Thread: Re: [GENERAL] medical image on postgreSQL?
> Apologize.. this posting may not relevance enough to this group. I > am very much a newbie to posgreSQL database programming and would > like assistance. I am finding an example how to use the database > (postgreSQL) to store MRI/CT image data using C language > interface. I heard something pronounced like: Content-Based Image > Retrieval.. but I still do not have any idea for a HowTo do on > postgreSQL database. This is the 3rd such case that I've heard someone using PostgreSQL to store MRI images. While it's non-portable (works on FreeBSD/Linux), sendfile() and recvfile() would be huge wins for folks in that crowd (or anyone storing/fetching large files). There'd be some large #ifdef sections (~100 lines?) in the backend, possibly in the fe ('nother ~100 lines), but would patches for this be accepted into the tree if I did the legwork given sendfile()'s non-universal portability (which seems to be, IMHO, an overly important criteria)? -sc -- Sean Chittenden
On Fri, 11 Apr 2003, Sean Chittenden wrote: > > Apologize.. this posting may not relevance enough to this group. I > > am very much a newbie to posgreSQL database programming and would > > like assistance. I am finding an example how to use the database > > (postgreSQL) to store MRI/CT image data using C language > > interface. I heard something pronounced like: Content-Based Image > > Retrieval.. but I still do not have any idea for a HowTo do on > > postgreSQL database. > > This is the 3rd such case that I've heard someone using PostgreSQL to > store MRI images. While it's non-portable (works on FreeBSD/Linux), > sendfile() and recvfile() would be huge wins for folks in that crowd > (or anyone storing/fetching large files). There'd be some large > #ifdef sections (~100 lines?) in the backend, possibly in the fe > ('nother ~100 lines), but would patches for this be accepted into the > tree if I did the legwork given sendfile()'s non-universal portability > (which seems to be, IMHO, an overly important criteria)? -sc I'm not familiar with sendfile() recfile(). Are they in contrib somewhere?
> > > Apologize.. this posting may not relevance enough to this group. > > > I am very much a newbie to posgreSQL database programming and > > > would like assistance. I am finding an example how to use the > > > database (postgreSQL) to store MRI/CT image data using C > > > language interface. I heard something pronounced like: > > > Content-Based Image Retrieval.. but I still do not have any idea > > > for a HowTo do on postgreSQL database. > > > > This is the 3rd such case that I've heard someone using PostgreSQL > > to store MRI images. While it's non-portable (works on > > FreeBSD/Linux), sendfile() and recvfile() would be huge wins for > > folks in that crowd (or anyone storing/fetching large files). > > There'd be some large #ifdef sections (~100 lines?) in the > > backend, possibly in the fe ('nother ~100 lines), but would > > patches for this be accepted into the tree if I did the legwork > > given sendfile()'s non-universal portability (which seems to be, > > IMHO, an overly important criteria)? -sc > > I'm not familiar with sendfile() recfile(). Are they in contrib > somewhere? :) They're system calls, like write() && read() except they're zero copy socket operations. If the OS has sendfile(), the OS basically DMA's the data from the disk read directly to the network card averting copying the data to the userland and back to the kernel. I actually think it'd be interesting to get this in use for general reads. sendfile() lets you send headers/trailers to the data being sent, similar to writev(). Other zero copy socket operations are mmap() + write(), but last I heard, that was a FreeBSD only thing... for now. man 2 sendfile err... there is no recvfile though... I thought there was an fd based call similar to recvfrom called recvfile... I wonder where I saw that... hrm, I think I may add that to -CURRENT for orthogonality's sake. -sc -- Sean Chittenden
Sean Chittenden <sean@chittenden.org> writes: > Other zero copy socket operations are mmap() + write(), but last I heard, > that was a FreeBSD only thing... for now. man 2 sendfile There's a lot of resistance to the optimizating mmap+write in the linux camp. It isn't just a matter of time, the developers there actively think this is a bad idea. In fact the code has been written several times and is never accepted. They think developers should be encouraged to use sendfile and the common code path for write shouldn't be wasting cycles checking for special cases in the page table. Note that there are some protocol requirements for sendfile to be feasible. There has to be zero alterations made to the data in flight. No escaping, decompression, etc. And there has to be no cases when the program would want to stop transmitting partway through. I think you can send a portion of a file but you would have to know the size of the chunk up front and the best performance would be if the chunk is very large. -- greg
> > Other zero copy socket operations are mmap() + write(), but last I > > heard, that was a FreeBSD only thing... for now. man 2 sendfile > > There's a lot of resistance to the optimizating mmap+write in the > linux camp. It isn't just a matter of time, the developers there > actively think this is a bad idea. In fact the code has been written > several times and is never accepted. They think developers should be > encouraged to use sendfile and the common code path for write > shouldn't be wasting cycles checking for special cases in the page > table. Well, I won't go into how well/poorly Linux's VM is written... that said, I suppose I sympathize with the developers in the linux camp that want to avoid this issue... this isn't easy to do right/elegantly and it took BSD quite a while to get right, iirc. > Note that there are some protocol requirements for sendfile to be > feasible. There has to be zero alterations made to the data in > flight. No escaping, decompression, etc. And there has to be no > cases when the program would want to stop transmitting partway > through. I think you can send a portion of a file but you would have > to know the size of the chunk up front and the best performance > would be if the chunk is very large. I can speak from personal experience under huge loads (60K+ connections to a single webserver) that for small files, it is advantageous to use mmap() + write() instead of sendfile(). sendfile() has a pretty funky API that isn't the cleanest out there and requires a small state machine per file being sent and is more complex for nonblocking IO, but it's still better. As for performance, mmap() + write() is _faster_ than sendfile() for small files that can be cached by the FS cache layer. What's odd, however, is that I found it only marginally faster (1-3ms?) and I'm not convinced that the speed up wasn't from sending data from the local box (mmap()) instead of being pulled over NFS (sendfile()). sendfile() is pretty slick and I'd recommend its use anywhere over read() + write(). FWIW, cache coherency isn't an issue for well written VMs though (*rub*). The data can change under sendfile()'s feet and that's okay, BSD handles this correctly (nevermind MVCC prevents this from being a problem). Writing data to a page that's mmap()'ed is also sync'ed and cache coherency isn't an issue for so long as the page is shared and sync'ed with disk periodically. -sc -- Sean Chittenden