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Fast forward solver for EIT
Set the .yaml
accordingly.
Hi there,
I am trying to prepare a call the PEITS solver from octave, where an input is the EIDORS fmdl structure (see fmdl_cyl.mat in the attached zip file) with cylinder equipped by circular electrodes. After executing my code (see call_peits.m in the attached zip file), I have received the following error:
octave:8> out = call_peits('JOB1'); Warning: Unable to read parameter file '../data/parameter' Error: ParameterNotFound [map:/home/jc/PEITS_root/PEITS/dune-fem-1.4.0/dune/fem/io/parameter.hh:734]: Parameter 'electrode.use_node_assignment' not found. Warning: Unable to read parameter file '../data/parameter' Error: ParameterNotFound [map:/home/jc/PEITS_root/PEITS/dune-fem-1.4.0/dune/fem/io/parameter.hh:734]: Parameter 'electrode.use_node_assignment' not found. ...
I would like to ask for advice. Are all parameters in the right place?
In a summary, I have the following files in the directory PEITS_root/PEITS/data/
standardparams
parameter
current_protocol_3Dcyl.txt
electrode_nodes_3Dcyl.txt
param_3Dcyl
3Dcyl.dgf
which are also part of the attached zip file: call_peits.zip
Thank you in advance for any advice.
module load openblas/0.2.14/intel-2015-update2
PEITS verison is old dune_peits version has specifying nodes, should update
Will the PEITS installation package be updated? There are always errors in the installation, and some packages have failed.
Kirill had something weird where the X, Y and Z coordinates of the mesh encopassed the origin, that a whole section of the result was all fucked up. Translating the coordinates of the mesh so they were all positive fixed this...
Installing on windows system for linux which doesnt have everything installed as normal ubuntu highlighted that some other packages were needed:
pkg-config
its still not compiling so there is something else too
when making zoltan
Makefile:1053: recipe for target 'install-exec-hook' failed
make[3]: *** [install-exec-hook] Error 255
make[3]: Leaving directory '/home/james/PEITS_root/Zoltan_v3.8/BUILD_DIR'
Makefile:916: recipe for target 'install-exec-am' failed
make[2]: *** [install-exec-am] Error 2
make[2]: Leaving directory '/home/james/PEITS_root/Zoltan_v3.8/BUILD_DIR'
Makefile:863: recipe for target 'install-am' failed
make[1]: *** [install-am] Error 2
make[1]: Leaving directory '/home/james/PEITS_root/Zoltan_v3.8/BUILD_DIR'
Makefile:534: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1
things missing from markus' dune peits wiki readme
Voltages are ~x10 higher than expected when using a sigma =2 for all elements. Setting it to 2.0001 works.
load_sigma_vector_binary gives expected values of 2, so likely inside the solver somewhere.
This was a day of my life you took away from me markus, and I want it back
the date part of the output filenames have : in them. Which windows is not happy with. Makes copying them around a pain
In particular, this means:
Since Dune has a full CMake
build process, I am trying to replace the Automake
, sh INSTALL
process with a coherent CMake
one for a dune-peits
module.
Develop a Dockerfile to set up the full environment including PETSc, Zoltan and dune on Ubuntu18 to get the latest LTR updates.
What needs to be included next:
dune_exporter.m currently has this bit of code:
fprintf(paramfile, ['electrode.nodes: ../data/electrode_nodes_TA052_meters']); % If electrodes should be defined by nodes, change this file
fprintf(paramfile, ['surface.coordinates: ../data/surface_coordinates_TA052_precise']);
But in most cases we aren't generating these files so it produces an error when PEITS is running.
Quick fix: remove these lines
dune-peits
using a simplistic algorithm
data
This is annoying
Fails when running sh INSTALL
with the following error
/usr/include/c++/7/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
#error This file requires compiler and library support \
Its probably related to the newer GCC, there are so many places where build and compiler flags are set that I am unsure where to set -std=c++11 or -std=gnu++11
Too many hard coded paths
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