D4science

Jun 17, 2015

12:19 PM D4Science Infrastructure Task #87: Make new gCube and D4Science wiki available only on https

Remember that the configuration steps can chagne depending on the number of VMs. See ticket #85 Andrea Dell'Amico

11:46 AM D4Science Infrastructure Task #85: Deploy wikimedia on wiki.gcube-system.org and wiki.d4science.org

Andrea Dell'Amico wrote:
> The two mediawiki instances will run on the same server or there will be two separate VMs... Andrea Dell'Amico

Jun 15, 2015

11:58 PM D4Science Infrastructure Task #110: Create 3 Virtual Machine for developement to host new noSQL Db cluster

Do we have a hint about the couchdb architecture that is to be implemented?
Andrea Dell'Amico

02:52 PM D4Science Infrastructure Task #176 (In Progress): Configure DSS to support EUDAT-D4Science integration

New document from Cineca: http://eudat.eu/User%20Documentation%20-%20B2STAGE.html
Andrea Dell'Amico

Jun 12, 2015

06:22 PM D4Science Infrastructure Task #85: Deploy wikimedia on wiki.gcube-system.org and wiki.d4science.org

The two mediawiki instances will run on the same server or there will be two separate VMs?
Andrea Dell'Amico

06:19 PM D4Science Infrastructure Task #87 (In Progress): Make new gCube and D4Science wiki available only on https

The SSL configuration is ready to be deployed.
Before switching to ssl it should be better to test if the site works... Andrea Dell'Amico

02:27 PM D4Science Infrastructure Task #172: Shut down the old d4science Trac instance

Any news?
Andrea Dell'Amico

02:26 PM D4Science Infrastructure Task #98 (Closed): MongoDB in production: allow only trusted connections

Andrea Dell'Amico

01:24 PM D4Science Infrastructure Task #99: run mongoDB as unprivileged user

I assume the nodes are:
~~~
node58.p.d4science.research-infrastructures.eu
node67.p.d4science.research-infrastru... Andrea Dell'Amico

Jun 11, 2015

07:28 PM D4Science Infrastructure Task #176: Configure DSS to support EUDAT-D4Science integration

We had a conference call with Giovanni Morelli, he asked to wait for more precise guidelines. He will send them in th... Andrea Dell'Amico

05:37 PM D4Science Infrastructure Task #248 (Closed): No mongodb server rotates its logs

All the mongodb instances never rotate their log files. The production cluster log files are over 1GB on every node.
Andrea Dell'Amico

04:29 PM D4Science Infrastructure Task #98 (Feedback): MongoDB in production: allow only trusted connections

The iptables rules are now active.
Andrea Dell'Amico

03:35 PM D4Science Infrastructure Task #98 (In Progress): MongoDB in production: allow only trusted connections

I did not found any connections from .tw hosts, but I composed a list that includes more that what initially asked:
... Andrea Dell'Amico

Jun 10, 2015

05:07 PM D4Science Infrastructure Task #98: MongoDB in production: allow only trusted connections

I've found some networks recently used to protect another service on node21.p.d4science.research-infrastructures.eu:
... Andrea Dell'Amico

04:35 PM D4Science Infrastructure Support #238 (Rejected): The nagios check 'gcube search' goes often in critical state

Andrea Dell'Amico

04:07 PM D4Science Infrastructure Support #238: The nagios check 'gcube search' goes often in critical state

It's working correctly since the start of the month, but it flipped a lot in May.
When if fails it's always becaus... Andrea Dell'Amico

01:00 PM D4Science Infrastructure Support #238: The nagios check 'gcube search' goes often in critical state

I attach the two scripts to clarify.
Andrea Dell'Amico

12:55 PM D4Science Infrastructure Support #238: The nagios check 'gcube search' goes often in critical state

Sorry, I just noted that the formatting lost a part of the script. The line
~~~
wget http://$1/images/report/xml ... Andrea Dell'Amico

Jun 09, 2015

05:11 PM D4Science Infrastructure Task #100: Increase ram Memory on IS-Collector services in production

It needs to be done during the next downtime.
Andrea Dell'Amico

05:09 PM D4Science Infrastructure Task #85: Deploy wikimedia on wiki.gcube-system.org and wiki.d4science.org

It seems that we only need to ask for the wiki backups.
Tommaso is going to email the Greeks.
After that we will ... Andrea Dell'Amico

01:16 PM D4Science Infrastructure Incident #232 (Closed): node51.p.d4science.research-infrastructures.eu webapp unresponsive. The ajp port is open with connections from China

The iptables rules are active. Andrea Dell'Amico

12:37 PM D4Science Infrastructure Incident #232: node51.p.d4science.research-infrastructures.eu webapp unresponsive. The ajp port is open with connections from China

John Gerbesiotis wrote:
> Yes searchsystem uses ehcache and the default port of ehcache is 4446.
And that port is... Andrea Dell'Amico

Jun 08, 2015

06:31 PM D4Science Infrastructure Support #238 (Rejected): The nagios check 'gcube search' goes often in critical state

The "Gcube search" nagios check on portal.i-marine.d4science.org is often in critical state. The script source code i... Andrea Dell'Amico

06:19 PM D4Science Infrastructure Task #213 (Closed): Create a new machine to host the mongodb server used by the accounting service

The nagios checks are active.
Andrea Dell'Amico

06:02 PM D4Science Infrastructure Support #229 (Closed): Create a new virtual machine to host the ic-proxy webapp managed by smartgears

Andrea Dell'Amico

04:23 PM D4Science Infrastructure Incident #232: node51.p.d4science.research-infrastructures.eu webapp unresponsive. The ajp port is open with connections from China

Port 8009 is now closed. What's worrying me is udp 4446, it's opened by one of the tomcat webapps but I don't know if... Andrea Dell'Amico

11:38 AM D4Science Infrastructure Incident #232: node51.p.d4science.research-infrastructures.eu webapp unresponsive. The ajp port is open with connections from China

It surely needs to be closed.
The ajp port is always of no use on our systems, because we always use the http port... Andrea Dell'Amico

12:05 PM D4Science Infrastructure Support #233 (In Progress): node65.p.d4science.research-infrastructures.eu increase memory RAM

I've just increased the available RAM in the xen configuration file for the machine. A shutdown is needed, let me kn... Andrea Dell'Amico

Jun 06, 2015

12:44 PM D4Science Infrastructure Incident #232 (Closed): node51.p.d4science.research-infrastructures.eu webapp unresponsive. The ajp port is open with connections from China

The 8080 (and 8005) tomcat port has been closed since last night.
The actual 'netstat -na' output is:
~~~
Active... Andrea Dell'Amico

Jun 05, 2015

04:51 PM D4Science Infrastructure Support #229 (Feedback): Create a new virtual machine to host the ic-proxy webapp managed by smartgears

Andrea Dell'Amico

04:51 PM D4Science Infrastructure Support #229 (In Progress): Create a new virtual machine to host the ic-proxy webapp managed by smartgears

The machine is ready.
There's a nginx frontend that runs on port 80 and act as a proxy for the tomcat instance.
Andrea Dell'Amico

03:28 PM D4Science Infrastructure Support #229: Create a new virtual machine to host the ic-proxy webapp managed by smartgears

The hostname will be node79.d4science.org, IP 146.48.122.79
Andrea Dell'Amico

Jun 04, 2015

05:31 PM D4Science Infrastructure Task #183: tomcat running as root user under port 80

Roberto Cirillo wrote:
> The following list contains all tomcat instances in production, running as root user under ... Andrea Dell'Amico

05:21 PM D4Science Infrastructure Task #183: tomcat running as root user under port 80

due to changes in a related task Andrea Dell'Amico

05:25 PM D4Science Infrastructure Task #217 (Closed): Automate the installation and configuration of the statistical-manager nodes

All the components need to be automatically deployed.
Andrea Dell'Amico

05:23 PM D4Science Infrastructure Task #206: Automate the installation of wps.statistical.d4science.org

The news is that R is not needed.
R is actually present maybe because the machine is a clone of one of the smartgear... Andrea Dell'Amico

05:21 PM D4Science Infrastructure Task #206: Automate the installation of wps.statistical.d4science.org

due to changes in a related task Andrea Dell'Amico

05:21 PM D4Science Infrastructure Task #207: Document the R installation on the statistical-manager nodes.

The packages list describes the installation on the statistical-manager* nodes. Andrea Dell'Amico

03:12 PM D4Science Infrastructure Task #172: Shut down the old d4science Trac instance

I see a lot of other virtualdomains on issue.research-infrastructures.eu. Some are trac instances, some are 'portals'... Andrea Dell'Amico

01:04 PM D4Science Infrastructure Task #213 (In Progress): Create a new machine to host the mongodb server used by the accounting service

We need the nagios checks.
Andrea Dell'Amico

12:57 PM D4Science Infrastructure Task #213 (Closed): Create a new machine to host the mongodb server used by the accounting service

There is a new playbook inside d4science-ghn-cluster that installs a configure a mongodb instance.
It can be extende... Andrea Dell'Amico

12:56 PM D4Science Infrastructure Task #213 (In Progress): Create a new machine to host the mongodb server used by the accounting service

The machine is up and running.
Andrea Dell'Amico

11:52 AM D4Science Infrastructure Task #213: Create a new machine to host the mongodb server used by the accounting service

node57.p.d4science.research-infrastructures.eu's IP address: 146.48.122.135 (needed to manage the firewall rules).
Andrea Dell'Amico

11:51 AM D4Science Infrastructure Task #213: Create a new machine to host the mongodb server used by the accounting service

Hostname: mongo-0-ut-d4s.d4science.org
IP address: 146.48.123.0
Andrea Dell'Amico

11:49 AM D4Science Infrastructure Task #213 (Closed): Create a new machine to host the mongodb server used by the accounting service

1. Install mongodb 2.x
2. Mount the /data dir now used by node57.p
3. monitor mongodb via nagios
4. mongodb ac... Andrea Dell'Amico

Jun 03, 2015

11:56 AM D4Science Infrastructure Task #98: MongoDB in production: allow only trusted connections

Roberto Cirillo wrote:
> 1. 28017 port should be closed from outside
Ok
> 2. I don't know if is possible to o... Andrea Dell'Amico

11:16 AM D4Science Infrastructure Support #135 (Closed): Add a Favicon to Redmine Service

Andrea Dell'Amico

May 30, 2015

08:34 PM D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure Support #135 (Feedback): Add a Favicon to Redmine Service

Andrea Dell'Amico

05:42 PM D4Science Infrastructure Support #135 (In Progress): Add a Favicon to Redmine Service

Done. Andrea Dell'Amico

May 29, 2015

07:42 PM D4Science Infrastructure 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

May 28, 2015

03:14 PM D4Science Infrastructure 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 D4Science Infrastructure Task #84 (In Progress): Create new virtual machines to host gCube and DScience WIKI

Andrea Dell'Amico

01:21 PM D4Science Infrastructure 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

01:01 PM D4Science Infrastructure Task #172: Shut down the old d4science Trac instance

The SVN sync is now disabled.
Andrea Dell'Amico

12:22 PM D4Science Infrastructure 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

11:02 PM D4Science Infrastructure 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

06:51 PM D4Science Infrastructure 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

06:24 PM D4Science Infrastructure 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

04:08 PM D4Science Infrastructure 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

May 26, 2015

11:59 PM D4Science Infrastructure Task #140: 36 new smartgears VMs are needed

The keys have been installed on all nodes.
Andrea Dell'Amico

May 25, 2015

06:17 PM D4Science Infrastructure 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

03:05 PM D4Science Infrastructure 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

03:03 PM D4Science Infrastructure Task #138 (Closed): Automate the installation of the R suite and its packages

Gp says that the installation is correctly working.
Andrea Dell'Amico

May 23, 2015

03:02 PM D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure Task #138 (Feedback): Automate the installation of the R suite and its packages

Andrea Dell'Amico

02:01 PM D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure Task #139 (Closed): Automate the smartgears installation and configuration

Andrea Dell'Amico

02:18 PM D4Science Infrastructure Task #139 (In Progress): Automate the smartgears installation and configuration

Andrea Dell'Amico

02:18 PM D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure 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

May 22, 2015

11:28 PM D4Science Infrastructure Task #131 (In Progress): Report the R Interpreter environment to reproduce on the Generic Worker nodes

Andrea Dell'Amico

11:24 PM D4Science Infrastructure Task #131 (Feedback): Report the R Interpreter environment to reproduce on the Generic Worker nodes

Andrea Dell'Amico

11:22 PM D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure 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 D4Science Infrastructure 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

11:18 AM D4Science Infrastructure 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