Activity

From May 08, 2015 to Jun 06, 2015

May 30, 2015

08:34 PM Task #207 (Closed): Document the R installation on the statistical-manager nodes.: The R installation of wps.statistical.d4science.org is more complex than the one that runs on the workers nodes.
W... Andrea Dell'Amico
08:31 PM Task #206 (Closed): Automate the installation of wps.statistical.d4science.org: 1. Web server frontend
2. Tomcat under an unprivileged user
3. R needs to be installed with the same version packag... Andrea Dell'Amico
08:29 PM Task #205 (Closed): Automate the installation and configuration of the geonetwork servers: Put them under ansible control, and install a web server frontend as we did for the geoservers. Andrea Dell'Amico
08:27 PM Task #183: tomcat running as root user under port 80: The tomcat on node57.p.d4science.research-infrastructures.eu is running as 'transact' user and it's listening on port... Andrea Dell'Amico
05:42 PM Support #135 (Feedback): Add a Favicon to Redmine Service: Andrea Dell'Amico
05:42 PM Support #135 (In Progress): Add a Favicon to Redmine Service: Done. Andrea Dell'Amico

May 29, 2015

07:42 PM Task #85: Deploy wikimedia on wiki.gcube-system.org and wiki.d4science.org: A mediawiki installation lives on wiki.d4science.org. I shut down the web server because I still don't know how the w... Andrea Dell'Amico
03:15 PM Task #117: Execute FAO MSY on the complete FAO Dataset: As it happened also in other cases (e.g. the Length-Weight algorithm), the effect of parallelising an R script is to ... Gianpaolo Coro
12:35 PM Task #140 (Closed): 36 new smartgears VMs are needed: Roberto Cirillo
12:25 PM Task #140 (Resolved): 36 new smartgears VMs are needed: Roberto Cirillo
12:28 PM Incident #163 (Rejected): Redmine - change the duration of the working day: Redmine perfectly calculate the time. The issue does not exist Luca Frosini
12:27 PM Incident #163 (In Progress): Redmine - change the duration of the working day: Luca Frosini
11:36 AM Task #184 (Closed): Ganglia monitoring, gCore based category: upgrade the VM running unsupported distributions: In this list there is a set of VMs with an OS (ubuntu 8.04 or 121.04) that are not supported by Ganglia and should be... Roberto Cirillo
11:24 AM Task #183 (Closed): tomcat running as root user under port 80: The following list contains all tomcat instances in production, running as root user under port 80:
node57.p.d4sci... Roberto Cirillo

May 28, 2015

05:32 PM Incident #171: Recently updated file for gCubeApps/BlueBridgeProject Folder error: I've attached the history of "Proposal" folder: I see at the same time a "cut" and an "add" operation of the "Old" f... Roberto Cirillo
05:02 PM Task #177 (Closed): Make Release Notes of Cube 3.7.0 Public Available: Massimiliano Assante
05:02 PM Task #177 (Closed): Make Release Notes of Cube 3.7.0 Public Available: The release notes coming from ETICS have been formed by Nikolas, I took care of formatting them in HTML and put in th... Massimiliano Assante
04:27 PM Incident #148 (Closed): Resource Sweeper does not sweep GHN Resources: Massimiliano Assante
04:26 PM Incident #148: Resource Sweeper does not sweep GHN Resources: is this activity terminated? if yes, please close the ticket. Pasquale Pagano
04:18 PM Task #176 (Closed): Configure DSS to support EUDAT-D4Science integration: According to what reported here: http://eudat.eu/User%20Documentation%20-%20Data%20Staging%20Script.html#UserDocument... Pasquale Pagano
03:21 PM Task #85: Deploy wikimedia on wiki.gcube-system.org and wiki.d4science.org: @roberto.cirillo do you have information regarding what Andrea is asking? Luca Frosini
03:14 PM Task #85 (In Progress): Deploy wikimedia on wiki.gcube-system.org and wiki.d4science.org: I'm going to install mediawiki with nginx as a front end web server loosely following those guides: [https://www.medi... Andrea Dell'Amico
03:13 PM Task #84 (In Progress): Create new virtual machines to host gCube and DScience WIKI: Andrea Dell'Amico
01:21 PM Task #172: Shut down the old d4science Trac instance: I just deleted the following DNS records:
issue.d4science-ii.research-infrastructures.eu
support.d4science.resear... Andrea Dell'Amico
01:02 PM Task #172: Shut down the old d4science Trac instance: The shutdown email should be communicated on the iMarine project TCom mailing list. Massimiliano Assante
01:01 PM Task #172: Shut down the old d4science Trac instance: Before shutting down the iMarine TRAC instance please give us a deadline (and 1 week of time) with repeated warning e... Massimiliano Assante
01:01 PM Task #172: Shut down the old d4science Trac instance: The SVN sync is now disabled.
Andrea Dell'Amico
12:44 PM Task #172: Shut down the old d4science Trac instance: I asked to involved people and I confirm that the SVN sync is not needed anymore. Luca Frosini
12:22 PM Task #172 (In Progress): Shut down the old d4science Trac instance: The server is now running only the redbox and social-isti trac instances.
Is the svn sync still needed?
Andrea Dell'Amico

May 27, 2015

11:22 PM Incident #171: Recently updated file for gCubeApps/BlueBridgeProject Folder error: All the files in the folder "Old" are not available, they are 35 files.
Today the folder "Old" and other folders hav... Valentina Marioli
09:33 PM Incident #171: Recently updated file for gCubeApps/BlueBridgeProject Folder error: This is not exact: the metadata fields are stored in MongoDB but the file payload is missing.
Could I have more deta... Roberto Cirillo
06:58 PM Incident #171: Recently updated file for gCubeApps/BlueBridgeProject Folder error: The file is in the storage, but it's not possible to download it.
Roberto, could you please check it? Valentina Marioli
06:52 PM Incident #171 (In Progress): Recently updated file for gCubeApps/BlueBridgeProject Folder error: Valentina Marioli
05:40 PM Incident #171 (Closed): Recently updated file for gCubeApps/BlueBridgeProject Folder error: The portlet receives the following exception in the backend, I checked the scope for the storage service endpoint and... Massimiliano Assante
11:17 PM Task #172: Shut down the old d4science Trac instance: RedBox has to be maintained as well.
Pasquale Pagano
11:02 PM Task #172: Shut down the old d4science Trac instance: The d-net guys say that redbox isn't their.
All the other instances can be closed. So it seems that only social.isti... Andrea Dell'Amico
07:56 PM Task #172: Shut down the old d4science Trac instance: I think the following ones can be turned off.
issue.d4science-ii.research-infrastructures.eu
support.d4science.re... Pasquale Pagano
06:51 PM Task #172: Shut down the old d4science Trac instance: There are several trac instances on that server:
issue.d4science-ii.research-infrastructures.eu
support.d4science... Andrea Dell'Amico
06:27 PM Task #172 (Closed): Shut down the old d4science Trac instance: The old trac instance available at https://support.d4science.research-infrastructures.eu can be shut down.
If the ho... Luca Frosini
06:24 PM Task #98: MongoDB in production: allow only trusted connections: Two considerations
1. 28017 is the http port that shows the server status. Is it really needed? even from outside?
... Andrea Dell'Amico
05:53 PM Incident #163 (Paused): Redmine - change the duration of the working day: I didn't find the solution yet. More investigation is needed Luca Frosini
12:49 PM Incident #163 (In Progress): Redmine - change the duration of the working day: Luca Frosini
11:49 AM Incident #163 (Closed): Redmine - change the duration of the working day: Redmine supports a working day with a duration of 24 hours.
You can change the configuration of Redmine to support ... Giancarlo Panichi
04:08 PM Task #169 (Closed): Verification of the smartgears nodes list: Ganglia is showing more smartgears workers than expected: [[http://monitoring.research-infrastructures.eu/ganglia/?c=... Andrea Dell'Amico
02:18 PM Task #117 (In Progress): Execute FAO MSY on the complete FAO Dataset: Tests have started for this huge computation.
I expect the computation time to be exponential descendant.
A linear... Gianpaolo Coro

May 26, 2015

11:59 PM Task #140: 36 new smartgears VMs are needed: The keys have been installed on all nodes.
Andrea Dell'Amico
06:00 PM Task #140: 36 new smartgears VMs are needed: It's also need to add the production key "d4science.research-infrastructures.eu.gcubekey" on all the new nodes config... Roberto Cirillo
06:01 PM Incident #148: Resource Sweeper does not sweep GHN Resources: The fix has been released in 3.7.0 and should build tonight. Massimiliano Assante
11:17 AM Incident #148: Resource Sweeper does not sweep GHN Resources: Please deploy the patch on the production portal. Pasquale Pagano

May 25, 2015

07:54 PM Task #150 (Closed): Add nagios check for sp.d4science.org tomcat: This machine hosts the Shibboleth service provider of the infrastructure.
The tomcat is the same and is installed ... Massimiliano Assante
07:48 PM Task #149 (Closed): Add nagios check for www.d4science.org and www.gcube-system.org websites: The tomcat is the same and is installed in /home/portal/liferay/tomcat/ of portal.d4science.org Massimiliano Assante
07:43 PM Incident #148 (Resolved): Resource Sweeper does not sweep GHN Resources: The new deserialisation is performed through the Resources class of org.gcube.common.resources instead of using JAXB,... Massimiliano Assante
05:14 PM Incident #148 (In Progress): Resource Sweeper does not sweep GHN Resources: Massimiliano Assante
05:14 PM Incident #148 (Closed): Resource Sweeper does not sweep GHN Resources: The Resource Sweeper is no longer able to sweep expired GHN resources. The problem seems to be in the resource deseri... Massimiliano Assante
06:17 PM Task #140 (Feedback): 36 new smartgears VMs are needed: All the nodes from node43.d4science.org to node78.d4science.org are now configured with the *production* scope.
Th... Andrea Dell'Amico
03:11 PM Task #140: 36 new smartgears VMs are needed: I have run precise tests to evaluate the work of this execution environment, both from the Statistical Manager and fr... Gianpaolo Coro
03:05 PM Task #140: 36 new smartgears VMs are needed: The configuration scripts are complete. The R installation has been tested, so I'm launching the configuration of all... Andrea Dell'Amico
02:46 PM Task #140: 36 new smartgears VMs are needed: Please update the %Done and let us understand the status of this activity. Pasquale Pagano
05:52 PM Task #109 (Closed): new VMs for new worker instances in production environment: Dismissed. Tommaso Piccioli
05:07 PM Task #109: new VMs for new worker instances in production environment: I'm going to dismiss the 3 nodes
node25.d4science.org
node26.d4science.org
node40.d4science.org
no other res... Tommaso Piccioli
02:45 PM Task #109 (In Progress): new VMs for new worker instances in production environment: Why this ticket is still open (it was still marked as New instead of In Progress) and why its %Done is still 0%? Plea... Pasquale Pagano
03:03 PM Task #138 (Closed): Automate the installation of the R suite and its packages: Gp says that the installation is correctly working.
Andrea Dell'Amico
02:47 PM Task #138: Automate the installation of the R suite and its packages: Gp please answer to the request for feedback. Pasquale Pagano
02:58 PM Task #131 (Closed): Report the R Interpreter environment to reproduce on the Generic Worker nodes: Gianpaolo Coro

May 23, 2015

03:02 PM Task #140: 36 new smartgears VMs are needed: node43.d4science.org and node44.d4sciece.org have been deployed with smartgears under the new tomcat package and R. s... Andrea Dell'Amico
02:13 PM Task #140: 36 new smartgears VMs are needed: The distribution must be Ubuntu precise as a R requirement.
Update, from Tom:
*The new nodes are up and running... Andrea Dell'Amico
02:09 PM Task #140 (Closed): 36 new smartgears VMs are needed: Gianpaolo needs 36 more smartgears worker nodes.
They need both the latest smartgears software and R installed as d... Andrea Dell'Amico
02:55 PM Task #138 (Feedback): Automate the installation of the R suite and its packages: Andrea Dell'Amico
02:01 PM Task #138 (In Progress): Automate the installation of the R suite and its packages: There's now a library playbook called 'R' that installs the base R packages and even additional packages.
The additi... Andrea Dell'Amico
02:54 PM Task #142 (Closed): New internal repository to distribute package backports on Ubuntu precise.: The new repository is called precise-backports and lives on ppa.research-infrastructures.eu.
There also is an ansi... Andrea Dell'Amico
02:50 PM Task #142 (Closed): New internal repository to distribute package backports on Ubuntu precise.: We need a new internal repository to distribute our package backports for Ubuntu precise. Andrea Dell'Amico
02:52 PM Task #141 (Closed): We need a newer tomcat package for the Ubuntu precise VMs: The packages are available on the new precise-backports repo on ppa.research-infrastructures.eu
Andrea Dell'Amico
02:16 PM Task #141 (Resolved): We need a newer tomcat package for the Ubuntu precise VMs: We now have a package for tomcat 7.0.55. I chose this one because is the last ubuntu/debian build that does not depen... Andrea Dell'Amico
02:15 PM Task #141 (Closed): We need a newer tomcat package for the Ubuntu precise VMs: The smartgears software doesn't work with tomcat 7.0.26, the version packaged for Ubuntu precise.
The smartgears n... Andrea Dell'Amico
02:19 PM Task #139 (Closed): Automate the smartgears installation and configuration: Andrea Dell'Amico
02:18 PM Task #139 (In Progress): Automate the smartgears installation and configuration: Andrea Dell'Amico
02:18 PM Task #139: Automate the smartgears installation and configuration: The smartgears role is available inside the d4science-ghn-cluster playbook. On Ubuntu precise the library role 'preci... Andrea Dell'Amico
02:05 PM Task #139 (Closed): Automate the smartgears installation and configuration: We need an ansible playbook that installs and configure a smartgears intance.
Andrea Dell'Amico
12:24 AM Task #131: Report the R Interpreter environment to reproduce on the Generic Worker nodes: Gianpaolo Coro wrote:
> The required JAGS version is 3.1.0.
> The packages compatible with the algorithms are the f... Andrea Dell'Amico
12:00 AM Task #131: Report the R Interpreter environment to reproduce on the Generic Worker nodes: The required JAGS version is 3.1.0.
The packages compatible with the algorithms are the following:
R2jags_0.03-08 ... Gianpaolo Coro

May 22, 2015

11:28 PM Task #131 (In Progress): Report the R Interpreter environment to reproduce on the Generic Worker nodes: Andrea Dell'Amico
11:24 PM Task #131 (Feedback): Report the R Interpreter environment to reproduce on the Generic Worker nodes: Andrea Dell'Amico
11:22 PM Task #131: Report the R Interpreter environment to reproduce on the Generic Worker nodes: I've automated the packages installation but some versions differ from your list:
~~~
Package Ver... Andrea Dell'Amico
07:23 PM Task #131: Report the R Interpreter environment to reproduce on the Generic Worker nodes: Which jags version is needed? The one distributed with Ubuntu precise is 3.1.0, via CRAN the 3.2.0, 3.3.0, 3.4.0 are ... Andrea Dell'Amico
11:27 PM Task #138: Automate the installation of the R suite and its packages: The result is the following:
Package Version
abind "abind" "1.4-3"
bayesmix "bayesmix" "0.7-3"
coda "coda" "0.1... Andrea Dell'Amico
11:26 PM Task #138 (Closed): Automate the installation of the R suite and its packages: Create an ansible playbook that installs R and the listed packages on Ubuntu precise Andrea Dell'Amico

May 21, 2015

06:43 PM Support #135 (Closed): Add a Favicon to Redmine Service: The favicon of the Redmine service should be revised by using the following one
https://www.d4science.org/documents... Leonardo Candela
11:18 AM Task #131: Report the R Interpreter environment to reproduce on the Generic Worker nodes: It seems that CRAN is also availabe as a Ubuntu repository: http://sites.psu.edu/theubunturblog/installing-r-in-ubunt... Andrea Dell'Amico
11:10 AM Task #131 (In Progress): Report the R Interpreter environment to reproduce on the Generic Worker nodes: The Worker nodes host a different R Environment with respect to the Statistical Managers. The latters are far more co... Gianpaolo Coro
11:03 AM Task #131 (Closed): Report the R Interpreter environment to reproduce on the Generic Worker nodes: In this ticket we will report the environment to install on a Generic Worker node to make it compliant with current a... Gianpaolo Coro

May 18, 2015

05:59 PM Support #119 (Closed): add new nagios check on bionym.d4science.org: A new Nagios check should be added for tomcat running on port 80 hosted at: bionym.d4science.org Roberto Cirillo
04:11 PM Task #117 (Closed): Execute FAO MSY on the complete FAO Dataset: FAO MSY needs to be executed on 5500 species. This requires empowering the production Cloud processing environment. Gianpaolo Coro

May 15, 2015

06:40 PM Task #110 (Closed): Create 3 Virtual Machine for developement to host new noSQL Db cluster: Please create the new machine as nodeXX.d.d4science.org Luca Frosini
05:22 PM Task #109 (Closed): new VMs for new worker instances in production environment: The following list contains all the VMs dismissed in release 3.7
{{{
node2.d4science.org
node6.p.d4science.researc... Roberto Cirillo
05:11 PM Incident #103 (Closed): statistical manager and new workers issue: Gianpaolo Coro
05:10 PM Incident #103 (In Progress): statistical manager and new workers issue: Gianpaolo Coro
05:03 PM Incident #103: statistical manager and new workers issue: The modifications have been deployed and tested with heterogeneous experiments on the Statistical Managers in product... Gianpaolo Coro
02:32 PM Incident #103: statistical manager and new workers issue: Two nested problems caused this issue:
1 - the storage manager destroyed one previously created smp link for a file ... Gianpaolo Coro
02:21 PM Incident #103: statistical manager and new workers issue: please put in progress this incidente and report the solution identified. Pasquale Pagano
03:50 PM Incident #95 (Closed): References on task in SVN commit corrupt referenced ticket: Tommaso Piccioli
02:23 PM Incident #95: References on task in SVN commit corrupt referenced ticket: is the issue solved? If yes, please close the incident. Pasquale Pagano
02:21 PM Incident #107 (Closed): gCubeApps/ENVRI VRE GenericResource missing: Massimiliano Assante
12:33 PM Incident #107 (Resolved): gCubeApps/ENVRI VRE GenericResource missing: Massimiliano Assante
12:32 PM Incident #107 (In Progress): gCubeApps/ENVRI VRE GenericResource missing: The generic resources of type VRE was recreated by issuing a new VRE Creation Massimiliano Assante
12:21 PM Incident #107 (Closed): gCubeApps/ENVRI VRE GenericResource missing: The gCubeApps/ENVRI is missing in the generic resources go type VRE, therefore we cannot perform any operation in the... Massimiliano Assante

May 14, 2015

07:35 PM Incident #103 (Closed): statistical manager and new workers issue: The new worker seems able to start more than one computation and this cause errors in accessing the statistical manag... Roberto Cirillo
06:45 PM Incident #95 (Resolved): References on task in SVN commit corrupt referenced ticket: Tommaso Piccioli
06:44 PM Incident #95 (In Progress): References on task in SVN commit corrupt referenced ticket: Plugin removed.
Anyway il seems that the pluginwas usefull for the tortoise svn users. Tommaso Piccioli
03:36 PM Incident #95: References on task in SVN commit corrupt referenced ticket: The problem is related to a plugin called **Redmine Add Subversion Links** and available here:
https://github.com/ma... Luca Frosini
11:06 AM Incident #95 (Closed): References on task in SVN commit corrupt referenced ticket: Redmine has the capability to link SVN commit to task using a keyword (refs, IssueId, fixes, ....) followed by #NN (N... Luca Frosini
05:46 PM Task #102 (Closed): AMQ in production: upgrade OS: The AMQ in production is hosted on:
message-broker.d4science.research-infrastructures.eu
with: ubuntu 9.04.
Th... Massimiliano Assante
05:44 PM Task #101 (Closed): Add new special nagios check for host: message-broker.d4science.research-infrastructures.eu: The following queues:
- D4ScienceJobAlternative
- D4ScienceJob
and every queue with prefix "D4ScienceJobRespon... Massimiliano Assante
05:39 PM Task #100 (Closed): Increase ram Memory on IS-Collector services in production: The following nodes have an instance of IS-Collector service that runs in production environment:
{{{
- node1.p.d... Massimiliano Assante
05:37 PM Task #99 (Closed): run mongoDB as unprivileged user: The mongoDB instances in production environment running as root user.
We should change the user as done in developme... Massimiliano Assante
05:34 PM Task #87: Make new gCube and D4Science wiki available only on https: I think the login should be on https but why we would want non logged user to use https? Massimiliano Assante
05:16 PM Task #98 (Closed): MongoDB in production: allow only trusted connections: Only allow trusted clients to connect to the port for the mongod instances.
The ports used are: 27017, 28017
Follo... Massimiliano Assante

May 13, 2015

03:32 PM Task #86 (Closed): Request new SSL Certificate globally recognized for wiki.gcube-system.org and wiki.d4science.org: Luca Frosini
03:26 PM Task #86 (Resolved): Request new SSL Certificate globally recognized for wiki.gcube-system.org and wiki.d4science.org: Tommaso Piccioli
03:25 PM Task #86 (In Progress): Request new SSL Certificate globally recognized for wiki.gcube-system.org and wiki.d4science.org: Tommaso Piccioli
03:22 PM Task #86: Request new SSL Certificate globally recognized for wiki.gcube-system.org and wiki.d4science.org: SSL Certificate for wiki.gcube-system.org and wiki.d4science.org already issued by CA Tommaso Piccioli
03:04 PM Task #86 (Closed): Request new SSL Certificate globally recognized for wiki.gcube-system.org and wiki.d4science.org: Luca Frosini
03:08 PM Task #84: Create new virtual machines to host gCube and DScience WIKI: The name of the machines will be
wiki.gcube-system.org
wiki.d4science.org
Luca Frosini
03:01 PM Task #84 (Closed): Create new virtual machines to host gCube and DScience WIKI: Luca Frosini
03:06 PM Task #88 (Closed): Migrate gCube and D4Science WIKI content on new installation: Luca Frosini
03:05 PM Task #87 (Closed): Make new gCube and D4Science wiki available only on https: Luca Frosini
03:02 PM Task #85 (Closed): Deploy wikimedia on wiki.gcube-system.org and wiki.d4science.org: Luca Frosini

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