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

Yuan Li bear0980 at gmail.com
Fri Jun 17 09:51:43 PDT 2016 

Hi Nathan,

Aha! "yt" executable did not exist! The installation went smoothly so I did
not even think about checking the log, but there were actually some error
messages related to Cython. I realized that a system python module was
automatically loaded upon login, so I unloaded it and reinstalled yt. It is
working now. Thank you!

Best,
Yuan

On Thu, Jun 16, 2016 at 4:49 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> 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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