About installing Escript in Ubuntu 16.04

Hi Zheng,

I have had some trouble reproducing this bug in Ubuntu Xenial, but I believe that you may be able to fix your issue by changing line 756 of site_scons/dependencies.py to read:

if p.returncode == 0 and 'libmpi' in gmshlibs.decode('utf-8'):

I have made changes to esys-escript so that this issue should not arise in the next release (5.7).

Best regards,

Adam

Hi Adam,

Thanks very much for your response. This modification indeed solved this problem. May I ask another question in this post?

After installation, I got the following messages as below:

customer@node01:~/Downloads/python-escript_5.5$ scons -j1 options_file=scons/xenial_py3_options.py
scons: Reading SConscript files ...
3.5.2 (default, Oct 7 2020, 17:19:02)
[GCC 5.4.0 20160609]
Using options in scons/xenial_py3_options.py.
/bin/sh: svnversion: command not found
Using svn revision information from file. Got revision = 6948
Checking whether the C++ compiler works... (cached) yes
Checking for C++ function gethostname()... (cached) yes
Checking for C++ header file byteswap.h... (cached) yes
Checking for C++ function SCbswap32()... (cached) yes
Checking for C++ header file sys/endian.h... (cached) no
Checking for C++ header file libkern/OSByteOrder.h... (cached) no
Checking for working complex std::acos()... (cached) yes
Checking for C++ header file Python.h... (cached) yes
Checking for C++ function Py_Exit()... (cached) yes
Checking for C++ library boost_python-py35... (cached) yes
Checking for C++ header file numpy/ndarrayobject.h... (cached) yes
Checking for C++ library netcdf_c++... (cached) yes
Checking for C++ library umfpack... (cached) yes
Checking for C++ library boost_iostreams... (cached) no
Chmod("utest.sh", 0755)
Generated utest.sh.
Chmod("itest.sh", 0755)
Generated itest.sh.
Chmod("/home/customer/Downloads/python-escript_5.5/bin/run-escript", 0755)
Delete(["lib/pythonMPI", "lib/pythonMPIredirect"])
Delete("bin/escript-overlord")
scons: done reading SConscript files.
scons: Building targets ...
/home/customer/Downloads/python-escript_5.5/bin/run-escript /home/customer/Downloads/python-escript_5.5/build/scripts/release_sanity.py
scons: done building targets.

*** Config Summary (see config.log and <prefix>/lib/buildvars for details) ***
Escript revision 6948

  Install prefix: /home/customer/Downloads/python-escript_5.5
          Python: python3 (Version 3.5.2)
           boost: /usr (Version 1.58.0)
     boost numpy: NO
        trilinos: NO
           numpy: YES (with headers)
            gmsh: YES, MPI-ENABLED
  Solver library: paso
   Direct solver: YES (umfpack)
         domains: dudley, finley, ripley, speckley
          netcdf: YES (3)
           weipa: YES
          openmp: YES
            gdal: YES
          pyproj: YES
           scipy: YES
           sympy: YES
         umfpack: YES

  DISABLED features: cppunit debug gzip lapack mkl mpi parmetis silo trilinos visit
  Treating warnings as errors

SUCCESS: build complete

Here I found the 'boost numpy' is not installed. I am not sure whether there would be some problems for the later usage. So I ran one of my simulations by restarting a former stress and strain data from *.nc files (also generated using Escript coupled with Yade). However, I got the following error:

customer@node01:~/Yade/cases/SlopeFailure_try$ yade -n GIM_seepage.py
Welcome to Yade 20200613-3983~91b2a7a~xenial1
Using python version: 3.5.2 (default, Oct 7 2020, 17:19:02)
[GCC 5.4.0 20160609]
TCP python prompt on localhost:9024, auth cookie `scdeuy'
XMLRPC info provider on http://localhost:21024
/usr/lib/python3/dist-packages/IPython/utils/path.py:310: UserWarning: IPython dir '/home/customer/.ipython' is not a writable location, using a temp directory.
  " using a temp directory."%ipdir)
Running script GIM_seepage.py
Traceback (most recent call last):
  File "/usr/bin/yade", line 342, in runScript
    execfile(script,globals())
  File "/usr/lib/python3/dist-packages/past/builtins/misc.py", line 82, in execfile
    exec_(code, myglobals, mylocals)
  File "GIM_seepage.py", line 50, in <module>
    prob = MultiScale(restart=True,dir='./result_dry/checkpoint/',time=10,domain=mydomain,pore0=pore,perm=perm,kf=kf,dt=dt,ng=numg,np=nump,useMPI=mpi,rtol=1.e-2,verbose=True)
  File "/home/customer/Yade/cases/SlopeFailure_try/FEMxDEM/msFEMup.py", line 107, in __init__
    self.__stress=escript.load(dir+'stress_10.nc')
Boost.Python.ArgumentError: Python argument types in
    esys.escriptcore.escriptcpp.load(str)
did not match C++ signature:
    load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > fileName, escript::AbstractDomain domain)
[[ ^L clears screen, ^U kills line. F8 plot. ]]

What might be the possible reason for such error? I have recompiled Escript but got the same error. Could you please give me any clues?

Thanks and best regards,

Zheng

Thanks Adam Ellery, that solved my question.