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JiaweiZhuang / cloud-gchp-paper

Code to reproduce GCHP-on-cloud paper
MIT License
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Installing NetCDF with Spack failing #5

Closed rsignell-usgs closed 4 years ago

rsignell-usgs commented 4 years ago

The netcdf installation command: 

 spack -v install netcdf-fortran %intel ^netcdf~mpi ^hdf5~mpi+fortran+hl

is returning

==> No binary for netcdf found: installing from source
==> Fetching https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-c-4.7.0.tar.gz

curl: (22) The requested URL returned error: 404 Not Found

@JiaweiZhuang , this should get resolved when https://github.com/spack/spack/pull/15641 is accepted, right?

Is there a workaround?

rsignell-usgs commented 4 years ago

@JiaweiZhuang I'm still having an issue installing netcdf, and while I'm happy to raise an issue on Spack, I wanted to check here first to make sure it's not just a dumb user error.

When I do:

spack install netcdf-fortran@4.5.2 netcdf@4.7.4

I get a failure:

curl: (22) The requested URL returned error: 404 Not Found
==> Fetching from https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-c-4.7.0.tar.gz failed.

indeed, if I look at https://www.gfd-dennou.org/arch/netcdf/unidata-mirror, there is no netcdf-c-4.7.0.tar.gz, but there is a netcdf-c-4.7.4.tar.gz, which is what I asked for.

Is this a Spack bug, user error, or something else?

Thanks!

[centos@ip-10-0-0-80 ~]$ spack install netcdf-fortran@4.5.2 netcdf@4.7.4 ==> libsigsegv is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libsigsegv-2.11-qpmaxx6z62df4s4hwyehdwptv6kmrfhf ==> m4 is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/m4-1.4.18-cdmdgcjw5owv2olhgygcbhirab4ti4ae ==> pkgconf is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/pkgconf-1.6.1-zyia6fm5vvznsxxla43wto6vezv3jciz ==> ncurses is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/ncurses-6.1-rqw3cmcwvd76h4rjgtaxpvrqg47prwkg ==> readline is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/readline-7.0-b4z2xcjalfc4z7tgktx7txhe2my3wlfd ==> gdbm is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gdbm-1.18.1-dv2qksj2dheh7hzmu7iftqhxlkqrinwt ==> perl is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.26.2-7tmxubxk4qnty7decxqsz5yu5v3p3lqq ==> autoconf is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/autoconf-2.69-dzuvqtysoqchxxlnfcfdvflwlvnwl542 ==> automake is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/automake-1.16.1-33xp7xdltlskzu4kkd3mqv7gaiqt4hbj ==> libtool is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libtool-2.4.6-bcbiddkmbu4gy7wx6ftntmxqe3c5br3z ==> util-macros is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/util-macros-1.19.1-p66qdrtaslf2cq4wyc6mitrxzhnyujhc ==> libpciaccess is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libpciaccess-0.13.5-5chyfxo6gpmcf74gpv3sqni2aa6v5x57 ==> libiconv is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libiconv-1.15-bli6oh4rawy6bwdqa7ylbp7wt5tkynyv ==> xz is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/xz-5.2.4-agv5zlv7phi4ye3evlpv3t4ypgve4bpe ==> zlib is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/zlib-1.2.11-64vg6e4evdrlqgx7iicwhu2hs7lv6gpz ==> libxml2 is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libxml2-2.9.9-7mziu5hpmcz6mzurl4tnfvr3edkcacjl ==> numactl is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/numactl-2.0.12-i43do2bjh7xwr7akweicmxacdnfkhihd ==> hwloc is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/hwloc-1.11.11-nitrbjdrggydfh37c4na2airsjajvlm7 ==> openmpi is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openmpi-3.1.4-2e57mrcnrgpww35cgci4ema7xu5mnph6 ==> hdf5 is already installed in /home/centos/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/hdf5-1.10.5-jupy7sbj7jptxkixx42jwgxfmxp34wdk ==> Installing netcdf ==> Searching for binary cache of netcdf ==> Warning: No Spack mirrors are currently configured ==> No binary for netcdf found: installing from source ==> Fetching https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-c-4.7.0.tar.gz curl: (22) The requested URL returned error: 404 Not Found ==> Fetching from https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-c-4.7.0.tar.gz failed. ==> Error: FetchError: All fetchers failed for netcdf-4.7.0-a34weikstzx2seizzpffse6uhspgn4sc /home/centos/spack/lib/spack/spack/package.py:1061, in do_fetch: 1058 raise FetchError("Will not fetch %s" % 1059 self.spec.format('{name}{@version}'), ck_msg) 1060 >> 1061 self.stage.create() 1062 self.stage.fetch(mirror_only) 1063 self._fetch_time = time.time() - start_time 1064
rsignell-usgs commented 4 years ago

I didn't do anything, and I don't see any recently closed spack PRs that would have made any difference, but I just tried

spack install netcdf-fortran@4.5.2 netcdf@4.7.4

and now it's working. Doesn't make me feel too confident about Spack, but off we go! 😕

rsignell-usgs commented 4 years ago

And the instructed installation of non-MPI NetCDF (which is what we actually want for building the Coupled Ocean Atmosphere Wave and Sediment Transport (COAWST) model) worked also:

spack -v install netcdf-fortran %intel ^netcdf~mpi ^hdf5~mpi+fortran+hl