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

[Yuan Li]

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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