New installation, yt loading error
Hi, I recently tried to re-install yt on my home directory of a local cluster. I used the all in one script. After installation I added the yt path to the PATH environment variable. The installation looks ok, and the command "yt --help" works. However, when I try to load data, which worked with a previous installation, I get this error: Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:53:17) [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux Type "help", "copyright", "credits" or "license" for more information.
import yt
yt.load("disk_mhdhdf5_chk_0020")
python: /home/conda/feedstock_root/build_artifacts/libnetcdf_1535659474245/work/libsrc4/nc4var.c:431: nc4_vararray_add: Assertion `var->varid == grp->vars.nelems' failed. Aborted (core dumped) Does anyone know what this means? I must have missed something in the setup. I haven't used conda before. Thanks! Paco
Hi, This is an issue with conda-forge’s netcdf4 library. If you don’t actually need netcdf4 you can just uninstall the library and this issue will go away. I’m a little concerned this is happening with a fresh yt installation, since I thought conda-forge had updated their netcdf4 package to turn off these debug checks. If you could share the dataset that triggers this I might be able to reproduce this and report it to conda-forge so the package can be fixed. Nathan On Wed, Sep 19, 2018 at 9:16 PM Paco Holguin <opaco450@gmail.com> wrote:
Hi,
I recently tried to re-install yt on my home directory of a local cluster. I used the all in one script. After installation I added the yt path to the PATH environment variable.
The installation looks ok, and the command "yt --help" works. However, when I try to load data, which worked with a previous installation, I get this error:
Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:53:17)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
import yt
yt.load("disk_mhdhdf5_chk_0020")
python: /home/conda/feedstock_root/build_artifacts/libnetcdf_1535659474245/work/libsrc4/nc4var.c:431: nc4_vararray_add: Assertion `var->varid == grp->vars.nelems' failed.
Aborted (core dumped)
Does anyone know what this means? I must have missed something in the setup. I haven't used conda before.
Thanks!
Paco
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Hi Nathan, Removing netcdf4 fixed the issue. Thanks for the help! I'll see if I can get a link to the dataset to you. -Paco On Wed, Sep 19, 2018 at 11:03 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi,
This is an issue with conda-forge’s netcdf4 library. If you don’t actually need netcdf4 you can just uninstall the library and this issue will go away.
I’m a little concerned this is happening with a fresh yt installation, since I thought conda-forge had updated their netcdf4 package to turn off these debug checks. If you could share the dataset that triggers this I might be able to reproduce this and report it to conda-forge so the package can be fixed.
Nathan
On Wed, Sep 19, 2018 at 9:16 PM Paco Holguin <opaco450@gmail.com> wrote:
Hi,
I recently tried to re-install yt on my home directory of a local cluster. I used the all in one script. After installation I added the yt path to the PATH environment variable.
The installation looks ok, and the command "yt --help" works. However, when I try to load data, which worked with a previous installation, I get this error:
Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:53:17)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
import yt
yt.load("disk_mhdhdf5_chk_0020")
python: /home/conda/feedstock_root/build_artifacts/libnetcdf_ 1535659474245/work/libsrc4/nc4var.c:431: nc4_vararray_add: Assertion `var->varid == grp->vars.nelems' failed.
Aborted (core dumped)
Does anyone know what this means? I must have missed something in the setup. I haven't used conda before.
Thanks!
Paco
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
This should be fixed now. Thank you for the report! If you're curious about what happened, see: https://github.com/conda-forge/netcdf4-feedstock/issues/61 On Wed, Sep 19, 2018 at 11:58 PM, Paco Holguin <opaco450@gmail.com> wrote:
Hi Nathan,
Removing netcdf4 fixed the issue. Thanks for the help!
I'll see if I can get a link to the dataset to you.
-Paco
On Wed, Sep 19, 2018 at 11:03 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi,
This is an issue with conda-forge’s netcdf4 library. If you don’t actually need netcdf4 you can just uninstall the library and this issue will go away.
I’m a little concerned this is happening with a fresh yt installation, since I thought conda-forge had updated their netcdf4 package to turn off these debug checks. If you could share the dataset that triggers this I might be able to reproduce this and report it to conda-forge so the package can be fixed.
Nathan
On Wed, Sep 19, 2018 at 9:16 PM Paco Holguin <opaco450@gmail.com> wrote:
Hi,
I recently tried to re-install yt on my home directory of a local cluster. I used the all in one script. After installation I added the yt path to the PATH environment variable.
The installation looks ok, and the command "yt --help" works. However, when I try to load data, which worked with a previous installation, I get this error:
Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:53:17)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
import yt
yt.load("disk_mhdhdf5_chk_0020")
python: /home/conda/feedstock_root/build_artifacts/libnetcdf_1535659 474245/work/libsrc4/nc4var.c:431: nc4_vararray_add: Assertion `var->varid == grp->vars.nelems' failed.
Aborted (core dumped)
Does anyone know what this means? I must have missed something in the setup. I haven't used conda before.
Thanks!
Paco
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
participants (2)
-
Nathan Goldbaum -
Paco Holguin