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

[Yuan Li]

Hi Nathan,

On Comet:
I set PYTHONPATH in bash_profile, but maybe that was not enough. Now in my
script, I do "mpirun -np 96 /home/yuan/source/yt-conda/bin/python **.py",
and it seems to be working. Yay!


On Smic:
I reinstalled yt with INST_YT_SOURCE=1. I set PATH & YT_DEST in my
bash_profile. However, the system does not recognize yt.
 -bash: yt: command not found
even after I do "source ~/source/yt-conda/bin/activate". I thought I set up
everything just the same as Comet...


Yuan

On Wed, Jun 15, 2016 at 4:50 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> 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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