The current bottleneck with file systems is the speed of getting data
on or off the magnetic surface. So filesystem compression helps, as
less data needs to be physically written or read per image. The CPU
time spent compressing the data is less than the time saved in writing
less data to the surface.
I would be interested to see if the speed up is the same with a solid
state drive, as there is near 'random access' here, unlike with a
magnetic drive where the seek time is one of the bottlenecks. For
example, mechanical hard drives are limited to about 130MB/s, whereas
SSDs can already manage 200MB/s (faster than a first generation SATA
interface at 150MB/s can cope with and one of the drivers behind the
2nd (300MB/s) and 3rd generation (600MB/s) SATA intefaces). The large
size of our image files should make them ideal for use with SSDs.
Quoting "James Holton" <[log in to unmask]>:
> I think it important to point out that despite the subject line, Dr.
> Scott's statement was:
> "I think they process a bit faster too"
> Strangely enough, this has not convinced me to re-format my RAID
> array with an new file system nor re-write all my software to
> support yet another new file format. I guess I am just lazy that
> way. Has anyone measured the speed increase? Have macs become
> I/O-bound again? In any case, I think it is important to remember
> that there are good reasons for leaving image file formats
> uncompressed. Probably the most important is the activation barrier
> to new authors writing new programs that read them. "fread()" is
> one thing, but finding the third-party code for a particular
> compression algorithm, navigating a CVS repository and linking to a
> library are quite another! This is actually quite a leap for those
> of us who never had any formal training in computer science.
> Personally, I still haven't figured out how to read pck images, as
> it is much easier to write "jiffy" programs for uncompressed data.
> For example, if all you want to do is extract a group of pixels
> (such as a spot), then you have to decompress the whole image! In
> computer speak: fseek() is rendered useless by compression. This
> could be why Mar opted not to use the pck compression for their
> newer CCD-based detectors?
>
> That said, compressed file systems do appear particularly attractive
> if space is limiting. Apparently HFS can do it, but what about
> other operating systems? Does anyone have experience with a Linux
> file system that both supports compression and doesn't get corrupted
> easily?
>
> -James Holton
> MAD Scientist
>
>
> Graeme Winter wrote:
>> Hi David,
>>
>> If the data compression is carefully chosen you are right: lossless
>> jpeg2000 compression on diffraction images works very well, but is a
>> spot slow. The CBF compression using the byte offset method is a
>> little less good at compression put massively faster... as you point
>> out, this is the one used in the pilatus images. I recall that the
>> .pck format used for the MAR image plates had the same property - it
>> was quicker to read in a compressed image that the raw equivalent.
>>
>> So... once everyone is using the CBF standard for their images, with
>> native lossless compression, it'll save a fair amount in disk space
>> (=£/$), make life easier for people and - perhaps most importantly -
>> save a lot of data transfer time.
>>
>> Now the funny thing with this is that if we compress the images before
>> we store them, the compression implemented in the file system will be
>> less effective... oh well, can't win em all...
>>
>> Cheers,
>>
>> Graeme
>>
>>
>>
>> 2009/9/18 Waterman, David (DLSLtd,RAL,DIA) <[log in to unmask]>:
>>
>>> Just to comment on this, my friend in the computer game industry insists
>>> that compression begets speed in almost all data handling situations.
>>> This will be worth bearing in mind as we start to have more fine-sliced
>>> Pilatus 6M (or similar) datasets to deal with.
>>>
>>> Cheers,
>>> David.
>>>
>>> -----Original Message-----
>>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
>>> William G. Scott
>>> Sent: 17 September 2009 22:48
>>> To: [log in to unmask]
>>> Subject: [ccp4bb] I compressed my images by ~ a factor of two, and they
>>> load and process in mosflm faster
>>>
>>> If you have OS X 10.6, this will impress your friends and save you some
>>> disk space:
>>>
>>> % du -h -d 1 mydata
>>> 3.5G mydata
>>>
>>> mv mydata mydata.1
>>>
>>> sudo ditto --hfsCompression mydata.1 mydata rm -rf mydata.1
>>>
>>> % du -h -d 1 mydata
>>> 1.8G mydata
>>>
>>> This does hfs filesystem compression, so the images are still recognized
>>> by mosflm, et al. I think they process a bit faster too, because half
>>> the information is packed into the resource fork.
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