D4Science Infrastructure

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