Project

General

Profile

D64 OpenAIRE Maintenance Report » History » Version 75

Marek Horst, 14/06/2018 02:17 PM
updating unplanned downtime date and description

1 1 Marek Horst
h1. D6.4 OpenAIRE Maintenance Report (v1, 9th of December 2016)
2
3
{{toc}}
4
5
h2. Overview
6
7 65 Marek Horst
This document contains information about the status of OpenAIRE2020 workflows, services and content. It provides details about deployment and history of major modifications of the system hosted at ICM, Poland and Zenodo repository hosted at CERN, Switzerland. The official maintenance of the OpenAIRE2020 services began on January 1st, 2015 when the project started.
8 1 Marek Horst
9 70 Marek Horst
_Information Space Data_ section focuses on OpenAIRE data model including stats for main entities, inferred relations, funders, available data sources and records stored in Zenodo repository. 
10 1 Marek Horst
11 70 Marek Horst
_OpenAIRE workflows_ describes in depth all subsequent phases of data processing:
12 65 Marek Horst
* aggregation
13
* Information Space population
14
* deduplication
15
* inference generation
16 67 Alessia Bardi
* Information Space monitoring and publishing
17 65 Marek Horst
18 67 Alessia Bardi
The last section gives insight into software life-cycle of all major services involved in the project, whole infrastructure and most important architectural changes.
19 1 Marek Horst
20 69 Marek Horst
h2. Information Space Data
21 1 Marek Horst
22 53 Marek Horst
The OpenAIRE [[Core Data Model]] comprises the following interlinked entities: 
23
* results ( in form of publications, datasets and patents)
24
* persons
25
* organisations
26
* funders
27
* funding streams
28
* projects
29
* data sources (in form of institutional, thematic, and data repositories, Current Research Information Systems (CRIS), thematic and national aggregators, publication catalogues and entity registries)
30 43 Jochen Schirrwagen
31 56 Marek Horst
h3. Content Status
32
33
First table presents numbers for different InformationSpace main entities and fulltexts:
34
35
|*data type*|*count*|
36
|publication metadata|17460368|
37
|dataset metadata|3226586|
38
|projects|653268|
39
|organizations|64591|
40
|authors|16188328|
41
|EuropePMC XML fulltext|1574358|
42
|PDF fulltext|2227458|
43
44
Second table provides numbers related to inferences generated by IIS:
45
46
|*inference type*|*count*|
47 66 Marek Horst
|dataset references|88610|
48
|project references|351302|
49 56 Marek Horst
|software urls references|21481|
50
|protein db references|196462|
51
|research initiatives references|7294|
52
|documents classified|2405869|
53
|similar documents found|164602477|
54
|citations matched by reference text|11390293|
55
|citations matched by id|3929053|
56
57
Both tables are based on IIS report generated on November 20, 2016 for OpenAIRE production infrastructure.
58
59
h3. Funders
60
61 60 Marek Horst
Table below presents number of publications funded by different funders:
62 56 Marek Horst
63 60 Marek Horst
|*funder/funding*|*count*|
64
|EC - FP7|195151|
65
|EC - H2020|1782|
66
|FCT|23849|
67
|WT|16108|
68
|NSF (US)|119550|
69
|NHMRC (AU)|5785|
70
|ARC (AU)|8053|
71 56 Marek Horst
72 71 Marek Horst
Presented numbers are based on production infrastructure state as of December 14, 2016.
73 56 Marek Horst
74 47 Jochen Schirrwagen
h3. Data Sources
75 48 Jochen Schirrwagen
76 1 Marek Horst
Data sources in OpenAIRE are divided in: 
77 71 Marek Horst
* data providers (~805) OpenAIRE continuously collects information from. Need to comply with the "OpenAIRE Guidelines":https://guidelines.openaire.eu
78 57 Jochen Schirrwagen
* data sources (~6562) where metadata are collected from compatible data providers (usually aggregators) and represented in the OpenAIRE portal as links to the publications and datasets (_downloadFrom_).
79 1 Marek Horst
80 51 Jochen Schirrwagen
The table below presents number of data sources grouped by OpenAIRE compatibility level and data source type:
81 52 Marek Horst
82 49 Jochen Schirrwagen
|*data source type*|*compatibility*|*count*|
83 20 Jochen Schirrwagen
|institutional repository |openaire-3.0 |122 |
84 18 Alessia Bardi
| |openaire-2.0+ |103 |
85 55 Marek Horst
| |openaire-2.0 |10 |
86
| |openaire-basic |252 |
87 45 Jochen Schirrwagen
|thematic repository |openaire-3.0 |5 |
88
| |openaire-2.0+ |9 |
89 1 Marek Horst
| |openaire-basic |22 |
90
|other publication repository |openaire-3.0 |8 |
91 18 Alessia Bardi
| |openaire-2.0+ |1 |
92 20 Jochen Schirrwagen
| |openaire-2.0 |2 |
93
| |openaire-basic |34 |
94 1 Marek Horst
|data repository |openaire-data-2.0 |11 |
95 55 Marek Horst
|publication repository aggregator |openaire-3.0 |5 |
96
| |openaire-2.0 |1 |
97 29 Marek Horst
| |openaire-basic |7 |
98
|data repository aggregator |openaire-data |1 |
99
|journals |openaire-3.0 |71 |
100
| |openaire-2.0 |2 |
101
| |openaire-basic |77 |
102
|journal aggregator / publisher |openaire-3.0 |4 |
103
| |openaire-basic |26 |
104
| |proprietary |1 |
105
|publication catalogue |proprietary |12 |
106
|repository registries|proprietary|2 |
107 1 Marek Horst
|funder databases |proprietary |8 |
108
109 30 Marek Horst
The number of data sources is based on the OpenAIRE-index from December 15, 2016.
110
111
h3. Zenodo Content Status
112
113
|*data type*|*count or size*|
114
|records|96771|
115 1 Marek Horst
|managed files|181778|
116 30 Marek Horst
|files total size|8TB|
117
118 52 Marek Horst
Presented numbers are based on Zenodo repository status on December 14, 2016.
119 18 Alessia Bardi
120
h2. [[OpenAIRE workflows]]
121
122
The OpenAIRE aggregation system is based on the "D-NET software toolkit":http://www.d-net.research-infrastructures.eu/. D-NET is a service-oriented framework specifically designed to support developers at constructing custom aggregative infrastructures in a cost-effective way. D-NET offers data management services capable of providing access to different kinds of external data sources, storing and processing information objects of any data models, converting them into common formats, and exposing information objects to third-party applications through a number of standard access API. Most importantly, D-NET offers infrastructure enabling services that facilitate the construction of domain-specific aggregative infrastructures by selecting and configuring the needed services and easily combining them to form autonomic data processing workflows. 
123
124
The Enabling Layer contains the Services supporting the application framework. These provide functionalities such as Service registration, discovery, subscription and notification and data transfer mechanisms through ResultSet Services. Most importantly, these Services are configured to orchestrate Services of other layers to fulfil the OpenAIRE specific requirements and implement the *[[OpenAIRE workflows]]*.
125
126
h2. Services
127
128
h3. Software life-cycle
129
130
h4. D-NET services
131 1 Marek Horst
132 73 Claudio Atzori
The D-NET services are shipped as web applications and deployed on the tomcat application server (v7.0.52) on three distinct systems: dev, beta, production. To support the deployment process all the software codebase is versioned on "SVN":https://svn-public.driver.research-infrastructures.eu/driver/dnet45 and the project is managed with maven, whose artifacts are automatically built on a continuous integration system ("Jenkins":https://jenkins-dnet.d4science.org) and hosted on a dedicated maven repository ("nexus":http://maven.research-infrastructures.eu/nexus), while webapp builds are made available via "http server":http://ppa.research-infrastructures.eu/ci_upload. The mentioned tools supporting the software lifecycle are maintained by CNR.
133 1 Marek Horst
134
The D-NET services deployment is performed in subsequent stages:
135
* The development infrastructure plays the role of test bench for the integration of the software developed by different institutions. It is maintained by CNR and runs mostly un-released code and contains mock or subsets of the data available on the production system.
136
* The beta infrastructure runs only released code. It is maintained by ICM and consists of the final integration stage where all the system workflows are tested on the real data (not necessarily the same data as the production system) before making them available to the production system. Although the software running on the beta system is not yet production ready, its portal is publicly accessible in order to showcase new features and data.
137
* The production infrastructure is maintained by ICM and runs only code that was tested on the beta system.
138 18 Alessia Bardi
139 1 Marek Horst
D-NET backend services are packed in four different web applications, each of them running on a dedicated tomcat instance.
140 18 Alessia Bardi
141 1 Marek Horst
h4. Information Inference Service
142 26 Marek Horst
143 59 Marek Horst
"Information Inference Service":https://github.com/openaire/iis is an oozie application providing set of inference algorithms deployed on Hadoop cluster. Each new IIS release is deployed into unique, dedicated HDFS location. This way different IIS versions can be utilized by different D-Net environments: beta and production. 
144 1 Marek Horst
145 59 Marek Horst
Formerly IIS was being deployed on CDH4 cluster. Since October 1st, 2015 dedicated "cdh5 branch":https://github.com/openaire/iis/commits/cdh5 was created where new SPARK modules were introduced and existing modules were optimized. On November 20, 2016 for the first time all inferences in production infrastructure were generated by IIS deployed on new CDH5 OCEAN cluster. Both stability and major performance increase were noticed.
146
147 63 Marek Horst
Currently IIS heavily depends on the following technologies:
148 68 Marek Horst
* "Java Platform Standard Edition (Java SE) 8":http://docs.oracle.com/javase/8/docs/
149 63 Marek Horst
* "Apache Avro":https://avro.apache.org/ hdfs data serialization
150
* "Apache Hadoop":http://hadoop.apache.org/ framework for distributed computing
151 64 Marek Horst
* "Apache Oozie":http://oozie.apache.org/ workflow definitions
152 63 Marek Horst
* "Apache Pig":https://pig.apache.org transformers, documents similarity
153
* "Apache Spark":http://spark.apache.org affiliation and citation matching algorithms
154 72 Marek Horst
* "Kryo":https://github.com/EsotericSoftware/kryo serialization framework
155 63 Marek Horst
* "Cermine":https://github.com/CeON/CERMINE metadata and text extraction from PDF documents
156
* "Madis":https://github.com/madgik/madis documents classification and reference extraction algorithms
157
158 1 Marek Horst
"Continuous Integration System":http://ci.ceon.pl/view/IIS/ hosted @ICM allows both building IIS artifacts and running full suite of integration tests which are triggered nightly.
159 59 Marek Horst
160 63 Marek Horst
More details on service versioning and deployment can be found on "IIS versioning and deployment":https://issue.openaire.research-infrastructures.eu/projects/openaire/wiki/IIS_versioning_and_deployment wiki page.
161 18 Alessia Bardi
162 1 Marek Horst
h4. Portal
163 23 Marek Horst
164
OpenAIRE portal is hosted at ICM. It uses Joomla! 3.6.2, a free dynamic portal engine and content management system (CMS).
165
166
The Joomla! depends on other upstream applications:
167
168
* Apache 2.4.7
169
* PHP 5.5.9
170
* MySQL 5.5.53
171 1 Marek Horst
* OpenLDAP 2.4.31
172 18 Alessia Bardi
173 1 Marek Horst
h4. Zenodo
174
175
Zenodo repository employs an instance of the Invenio software, developed by CERN.
176 31 Marek Horst
177
Repository is deployed in a production system (https://zenodo.org) and a QA system (https://sandbox.zenodo.org). In total the two systems are running on 30 VMs hosted in CERNs OpenStack infrastructure. All machines are configured using Puppet and are running on top of CERN CentOS 7.2.
178
179
Zenodo/Invenio depends on the following applications:
180
- HAProxy for load balancing
181
- Nginx for serving static content and proxying request to application server
182
- UWSGI as application server for Zenodo/Invenio application
183
- Redis for memory cache
184
- RabbitMQ as message broker
185
- Celery as distributed task queue
186
- PostgreSQL as database
187
- Elasticsearch as search engine
188
189 1 Marek Horst
Deployment process is described at http://zenodo.readthedocs.io/projectlifecycle.html#release-process
190 33 Marek Horst
191
See https://github.com/zenodo/zenodo/commits/production for changes to Zenodo production system (does not include changes to Invenio modules).
192 35 Marek Horst
193
Zenodo repository was relaunched on Invenio v3 alpha on September 12, 2016.
194 18 Alessia Bardi
195 1 Marek Horst
h3. Infrastructure services
196 18 Alessia Bardi
197 1 Marek Horst
Because OpenAIRE2020 services are a continuation and incremental extension of the services already present that resulted from OpenAIRE+ project, so they are still hosted on that same machines. More details are available at "OpenAIRE+ WP5 Maintenance Report":http://wiki.openaire.eu/xwiki/bin/view/OpenAIREplus%20Specific/WP5%20Maintenance%20Report.
198 18 Alessia Bardi
199 1 Marek Horst
h4. Hadoop clusters
200 18 Alessia Bardi
201 1 Marek Horst
h5. DM hadoop cluster
202
203
CDH version: @cdh4.3.1@
204
205
h5. IIS hadoop cluster
206 24 Marek Horst
207
There were two IIS clusters deployed:
208 39 Marek Horst
* old CDH4 IIS cluster, version @cdh4.3.1@, in operation until December 9, 2016 
209 1 Marek Horst
* new CDH5 IIS cluster deployed on March 22, 2016 in OCEAN infrastructure, supports MRv2 on YARN and SPARK
210 24 Marek Horst
211
CDH5 cluster version history:
212 27 Marek Horst
** @5.5.2@ deployment on March 22, 2016
213
** @5.5.2 -> 5.7.5@ upgrade on November 30, 2016
214 24 Marek Horst
** @5.7.5 -> 5.9.0@ upgrade on December 8, 2016
215 1 Marek Horst
216
h4. Databases
217 28 Marek Horst
218
|_database type_|_usage_|_version_|
219 24 Marek Horst
| postgress | statistics | @9.1.23@ |
220
| postgress | DNet services | @9.3.14@ |
221
| mongodb | DNet services | @3.2.6@ |
222 1 Marek Horst
| virtuoso | LOD | @7.2@ |
223 41 Marek Horst
224 18 Alessia Bardi
h4. Piwik analytics platform
225 24 Marek Horst
226
Currently deployed Piwik version: @2.17.1@, since December 6, 2016.
227 40 Marek Horst
228 24 Marek Horst
h4. ownCloud filesync platform
229 40 Marek Horst
230 18 Alessia Bardi
Deployed at https://box.openaire.eu. Current version: @8.2.7@, since October 19, 2016.
231 1 Marek Horst
232 22 Marek Horst
h3. Architectural changes
233 1 Marek Horst
234 58 Marek Horst
Detailed list of all administrative operations undertaken @ICM is available on [[D64_Servers_Administration_Operations_Changelog|changelog for servers administration operations]] wiki page.
235 18 Alessia Bardi
236 62 Marek Horst
h4. Introducing CDH5 IIS cluster hosted in ICM OCEAN infrastructure
237 1 Marek Horst
238
Slave node specification:
239
* Huawei RH1288 V3
240
* CPU: 2x Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz (24 cores, 48 threads)
241
* RAM: 128GB
242
* HDD: 4x SATA 6TB 7.2K RPM (HDFS)
243
244
Cluster summary (16 slaves):
245
* CPU: 384 cores, 768 threads
246
* RAM: 2048GB
247
* HDD: 384TB (HDFS)
248
249
YARN available resources:
250
* vcores: 640
251
* memory: 1.44TB
252 18 Alessia Bardi
* HDFS: 344TB
253 1 Marek Horst
254
h4. Incorporating resources from old CDH4 IIS cluster into existing DM CDH4 cluster
255 25 Marek Horst
256 1 Marek Horst
This task was possible after shutting down old IIS CDH4 cluster what happened on December 9, 2016.
257 25 Marek Horst
258
h4. Deploying DNet postgress and mongodb databases on separate machines
259
260
Separating @openaire-services@ database instances into dedicated ones (since June 27, 2016):
261
* @openaire-services-postgresql@
262
* @openaire-services-mongodb@
263 34 Marek Horst
264 1 Marek Horst
h4. Updating Zenodo repository infrastructure at CERN
265 34 Marek Horst
266
Several architectural changes were introduced in CERN's infrastructure:
267
* changed storage backend from OpenAFS to CERN EOS (18 PB disk cluster) for better scalability
268
* changed from self-managed MySQL database to CERN Database Team managed PostgreSQL database
269
* deployment of Elasticsearch clusters (6 VMs)
270
* SLC to CentOS 7 on all 30 VMs
271 1 Marek Horst
272
h3. System downtimes
273 36 Marek Horst
274
h4. @ICM
275 1 Marek Horst
276 75 Marek Horst
* [unplanned] November 13, 2017, 8 hours. #3284 main openaire.eu site becoming unavailable, two hard drives down one after another in a 8h period overnight
277 36 Marek Horst
* [planned] November 14, 2016, 2 hours. #2423 dealing with Linux Dirty COW vulnerability: kernel upgrade, OpenAIRE services restart.
278
279
h4. @CERN
280
281
* [unplanned] September 16, 2016, 3 hours. Preparation of a new load balancer caused an automatic update of CERN outerperimeter firewall that automatically closed access to the operational load balancers.
282
* [planned] September 12, 2016, 8 hours. Complete migration from old infrastructure to new infrastructure
283 1 Marek Horst
* minor incidents until September 12, 2016 due to overload of the legacy system