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[netCDFJava #MQO-415619]: Efficiently serializing NetCDF in memory objects

Proposal:
I am in the process of adding support for retrieving
the final file image for an in-memory file. This would
extend the existing nc_open_mem functionality.

This involves several changes.
1. nc_open_mem() would now allow the NC_WRITE mode flag
   so a chunk of memory can be passed in and be modified
2. nc_create() would now allow the NC_INMEMORY flag to be set
   to cause the created file to be kept in memory.
3. the ability would be provided to obtain the in-memory contents
   of a file at the point it is closed using a new function
        nc_close_mem(int ncid, size_t* sizep, void** memory)
Note the following.
1. If nc_open_mem is called with NC_WRITE, then a copy of the incoming
   memory would be made internally (dictated by HDF5 functionality).
   If instead, the file is read-only, no copy would be made.
2. The memory returned by nc_close_mem would be a COPY of the current
   contents if the original was writeable (again HDF5 forced).

I also have a couple of thoughts.
1. Instead of nc_close_mem, I could separate out the memory extraction
   from the close operation. Hence one would call something like
   nc_get_mem() and then nc_close() instead of nc_close only.
   I prefer the nc_close_mem solution, but can anyone provide a
   use case where the separate functions is better?
2. I could always make it so that the incoming and extracted memory
   chunks were copies. This would mean that read-only opening
   a memory chunk would pay the copy cost when it did not have to.
   But the always copy soln might be simpler for the user to understand
   and use.
Note that this is all preliminary and is subject to change if,
for example, I cannot get some piece of functionality to work.




> Sorry, I posted the proposal to the netcdf news group and forgot to copy
> to the gihub site. I will do that ASAP.
> 
> >
> > This is good news. I am eager to provide feedback on your proposal.
> > I did not find any proposal in the linked issue. Did you forget to push :) ?
> >
> > Also, it has not been updated with our latest discussions. Do you want me
> > to fix that ?
> >
> > Regards,
> >
> > Michaël
> >
> > address@hidden>:
> >
> > > It appears I can do this. You might examine my proposed
> > > API and tell me if it will serve your purposes.
> > > See https://github.com/Unidata/netcdf-c/issues/708
> > >
> > > > I will investigate and see if I can use this function
> > > > to get the desired effect.
> > > > Thanks for bringing it to my attention.
> > > >
> > > > >
> > > > > The HDFgroup forum has pointed me to the H5Pset_file_image
> > > > > <https://support.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#
> > > Property-SetFileImage>
> > > > > function. This is documented further here
> > > > > <https://support.hdfgroup.org/HDF5/doc/Advanced/FileImageOperations/
> > > HDF5FileImageOperations.pdf>
> > > > > and seems to be available from HDF5 1.8.9 upwards.
> > > > > So, I should rejoice as the limitations no longer comes from the HDF5
> > > > > software. Yet, I am a bit suspicious because this feature has been
> > > > > available from mid-2012 and I fear you are not using it for a good
> > > reason.
> > > > >
> > > > > What do you think ? I am willing to try implementing it if someone can
> > > > > mentor me.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Michaël
> > > > >
> > > > > address@hidden>:
> > > > >
> > > > > > I think that as long as the mmap is set up with non-persist, then
> > > > > > the only writes to disk will occur with paging.
> > > > > >
> > > > > > > Actually, my solution is less than optimal since, using mmap, data
> > > is
> > > > > > still
> > > > > > > written to disk eventually.
> > > > > > >
> > > > > > > The goal is to avoid both writes to disk and data copies. This is
> > > > > > sometimes
> > > > > > > called "zero copy" optimization and would work because in my
> > > application,
> > > > > > > we enforce that input data is read only. Output data is modified
> > > > > > obviously
> > > > > > > but can be seen as read only just before transmission.
> > > > > > >
> > > > > > > I have started a thread on the HDF forum on the topic. I am also
> > > looking
> > > > > > > into Apache Common VFS Ram filesystem as a fallback workaround.
> > > > > > >
> > > > > > > Regards,
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > address@hidden>:
> > > > > > >
> > > > > > > > Actually, we do use mmap already. The problem is that the mapped
> > > memory
> > > > > > > > is hidden deep in, for example, the hdf5 memory driver. So there
> > > is no
> > > > > > > > way I can see to get access to it. If we did have access to it,
> > > then
> > > > > > > > of course, we could copy it out and give you the functionality
> > > you
> > > > > > desire .
> > > > > > > >
> > > > > > > > >
> > > > > > > > > My ideal use case would allow users to create/modify NetCDF4
> > > datasets
> > > > > > > > > in-memory. Once done, my software would read the binary data
> > > and
> > > > > > send it
> > > > > > > > > over the network.
> > > > > > > > > One workaround I see is to use POSIX memory mapped file
> > > > > > > > > <https://en.wikipedia.org/wiki/Memory-mapped_file> to trick
> > > the
> > > > > > library
> > > > > > > > > into working in-memory.
> > > > > > > > >
> > > > > > > > > I now understand this issue originates from a limitation of
> > > the HFD5
> > > > > > > > > library. I can raise this issue to the HDF group. Publications
> > > such
> > > > > > as
> > > > > > > > this
> > > > > > > > > one 
> > > > > > > > > <https://support.hdfgroup.org/pubs/papers/Big_HDF_FAQs.pdf>
> > > (see
> > > > > > > > also
> > > > > > > > > this
> > > > > > > > > <https://www.hdfgroup.org/2015/03/from-hdf5-datasets-to-
> > > > > > > > apache-spark-rdds/>)
> > > > > > > > > seems to indicate they would be interested bythe feature.
> > > Indeed,
> > > > > > > > avoiding
> > > > > > > > > unecessary transfers to disk is key to achieving good
> > > performance in
> > > > > > Big
> > > > > > > > > Data systems (this is the whole point of Apache Spark BTW).
> > > > > > > > >
> > > > > > > > > Regards,
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > address@hidden>:
> > > > > > > > >
> > > > > > > > > > This question has come up before.
> > > > > > > > > > This is currently not possible for netcdf-4 files.
> > > > > > > > > > Using the NC_DISKLESS mode flag allows for keeping
> > > > > > > > > > the file in memory. The nc_open_mem function allows for the
> > > > > > > > > > read only access to treat a chunk of memory as if it was
> > > > > > > > > > a netcdf file. Unfortunately, for netcdf-4, we ultimately
> > > > > > > > > > depend on the HDF5 operation H5P_set_core
> > > > > > > > > > (https://support.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#
> > > > > > > > Property-SetFaplCore
> > > > > > > > > > ).
> > > > > > > > > > Upon close(), this can optionally store the memory buffer in
> > > a
> > > > > > file.
> > > > > > > > > > Unfortunately, it does not (currently) provide an option to
> > > copy
> > > > > > out
> > > > > > > > the
> > > > > > > > > > memory.
> > > > > > > > > > The only solution I can see for now is to build an
> > > alternative to
> > > > > > the
> > > > > > > > core
> > > > > > > > > > driver
> > > > > > > > > > that provides access (somehow) to the memory.
> > > > > > > > > > BTW, this is all going on at the netcdf-c library level. Our
> > > pure
> > > > > > jave
> > > > > > > > HDF5
> > > > > > > > > > reader is read-only, hence cannot create or modify files.
> > > > > > > > > >
> > > > > > > > > > I have created an issue for this
> > > > > > > > > > (https://github.com/Unidata/netcdf-c/issues/708)
> > > > > > > > > > but it is not likely to get implemented anytime soon.
> > > > > > > > > >
> > > > > > > > > > You will have to be content with writing the contents to a
> > > file.
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > I am using NetCDF Java library 4.6.10.
> > > > > > > > > > >
> > > > > > > > > > > My goal is to efficiently send NetcdfFile
> > > > > > > > > > > <https://www.unidata.ucar.edu/software/thredds/current/
> > > > > > > > > > netcdf-java/javadoc/ucar/nc2/NetcdfFile.html>
> > > > > > > > > > > objects over the network using a communication library
> > > (such as
> > > > > > > > ZeroMQ) .
> > > > > > > > > > > Because the NetcdfFile
> > > > > > > > > > > <https://www.unidata.ucar.edu/software/thredds/current/
> > > > > > > > > > netcdf-java/javadoc/ucar/nc2/NetcdfFile.html>
> > > > > > > > > > > class
> > > > > > > > > > > does not implement Serializable, I need to implement that
> > > step
> > > > > > > > myself.
> > > > > > > > > > >
> > > > > > > > > > > Since NetCDF is a machine independent data format, I would
> > > like
> > > > > > to
> > > > > > > > access
> > > > > > > > > > > the raw binary data.
> > > > > > > > > > >
> > > > > > > > > > > This is trivial if the data kas been written to a file on
> > > the
> > > > > > disk.
> > > > > > > > But,
> > > > > > > > > > > what about in memory datasets ? If possible, I would like
> > > to
> > > > > > access
> > > > > > > > to
> > > > > > > > > > > binary data without writing it to disk...
> > > > > > > > > > >
> > > > > > > > > > > Can I access the buffer of an in-memory NetcdfFile
> > > > > > > > > > > <https://www.unidata.ucar.edu/software/thredds/current/
> > > > > > > > > > netcdf-java/javadoc/ucar/nc2/NetcdfFile.html>
> > > > > > > > > > > object
> > > > > > > > > > > from the Java API ? Any pointers will be appreciated.
> > > > > > > > > > >
> > > > > > > > > > > Kind regards,
> > > > > > > > > > >
> > > > > > > > > > > Michaël
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > =Dennis Heimbigner
> > > > > > > > > >   Unidata
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > Ticket Details
> > > > > > > > > > ===================
> > > > > > > > > > Ticket ID: MQO-415619
> > > > > > > > > > Department: Support netCDF Java
> > > > > > > > > > Priority: Normal
> > > > > > > > > > Status: Open
> > > > > > > > > > ===================
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> > > > > > > > > > this way, you must let us know in each email you send to us 
> > > > > > > > > > .
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> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > > =Dennis Heimbigner
> > > > > > > >   Unidata
> > > > > > > >
> > > > > > > >
> > > > > > > > Ticket Details
> > > > > > > > ===================
> > > > > > > > Ticket ID: MQO-415619
> > > > > > > > Department: Support netCDF Java
> > > > > > > > Priority: Normal
> > > > > > > > Status: Open
> > > > > > > > ===================
> > > > > > > > NOTE: All email exchanges with Unidata User Support are recorded
> > > in the
> > > > > > > > Unidata inquiry tracking system and then made publicly available
> > > > > > through
> > > > > > > > the web.  If you do not want to have your interactions made
> > > available
> > > > > > in
> > > > > > > > this way, you must let us know in each email you send to us.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > =Dennis Heimbigner
> > > > > >   Unidata
> > > > > >
> > > > > >
> > > > > > Ticket Details
> > > > > > ===================
> > > > > > Ticket ID: MQO-415619
> > > > > > Department: Support netCDF Java
> > > > > > Priority: Normal
> > > > > > Status: Open
> > > > > > ===================
> > > > > > NOTE: All email exchanges with Unidata User Support are recorded in
> > > the
> > > > > > Unidata inquiry tracking system and then made publicly available
> > > through
> > > > > > the web.  If you do not want to have your interactions made
> > > available in
> > > > > > this way, you must let us know in each email you send to us.
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > > > =Dennis Heimbigner
> > > > Unidata
> > > >
> > >
> > > =Dennis Heimbigner
> > >   Unidata
> > >
> > >
> > > Ticket Details
> > > ===================
> > > Ticket ID: MQO-415619
> > > Department: Support netCDF Java
> > > Priority: Normal
> > > Status: Open
> > > ===================
> > > NOTE: All email exchanges with Unidata User Support are recorded in the
> > > Unidata inquiry tracking system and then made publicly available through
> > > the web.  If you do not want to have your interactions made available in
> > > this way, you must let us know in each email you send to us.
> > >
> > >
> > >
> >
> >
> 
> =Dennis Heimbigner
> Unidata
> 

=Dennis Heimbigner
  Unidata


Ticket Details
===================
Ticket ID: MQO-415619
Department: Support netCDF Java
Priority: Normal
Status: Open
===================
NOTE: All email exchanges with Unidata User Support are recorded in the Unidata 
inquiry tracking system and then made publicly available through the web.  If 
you do not want to have your interactions made available in this way, you must 
let us know in each email you send to us.