infrastructure Task #12798 (In Progress): Upgrade the oVirt cluster

Upgraded:
dlib19x
dlib18x
dlib16x
The upgrade of dlib15x just started. Andrea Dell'Amico

06:36 PM D4Science Infrastructure Task #12798 (Closed): Upgrade the oVirt cluster

The fix for the gluster leak has been released some weeks ago and it seems stable. Also, we are running out of memory... Andrea Dell'Amico

06:42 PM ISTI Open Access Feature #12721 (In Progress): Beautify the object identifiers

I'm ready to provision the nginx configuration, but I'll do it when @michele.artini@isti.cnr.it is present so that we... Andrea Dell'Amico

Oct 26, 2018

07:12 PM D4Science Infrastructure Task #12792: Apache Server - The response in servlets no longer works correctly

Did you try any other servlet?
Andrea Dell'Amico

Oct 25, 2018

12:41 PM D4Science Infrastructure Task #12742: DataMiner - Support Python 3.6

Done. Andrea Dell'Amico

Oct 24, 2018

07:07 PM D4Science Infrastructure Task #12742: DataMiner - Support Python 3.6

python 3.6 is installed on dataminer1-d-d4s.d4science.org, dataminer2-d-d4s.d4science.org, dataminer1-devnext.d4scien... Andrea Dell'Amico

02:07 PM D4Science Infrastructure Task #12742 (In Progress): DataMiner - Support Python 3.6

Andrea Dell'Amico

Oct 23, 2018

05:06 PM D4Science Infrastructure Incident #12756 (In Progress): ShareLatex on VRE CollabResearch crashes very often

I don't see anything strange on the service side. The *session expiring* error could be date related, is your worksta... Andrea Dell'Amico

Oct 18, 2018

03:27 PM D4Science Infrastructure VM Creation #12661 (Feedback): create a new VM same as data-d.d4science.org to test the new URIResolver

Done. Now the configuration correctly reports data1-d.d4science.net.
Andrea Dell'Amico

03:21 PM D4Science Infrastructure VM Creation #12661 (In Progress): create a new VM same as data-d.d4science.org to test the new URIResolver

There's a problem with the hostname, the VM was created as data1-d.d4science.org. Working on it.
Andrea Dell'Amico

02:46 PM D4Science Infrastructure VM Creation #12661 (Feedback): create a new VM same as data-d.d4science.org to test the new URIResolver

Andrea Dell'Amico

02:46 PM D4Science Infrastructure VM Creation #12661: create a new VM same as data-d.d4science.org to test the new URIResolver

The hostname is data1-d.d4science.net, Lucio has gcube and root access.
Andrea Dell'Amico

02:32 PM D4Science Infrastructure VM Creation #12661: create a new VM same as data-d.d4science.org to test the new URIResolver

The VM is ready, smartgears 2.2.0-4.12.1-162179 is installed. Let us know if you need a different version.
Note th... Andrea Dell'Amico

12:43 PM D4Science Infrastructure VM Creation #12661: create a new VM same as data-d.d4science.org to test the new URIResolver

OK. Last question, smartgears from snapshots or staging?
Andrea Dell'Amico

11:42 AM D4Science Infrastructure VM Creation #12661: create a new VM same as data-d.d4science.org to test the new URIResolver

You are right. Can you give us the maven coordinates for the uri-resolver? until now the applications on data*.d4scie... Andrea Dell'Amico

Oct 17, 2018

08:22 PM D4Science Infrastructure Task #12516 (Closed): PF-KPIs VRE: new PostgreSQL database is needed

Andrea Dell'Amico

02:47 PM D4Science Infrastructure Task #12711: GeoNetwork connector provisioning on GN 3.2.1

Fabio Sinibaldi wrote:
> I don't have the configuration rights on production portals.
@massimiliano.assante@isti.... Andrea Dell'Amico

02:13 PM D4Science Infrastructure Task #12599 (In Progress): Is it possible to install rJava on RStudioLab?

I'm still not able to find the reason why the load of the library fails from inside rstudio while it works from a she... Andrea Dell'Amico

Oct 16, 2018

07:38 PM D4Science Infrastructure Task #12711 (Feedback): GeoNetwork connector provisioning on GN 3.2.1

The connector has been installed into geonetwork-spatialdata.d4science.org too. Andrea Dell'Amico

05:30 PM D4Science Infrastructure Task #12711: GeoNetwork connector provisioning on GN 3.2.1

geonetwork.pre.d4science.net is ready to be tested.
Andrea Dell'Amico

05:20 PM D4Science Infrastructure Task #12711: GeoNetwork connector provisioning on GN 3.2.1

The playbook is ready to be tested. I only need to know where. Andrea Dell'Amico

03:02 PM D4Science Infrastructure Task #12711 (In Progress): GeoNetwork connector provisioning on GN 3.2.1

Andrea Dell'Amico

04:06 PM D4Science Infrastructure Task #12714: DataMiner - Check svn configuration of dataminer-ghost-d.dev.d4science.org

Roberto Cirillo wrote:
> The dataminer ghost: dataminer-ghost-d.dev.d4science.org is an ALIAS of dataminer1-devnext ... Andrea Dell'Amico

12:47 PM D4Science Infrastructure Task #12678: Ansible-dataminer: manage parallel computation as parameter in web.xml

Roberto Cirillo wrote:
> The new dataminer app has been installed successfully: The new web.xml is properly managed.... Andrea Dell'Amico

10:26 AM D4Science Infrastructure Task #12703: Public pages visualised by data miner services and proxies

I'm reassigning to Giancarlo, when he'll have the new index.html ready I'll change the playbook to replace the origin... Andrea Dell'Amico

Oct 15, 2018

06:41 PM D4Science Infrastructure VM Creation #8561 (In Progress): Move authorization service instance on a new VM called auth-dev.d4science.org

I just added the CNAME again, some services still break.
Andrea Dell'Amico

05:12 PM D4Science Infrastructure Incident #12696 (In Progress): geonetwork-spatialdata.d4science.org denied access to database

I just reloaded the postgresql service to be on the safe side, but in the logs I saw:'
~~~
2018-10-15 16:59:43.41... Andrea Dell'Amico

03:47 PM D4Science Infrastructure Incident #12695 (Closed): virtuoso.i-marine.d4science.org certificate is expired, so the service is not working inside the VRE

The embedded services, eg https://services.d4science.org/group/biodiversitylab/sparql-search show an empty page bec... Andrea Dell'Amico

03:05 PM D4Science Infrastructure Task #8673 (Closed): Reconfigure the authorization clients in dev to use https://auth-d.dev.d4science.org/ as the URL for the authentication service

I just removed node7.d.d4science.research-infrastructures.eu record from the DNS.
Andrea Dell'Amico

02:35 PM D4Science Infrastructure Task #8673: Reconfigure the authorization clients in dev to use https://auth-d.dev.d4science.org/ as the URL for the authentication service

Any news on this one? Andrea Dell'Amico

02:31 PM D4Science Infrastructure Task #10505 (Closed): R processes out of control on dataminer0-proto.d4science.org

Closing, as nobody is interested. Andrea Dell'Amico

12:53 PM D4Science Infrastructure VM Creation #12661: create a new VM same as data-d.d4science.org to test the new URIResolver

As we have to introduce smartgears, the playbook must be changed. We are going to switch from apache to nginx too. Andrea Dell'Amico

Oct 12, 2018

11:43 AM ISTI Open Access Bug #12670: Memory problem

It would be better to do the math for the maximum php memory consumption: there are limits to the max memory for each... Andrea Dell'Amico

11:29 AM ISTI Open Access Bug #12669: Wrong encoding after startup

What portal? I know that *ISTI Open Portal* has a meaning to you, but I need the hostname(s). Andrea Dell'Amico

Oct 10, 2018

12:47 AM D4Science Infrastructure Task #12599: Is it possible to install rJava on RStudioLab?

I just tried RStudioLab (my instance was rstudio1.d4science.org) and rJava loaded, here is a screenshot.
I've also ... Andrea Dell'Amico

Oct 09, 2018

12:47 PM D4Science Infrastructure Task #12599: Is it possible to install rJava on RStudioLab?

On what instance? I’ll try to reproduce from inside studio, because the library always loads successfully when I run ... Andrea Dell'Amico

11:39 AM D4Science Infrastructure Task #12599: Is it possible to install rJava on RStudioLab?

It's not even that. it seems that I have to setup a full java environment before running `R CMD javareconf`. The comm... Andrea Dell'Amico

11:01 AM D4Science Infrastructure Task #12599: Is it possible to install rJava on RStudioLab?

It seems that `rJava` wants `JAVA_HOME="/usr/lib/jvm/java-8-oracle/jre"`, while that variable is usually `JAVA_HOME="... Andrea Dell'Amico

Oct 04, 2018

10:22 AM D4Science Infrastructure Task #12578 (Feedback): Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested

Lars Valentin wrote:
> > It's a different problem: knime wants to write inside the knime distribution somehow, when ... Andrea Dell'Amico

Oct 03, 2018

06:59 PM D4Science Infrastructure Task #12599 (Feedback): Is it possible to install rJava on RStudioLab?

rJava is going to be installed on every rstudio instance in the next minutes. Andrea Dell'Amico

03:02 PM D4Science Infrastructure Task #12599 (In Progress): Is it possible to install rJava on RStudioLab?

The problem is still the same (the JDK was updated from 7 to 8 in the meantime). I'm going to install the package glo... Andrea Dell'Amico

Oct 02, 2018

05:48 PM D4Science Infrastructure Task #12578 (Feedback): Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested

Andrea Dell'Amico

05:48 PM D4Science Infrastructure Task #12578: Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested

Lars Valentin wrote:
> Thanks for the effort! If I understand you right the dataminer does not yet behave as expecte... Andrea Dell'Amico

02:12 PM D4Science Infrastructure Task #12578: Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested

I also run successfully:
~~~
/usr/local/bin/knime -reset -consoleLog -nosplash -application org.knime.product.KNI... Andrea Dell'Amico

01:47 PM D4Science Infrastructure Task #12578: Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested

I also run the same workflow adding the option `-destFile=workflow.zip`. The result is attached. Andrea Dell'Amico

01:45 PM D4Science Infrastructure Task #12578: Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested

Lars Valentin wrote:
> great, I am looking forward that this will lead to a finally working version. Please let me k... Andrea Dell'Amico

12:08 PM D4Science Infrastructure Task #12578: Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested

Lars Valentin wrote:
> Thank you for testing. As stated above FSK seems to be still installed in Version=\"0.1.0.201... Andrea Dell'Amico

11:49 AM D4Science Infrastructure Task #12578 (In Progress): Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested

The installation of the plugin failed because of a bug in my script that only shows up when run by cron. I'm fixing i... Andrea Dell'Amico

11:53 AM D4Science Infrastructure Support #12580: WP6: Question on KNIME instances and DM

Yes, the installed KNIME version is 3.6.0 that will become 3.6.1 in the next days.
R is 3.4.4 everywhere.
Andrea Dell'Amico

Oct 01, 2018

07:58 PM D4Science Infrastructure Task #12578 (Feedback): Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested

Scripts and cron job have been installed. I tested the procedure on the dev environment and the plugin installed succ... Andrea Dell'Amico

07:29 PM D4Science Infrastructure Task #12578 (In Progress): Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested

The one I get installed is `1.2.1.201809271338`. I'm adding a cron job that (re)installs the plugin daily. By tomorro... Andrea Dell'Amico

05:51 PM D4Science Infrastructure Task #12578: Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested

(I do not have access to that VRE, FYI). Andrea Dell'Amico

03:23 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

Lars Valentin wrote:
>
> What Andrea was referring to was the direct use of a .knwf file (KNime WorkFlow).
>
> ... Andrea Dell'Amico

03:19 PM D4Science Infrastructure Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins

Leonardo Candela wrote:
> the effort and time needed to install another version of KNIME will be reported. From a pr... Andrea Dell'Amico