Re: [Anuga-user] Problem with runtests.py / _intel_fast_memset issue

[Stephen R. <ste...@an...>]

Hi Christos,


It would be interesting to see the output of


python setup.py clean

python setup.py build 2>&1 | tee build.log


The content of build.log might give us a hint as to where the intel command is coming from.


I suppose you have talked to your system admin people?


Some interesting discussions


https://mail.python.org/pipermail//scikit-image/2015-October/004333.html


https://groups.google.com/forum/#!topic/scikit-image/iSgNGBG0ZqU



and


https://christoph-conrads.name/building-numpy-and-scipy-with-intel-compilers-and-intel-mkl/


It has been a while but we have compiled anuga using the intel compilers, so this third link might be an option.



Cheers

Steve


==============================
Stephen Roberts
Undergraduate Convenor
Mathematical Sciences Institute
Room 4.74 Hanna Neumann Building #145
The Australian National University
Canberra, ACT 2600 AUSTRALIA
Ph: +61 2 61254445
CRICOS: 00120C

________________________________
From: Christos Altantzis <alt...@gm...>
Sent: Friday, 2 August 2019 8:48:48 PM
To: Anu...@li... <Anu...@li...>
Subject: [Anuga-user] Problem with runtests.py / _intel_fast_memset issue

Hi Group,

I have been using anuga for more than a year now and I have to admit that the developers have done an excellent job. I really thank you for this. Until now I have been working on local machines and I never had a problem.

Currently, I am trying ti install ANUGA on a cluster where I do not have superuser rights, so I am trying to install the code from source. I have managed to install all the dependencies and all of them seem to be working properly. Build_all.py works without problems and the installation seems to be fine. Then when I am trying to import anuga or run the runtests.py I get the following error:

Building, see build.log...
Build OK
Traceback (most recent call last):
  File "runtests.py", line 402, in <module>
    main(argv=sys.argv[1:])
  File "runtests.py", line 201, in main
    __import__(PROJECT_MODULE)
  File "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/__init__.py", line 69, in <module>
    from anuga.shallow_water.shallow_water_domain import Domain
  File "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py", line 100, in <module>
    from anuga.abstract_2d_finite_volumes.generic_domain \
  File "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/abstract_2d_finite_volumes/generic_domain.py", line 22, in <module>
    from quantity import Quantity
  File "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py", line 30, in <module>
    from anuga.fit_interpolate.fit import fit_to_mesh
  File "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/fit_interpolate/fit.py", line 33, in <module>
    from anuga.fit_interpolate.general_fit_interpolate import FitInterpolate
  File "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/fit_interpolate/general_fit_interpolate.py", line 26, in <module>
    from anuga.utilities.sparse import Sparse, Sparse_CSR
  File "/cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/utilities/sparse.py", line 335, in <module>
    from sparse_ext import csr_mv
ImportError: /cluster/home/caltantz/Simulations/ANUGA/anuga_core/build/testenv/lib64/python2.7/site-packages/anuga/utilities/sparse_ext.so: undefined symbol: _intel_fast_memset

The problem is this _intel_fast_memset. I made sure that I do not load any icc in my bashrc and that only gcc is used, and still I see this problem. Is it possible that this happens due to the fact that some of the dependencies might have been built with icc?? Have you encountered such an issue in the past?? I am struggling to resolve this issue but I am out of ideas.

If anything else fails I will try to install locally conda and do everything through conda, but if somebody has some experience with a similar problem I would appreciate sharing his/her experience.

Best
Christos