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

[Nathan Goldbaum]

On Wed, Jun 15, 2016 at 3:41 PM, Yuan Li <bear0980 at gmail.com> wrote:

> 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/".
>

Ah, so it looks like you used INST_YT_SOURCE=0 here as well. By default it
uses a binary conda package, so no yt-hg folder.


>
> 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
>
>
Are you sure you're using yt's python and numpy here? It looks like you're
importing yt's numpy using an incompatible python interpreter (e.g. the
comet system python).


>
> 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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