I'm a grad student in astrophysics. I run big simulations using codes mostly developed by others over a decade or so. For examples of these codes, you can check out gadget http://www.mpa-garching.mpg.de/gadget/ and enzo http://code.google.com/p/enzo/. Those are definitely the two most mature codes (they use different methods).
The outputs from these simulations are huge. Depending on your code, your data is a bit different, but it's always big data. You usually take billions of particles and cells to do anything realistic. The biggest runs are terabytes per snapshot and hundreds of snapshots per simulation.
Currently, it seems that the best way to read and write this kind of data is to use HDF5 http://www.hdfgroup.org/HDF5/, which is basically an organized way of using binary files. It's a huge improvement over unformatted binary files with a custom header block (still give me nightmares), but I can't help but think there could be a better way to do this.
I imagine the sheer data size is the issue here, but is there some sort of datastore that can handle terabytes of binary data efficiently, or are binary files the only way at this point?
If it helps, we typically store data columnwise. That is, you have a block of all particle id's, block of all particle positions, block of particle velocites, etc. It's not the prettiest, but it is the fastest for doing something like a particle lookup in some volume.
edit: Sorry for being vague about the issues. Steve is right that this might just be an issue of data structure rather than the data storage method. I have to run now, but I will provide more details late tonight or tomorrow.
edit 2: So the more I look into this, the more I realize that this probably isn't a datastore issue anymore. The main issue with unformatted binary was all the headaches reading the data correctly (getting the block sizes and order right and being sure about it). HDF5 pretty much fixed that and there isn't going to be a faster option until the file system limitations are improved (thanks Matt Turk).
The new issues probably come down to data structure. HDF5 is as performant as we can get, even if it is not the nicest interface to query against. Being used to databases, I thought it would be really interesting/powerful to be able to query something like "give me all particles with velocity over x at any time". You can do something like that now, but you have to work at a lower level. Of course, given how big the data is and depending on what you are doing with it, it might be a good thing to work at a low level for performance sake.
- MongoDB: http://www.mongodb.org/
- Netezza Products: http://www.netezza.com/data-warehouse-appliance-products/skimmer.aspx
- Hadoop: http://hadoop.apache.org/
- Wikipedia's List of Distributed File Systems: http://en.wikipedia.org/wiki/List_of_file_systems#Distributed_file_systems
EDIT
Rationale for my lack of explanation / etc.:
- OP says: "[HDF5]'s a huge improvement over unformatted binary files with a custom header block (still give me nightmares), but I can't help but think there could be a better way to do this."
What does "better" mean? Better structured? He seems to allude to the "unformatted binary files" as being an issue - so maybe that's what he means by better. If so, he'll need something with some structure - hence the first couple suggestions.
- OP says: "I imagine the sheer data size is the issue here, but is there some sort of datastore that can handle terabytes of binary data efficiently, or are binary files the only way at this point?"
Yes, there are several. Both structured, and "unstructured" - does he want structure, or is he happy to leave them in some sort of "unformatted binary format"? We still don't know - so I suggest checking out some Distributed File Systems.
- OP says: "If it helps, we typically store data columnwise. That is, you have a block of all particle id's, block of all particle positions, block of particle velocites, etc. It's not the prettiest, but it is the fastest for doing something like a particle lookup in some volume."
Again, Does the OP want better structure, or doesn't he? Seems like he wants both - better structure AND faster.... maybe scaling OUT will give him this. This further reinforces the first few options I listed.
- OP says (in comments): "I don't know if we can take the hit on io though."
Are there IO requirements? Cost restrictions? What are they?
We can't get something for nothing here. There is no "silver-bullet" storage solution. All we have to go on here for requirements is "lots of data" and "I don't know if I like the lack of structure, but I'm not willing to increase my IO to accommodate any additional structure"... so I don't know what kind of answer he's expecting. He hasn't listed a single complaint about the current solution he has other than the lack of structure - and he's already said he's not willing to pay any overhead to do anything about that... so.... ?
来源：https://stackoverflow.com/questions/6513671/datastore-for-large-astrophysics-simulation-data