[yt-users] Installing yt on Xsede Smic and Comet

[Yuan Li]

Hi Nathan,

Thank you for the quick response!

On Smic: Where is this "clean.sh" file? In the old yt3, it is under
yt-x86_64/src/yt-hg, but I cannot find it in the new "/yt-conda/".

On Comet, after reinstalling yt following your instructions, I am able to
update yt now. However, when I submit a job, I get this error at "import
yt":
...
  File "/home/yuan/source/yt-conda/src/yt-hg/yt/__init__.py", line 78, in
<module>
    import numpy as np # For modern purposes
...
from . import multiarray
AttributeError: PyCapsule_Import "datetime.datetime_CAPI" is not valid


Any suggestions on how to fix this?

Yuan

On Wed, Jun 15, 2016 at 2:50 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> On Wed, Jun 15, 2016 at 1:42 PM, Yuan Li <yuan at astro.columbia.edu> wrote:
>
>> Hi all,
>>
>> I am having trouble installing/running the latest yt on Xsede Smic and
>> Comet clusters. I used to have yt3 on both machines and they were working
>> fine. Recently, after failing to update yt, I decided to delete the old one
>> and install the latest version. I am using the unmodified file from
>> http://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh
>>
>>
>> Here are the problems I have:
>> *On Smic*
>> When I do "yt update" on the login node, or when I try to submit a yt
>> job, I get this error message
>> ...
>> ValueError: numpy.dtype has the wrong size, try recompiling
>>
>> I have seen this error message before and fixed it somehow, but I do not
>> remember how...
>>
>
> Navigate to the checkout of the yt mercurial repository and do:
>
> $ ./clean.sh
> $ python setup.py develop
>
>
>>
>>
>> *On Comet*
>> When I do "yt update", I get this error message:
>> ...
>> YT site-packages not in path, so you must
>> update this installation manually by committing and
>> merging your modifications to the code before
>> updating to the newest changeset.
>>
>> I manually set YT_DEST in my bash_profile, but that does not seem to
>> help. I can however submit a yt job and it will run fine, but not in
>> parallel. Before I reinstalled yt, I was able to run yt3 in parallel on
>> Comet after loading mpi4py.
>>
>> Also, when I do
>> "source ~/source/yt-conda/bin/activate" I get this error message:
>> Error: no environment provided.
>> and it seems that I do not even need to activate yt anymore (is it
>> because I have "export PATH=/home/yuanli/source/yt-conda/bin:$PATH" in my
>> bash_profile?). Maybe I missed something in the doc. I am very confused.
>>
>
> It looks like you ran the install script with INST_YT_SOURCE=0 (the
> default). Try again with INST_YT_SOURCE=1. You will also likely need to do
> "pip install mpi4py" to get an mpi4py installation linked against comet's
> MPI libraries.
>
>
>>
>> Thanks in advance!
>> Yuan
>>
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>>
>
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