Bug 1886639 - Parallel support for NetCDF
Summary: Parallel support for NetCDF
Keywords:
Status: CLOSED NOTABUG
Alias: None
Product: Fedora EPEL
Classification: Fedora
Component: netcdf
Version: epel7
Hardware: All
OS: Linux
unspecified
medium
Target Milestone: ---
Assignee: Orion Poplawski
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2020-10-09 01:51 UTC by jeff.kopera
Modified: 2021-01-26 03:42 UTC (History)
5 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2021-01-26 03:42:27 UTC
Type: Enhancement


Attachments (Terms of Use)

Description jeff.kopera 2020-10-09 01:51:35 UTC
Would it be possible to adjust how this package is built to support the parallel I/O features of NetCDF?

Comment 1 Orion Poplawski 2020-10-09 02:23:48 UTC
What features exactly?

Comment 2 jeff.kopera 2020-10-09 02:31:33 UTC
Parallel access to netCDF-4/HDF5 files (https://www.unidata.ucar.edu/software/netcdf/docs/parallel_io.html)

I suspect there may be an issue with the hdf5 package it's built against that may prevent this, but these are the instructions from Unidata on how to build with parallel I/O support: https://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html#build_parallel

Comment 3 Orion Poplawski 2020-10-09 02:41:06 UTC
So, on the pnetcdf side the first step is that someone (probably me :() would need to package pnetcdf for Fedora.  Next concern is whether or not we would need to provide two versions - one with pnetcdf support and one without.

We do already build parallel hdf5 versions (mpich and openmpi) so that should be covered when we get to it.

Comment 4 jeff.kopera 2020-10-09 02:51:21 UTC
There may be desire it from others, but I don't think I have any need for pnetcdf support

Comment 5 Orion Poplawski 2020-10-09 03:02:59 UTC
So do the netcdf-openmpi or netcdf-mpich packages not do what you want already?

It appears that --enable-pnetcdf in the netcdf configure turns on both the pnetcdf and parallel HDF5 io support and appear to not be able to be independent.

Comment 6 jeff.kopera 2020-10-09 03:12:50 UTC
It appears I overlooked their existence. I'll look into it and get back to you on that.

I don't think --enable-pnetcdf is necessary to turn on parallel HDF5 support. I played around a little with this and was able to build hdf5 and netcdf from source, resulting in netcdf having parallel I/O support. Pretty much following the Building with Parallel I/O Support section from https://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html#build_parallel, stopping before the Building PnetCDF from source section.

Comment 7 jeff.kopera 2020-10-09 03:44:39 UTC
It does look like either netcdf-openmpi or netcdf-mpich can meet my needs. Thanks very much for making me aware of them


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