James, > I am advised that you should be able to get the following via > anonymous ftp: > > > ftp://ftp.exa.com/outgoing/netcdf/ > <ftp://ftp.exa.com/outgoing/netcdf/Fluid_Meas.fnc> Fluid_Meas.fnc > > ftp://ftp.exa.com/outgoing/netcdf/ > <ftp://ftp.exa.com/outgoing/netcdf/Fluid_Meas.fnc-nccopy-k3> > Fluid_Meas.fnc-nccopy-k3 > > ftp://ftp.exa.com/outgoing/netcdf/ > <ftp://ftp.exa.com/outgoing/netcdf/Fluid_Meas.snc> Fluid_Meas.snc > > ftp://ftp.exa.com/outgoing/netcdf/ > <ftp://ftp.exa.com/outgoing/netcdf/Fluid_Meas.snc-nccopy-k3> > Fluid_Meas.snc-nccopy-k3 Thanks, I see what you mean! We'll have to investigate why the netCDF-4 copies of these netCDF classic format files are so much larger than expected (e.g. 42 MB classic file but 96 MB netCDF-4 file, and ncdump shows not a lot of metadata). I don't currently have an explanation, but it could be a bug. --Russ > >> Thanks for the reply. If the difference were metadata, wouldn't we > >> expect to see the greatest difference between the netcdf-3 firnat > >> and HDF with smaller data files? In fact, we're finding the > >> opposite. > > > > Yes, if you only have a moderate amount of metadata and lots of data, > > HDF5 files would be much larger with a small amount of data but similar > > in size with a large amount of data. > > > > If, however, you had lots of metadata (for example 5000 variables and > > 5000 dimensions), then the HDF5 files might appear significantly larger > > even with lots of data. > > > >> We would like to share some larger data files with you guys in > >> order to better understand the situation. Would you be willing to > >> pick some data up from our ftp site? > > > > Yes, that would be useful. > > > > --Russ > > > >> > Hi James, > >> > > >> >> We recently began working on a transition from netcdf 3.6.2 to 4.1.1. > >> >> > >> >> The process was trouble free and things seem to be working, but we > >> have > >> >> been surprised to find the HDF variant producing extremely large > >> files > >> >> relative to the old netcdf native form. Our measurement files are > >> >> already > >> >> enormous, and further growth would be deadly. > >> >> > >> >> Has anyone else encountered this? > >> > > >> > There is a larger fixed-size overhead for metadata (names and > >> > properties of variables, dimensions, and attributes) in the HDF5-based > >> > netCDF-4 format, but in our experience, it's not significant for files > >> > with lots of data and only a moderate amount of metadata. And use of > >> > compression can make equivalent netCDF-4 files significantly smaller > >> > than netCDF-3 classic format files. > >> > > >> > As an example we use in our netCDF training workshop, a small netCDF > >> > classic format file with only one dimension of size 2 and one variable > >> > that uses that dimension is very small using netCDF classic or 64-bit > >> > offset formats: > >> > > >> > 88 test.nc1 # classic format > >> > 92 test.nc2 # 64-bit -offset format > >> > 5072 test.nc3 # netCDF-4 format > >> > 5108 test.nc4 # netCDF-4 -classic model format > >> > > >> > However, if you change the dimension size to 10000, the sizes are much > >> > closer: > >> > > >> > 40080 test.nc1 # classic format > >> > 40084 test.nc2 # 64-bit -offset format > >> > 45064 test.nc3 # netCDF-4 format > >> > 45101 test.nc4 # netCDF-4 -classic model format > >> > > >> > And if you apply level-1 compression to the variable in the netCDF-4 > >> > format, the netCDF-4 file is significantly smaller for this > >> > (artificial) data: > >> > > >> > 40080 test.nc1 # classic format > >> > 40084 test.nc2 # 64-bit -offset format > >> > 21055 test.nc3 # netCDF-4 format > >> > 21092 test.nc4 # netCDF-4 -classic model format > >> > > >> > Finally, if you apply the shuffle filter along with compression for > >> > this test file, the result is significantly better compression: > >> > > >> > 40080 test.nc1 # classic format > >> > 40084 test.nc2 # 64-bit -offset format > >> > 7777 test.nc3 # netCDF-4 format > >> > 7814 test.nc4 # netCDF-4 -classic model format > >> > > >> > It's easy to run little experiments like this with the "nccopy" > >> > utility in the latest netCDF snapshot release (soon to be in version > >> > 4.1.2), as you can specify conversions and compression on the command > >> > line: > >> > > >> > > >> > http://www.unidata.ucar.edu/netcdf/workshops/2010/utilities/NccopyExamples.html > >> > > >> > This is a very articficial example and it's unlikely you'll get > >> > results as good with your real data, but experimenting with nccopy's > >> > compression options on some real data could determine what you can > >> > expect in using netCDF 4 for your data. > >> > > >> > --Russ > >> > > >> > Russ Rew UCAR Unidata Program > >> > address@hidden http://www.unidata.ucar.edu > >> > > >> > > >> > > >> > Ticket Details > >> > =================== > >> > Ticket ID: AIQ-275071 > >> > Department: Support netCDF > >> > Priority: Normal > >> > Status: Closed > >> > > >> > >> > >> > > > > Russ Rew UCAR Unidata Program > > address@hidden http://www.unidata.ucar.edu > > > > > > > > Ticket Details > > =================== > > Ticket ID: AIQ-275071 > > Department: Support netCDF > > Priority: Normal > > Status: Closed > > > > > Russ Rew UCAR Unidata Program address@hidden http://www.unidata.ucar.edu Ticket Details =================== Ticket ID: AIQ-275071 Department: Support netCDF Priority: Normal Status: Closed
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