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

[Gaël Donval]

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.


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.
 * 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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