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new netCDF builds lack cdf5 support #9383

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JackPerdue opened this issue Nov 27, 2019 · 7 comments
Open

new netCDF builds lack cdf5 support #9383

JackPerdue opened this issue Nov 27, 2019 · 7 comments
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problem report
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4.x

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@JackPerdue
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We had a user lamenting the lack of cdf5 in the latest NCL with netCDF/4.6.1-intel-2018b. Apparently, changes from upstream at netCDF have disabled building cdf5 support by default. To build the latest, I made these changes

2a3
> versionsuffix = '-cdf5'
30,31c31,32
<     "-DBUILD_SHARED_LIBS=OFF ",
<     "-DBUILD_SHARED_LIBS=ON ",
---
>     "-DBUILD_SHARED_LIBS=OFF -DUSE_CDF5=ON ",
>     "-DBUILD_SHARED_LIBS=ON -DUSE_CDF5=ON ",

I'm just a sysop at this point and not much of a user. Is CDF5 something that EasyBuild should enable by default? (Our user seems happy with loading NCL and then loading netCDF-cdf5.)
@JackPerdue
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Note: while the build logs indicate CDF5 support enabled and the user seems happy, the 'nc-config --with-cdf5' command still returns 'no'. Not sure what's up with that.

@boegel boegel added this to the 4.x milestone Nov 28, 2019
@boegel
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boegel commented Nov 28, 2019

@JackPerdue Do you know why the netCDF folks have stopped enabling that by default?

Also, does -DUSE_CDF5=ON just enable additional capabilities, or does it change the functionality?
If it's the former, we can consider enabling it by default, but if it's the latter we'll need to be more careful...

@JackPerdue
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From random Googles I did to satisfy the researcher, I found things like this:

Unidata/netcdf-c#931

which seems to imply cdf5 was a default until netCDF 4.5 when a command line option was introduced which defaulted to "disable". In addition to the CMake option, there is a configure option. I'm not a CFD kinda person (as helpdesk/sysadm person). I just know that when I added that to the build, the user we had here that wanted NCL with cdf5 support was happy with the new version (they said it worked and I haven't heard otherwise from them [always a good thing])

@JackPerdue
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AFAIK, it only adds some 64-bit support in places and should still have the other stuff. But like I said, I'm not a netCDF user.

@JackPerdue
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[j-perdue@login2 (18:48) ~]$ grep -i cdf5 /sw/eb/sw/netCDF/*/easybuild/easybuild-netCDF-*.log  | grep -i cdf5 | grep -e yes -e no | grep Support:
/sw/eb/sw/netCDF/4.5.0-foss-2017b/easybuild/easybuild-netCDF-4.5.0-20180304.125037.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.5.0-foss-2017b/easybuild/easybuild-netCDF-4.5.0-20180304.125037.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.5.0-intel-2017b/easybuild/easybuild-netCDF-4.5.0-20190316.120947.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.5.0-intel-2017b/easybuild/easybuild-netCDF-4.5.0-20190316.120947.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.0-foss-2018a/easybuild/easybuild-netCDF-4.6.0-20181124.104607.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.0-foss-2018a/easybuild/easybuild-netCDF-4.6.0-20181124.104607.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.0-intel-2018a/easybuild/easybuild-netCDF-4.6.0-20181010.085206.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.0-intel-2018a/easybuild/easybuild-netCDF-4.6.0-20181010.085206.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-foss-2018b/easybuild/easybuild-netCDF-4.6.1-20181212.044241.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-foss-2018b/easybuild/easybuild-netCDF-4.6.1-20181212.044241.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-fosscuda-2018b/easybuild/easybuild-netCDF-4.6.1-20190925.220951.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-fosscuda-2018b/easybuild/easybuild-netCDF-4.6.1-20190925.220951.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-gompi-2017b/easybuild/easybuild-netCDF-4.6.1-20180509.180815.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-gompi-2017b/easybuild/easybuild-netCDF-4.6.1-20180509.180815.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-gompi-2017b-HDF5-1.8.19/easybuild/easybuild-netCDF-4.6.1-20190716.105625.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-gompi-2017b-HDF5-1.8.19/easybuild/easybuild-netCDF-4.6.1-20190716.105625.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-iimpi-2017b/easybuild/easybuild-netCDF-4.6.1-20180509.170950.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-iimpi-2017b/easybuild/easybuild-netCDF-4.6.1-20180509.170950.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-iimpi-2017b-HDF5-1.8.19/easybuild/easybuild-netCDF-4.6.1-20190716.133003.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-iimpi-2017b-HDF5-1.8.19/easybuild/easybuild-netCDF-4.6.1-20190716.133003.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-intel-2018b-cdf5/easybuild/easybuild-netCDF-4.6.1-20191126.123732.log:CDF5 Support:		yes
/sw/eb/sw/netCDF/4.6.1-intel-2018b-cdf5/easybuild/easybuild-netCDF-4.6.1-20191126.123732.log:CDF5 Support:		yes
/sw/eb/sw/netCDF/4.6.1-intel-2018b/easybuild/easybuild-netCDF-4.6.1-20181227.150001.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-intel-2018b/easybuild/easybuild-netCDF-4.6.1-20181227.150001.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-iomkl-2018b/easybuild/easybuild-netCDF-4.6.1-20191011.122322.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-iomkl-2018b/easybuild/easybuild-netCDF-4.6.1-20191011.122322.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-iompi-2017b/easybuild/easybuild-netCDF-4.6.1-20180509.173041.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-iompi-2017b/easybuild/easybuild-netCDF-4.6.1-20180509.173041.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-PGI-18.4-GCC-6.4.0-2.28/easybuild/easybuild-netCDF-4.6.1-20181109.104830.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-PGI-18.4-GCC-6.4.0-2.28/easybuild/easybuild-netCDF-4.6.1-20181109.104830.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-PGI-18.7-GCC-6.4.0-2.28/easybuild/easybuild-netCDF-4.6.1-20181110.083807.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.1-PGI-18.7-GCC-6.4.0-2.28/easybuild/easybuild-netCDF-4.6.1-20181110.083807.log:CDF5 Support:		no
/sw/eb/sw/netCDF/4.6.2-gompi-2019a/easybuild/easybuild-netCDF-4.6.2-20190309.175646.log:CDF5 Support:		yes
/sw/eb/sw/netCDF/4.6.2-gompi-2019a/easybuild/easybuild-netCDF-4.6.2-20190309.175646.log:CDF5 Support:		yes
/sw/eb/sw/netCDF/4.6.2-iimpi-2019a/easybuild/easybuild-netCDF-4.6.2-20190312.080145.log:CDF5 Support:		yes
/sw/eb/sw/netCDF/4.6.2-iimpi-2019a/easybuild/easybuild-netCDF-4.6.2-20190312.080145.log:CDF5 Support:		yes
/sw/eb/sw/netCDF/4.6.2-pompi-2019a/easybuild/easybuild-netCDF-4.6.2-20190719.154110.log:CDF5 Support:		yes
/sw/eb/sw/netCDF/4.7.1-gompi-2019b/easybuild/easybuild-netCDF-4.7.1-20191109.154056.log:CDF5 Support:		yes
/sw/eb/sw/netCDF/4.7.1-gompi-2019b/easybuild/easybuild-netCDF-4.7.1-20191109.154056.log:CDF5 Support:		yes

@akesandgren
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It adds the CDF-5 file format without changing anything else.
In 4.4.x there was no config/cmake option to enable it, it was always there.
from 4.6.2 it's been set to AUTO-ON unless SIZEOF_SIZE_T EQUAL 4

And CDF-5 is just 64bit enable file format.

So for 4.5 onwards we should probably enable it explicitly in the easyblock.

@JackPerdue
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"So for 4.5 onwards we should probably enable it explicitly in the easyblock."

Sounds good to me (with limited easyblock skills)

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