Hi Christian,
1) Regarding variable max cache size, thank you for the (speedy)
accommodation; it would likely solve my problem. However I can't help
wonder if this is best for the library. Use of variable (non-final)
statics effectively means employing globals. That's going to make it
much more difficult to reason about their state at a given moment.
Before they were hardcoded and final, so their value could be relied
upon. Now it will be subject to change by any thread at any time, and
new values will affect all default-using Variable instances everywhere
in the app, regardless of which file they are associated with.
I imagine it would be useful to be able to change max size on a
per-file-basis. Is there a point in the code where Variable objects are
being attached to the NetcdfFile object, where the limit could be set,
to a value previously specified on that NetcdfFile object? That way one
would have the opportunity to set a value appropriate to a particular
netcdf file, without the above perils. The static default value could
then remain constant, as-is.
Let me know what you think.
2) Regarding each NetcdfDataset having it's own set of cached Variable
data: it seems a consequence of this would be that in a multi-threaded
environment like a web server (as in our use-case), where many
NetcdfDataset objects would (by necessity) be 'checked out' (in use by
various threads) at any given time, there would then, after a period of
use during which the caches would populate, end up being multiple copies
of each cached Variable in memory.
For example, at the moment we are putting each of our netcdf files
entirely in memory, and as you might imagine that uses up an immense
amount of memory and of course is the most simplistic 'caching' solution
possible. As it turns out, we only actually use about 1/10th of the
variables in each netcdf file in question. So a lazy caching solution,
such as netcdf-java lib's, should be a distinct advantage, which is why
I was pursuing it, allowing us to reduce the amount of memory required
to very roughly 1/10 of current.
However, since each Netcdfdataset has its own copy of the same cached
Variable data, not only does it negate this advantage, it could actually
require vastly more memory since the number of request-servicing threads
would easily exceed 10.
Can you again validate that this is actually the situation we are facing
and that I'm not missing anything here?
Many thanks!
James
On 07/10/2017 04:33 PM, Christian Ward-Garrison wrote:
Hi James,
> is there a central place where one can change the max size of
variable to cache
There are 3, each used for a different purpose [1][2][3].
Unfortunately, none of them could be modified by the user, so I pushed
a commit [4] that fixes that. I also built a new SNAPSHOT version of
NetCDF-Java that includes the fix [5]. If you'd like to change those
values, you should grab that version. If you're using Maven or Gradle
to manage the dependencies of your program, follow these instructions
[6], but pull from the "unidata-snapshots" repository.
> Can you verify whether or not this is the case?
It is indeed the case. The data are cached on the Variable objects,
which are not shared among NetcdfDatasets.
Cheers,
Christian
[1]
https://github.com/cwardgar/thredds/blob/a88db4af71bac2c29429540bc1e5387741be7d68/cdm/src/main/java/ucar/nc2/Variable.java#L69
[2]
https://github.com/cwardgar/thredds/blob/a88db4af71bac2c29429540bc1e5387741be7d68/cdm/src/main/java/ucar/nc2/Variable.java#L70
[3]
https://github.com/cwardgar/thredds/blob/a88db4af71bac2c29429540bc1e5387741be7d68/cdm/src/main/java/ucar/nc2/dataset/CoordinateAxis.java#L76
[4]
https://github.com/cwardgar/thredds/commit/a88db4af71bac2c29429540bc1e5387741be7d68
[5]
http://artifacts.unidata.ucar.edu/content/repositories/unidata-snapshots/edu/ucar/netcdfAll/4.6.11-SNAPSHOT/
[6]
https://www.unidata.ucar.edu/software/thredds/current/netcdf-java/reference/BuildDependencies.html
On Thu, Jul 6, 2017 at 2:05 PM, James Gardner <james.gardner@xxxxxxxx
<mailto:james.gardner@xxxxxxxx>> wrote:
Hi,
If I might pick up where my coworker left off; I need to know a
couple of additional details about how caching is implemented in
the netcdf-java lib.
First, is there a central place where one can change the max size
of variable to cache, for instance on the netcdfFile/Dataset
object to which the variable belongs (or even some master
location), or must one use setSizeToCache on each separate variable?
My second question is regarding the way/location in which variable
data is cached.
If one is using netcdf file caching, it seems that all
netcdfDataset objects in the cache/pool which represent a given
actual netcdf file, each have their own cached variable data. In
other words, cached variable data is not shared between acquired
netcdfDataset objects.
I believe I have seen this reflected in the output of (the cache
status section of) getDetailInfo() when called on various such
netcdfDataset objects during runtime; some seem to reflect the
custom setSizeToCache changes I have made, and have cached data,
while others do not, indicating that they have their own copies of
variables, along with their own cache settings/thresholds.
Can you verify whether or not this is the case?
Cheers,
James
Hi Kevin,
I've done a little research and can provide some answers to
your questions.
> Then, next time that NetcdfDataset.acquireDataset() is
called it causes
the
> FileCache.acquireCacheOnly() to return null because the cached
NetcdfDataset.raf
> (RandomAccessFile) is null so it makes the lastModified = 0.
Prior to v4.6.5, this is indeed how caching of NetcdfDataset
worked. It was
broken. However, the commit I referenced earlier should've
fixed that.
> What does NetcdfDataset.acquireDataset() actually cache?
It caches the actual NetcdfDataset object, which is the result
of parsing a
dataset's metadata to form a hierarchical structure and then
optionally
"enhancing" that structure. Typical enhancements include
construction of
coordinate systems. These objects are heavyweight and
non-trivial to
create, so only making them once is a huge performance win,
especially if
the dataset aggregates smaller datasets.
> Can I avoid having to do a Variable.read() for every request?
> Shouldn't this data be cached inside of the netcdf file.
No, you can't avoid calling Variable.read(). However, if a
variable is
small enough its data will be cached automatically [1]. It
looks like the
limits are 4,000 bytes for normal variables and 40,000 bytes
for coordinate
variables, though you could set different limits by calling
Variable.setSizeToCache(). Alternatively, you could just
explicitly cache
the data yourself by calling Variable.setCachedData().
> Should I be using those caching options and just storing
those Variable
objects
> in memory in my own cache instead.
With the recent caching fix, you shouldn't need to hold on to
the Variable
objects yourself. NetcdfDatasets will be cached, including the
Variables
that they contain.
> Would it be a better option to use NetcdfFile.openInMemory().
You could try that, especially if hardware resources are no
object. I'd be
interested in the results. Actually, I'd be interested in any
performance
data you collect as you optimize your response times.
Just be aware that opening a file using the static methods or
constructors
in NetcdfFile will mean that enhancements won't be applied to
it. If you
need coordinate systems to be built, or calculation of
scale/offset/missing
values, you need to open with NetcdfDataset.
----
In your original message, you mentioned you're using
NetcdfDataset.initNetcdfFileCache(), which caches
NetcdfDataset objects.
Another potential performance improvement may come from
caching the
underlying RandomAccessFiles, via setGlobalFileCache(). If a
RandomAccessFile is acquired from the cache rather than
recreated, this
saves you from performing an open() system call, as well as
potentially a
seek() and fill of its buffer.
Here [3] are the global caches we run in the TDS. You don't
need to worry
about GribCdmIndex unless you're working with GRIB files.
Cheers,
Christian
[1]
https://github.com/Unidata/thredds/blob/v4.6.6/cdm/src/main/java/ucar/nc2/Variable.java#L848
<https://github.com/Unidata/thredds/blob/v4.6.6/cdm/src/main/java/ucar/nc2/Variable.java#L848>
[2]
https://github.com/Unidata/thredds/blob/v4.6.6/cdm/src/main/java/ucar/nc2/Variable.java#L69
<https://github.com/Unidata/thredds/blob/v4.6.6/cdm/src/main/java/ucar/nc2/Variable.java#L69>
[3]
https://github.com/Unidata/thredds/blob/v4.6.6/tds/src/main/java/thredds/server/config/CdmInit.java#L263
<https://github.com/Unidata/thredds/blob/v4.6.6/tds/src/main/java/thredds/server/config/CdmInit.java#L263>
On Wed, Jun 15, 2016 at 4:31 PM, Christian Ward-Garrison
<cwardgar@xxxxxxxx>
wrote:
> Hi Kevin,
>
> Sorry for the delay in respondingâI was busy with the
release of 4.6.6âbut
> I have some time to work on this issue now. A couple questions:
>
> 1. What does your webapp do? It sounds like it takes a
user-defined subset
> of the data in a NetCDF file and returns it in JSON format.
How similar is
> it to our NetCDF Subset Service (example
>
<http://thredds.ucar.edu/thredds/ncss/grib/NCEP/NAM/Alaska_11km/Best/dataset.html
<http://thredds.ucar.edu/thredds/ncss/grib/NCEP/NAM/Alaska_11km/Best/dataset.html>>
> )?
> 2. What version of NetCDF-Java are you using. I suspect that
much of the
> slowness you're encountering was already fixed
>
<https://github.com/cwardgar/thredds/commit/075e9a819ee10714d53b355481a7cccac88b1fb9#diff-99981060deed76f1a9ddedc4362acd7fL155
<https://github.com/cwardgar/thredds/commit/075e9a819ee10714d53b355481a7cccac88b1fb9#diff-99981060deed76f1a9ddedc4362acd7fL155>>
> in v4.6.5.
>
> Cheers,
> Christian
>
> On Wed, Jun 8, 2016 at 4:17 PM, Kevin Off - NOAA Affiliate <
> kevin.off@xxxxxxxx> wrote:
>
>> Hi all,
>>
>> I am trying to understand caching when it comes to the file
and the
>> actual data. The application that I am working on will
provide data from
>> 133 NetCDF files that range in size from 50 MB to 400 MB.
These are weather
>> forecast files that contain about 22 variables that we are
interested in .
>> Each variable has between 1 and 55 or so time steps as
dimensions.
>>
>> This is a Spring web application running in an embedded
tomcat instance.
>> All of the files on disk amount to about 22GB of data.
>>
>> When I receive a request I:
>>
>> 1. Re-project the lat lon to the dataset's projection
(Lambert
>> Convormal)
>> 2. Lookup the index of the data from the coordinate variabls
>> 3. loop through every variable
>> 4. Perform the Array a = var.read()
>> 5. Loop through every time step and retrieve the value
at the
>> specified point
>> 6. Return it all in a JSON document.
>>
>> This application needs to be extremely fast. We will be
serving thousands
>> of requests per second (in production on a scaled system)
depending on
>> weather conditions.
>>
>> I have been told that hardware is not an obstacle and that
I can use as
>> much memory as I need.
>> During my coding and debugging I have been able to achieve
a response
>> time of about 200ms - 400ms on average (this does not
include any network
>> time).
>> As I add timers to every part of the application I find
that most of the
>> time is spent in the Variable.read() function.
>>
>> Here is a summary of the the configuration of the app.
>>
>> NetcdfDataset.initNetcdfFileCache(100, 200, 0);
>> NetcdfDataset nc = NetcdfDataset.acquireDataset(filename, null)
>> for each coverage{
>> Variable v = ds.findVariable(name)
>> Array d = v.read()
>> for each time step {
>> value = d.read(time, y, x)
>> }
>> }
>> nc.close()
>>
>> I have several questions.
>>
>> 1. I noticed that when the NetcdfDataset.close()
function is called
>> it detects that I am using caching and performs
releases. This causes the
>> IOServiceProvider (AbstractIOServiceProvider).release()
to be called which
>> closes and nulls the RandomAccessFile. Then, next time that
>> NetcdfDataset.acquireDataset() is called it causes the
>> FileCache.acquireCacheOnly() to return null because the
cached
>> NetcdfDataset.raf (RandomAccessFile) is null so it makes
the lastModified >> =
>> 0. Am I missing something or is there no way to reuse
the NetcdfDataset
>> after you call close()?
>> 2. What does NetcdfDataset.acquireDataset() actually
cache? Is it
>> just the metadata or does it actually read in the data
to all of the
>> variables?
>> 3. Can I avoid having to do a Variable.read() for every
request?
>> Shouldn't this data be cached inside of the netcdf file.
>> 4. I see that there are caching functions on the
Variable object.
>> Should I be using those caching options and just storing
those Variable
>> objects in memory in my own cache instead.
>> 5. Would it be a better option to use
NetcdfFile.openInMemory().
>>
>> I know this is a bit long winded but I just want to make
sure to explore
>> all of my options. I have spent a lot of time stepping
through the ucar
>> library and have already learned a lot. I just need a
little guidance
>> regarding some of the more abstract caching functionality.
Thanks for your
>> help.
>>
>> --
>> Kevin Off
>> Internet Dissemination Group, Kansas City
>> Shared Infrastructure Services Branch
>> National Weather Service
>> Software Engineer / Ace Info Solutions, Inc.
>> <http://www.aceinfosolutions.com
<http://www.aceinfosolutions.com>>
>>
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