[yt-dev] conda and external libraries

j s oishi jsoishi at gmail.com
Tue Oct 22 08:40:56 PDT 2013


daikaiju:/data/../96_Ra10000 [10:39]$ python 2d_gmode_kx1_kz1.py


Traceback (most recent call last):
  File "2d_gmode_kx1_kz1.py", line 26, in <module>
    from dedalus.mods import *
  File "/home/jsoishi/hg-projects/dedalus/dedalus/mods.py", line 30, in
<module>
    from dedalus.utils.logger import mylog
  File "/home/jsoishi/hg-projects/dedalus/dedalus/utils/logger.py", line
30, in <module>
    from dedalus.utils.parallelism import com_sys
  File "/home/jsoishi/hg-projects/dedalus/dedalus/utils/parallelism.py",
line 52, in <module>
    com_sys = CommunicationSystem()
  File "/home/jsoishi/hg-projects/dedalus/dedalus/utils/parallelism.py",
line 43, in __init__
    from dedalus.utils.fftw import fftw
ImportError: /home/jsoishi/build/yt-conda/bin/../lib/libm.so.6: version
`GLIBC_2.15' not found (required by /home/jsoishi/build/lib/libfftw3.so.3)



On Tue, Oct 22, 2013 at 11:39 AM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:

> Hi Jeff,
>
> Can you paste the error messages you're seeing?
>
> Nathan
>
>
> On Tuesday, October 22, 2013, j s oishi wrote:
>
>> Hi all,
>>
>> So I've been playing with the new conda installed yt. In principle, I
>> really like the idea: a simple, completely isolated python distribution
>> that does dependency management. However, I'm running into some problems
>> that are potentially big problems for yt down the road. My issue is that
>> I'm trying to install Dedalus into the yt-provided conda install. However,
>> to do that, I need to interface with external libraries--ones that I do
>> *not* want to have built as conda packages. The two that come up first are
>> MPI and FFTW. Since the Dedalus FFTW bindings are actually used in yt for
>> its FFT analysis, this is relevant for yt too.
>>
>> On a supercomputing center, one would very much want to use their MPI and
>> FFT libraries, rather than some binary blob from conda, I think we need to
>> figure out how to do this. The problem I'm getting specifically is that if
>> I build FFTW (for example) myself, I want to link against the system libm.
>> But conda provides its OWN libm, which, it turns out is not GLIBC
>> compatible with what FFTW was built against. I believe this is because libm
>> from conda was not built against the same glibc as my libm, which FFTW was
>> built against. I don't know how to solve this problem, since I don't really
>> understand dynamic libraries, nor conda. Does anyone have any ideas about
>> this? Is this something I should take up with the conda list?
>>
>> My apologies if this is unclear. I am not fully sure I understand what is
>> happening myself.
>>
>> thanks,
>>
>> j
>>
>
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