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

Thu Jun 16 13:49:08 PDT 2016

Does yt's bin directory show up in your PATH environment variable? If so,
does a "yt" executable exist in that directory? If not, how are you setting
your PATH? Does it work if you prepend yt's bin directory to your PATH
manually in your current ssh session?

On Thu, Jun 16, 2016 at 3:43 PM, Yuan Li <bear0980 at gmail.com> wrote:

> Yes I did that but it did not seem to do anything.
>
> Maybe I should email Smic people for help?
>
> Yuan
>
> On Thu, Jun 16, 2016 at 4:39 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> On Thu, Jun 16, 2016 at 3:34 PM, Yuan Li <bear0980 at gmail.com> wrote:
>>
>>> 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...
>>>
>>
>> With the new install script, the activate script is unnecessary. Simply
>> prepend the location of the yt installation's bin directory to your PATH.
>> The install script should print out explicit code that you can copy/paste
>> into your .bashrc when the script finishes.
>>
>>
>>>
>>>
>>> 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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