I have a collection of text files containing anonymised medical data (age, country, symptoms, diagnosis etc). This data goes back for at least 30 years so as you can imagine I have quite a large sized data set. In total I have around 20,000 text files totalling approx. 1TB.
Periodically I will be needing to search these files for occurances of a particular string (not regex). What is the quickest way to search through this data?
I have tried using grep and recursively searching through the directory as follows:
LC_ALL=C fgrep -r -i "searchTerm" /Folder/Containing/Files
The only problem with doing the above is that it takes hours (sometimes half a day!) to search through this data.
Is there a quicker way to search through this data? At this moment I am open to different approaches such as databases, elasticsearch etc. If I do go down the database route, I will have approx. 1 billion records.
My only requirements are:
1) The search will be happening on my local computer (Dual-Core CPU and 8GB RAM)
2) I will be searching for strings (not regex).
3) I will need to see all occurances of the search string and the file it was within.
There are a lot of answers already, I just wanted to add my two cents:
Having this much huge data(1 TB) with just 8 GB of memory will not be good enough for any approach, be it using the Lucene or Elasticsearch(internally uses Lucene) or some grep command if you want faster search, the reason being very simple all these systems hold the data in fastest memory to be able to serve faster and out of 8 GB(25% you should reserve for OS and another 25-50% at least for other application), you are left with very few GB of RAM.
Upgrading the SSD, increasing RAM on your system will help but it's quite cumbersome and again if you hit performance issues it will be difficult to do vertical scaling of your system.
Suggestion
I know you already mentioned that you want to do this on your system but as I said it wouldn't give any real benefit and you might end up wasting so much time(infra and code-wise(so many approaches as mentioned in various answers)), hence would suggest you do the top-down approach as mentioned in my another answer for determining the right capacity. It would help you to identify the correct capacity quickly of whatever approach you choose.
About the implementation wise, I would suggest doing it with Elasticsearch(ES), as it's very easy to set up and scale, you can even use the AWS Elasticsearch which is available in free-tier as well and later on quickly scale, although I am not a big fan of AWS ES, its saves a lot of time of setting up and you can quickly get started if you are much familiar of ES.
In order to make search faster, you can split the file into multiple fields(title,body,tags,author etc) and index only the important field, which would reduce the inverted index size and if you are looking only for exact string match(no partial or full-text search), then you can simply use the keyword field which is even faster to index and search.
I can go on about why Elasticsearch is good and how to optimize it, but that's not the crux and Bottomline is that any search will need a significant amount of memory, CPU, and disk and any one of becoming bottleneck would hamper your local system search and other application, hence advising you to really consider doing this on external system and Elasticsearch really stands out as its mean for distributed system and most popular open-source search system today.
You clearly need an index, as almost every answer has suggested. You could totally improve your hardware but since you have said that it is fixed, I won’t elaborate on that.
I have a few relevant pointers for you:
Index only the fields in which you want to find the search term rather than indexing the entire dataset;
Create multilevel index (i.e. index over index) so that your index searches are quicker. This will be especially relevant if your index grows to more than 8 GB;
I wanted to recommend caching of your searches as an alternative, but this will cause a new search to again take half a day. So preprocessing your data to build an index is clearly better than processing the data as the query comes.
Minor Update:
A lot of answers here are suggesting you to put the data in Cloud. I'd highly recommend, even for anonymized medical data, that you confirm with the source (unless you scraped the data from the web) that it is ok to do.
To speed up your searches you need an inverted index. To be able to add new documents without the need to re-index all existing files the index should be incremental.
One of the first open source projects that introduced incremental indexing is Apache Lucense. It is still the most widely used indexing and search engine although other tools that extend its functionality are more popular nowadays. Elasiticsearch and Solr are both based on Lucense. But as long as you don't need a web frontend, support for analytical querying, filtering, grouping, support for indexing non-text files or an infrastrucutre for a cluster setup over multiple hosts, Lucene is still the best choice.
Apache Lucense is a Java library, but it ships with a fully-functional, commandline-based demo application. This basic demo should already provide all the functionality that you need.
With some Java knowledge it would also be easy to adapt the application to your needs. You will be suprised how simple the source code of the demo application is. If Java shouldn't be the language of your choice, its wrapper for Pyhton, PyLucene may also be an alternative. The indexing of the demo application is already reduced nearly to the minimum. By default no advanced functionlity is used like stemming or optimization for complex queries - features, you most likely will not need for your use-case but which would increase size of the index and indexing time.
I see 3 options for you.
You should really consider upgrading your hardware, hdd -> ssd upgrade can multiply the speed of search by times.
Increase the speed of your search on the spot.
You can refer to this question for various recommendations. The main idea of this method is optimize CPU load, but you will be limited by your HDD speed. The maximum speed multiplier is the number of your cores.
You can index your dataset.
Because you're working with texts, you would need some full text search databases. Elasticsearch and Postgres are good options.
This method requires you more disk space (but usually less than x2 space, depending on the data structure and the list of fields you want to index).
This method will be infinitely faster (seconds).
If you decide to use this method, select the analyzer configuration carefully to match what considered to be a single word for your task (here is an example for Elasticsearch)
Worth covering the topic from at two level: approach, and specific software to use.
Approach:
Based on the way you describe the data, it looks that pre-indexing will provide significant help. Pre-indexing will perform one time scan of the data, and will build a a compact index that make it possible to perform quick searches and identify where specific terms showed in the repository.
Depending on the queries, it the index will reduce or completely eliminate having to search through the actual document, even for complex queries like 'find all documents where AAA and BBB appears together).
Specific Tool
The hardware that you describe is relatively basic. Running complex searches will benefit from large memory/multi-core hardware. There are excellent solutions out there - elastic search, solr and similar tools can do magic, given strong hardware to support them.
I believe you want to look into two options, depending on your skills, and the data (it will help sample of the data can be shared) by OP.
* Build you own index, using light-weight database (sqlite, postgresql), OR
* Use light-weight search engine.
For the second approach, using describe hardware, I would recommended looking into 'glimpse' (and the supporting agrep utility). Glimple provide a way to pre-index the data, which make searches extremely fast. I've used it on big data repository (few GB, but never TB).
See: https://github.com/gvelez17/glimpse
Clearly, not as modern and feature rich as Elastic Search, but much easier to setup. It is server-less. The main benefit for the use case described by OP is the ability to scan existing files, without having to load the documents into extra search engine repository.
Can you think about ingesting all this data to elasticsearch if they have a consistent data structure format ?
If yes, below are the quick steps:
1. Install filebeat on your local computer
2. Install elasticsearch and kibana as well.
3. Export the data by making filebeat send all the data to elasticsearch.
4. Start searching it easily from Kibana.
Fs Crawler might help you in indexing the data into elasticsearch.After that normal elasticsearch queries can you be search engine.
I think if you cache the most recent searched medical data it might help performance wise instead of going through the whole 1TB you can use redis/memcached
According to the neo4j documentation, indexing can be done i 2 ways"
Indexing in Neo4j can be done in two different ways:
1. The database itself is a natural index consisting of its relationships of different types between nodes. For example a tree
structure can be layered on top of the data and used for index lookups
performed by a traverser.
2. Separate index engines can be used, with Apache Lucene being the default
backend included with Neo4j.
But there is no comparison which is better in what and what is better in which cases.
Which one is better and why?
Is this a data warehouse/mart or reporting database? If you have both transactions and search going against the database it might give interesting pros or cons.
Lucene exists for one reason search and it does it really well. If you have a large system with multiple services, for ultimate scalability it is always to split the services up and keep them doing their single responsibility. This would give you flexibility of using that Lucene index against other services if necessary...also if you ever got rid off neo4j, then you still have your index/search artifacts around not coupled to Neo4j.
I would look at it from the overall system architecture not just specific functionality.
I am developing an Azure based website and I want to provide search capabilities using Lucene. (structured json objects would be indexed and stored in Lucene and other content such as Word documents, etc. would be indexed in lucene but stored in blob storage) I want the search to be secure, such that one user would never see a document belonging to another user. I want to allow ad-hoc searches as typed by the user. Lastly, I want to query programmatically to return predefined sets of data, such as "all notes for user X". I think I understand how to add properties to each document to achieve these 3 objectives. (I am listing them here so if anyone is kind enough to answer, they will have better idea of what I am trying to do)
My questions revolve around performance and security.
Can I improve document security by having a separate index for each user, or is including the user's ID as a parameter in each search sufficient?
Can I improve indexing speed and total throughput of the system by having a separate index for each user? My thinking is that having separate indexes would allow me to scale the system by having multiple index writers (perhaps even on different server instances) working at the same time, each on their own index.
Any insight would be greatly appreciated.
Regards,
Nate
Of course, one index.
You can do even better than what you suggested by using ManifoldCF (Apache product that knows how to handle Solr) to manage security.
And one off topic, uninformed suggestion: I'd rather use CloudBees or Heroku (or Amazon) instead of Azure.
Until you will use several machines for indexing I guess it's more convenient to use single index. Lucene community done a lot of work to make indexing process as efficient as it can. So unless you intentionally want to implement distributed indexing I doesn't recommend you to split indexes.
However there are several reasons why you would want to split indexes:
if your machine have several IO devices which could be utilized in parallel. In this case, if you are IO bound, splitting indexes is good idea.
splitting document fields between indexes (this is what ParallelReader is supposed for). This is more exotic form of splitting, but it may be a good idea if search is performed using different groups of fields. Suppose, we have two search query types: the first is using field name and type, and the second is using fields price and discount. If those fields are updated at different rate (I guess, name updates are far more rarely than price updates), updating only part of index would require less IO resources. This will give more overall throughput to the system.
Let us say, I am maintaining an index of a lot of documents. I want to update the index for newly arriving data to make it as real time as possible. What kind of indexing tool do I need to look at ? I have looked at Sphinx and Lucene and from previous posts, they are recommended for real time indexing.
The delta indexing mechanism used in Sphinx looks like a pretty neat idea.
Some questions I have are
1) How quickly can the document be searchable once it arrives ?
2) How efficient is the index merge process ? (merging the delta index and the main Index)
I understand these are very general questions and I wanted to get an idea if using Sphinx would be the right way to go about this problem.
Sphinx have real-time indexes which allow add/update/delete indexes on the fly.
You can look at Apache Solr (NRT) and Elastic Search for real-time implementations using Lucene. You can look at some benchmarks.
We own SiteA and SiteB and they share the same server and database where we have full control.
SiteC , siteD and siteE are some of the sites we own as well but reside on a different web hosts.
The goal is to create a unified search functionality for all of the sites mentioned above. That is if somebody search for a term in SiteA, the search result will automatically come up with results from SiteB,SiteC,SiteD and Site E too. The search results should be shown under the website they were found in.
All these websites content are stored in their own databases.
If I use SphinxSearch to index the above sites,I would then require those sites that we dont have complete control with to setup a web service where i can download a database dump or csv file for indexing.
Im not quite sure about how a sphider will come into play here so need your opinion.
Sphinx or a spider?
THanks!
If you can ask the owner of other websites to give you content for free, then there is no need for a spider. Just use sphinxsearch to index the content.
If you can't get content directly from them, a spider is the only choice for you. There is little to think about this issue.
Sphinx is a full-text search engine solution, while a spider is for fetching contents from internet. They are not replacements to each other. Even if you use a spider, you still have to use some full-text search engine software for example sphinx or lucene/solr.
So you have to make a decision first: Do I want to use sphinx for searching? If the answer is yes, then there is only one thing left: how can I index the contents for searching?
sphinx supports using database or XML as data source. Database as data source is more popular because preparing and updating XML documents in a specific format is very tedious(compared to maintaining a database table). So I guess finally you have to store all of the data into database. As you described, all of the data are all ready in databases, but some of the databases are out of your control. For you own database, there is no problem. For the databases that out of your control, I suggest that you use distributed sphinx searching: http://sphinxsearch.com/docs/2.0.6/distributed.html
The key idea is to horizontally partition (HP) searched data accross
search nodes and then process it in parallel.
Partitioning is done manually. You should
setup several instances of Sphinx programs (indexer and searchd) on
different servers;
make the instances index (and search) different parts of data;
configure a special distributed index on some of the searchd
instances;
and query this index.
This index only contains references to other local and remote indexes
- so it could not be directly reindexed, and you should reindex those indexes which it references instead.