Archive for the ‘Technical’ Category

Solr Superclusters for improved federated search

As part of our BioSolr project, we’ve been discussing how best to create a federated search over several Apache Solr instances. In this case various research institutions across the world are annotating data objects representing proteins and it would be useful to search not just the original protein data, but what others have added to the body of knowledge. If an institution wants to use the annotations, the usual approach is to download the extra data regularly and add it into a local Solr index.

Luckily Solr is widely used in the bioinformatics community so we have commonality in the query API. The question is would it be possible to use some of the distributed querying capabilities of SolrCloud to search not just the shards of a single index, but a group of Solr/SolrCloud indices – a supercluster.

This is a bit like a standard federated search, where queries are farmed out to various disparate search engines and the results then combined and displayed in some fashion. However, since we are sharing a single technology, powerful features such as result grouping would be possible.

For this to work at all, there would need to be some agreed standard between the various Solr systems: a globally unique record identifier for example (possibly implemented with a prefix unique to each institution). Any data that was required for result grouping would have to share a schema across the entire supercluster – let’s call this the primary schema – but basic searching and faceting could still be carried out over data with a differing, secondary schema. Solr dynamic fields might be useful for this secondary schema.

Luckily, research institutions are used to working as part of a consortium, and one of the conditions for joining would be agreeing to some common standards. A single Solr query API would then be available to all members of the consortium, to search not just their own data but everything available from their partners, without the slow and error-prone process of copying the data for local indexing.

We’re currently evaluating the feasibility of this idea and would welcome input from others – let us know what you think in the comments!

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Posted in Technical

January 20th, 2015

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Elasticsearch London user group – The Guardian & Orchestrate test the limits

Last week I popped into the Elasticsearch London meetup, hosted this time by The Guardian newspaper. Interestingly, the overall theme of this event was not just what the (very capable and flexible) Elasticsearch software is capable of, but also how things can go wrong and what to do about it.

Jenny Sivapalan and Mariot Chauvin from the Guardian’s technical team described how Elasticsearch powers the Content API, used not just for the newspaper’s own website but internally and by third party applications. Originally this was built on Apache Solr (I heard about this the last time I attended a search meetup at the Guardian) but this system was proving difficult to scale elastically, taking a few minutes before new content was available and around an hour to add a new server. Instead of upgrading to SolrCloud (which probably would have solved some of these issues) the team decided to move to Elasticsearch with targets of less than 5 seconds for new content to become live and generally a quicker response to traffic peaks. The team were honest about what had gone wrong during this process: oversharding led to problems caused by Java garbage collection, some of the characteristics of the Amazon cloud hosting used (in particular, unexpected server shutdowns for maintenance) required significant tweaking of the Elasticsearch startup process and they were keen to stress that scripting must be disabled unless you want your search servers to be an easy target for hackers. Although Elasticsearch promises that version upgrades can usually be done on a live cluster, the Guardian team found this unreliable in a majority of cases. Their eventual solution for version upgrades and even more simple configuration changes was to spin up an entirely new cluster of servers, switch over by changing DNS settings and then to turn off the old cluster. They have achieved their performance targets though, with around 375 requests/second supported and less than 15 minutes for a failed node to recover.

After a brief presentation from Colin Goodheart-Smithe of Elasticsearch (the company) on scripted aggregrations – a clever way to gather statistics, but possibly rather fiddly to debug – we moved on to Ian Plosker of, who provide a ‘database as a service’ backed by HBase, Elasticsearch and other technologies, and his presentation on Schemalessness Gone Wrong. Elasticsearch allows you submit data for indexing without pre-defining a schema – but Ian demonstrated how this feature isn’t very reliable in practice and how his team had worked around it but creating a ‘tuplewise transform’, restructuring data into pairs of ‘field name, field value’ before indexing with Elasticsearch. Ian was questioned on how this might affect term statistics and thus relevance metrics (which it will) but replied that this probably won’t matter – it won’t for most situations I expect, but it’s something to be aware of. There’s much more on this at Orchestrate’s own blog.

We finished up with the usual Q&A which this time featured some hard questions for the Elasticsearch team to answer – for example why they have rolled their own distributed configuration system rather than used the proven Zookeeper. I asked what’s going to happen to the easily embeddable Kibana 3 now Kibana 4 has its own web application (the answer being that it will probably not be developed further) and also about the licensing and availability of their upcoming Shield security plugin for Elasticsearch. Interestingly this won’t be something you can buy as a product, rather it will only be available to support customers on the Gold and Platinum support subscriptions. It’s clear that although Elasticsearch the search engine should remain open source, we’re increasingly going to see parts of its ecosystem that aren’t – users should be aware of this, and that the future of the platform will very much depend on the business direction of Elasticsearch the company, who also centrally control the content of the open source releases (in contrast to Solr which is managed by the Apache Foundation).

Elasticsearch meetups will be more frequent next year – thanks Yann Cluchey for organising and to all the speakers and the Elasticsearch team, see you again soon I hope.

Comparing Solr and Elasticsearch – here’s the code we used

A couple of weeks ago we presented the initial results of a performance study between Apache Solr and Elasticsearch, carried out by my colleague Tom Mortimer. Over the last few years we’ve tested both engines for client projects and noticed some significant performance differences, which we thought deserved fuller investigation.

Although Flax is partnered with Solr-powered Lucidworks we remain completely independent and have no particular preference for either Solr or Elasticsearch – as Tom says in his slides they’re ‘both awesome’. We’re also not interested in scoring points for or against either engine or the various commercial companies that are support their development; we’re actively using both in client projects with great success. As it turned out, the results of the study showed that performance was broadly comparable, although Solr performed slightly better in filtered searches and seemed to support a much higher maximum queries per second.

We’d like to continue this work, but client projects will be taking a higher priority, so in the hope that others get involved both to verify our results and take the comparison further we’re sharing the code we used as open source. It would also be rather nice if this led to further performance tuning of both engines.

If you’re interested in other comparisons between Solr and Elasticsearch, here are some further links to try.

Do let us know you get on, what you discover and how we might do things better!

Searching & monitoring the Unified Log

This week I dropped into the Unified Log Meetup held at the rather hard to find offices of Just Eat (luckily there was some pizza left). The Unified Log movement is interesting and there’s a forthcoming book on the subject from Snowplow’s Alex Dean – the short version is this is all about massive scale logging of everything a business does in a resilient fashion and the eventual insights one might gain from this data. We’re considering streams of data rather than silos or repositories we usually index here, and I was interested to see how search technology might fit into the mix.

The first talk by Ian Meyers from AWS was about Amazon Kinesis, a hosted platform for durable storage of stream data. Kinesis focuses on durability and massive volume – 1 MB/sec was mentioned as a common input rate, and data is stored across multiple availability zones. The price of this durability is latency (from a HTTP PUT to the associated GET might be as much as three seconds) but you can be pretty sure that your data isn’t going anywhere unexpectedly. Kinesis also allows processing on the data stream and output to more permanent storage such as Amazon S3, or Elasticsearch for indexing. The analytics options allow for counting, bucketing and some filtering using regular expressions, for real-time stream analysis and dashboarding, but nothing particularly advanced from a search point of view.

Next up was Martin Kleppman (taking a sabbatical from LinkedIn and also writing a book) to talk about some open source options for stream handling and processing, Apache Kafka and Apache Samza. Martin’s slides described how LinkedIn handles 7-8 million messages a second using Kafka, which can be thought of an append-only file – to get data out again, you simply start reading from a particular place in the file, with all the reliable storage done for you under the hood. It’s a much simpler system than RabbitMQ which we’ve used on client projects at Flax in the past.

Martin explored how Samza can be used as a stream processing layer on top of Kafka, and even how oft-used databases can be moved into local storage within a Samza process. Interestingly, he described how a database can be expressed simply as a change log, with Kafka’s clever log compaction algorithms making this an efficient way to represent it. He then moved on to describe a prototype integration with our Luwak stored query library, allowing for full-text search within a stream, with the stored queries and matches themselves being of course just more Kafka streams.

It’s going to be interesting to see how this concept develops: the Unified Log movement and stream processing world in general seems to lack this kind of advanced text matching capability, and we’ve already developed Luwak as a highly scalable solution for some of our clients who may need to apply a million stored queries to a million new stories a day. The volumes discussed at the Meetup are a magnitude beyond that of course but we’re pretty confident Luwak and Samza can scale. Watch this space!

A new Meetup for Lucene & Solr

Last Friday we held the first Meetup for a new Apache Lucene/Solr User Group we’ve recently created (there’s a very popular one for Elasticsearch so it seemed only fair Solr had its own). My co-organiser Ramkumar Aiyengar of Bloomberg provided the venue – Bloomberg’s huge and very well-appointed presentation space in their headquarters building off Finsbury Square, which impressed attendees. As this was the first event we weren’t expecting huge numbers but among the 25 or so attending were glad to see some from Flax clients including News UK, Alfresco and

Shalin Mangar, Lucene/Solr committer and SolrCloud expert started us off with a Deep Dive into some of the recent work performed on testing resilience against network failures. Inspired by this post about how Elasticsearch may be subject to data loss under certain conditions (and to be fair I know the Elasticsearch team are working on this), Shalin and his colleagues simulated a number of scary-sounding network fault conditions and tested how well SolrCloud coped – the conclusion being that it does rather well, with the Consistency part of the CAP theorem covered. You can download the Jepsen-based code used for these tests from Shalin’s employer Lucidworks own repository. It’s great to see effort being put into these kind of tests as reliable scalability is a key requirement these days.

I was up next to talk briefly about a recent study we’ve been doing into a performance comparison between Solr and Elasticsearch. We’ll be blogging about this in more detail soon, but as you can see from my colleague Tom Mortimer’s slides there aren’t many differences, although Solr does seem to be able to support around three times the number of queries per second. We’re very grateful to BigStep (who offer some blazingly fast hosting for Elasticsearch and other platforms) for assisting with the study over the last few weeks – and we’re going to continue with the work, and publish our code very soon so others can contribute and/or verify our findings.

Next I repeated my talk from Enterprise Search and Discovery on our work with media monitoring companies on scalable ‘inverted’ search – this is when one has a large number of stored queries to apply to a stream of incoming documents. Included in the presentation was a case study based on our work for Infomedia, a large Scandinavian media analysis company, where we have replaced Autonomy IDOL and Verity with a more scalable open source solution. As you might expect the new system is based on Apache Lucene/Solr and our Luwak library.

Thanks to Shalin for speaking and all who came – we hope to run another event soon, do let us know if you have a talk you would like to give, can offer sponsorship and/or a venue.

Cambridge Search Meetup – Elasticsearch Hackday

Last Friday we hosted a hackday featuring Elasticsearch in Cambridge, following a similar event last year focused on Apache Lucene/Solr. Around 20 people attended from organisations working in sectors including analytics, digital music, bioinformatics and e-commerce, and all the Flax team were there as well.

We started with a brief presentation on Elasticsearch and asked around the room for any data collections we might be able to use. Lee from Elasticsearch (the company) had brought collections of UK crime data and the complete works of Shakespeare; we also had several million rows of digital music metadata, Wikipedia edit data for all UK MPs (to follow last year’s theme!) and several years of data describing Premier League football. Unlike our Solr hackday where each team worked on the same general task, this time we split into four different teams who worked on all of the above except the Wikipedia edits. We’d also been provided with a very high-performance Elasticsearch cluster by BigStep for our use, which meant it was very quick to index the above data and start working with it.

By lunchtime (the food was sponsored by Elasticsearch, who also provided stickers, plush ELKs and lollypops – thanks guys!) we had some very basic information about the various datasets – such as which scene in which Shakespeare play has the most characters on stage (the answer is 21 in Richard III), and which football teams seemed to gain the most advantage from playing at home. Note that we had already moved beyond basic search functionality to use Elasticsearch as an analytic platform, answering particular questions, using features such as aggregations.

We continued during the afternoon to develop the various applications and finished with a ’show and tell’. Some of the teams had managed to develop user interfaces for Elasticsearch, the most polished being a clickable Google Map that would show you which types of crime were significantly above and below the national average for the area you selected – unsurprisingly in Cambridge, stolen bicycles were very common! By the end of the day, everyone had gained experience of Elasticsearch, some for the first time. We finished the day, as is traditional, with a swift pint and further networking.

Thanks to Cambridge Business Lounge (a highly recommended co-working space) for the venue, BigStep for hosting and Elasticsearch for sponsoring lunch and providing the swag, and of course to all who attended. We’ll return with a further Cambridge Search Meetup soon!

BioSolr begins with a workshop day

Last Thursday we attended a workshop day at the European Bioinformatics Institute as part of our joint BioSolr project. This was an opportunity for us to give some talks on particular aspects of Apache Lucene/Solr and hear from the various teams there on how they are using the software. The workshop was oversubscribed – it seems that there are even more people interested in Solr on the Wellcome Campus than we thought! We were also happy to welcome Giovanni Tummarello from Siren Solutions in Galway, Ireland and Lewis Geer from the EBI’s sister organisation in the USA, the NCBI.

We started with a brief introduction to BioSolr from Dr. Sameer Velankar and Flax then talked on Best Practices for Indexing with Solr. Based very much on our own experience and projects, we showed how although Solr’s Data Import Handler can be used to carry out many of the various tasks necessary to import, convert and process data, we prefer to write our own indexing systems, allowing us to more easily debug complex indexing tasks and protect the system from less stable external processing libraries. We then moved on to a presentation on Distributed Indexing, describing the older master/slaves technique and the more modern SolrCloud architecture we’ve used for several recent projects. We finished the morning’s talks with a quick guide to how to migrate from Apache Lucene to Apache Solr (which of course uses Lucene under the hood but is a much easier and full featured system to work with).

After lunch and some networking, we gave a further short presentation on comparing Elasticsearch to Solr, as some teams at the EBI have been considering its use. We then heard from Giovanni on Siren Solutions‘ innovative method for indexing heirarchical data with Solr using XML. His talk mentioned how by encoding tree positions directly within the index, far fewer Solr documents need to be created, with an index size reduction of 50% and up to twice the query speed. Siren have recently released open source plugins for both Solr and Elasticsearch based on this idea which are certainly worth investigating.

Following this talk, Lewis Geer described how the NCBI have built a large scale bioinformatics search platform backed both by Solr, built on commodity hardware and supporting up to 500 queries per second. To enable queries using various methods (Solr, SQL or even BLAST) they have built their own internal query language, standard result schemas and also collaborated with Heliosearch to develop improved JOIN facilities for Solr. The latter is a very exciting development as JOINs are heavily used in bioinformatics queries and we believe these features (made available recently as Solr patches) can be of use to the EBI as well. We’ll be investigating further how we can both use these features and help them to be committed to Solr.

Next were a collection of short talks from various teams from the Wellcome campus on how they were using Solr, Lucene and related tools. We heard from the PDBE, SPOT, Ensembl, UniProt, Sanger Core Services and Literature Services on a varied range of use cases, from searching proteins using Solr to scientific papers using Lucene. It was clear that we’ve still only scratched the surface of what is being done with both Lucene and Solr, and as the project progresses we hope to be able to generate repositories of useful software, documentation, best practises, guidance on migration and scaling and also learn a huge amount more about how search can be used in bioinformatics.

Over the next few weeks members of the Flax team will be visiting the EBI to work directly with the PDB and SPOT teams, to find out where we might be most effective. We’ll also be running Solr user group meetings at both the EBI and in Cambridge, of which more details soon. Do let us know if you’re interested! Thanks to the EBI for hosting the workshop day and of course the BBSRC for funding the BioSolr project.

Solr geolocation searches using WKT – latitude or longitude first?

Matt Pearce writes:

We have been working with a client who needs to search for documents based on location, either using a single point or (sometimes very) complex polygons. They supplied the location data in WKT format which we assumed we could feed directly into our search engine (in this case Solr) without any modifications being necessary.

Then we started testing the location searches using parameters in lat, long format. These were translated into a Solr filter query such as:

{!geofilt sfield=location pt=53.45,-0.25 d=20}

which produced no results, even though we knew there were documents well within the bounds of the search range. Reversing the coordinates did produce results though, and that seemed like a quick solution, so we assumed there was a problem in Solr that needed to be flagged.

This seemed like a problem that other Solr users would have come across, so I checked in JIRA, but nobody had raised it as an issue. That was a red flag to me, so I took a look at the code, and discovered that in the situation above, the first number is taken to be the y-coordinate, while the second is the x-coordinate. Very strange. I still didn’t want to raise a new issue, since it was looking increasingly like a problem with either our data or the request.

It turns out that in WKT format, the longitude coordinate comes first. We could safely reverse the coordinates in our search string because all our locations were in the UK, but this wouldn’t work for points in the US, for example, where longitudes go beyond -90. The coordinate order is mentioned in the GeoJSON specification, and on the Elasticsearch Geo Shape Type page, although I initially found it in some helper pages for SQL Server 2008! Unfortunately, it is not mentioned in the Solr documentation, as far as I can see, nor the Wikipedia entry for WKT.

In short, if you are representing geographical location data in WKT (and storing it in Solr or Elasticsearch), longitude comes first!

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Posted in Technical

September 12th, 2014

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London Elasticsearch User Group – September Meetup

Last night I joined a good-sized crowd at a venue on Hoxton Square for some talks on Elasticsearch – this Meetup group is very popular and always attracts a good proportion of people new to the world of search, as well as some familiar faces. I started with a quick announcement of our own Elasticsearch hackday in a few weeks time.

First of the speakers was Richard Pijnenburg with a surprisingly brief talk on Puppet and Elasticsearch – brief, because integrating the two is apparently very simple, requiring only a few lines of Puppet code. Some questions from the floor sparked a discussion of combining Puppet and Vagrant for setting up Elasticsearch instances: apparently very soon we’ll see a complete demo instance of Elasticsearch built using these technologies and including some example data, which will be very useful for those wanting to get started with the engine (here’s some more on this combination).

Next was Amit Talhan, ably assisted by Geza Kerekes, both from AlignAlytics who have been using Elasticsearch both as a data store, reporting store and more recently for analysing data from a survey of all the retail outlets in Nigeria. Generating a wealth of data across up to 1000 fields, including geolocation data harvested every five seconds, this survey could have been difficult if not impossible to handle using a traditional SQL database, but many of their colleagues were very used to SQL syntax and methods for analyzing data. Amit and Geza explained how they have used Elasticsearch and in particular aggregations to provide functionality such as checking for bad reporting by surveyors and unexpectedly high density areas (such as markets, where there may be 200 retail outlets in a few square metres). One challenge seems to have been how to explain to colleagues from the data analysis community that Elasticsearch can provide some, but not all of the functionality of a traditional database, but that alternative ways of indexing and querying data can be used to solve the same problems. Interestingly, performance testing by AlignAlytics proved that BigStep, a provider of ‘bare metal’ cloud hosting, could provide much better performance than their own dedicated servers.

Next was Mark Harwood with another of his fascinating investigations into how Elasticsearch can be used for analysis of user behaviour, showing how after a bad personal experience buying a new battery that turned out to be second-hand, he identified vendors with suspiciously positive reviews. He also discussed how behaviour-based term suggesters might be built using Elasticsearch’s significant_terms aggregration. His demonstration did remind me slightly of Xapian’s relevance feedback feature. I heard several people later say that they wished they had time for some of the fun projects Mark seems to work on!

The event finished with some lively discussion and some free pizza courtesy of Elasticsearch (the company). Thanks to Yann Cluchey as ever for organising the event and I look forward to seeing a few of the attendees in Cambridge soon – we’re only an hour or so by train from Cambridge plus a ten minute walk to the venue, so it should be an easy trip!

Why GCloud search is badly broken & how to fix it

The GCloud initiative and the associated CloudStore are a great idea – hoping to level the field of UK government IT supply, take advantage of flexible and agile delivery of software and services and help SMEs like ourselves compete against the large System Integrators (SIs) that dominate this market. GCloud sales have now reached £154m although this is still a fraction of what the UK government spends on IT. We’re on GCloud 5 ourselves by the way so I have a vested interest in helping potential customers find us, and we’ve helped with government systems before.

Unfortunately the Cloudstore itself has a search facility that is badly broken. There are several obvious issues: many of the entries created by the larger suppliers have been keyword stuffed – here’s a particularly egregious example from Atos which seems to include most of the terms used in software in the last few years. I found this using the search terms ‘enterprise search’ which produces very few relevant looking results. The online guidance for CloudStore search suggests putting double quotes around my terms (sadly I think few users will think of this) which improves things a little but there are still a lot of irrelevant results – an online conferencing system is fifth for example.

Fortunately all is not lost and in the next iteration of GCloud we are promised major improvements to the search engine. I’m hoping this will include phrase boosting. However, if the big SIs and others are allowed to create the sort of bad-quality content I have shown above, no search engine in the world will be able to sort the wheat from the chaff. It is essential that CloudStore entries are subject to some kind of curation and that keyword stuffing is banned and/or heavily penalised, otherwise SMEs like ourselves will still find it very hard to compete with the big SIs.

Update: it seems there is a new system under construction, and the search works a lot better. Let’s hope it comes out of alpha soon and can be used by purchasers!

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Posted in Business, Technical

June 26th, 2014

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