[gpaw-users] Installation question. Lapack and scalapack.

Jens Jørgen Mortensen jjmo at dtu.dk
Thu Nov 23 08:12:05 CET 2017 

Den 22-11-2017 kl. 13:37 skrev Aleksei via gpaw-users:
> Hello Gaël,
>
>
> On 20.11.2017 16:25, Gaël Donval via gpaw-users wrote:
>> Hi Aleksei,
>>> Hello Gaël,
>>>
>>>      Thank you for your reply.
>>>
>>>>> /home/aleksei/anaconda3/compiler_compat/ld:
>>>>> /home/aleksei/Programs/scalapack/lib/../lib/liblapack.a(zlarf.o):
>>>>> relocation R_X86_64_32 against `.rodata' can not be used when
>>>>> making
>>>>> a
>>>>> shared object; recompile with -fPIC
>>>>> /home/aleksei/anaconda3/compiler_compat/ld: final link failed:
>>>>> Nonrepresentable section on output
>>>>> collect2: error: ld returned 1 exit status
>>>>> error: command 'gcc' failed with exit status 1
>>>>>
>>>>> Has anybody seen these errors and do you know solution around
>>>>> this?
>>>> Did you try to... recompile with -fPIC? :)
>>> :)
>>>
>>> I am so bad at this that I did not realize that I had to add -fPIC to
>>> extra_compile_args, right?
>> I don't know if that's required in that file (the installer could add
>> it itself).
>>
>> Anyway, you need to compile blas/lapack/scalapack with -fPIC, not only
>> GPAW... well, if you indeed need it (see comments below).
>>
>>> As you suggested before, I installed intel mkl library. Then I found
>>> in gpaw archive customize.py file and changed it a bit (see attached)
>>> with intel compiler and gpaw was installed without any errors. Also I
>>> use now intel distribution of python,  even just 'python
>>> gpaw_script.py' uses 4 cores and calculations are much more faster.
>>> But, for some reason it seems that scalapck is not used. At least
>>> gpaw -info shows it. Also, when I type 'gpaw-python $(which gpaw)
>>> info' I get this error:
>> I have a limited experience with Intel libs but to my knowledge, they
>> provide their own scalapack. If you go with Intel, it's far easier to
>> use their full stack. You most likely want to use and link to that
>> library instead of compiling your own.
>>
>> Two important comments:
>>
>>   * Scalapack is harmful (performance-wise) for small systems and is
>>     definitely unnecessary if you don't use "many" CPU cores. So you may
>>     want it but you might not actually need it.
>>   * Compiling and setting things up is, most of the time, not a very
>>     involved process and yet it requires quite a lot of knowledge and
>>     experience! In other words, setting things up yourself is insanely
>>     hard if you don't know precisely what you are doing. Don't worry,
>>     you won't blow up your computer if you make a mistake! :) But you
>>     will go through an endless stream of weird errors that won't make
>>     any sense to you. In your case, all the new errors you describe stem
>>     from a misconfiguration of your Python environment (so nothing to do
>>     with GPAW or scalapack anymore). You can try to solve it yourself if
>>     you want, but I won't help you with it.
>>
>
> Yes, the problem now is with a misconfiguration of my Python 
> environment. Interesting that I do not have any problems when I run 
> gpaw calculations (or any other calculations) using python 
> interpreter, but I can not use only gpaw-python.  In requirements it 
> says that I need to have python 2.7-3.5, but I use python 3.6.3. I was 
> wondering if it can be the reason.

Python 3.6.3 should be fine.

Jens Jørgen

> Anyway, I will try to figure out how I can use gpaw-python since I 
> need to run parallel calculations on my laptop.
>
>> So what should you do?
>>
>>   * If you are on your own computer, just activate your anaconda3
>>     environment and type `pip install -U gpaw` to install gpaw. Then use
>>     as it is: in that case scalapack is definitely unnecessary.
>
> Before I always did this way, but I could not get 'gpaw-python' (I had 
> mpi and other dependences installed with intel distribution) and I 
> could not run parallel calculations, so I decided to try to install it 
> myself.
>
> Thank you for clarifying the situation.
>
> Best wishes,
> Aleksei
>>   * If you are on a HPC cluster, ask your local HPC services for
>>     support: chances are high that almost everything required is already
>>     there and they'll know what to do.
>>   * Or learn yourself, step by step, what you are doing when
>>     "installing" GPAW and related packages so that you make everything
>>     work.
>>
>> Best regards,
>> Gaël
>>
>>
>>
>>
>>
>>> Could not find platform independent libraries <prefix>
>>> Could not find platform dependent libraries <exec_prefix>
>>> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
>>> Fatal Python error: Py_Initialize: Unable to get the locale encoding
>>> ModuleNotFoundError: No module named 'encodings'
>>>
>>> Current thread 0x00007f91d4861700 (most recent call first):
>>> Aborted (core dumped)
>>>
>>> Seems that I need to set PYHTONHOME like this
>>>
>>>       export PYTHONHOME="/home/aleksei/anaconda3/envs/idp:$PYTHONHOME"
>>>
>>> but while this error is fixed I obtain another:
>>>
>>> File "/home/aleksei/anaconda3/envs/idp/lib/python3.6/struct.py", line
>>> 13, in <module>
>>>       from _struct import *
>>> ModuleNotFoundError: No module named '_struct'
>>>
>>>
>>> So, I am trying to fix it but always obtain one or another error and
>>> can not run gpaw-python.
>>>
>>> Have you seen similar issues?
>>>
>>>
>>> Best wishes,
>>> Aleksei
>>>
>>>
>>>
>>>> Best regards,
>>>> Gaël
>>>>
>>>>
>>>>> Thanks for help and your time!
>>>>>
>>>>> Best wishes,
>>>>>
>>>>> Aleksei
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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