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We have 20.000.000 generated textfiles every year, average size is approx 250 Kb each (35 Kb zipped).
We must put these files in some kind of archive for 10 years. No need to search inside textfiles, but we must be able to find one texfile by searching on 5-10 metadata fields such as "productname", "creationdate", etc.
I'm considering zipping each file and storing them in a SQL Server database with 5-10 searchable (indexed) columns and a varbinary(MAX) column for the zipped file data.
The database will be grow huge over the years; 5-10 Tb. So I think we need to partition data for example by keeping one database per year.
I've been looking into using FILESTREAM in SQL Server for the varbinary column that holds the data, but it seems this is more suitable for blobs > 1 Mb?
Any other suggestions on how to manage such data volumes?
I'd say keeping the files in the filesystem would be a better idea. And you can keep file name and path in the DB. Here's a similar question.
Filestream is definitely more suited to larger blobs (750kB-1MB) as the overhead required to open the external file begins to impact read and write performance vs. vb(max) blob storage for small files. If this is not so much of an issue (ie. reads of blob data after the initial write are infrequent, and the blobs are effectively immutable) then it's definitely an option.
I would probably suggest keeping the files directly in a vb(max) column if you can guarantee they won't get much larger in size, but have this table stored in a seperate filegroup using the TEXTIMAGE_ON option which would allow you to move it to different storage from the rest of the metadata if necessary. Also, make sure to design your schema so the actual storage of blobs can be split over multiple filegroups either using partitions or via some multiple table scheme so you can scale to different disks if necessary in the future.
Keeping the blobs directly associated with the SQL metadata either via Filestream or direct vb(max) storage has many advantages over dealing with filesystem / SQL inconsistencies not limited to ease of backup and other management operations.
I assume by "generated" you mean something like data are being injected into document templates, and so there's much repetition of text content, i.e. "boilerplate" ?
20 million of such "generated" files per year is ~55,000 per day, ~2300 per hour!
I would manage such volume by not generating text files in the first place, and instead by creating database abstracts that contain the data that are pumped into the generated text, so that you can reconstitute the full document if necessary.
If you mean something else by "generated" could you elaborate?
We have flat files (CSV) with >200,000,000 rows, which we import into a star schema with 23 dimension tables. The biggest dimension table has 3 million rows. At the moment we run the importing process on a single computer and it takes around 15 hours. As this is too long time, we want to utilize something like 40 computers to do the importing.
My question
How can we efficiently utilize the 40 computers to do the importing. The main worry is that there will be a lot of time spent replicating the dimension tables across all the nodes as they need to be identical on all nodes. This could mean that if we utilized 1000 servers to do the importing in the future, it might actually be slower than utilize a single one, due to the extensive network communication and coordination between the servers.
Does anyone have suggestion?
EDIT:
The following is a simplification of the CSV files:
"avalue";"anothervalue"
"bvalue";"evenanothervalue"
"avalue";"evenanothervalue"
"avalue";"evenanothervalue"
"bvalue";"evenanothervalue"
"avalue";"anothervalue"
After importing, the tables look like this:
dimension_table1
id name
1 "avalue"
2 "bvalue"
dimension_table2
id name
1 "anothervalue"
2 "evenanothervalue"
Fact table
dimension_table1_ID dimension_table2_ID
1 1
2 2
1 2
1 2
2 2
1 1
You could consider using a 64bit hash function to produce a bigint ID for each string, instead of using sequential IDs.
With 64-bit hash codes, you can store 2^(32 - 7) or over 30 million items in your hash table before there is a 0.0031% chance of a collision.
This would allow you to have identical IDs on all nodes, with no communication whatsoever between servers between the 'dispatch' and the 'merge' phases.
You could even increase the number of bits to further lower the chance of collision; only, you would not be able to make the resultant hash fit in a 64bit integer database field.
See:
http://en.wikipedia.org/wiki/Fowler_Noll_Vo_hash
http://code.google.com/p/smhasher/wiki/MurmurHash
http://www.partow.net/programming/hashfunctions/index.html
Loading CSV data into a database is slow because it needs to read, split and validate the data.
So what you should try is this:
Setup a local database on each computer. This will get rid of the network latency.
Load a different part of the data on each computer. Try to give each computer the same chunk. If that isn't easy for some reason, give each computer, say, 10'000 rows. When they are done, give them the next chunk.
Dump the data with the DB tools
Load all dumps into a single DB
Make sure that your loader tool can import data into a table which already contains data. If you can't do this, check your DB documentation for "remote table". A lot of databases allow to make a table from another DB server visible locally.
That allows you to run commands like insert into TABLE (....) select .... from REMOTE_SERVER.TABLE
If you need primary keys (and you should), you will also have the problem to assign PKs during the import into the local DBs. I suggest to add the PKs to the CSV file.
[EDIT] After checking with your edits, here is what you should try:
Write a small program which extract the unique values in the first and second column of the CSV file. That could be a simple script like:
cut -d";" -f1 | sort -u | nawk ' { print FNR";"$0 }'
This is a pretty cheap process (a couple of minutes even for huge files). It gives you ID-value files.
Write a program which reads the new ID-value files, caches them in memory and then reads the huge CSV files and replaces the values with the IDs.
If the ID-value files are too big, just do this step for the small files and load the huge ones into all 40 per-machine DBs.
Split the huge file into 40 chunks and load each of them on each machine.
If you had huge ID-value files, you can use the tables created on each machine to replace all the values that remained.
Use backup/restore or remote tables to merge the results.
Or, even better, keep the data on the 40 machines and use algorithms from parallel computing to split the work and merge the results. That's how Google can create search results from billions of web pages in a few milliseconds.
See here for an introduction.
This is a very generic question and does not take the database backend into account. Firing with 40 or 1000 machines on a database backend that can not handle the load will give you nothing. Such a problem is truly to broad to answer it in a specific way..you should get in touch with people inside your organization with enough skills on the DB level first and then come back with a more specific question.
Assuming N computers, X files at about 50GB files each, and a goal of having 1 database containing everything at the end.
Question: It takes 15 hours now. Do you know which part of the process is taking the longest? (Reading data, cleansing data, saving read data in tables, indexing… you are inserting data into unindexed tables and indexing after, right?)
To split this job up amongst the N computers, I’d do something like (and this is a back-of-the-envelope design):
Have a “central” or master database. Use this to mangae the overall process, and to hold the final complete warehouse.
It contains lists of all X files and all N-1 (not counting itself) “worker” databases
Each worker database is somehow linked to the master database (just how depends on RDBMS, which you have not specified)
When up and running, a "ready" worker database polls the master database for a file to process. The master database dolls out files to worker systems, ensuring that no file gets processed by more than one at a time. (Have to track success/failure of loading a given file; watch for timeouts (worker failed), manage retries.)
Worker database has local instance of star schema. When assigned a file, it empties the schema and loads the data from that one file. (For scalability, might be worth loading a few files at a time?) “First stage” data cleansing is done here for the data contained within that file(s).
When loaded, master database is updated with a “ready flagy” for that worker, and it goes into waiting mode.
Master database has it’s own to-do list of worker databases that have finished loading data. It processes each waiting worker set in turn; when a worker set has been processed, the worker is set back to “check if there’s another file to process” mode.
At start of process, the star schema in the master database is cleared. The first set loaded can probably just be copied over verbatim.
For second set and up, have to read and “merge” data – toss out redundant entries, merge data via conformed dimensions, etc. Business rules that apply to all the data, not just one set at a time, must be done now as well. This would be “second stage” data cleansing.
Again, repeat the above step for each worker database, until all files have been uploaded.
Advantages:
Reading/converting data from files into databases and doing “first stage” cleansing gets scaled out across N computers.
Ideally, little work (“second stage”, merging datasets) is left for the master database
Limitations:
Lots of data is first read into worker database, and then read again (albeit in DBMS-native format) across the network
Master database is a possible chokepoint. Everything has to go through here.
Shortcuts:
It seems likely that when a workstation “checks in” for a new file, it can refresh a local store of data already loaded in the master and add data cleansing considerations based on this to its “first stage” work (i.e. it knows code 5484J has already been loaded, so it can filter it out and not pass it back to the master database).
SQL Server table partitioning or similar physical implementation tricks of other RDBMSs could probably be used to good effect.
Other shortcuts are likely, but it totally depends upon the business rules being implemented.
Unfortunately, without further information or understanding of the system and data involved, one can’t tell if this process would end up being faster or slower than the “do it all one one box” solution. At the end of the day it depends a lot on your data: does it submit to “divide and conquer” techniques, or must it all be run through a single processing instance?
The simplest thing is to make one computer responsible for handing out new dimension item id's. You can have one for each dimension. If the dimension handling computers are on the same network, you can have them broadcast the id's. That should be fast enough.
What database did you plan on using with a 23-dimensional starscheme? Importing might not be the only performance bottleneck. You might want to do this in a distributed main-memory system. That avoids a lot of the materalization issues.
You should investigate if there are highly correlating dimensions.
In general, with a 23 dimensional star scheme with large dimensions a standard relational database (SQL Server, PostgreSQL, MySQL) is going to perform extremely bad with datawarehouse questions. In order to avoid having to do a full table scan, relational databases use materialized views. With 23 dimensions you cannot afford enough of them. A distributed main-memory database might be able to do full table scans fast enough (in 2004 I did about 8 million rows/sec/thread on a Pentium 4 3 GHz in Delphi). Vertica might be an other option.
Another question: how large is the file when you zip it? That provides a good first order estimate of the amount of normalization you can do.
[edit] I've taken a look at your other questions. This does not look like a good match for PostgreSQL (or MySQL or SQL server). How long are you willing to wait for query results?
Rohita,
I'd suggest you eliminate a lot of the work from the load by sumarising the data FIRST, outside of the database. I work in a Solaris unix environment. I'd be leaning towards a korn-shell script, which cuts the file up into more managable chunks, then farms those chunks out equally to my two OTHER servers. I'd process the chunks using a nawk script (nawk has an efficient hashtable, which they call "associative arrays") to calculate the distinct values (the dimensions tables) and the Fact table. Just associate each new-name-seen with an incrementor-for-this-dimension, then write the Fact.
If you do this through named pipes you can push, process-remotely, and readback-back the data 'on the fly' while the "host" computer sits there loading it straight into tables.
Remember, No matter WHAT you do with 200,000,000 rows of data (How many Gig is it?), it's going to take some time. Sounds like you're in for some fun. It's interesting to read how other people propose to tackle this problem... The old adage "there's more than one way to do it!" has never been so true. Good luck!
Cheers. Keith.
On another note you could utilize Windows Hyper-V Cloud Computing addon for Windows Server:http://www.microsoft.com/virtualization/en/us/private-cloud.aspx
It seems that your implementation is very inefficient as it's loading at the speed of less than 1 MB/sec (50GB/15hrs).
Proper implementation on a modern single server (2x Xeon 5690 CPUs + RAM that's enough for ALL dimensions loaded in hash tables + 8GB ) should give you at least 10 times better speed i.e at least 10MB/sec.
I am dealing with large amounts of scientific data that are stored in tab separated .tsv files. The typical operations to be performed are reading several large files, filtering out only certain columns/rows, joining with other sources of data, adding calculated values and writing the result as another .tsv.
The plain text is used for its robustness, longevity and self-documenting character. Storing the data in another format is not an option, it has to stay open and easy to process. There is a lot of data (tens of TBs), and it is not affordable to load a copy into a relational database (we would have to buy twice as much storage space).
Since I am mostly doing selects and joins, I realized I basically need a database engine with .tsv based backing store. I do not care about transactions, since my data is all write-once-read-many. I need to process the data in-place, without a major conversion step and data cloning.
As there is a lot of data to be queried this way, I need to process it efficiently, utilizing caching and a grid of computers.
Does anyone know of a system that would provide database-like capabilities, while using plain tab-separated files as backend? It seems to me like a very generic problem, that virtually all scientists get to deal with in one way or the other.
There is a lot of data (tens of TBs), and it is not affordable to load a copy into a relational database (we would have to buy twice as much storage space).
You know your requirements better than any of us, but I would suggest you think again about this. If you have 16-bit integers (0-65535) stored in a csv file, your .tsv storage efficiency is about 33%: it takes 5 bytes to store most 16-bit integers plus a delimiter = 6 bytes, whereas the native integers take 2 bytes. For floating-point data the efficiency is even worse.
I would consider taking the existing data, and instead of storing raw, processing it in the following two ways:
Store it compressed in a well-known compression format (e.g. gzip or bzip2) onto your permanent archiving media (backup servers, tape drives, whatever), so that you retain the advantages of the .tsv format.
Process it into a database which has good storage efficiency. If the files have a fixed and rigorous format (e.g. column X is always a string, column Y is always a 16-bit integer), then you're probably in good shape. Otherwise, a NoSQL database might be better (see Stefan's answer).
This would create an auditable (but perhaps slowly accessible) archive with low risk of data loss, and a quickly-accessible database that doesn't need to be concerned with losing the source data, since you can always re-read it into the database from the archive.
You should be able to reduce your storage space and should not need twice as much storage space, as you state.
Indexing is going to be the hard part; you'd better have a good idea of what subset of the data you need to be able to query efficiently.
One of these nosql dbs might work. I highly doubt any are configurable to sit on top of flat, delimited files. You might look at one of the open source projects and write your own database layer.
Scalability begins at a point beyond tab-separated ASCII.
Just be practical - don't academicise it - convention frees your fingers as well as your mind.
I would upvote Jason's recommendation if I had the reputation. My only add is that if you do not store it in a different format like the database Jason was suggesting you pay the parsing cost on every operation instead of just once when you initially process it.
You can do this with LINQ to Objects if you are in a .NET environment. Streaming/deferred execution, functional programming model and all of the SQL operators. The joins will work in a streaming model, but one table gets pulled in so you have to have a large table joined to a smaller table situation.
The ease of shaping the data and the ability to write your own expressions would really shine in a scientific application.
LINQ against a delimited text file is a common demonstration of LINQ. You need to provide the ability to feed LINQ a tabular model. Google LINQ for text files for some examples (e.g., see http://www.codeproject.com/KB/linq/Linq2CSV.aspx, http://www.thereforesystems.com/tutorial-reading-a-text-file-using-linq/, etc.).
Expect a learning curve, but it's a good solution for your problem. One of the best treatments on the subject is Jon Skeet's C# in depth. Pick up the "MEAP" version from Manning for early access of his latest edition.
I've done work like this before with large mailing lists that need to be cleansed, dedupped and appended. You are invariably IO bound. Try Solid State Drives, particularly Intel's "E" series which has very fast write performance, and RAID them as parallel as possible. We also used grids, but had to adjust the algorithms to do multi-pass approaches that would reduce the data.
Note I would agree with the other answers that stress loading into a database and indexing if the data is very regular. In that case, you're basically doing ETL which is a well understood problem in the warehouseing community. If the data is ad-hoc however, you have scientists that just drop their results in a directory, you have a need for "agile/just in time" transformations, and if most transformations are single pass select ... where ... join, then you're approaching it the right way.
You can do this with VelocityDB. It is is very fast at reading tab seperated data into C# objects and databases. The entire Wikipedia text is a 33GB xml file. This file takes 18 minutes to read in and persist as objects (1 per Wikipedia topic) and store in compact databases. Many samples are shown for how to read in tab seperated text files as part of the download.
The question's already been answered, and I agree with the bulk of the statements.
At our centre, we have a standard talk we give, "so you have 40TB of data", as scientists are newly finding themselves in this situation all the time now. The talk is nominally about visualization, but primarly about managing large amounts of data for those that are new to it. The basic points we try to get across:
Plan your I/O
Binary files
As much as possible, large files
File formats that can be read in parallel, subregions extracted
Avoid zillions of files
Especially avoid zillions of files in single directory
Data Management must scale:
Include metadata for provenance
Reduce need to re-do
Sensible data management
Hierarchy of data directories only if that will always work
Data bases, formats that allow metadata
Use scalable, automatable tools:
For large data sets, parallel tools - ParaView, VisIt, etc
Scriptable tools - gnuplot, python, R, ParaView/Visit...
Scripts provide reproducability!
We have a fair amount of stuff on large-scale I/O generally, as this is an increasingly common stumbling block for scientists.
What I want to create is a huge index over an even bigger collection of data. The data is a huge collection of images (and I mean millions of photos!) and I want to build an index on all unique images.
So I calculate a hash value of every image and append this with the width, height and file size of the image. This would generate a very unique key for every image. This would be combined with the location of the image, or locations in case of duplicates.
Technically speaking, this would fit perfectly in a single database table. An unique index on file name, plus an additional non-unique index on hash-width-height-size would be enough. However, I could use an existing database system to solve this, or just write my own, optimized version. It will be a single-user application anyway and the main purpose is to detect when I add a duplicate image to the collection so it will warn me that I already have it in my collection and display the locations where the other copies are. I can then decide to still add the duplicate or to discard it.
I've written hash-table implementations before and it's not that difficult once you know what you have to be aware of. So I could just implement my own file format for this data. It's unlikely that I'll ever need to add more information to these images and I'm not interested in similar images, just exact images. I'm not storing the original images in this file either, just the hash, size and location.
From experience, I know this could run extremely fast. I've done it before and have been doing similar things for nearly three decades so it's likely that I will chose this solution.
But I do wonder... Doing the same with an existing database system like SQL Server, Oracle, Interbase or MySQL, would performance still be high enough? There would be about 750 TB of images indexed in this database, which roughly translates to around 30 million records in a single, small table. Is it even worth considering the use of a regular database?
I have doubts about the usability of a database for this project. The amount of data is huge, yet the structure is real simple. I don't need multi-user support or most other features that most databases provide. So I don't see a need for a database. But I'm interested in the opinions of other programmers about this. (Although I expect most will agree with me here.)
The project itself, which is still just an idea in my head, is supposed to be some tool or add-on for explorer or whatever. Basically, it builds an index for any external hard disk that I attach to the system and when I copy an image to this disk somewhere, it's supposed to tell me if the image already exists at this disk. It will allow me to avoid filling up my backup disks with duplicates, although I sometimes would like to add duplicates. (E.g. because they're part of a series.) Since I like to create my own rendered artwork I have plenty of images. Plus, I've been taking digital pictures with digital cameras since 1996 so I also have a huge collection of photos. Add some other large collections to this and you'll soon realise that the amount of data will be huge. (And yes, there are already plenty of duplicates in my collection...)
Since it's a single-user application that you are considering, I'd probably have a look at SQLite. It ought to fit your other requirements rather nicely, I'd say.
I just tested the performance of PostgreSQL on my laptop (Core 2 Duo T5800 2.0 GHz 3.0 GiB RAM). I have a table with slightly more than 100M records, 5 columns and some indexes. I performed a range query on one indexed column (not the primary key) and returned all columns. A mean query returned 75 rows and executed in 750ms. You have to decide if this is fast enough.
I would avoid DIY-ing it unless you know all the repocussions of what you're doing.
Transactional Consistency for example, is not trivial.
I would suggest designing your code in such a way the backend can be easily replaced later, and then run with something sane ( SQLite is a good starting choice ), develop it the most sane and rational way possible, and then try slotting in the alternative backing store.
Then profile the differences, and run regression tests against it to make sure your database is not worse than SQLite.
Exisiting database solutions tend to win because they've had years of improvement and fine tuning to get their benefits, an a naïve attempt will likely be slower, buggier, and do less, all the while Increasing your development load to purely MONUMENTAL proportions.
http://fetter.org/optimization.html
The first rule of Optimization is, you do not talk about Optimization.
The second rule of Optimization is, you DO NOT talk about Optimization.
If your app is running faster than the underlying transport protocol, the optimization is over.
One factor at a time.
No marketroids, no marketroid schedules.
Testing will go on as long as it has to.
If this is your first night at Optimization Club, you have to write a test case.
Also, with databases, there is one thing you utterly MUST get ingrained.
Speed is unimportant
Your data being there when you need it, that is important.
When you have the assuredness that your data will always be there, then you may worry about trivial concerns like speed.
Hashes
You also lament that you'll be using image SHA's/MD5's etc to deduplicate images. This is a fallacious notion of its own, Hashes of files are only able to tell if the files are different, not if they're the same.
The logic is akin to asking 30 people to flip a coin, and you see the first one get heads, and thus decide to delete every other person who gets a head, because they're obviously the same person.
https://stackoverflow.com/questions/405628/what-is-the-best-method-to-remove-duplicate-image-files-from-your-computer
Although you may think it unlikely you'd have 2 different files with the same hash, your odds are about as good as winning the lotto. The chances of you winning the lotto are low, but somebody wins the lotto every day. Don't let it be you.
I have a system which is receiving log files from different places through http (>10k producers, 10 logs per day, ~100 lines of text each).
I would like to store them to be able to compute misc. statistics over them nightly , export them (ordered by date of arrival or first line content) ...
My question is : what's the best way to store them ?
Flat text files (with proper locking), one file per uploaded file, one directory per day/producer
Flat text files, one (big) file per day for all producers (problem here will be indexing and locking)
Database Table with text (MySQL is preferred for internal reasons) (pb with DB purge as delete can be very long !)
Database Table with one record per line of text
Database with sharding (one table per day), allowing simple data purge. (this is partitioning. However the version of mysql I have access to (ie supported internally) does not support it)
Document based DB à la couchdb or mongodb (problem could be with indexing / maturity / speed of ingestion)
Any advice ?
(Disclaimer: I work on MongoDB.)
I think MongoDB is the best solution for logging. It is blazingly fast, as in, it can probably insert data faster than you can send it. You can do interesting queries on the data (e.g., ranges of dates or log levels) and index and field or combination of fields. It's also nice because you can randomly add more fields to logs ("oops, we want a stack trace field for some of these") and it won't cause problems (as it would with flat text files).
As far as stability goes, a lot of people are already using MongoDB in production (see http://www.mongodb.org/display/DOCS/Production+Deployments). We just have a few more features we want to add before we go to 1.0.
I'd pick the very first solution.
I don't see why would you need DB at all. Seems like all you need is to scan through the data. Keep the logs in the most "raw" state, then process it and then create a tarball for each day.
The only reason to aggregate would be to reduce the number of files. On some file systems, if you put more than N files in a directory, the performance decreases rapidly. Check your filesystem and if it's the case, organize a simple 2-level hierarchy, say, using the first 2 digits of producer ID as the first level directory name.
I would write one file per upload, and one directory/day as you first suggested. At the end of the day, run your processing over the files, and then tar.bz2 the directory.
The tarball will still be searchable, and will likely be quite small as logs can usually compress quite well.
For total data, you are talking about 1GB [corrected 10MB] a day uncompressed. This will likely compress to 100MB or less. I've seen 200x compression on my log files with bzip2. You could easily store the compressed data on a file system for years without any worries. For additional processing you can write scripts which can search the compressed tarball and generate more stats.
Since you would like to store them to be able to compute misc. statistics over them nightly , export them (ordered by date of arrival or first line content) ... You're expecting 100,000 files a day, at a total of 10,000,000 lines:
I'd suggest:
Store all the files as regular textfiles using the following format : yyyymmdd/producerid/fileno.
At the end of the day, clear the database, and load all the textfiles for the day.
After loading the files, it would be easy to get the stats from the database, and post them in any format needed. (maybe even another "stats" database). You could also generate graphs.
To save space ,you could compress the daily folder. Since they're textfiles, they would compress well.
So you would only be using the database to be able to easily aggregate the data. You could also reproduce the reports for an older day if the process didn't work, by going through the same steps.
To my experience, single large table performs much faster then several linked tables if we talk about database solution. Particularly on write and delete operations. For example, splitting one table into three linked tables decreases performance 3-5 times. This is very rough, of course it depends on details, but generally this is the risk. It gets worse when data volumes get very large. Best way, IMO, to store log data is not in a flat text, but rather in a structured form, so that you can do efficient queries and formatting later. Managing log files could be pain, especially when there are lots of them and coming from many sources and locations. Check out our solution, IMO it can save you lots of development time.