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underworldcode / underworld2

underworld2: A parallel, particle-in-cell, finite element code for Geodynamics.
http://www.underworldcode.org/
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installing on WSL - may 2022 #606

Closed andrea-bistacchi closed 2 years ago

andrea-bistacchi commented 2 years ago

Hello, and thanks for making Underworld available to the community.

I have tried to follow different instructions to install Underworld2 on a clean Windows Subsystem for Linux (Ubuntu 22.04), but I always have some problem, generally related to installing PETSc.

These are the instructions I tried to follow unsuccessfully:

1) https://underworld2.readthedocs.io/en/latest/Installation.html

2) https://www.underworldcode.org/articles/setting-up-underworld-dependencies/

3) https://www.underworldcode.org/articles/using-python-virtual-environment-for-underworld-development/

I am not able to follow number (1) since the installation of libraries in the "Running Requirements" and "Build environment" are not described in details.

Number (2) is more detailed about PETSc installation, but at some point the configure script freezes and never gets to the end.

Regarding number (3), I do not understand if I need this for simply running Underworld (not developing new code).

I've also seen #587 (using conda) and I am wondering is it might be useful.

BTW, the reason I am trying to install on WSL instead of using Docker is that I have a good workstation with an AMD processor with 32 cores - 64 threads and a lot of RAM, and the Docker version seems to use just one thread.

Thanks very much!

rbeucher commented 2 years ago

Hi @andrea-bistacchi , Have you tried conda?

Romain

rbeucher commented 2 years ago

I'll see if I can come up with a tutorial specific to WSL. Pb is that will pin a specific version of PETSc.

jmansour commented 2 years ago

@andrea-bistacchi @rbeucher the WSL+Ubuntu@22.04 build process should be basically identical to the direct Ubuntu@22.04. Basically, a sudo apt install petsc-dev should be all that is required (for PETSc), assuming that the installed PETSc version is compatible with UW2.

@andrea-bistacchi note that detailed instructions for dependency installation is generally not provided as unfortunately it tends to go out of date very quickly and is difficulty to maintain. With regards to the Docker usage, I'd suggest you pull up your Docker settings via the Docker icon in the Windows task-menu. From there you should be able to decide how many cores Docker has access to.

andrea-bistacchi commented 2 years ago

Hello. I haven't tried conda. It should be just

conda install underworld

if all dependencies are correctly listed in conda-forge, correct?

rbeucher commented 2 years ago

Yes, make sure that you use conda-forge.

andrea-bistacchi commented 2 years ago

@jmansour

Yes WSL should be exactly as Ubuntu (unless we consider a GUI application).

Thanks for the Docker trick. Do you think in the end performances will be the same?

Thanks!

andrea-bistacchi commented 2 years ago

So I am following this article now (with some difference - see below):

https://www.underworldcode.org/articles/here-comes-conda/

This means installing Miniconda (no GUI in WSL), creating an environment, adding channels, and installing as follows:

 wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.11.0-Linux-x86_64.sh
sh ./Miniconda3-py39_4.11.0-Linux-x86_64.sh
conda update --all
conda create -n underworld2    # do not specify python version since some of them are not compatible with underworld
conda activate underworld2
conda config --add channels conda-forge
conda config --append channels geo-down-under
conda install -c conda-forge -c geo-down-under underworld2 lavavu uwgeodynamics badlands jupyterlab

Note that I am not installing stripythat I understand is not compatible with some other library, and that I had to add jupyterlab.

It looks like it works! I will confirm after some testing.

andrea-bistacchi commented 2 years ago

Hello, I tried to run some Jupyter notebook example from model_library and I got this kind of error, related to not finding the PETSc libray:

# Import some libraries we'll need
import underworld as uw
import glucifer
import numpy
import matplotlib.pyplot as plt
from scipy import interpolate

uw.matplotlib_inline()

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/tmp/ipykernel_21014/385265383.py in <module>
      1 # Import some libraries we'll need
----> 2 import underworld as uw
      3 import glucifer
      4 import numpy
      5 import matplotlib.pyplot as plt

~/miniconda3/envs/underworld2/lib/python3.7/site-packages/underworld/__init__.py in <module>
     75 import sys as _sys
     76 from . import timing
---> 77 from . import libUnderworld as _libUnderworld
     78 from . import _stgermain
     79 _data =  _libUnderworld.StGermain_Tools.StgInit( _sys.argv )

~/miniconda3/envs/underworld2/lib/python3.7/site-packages/underworld/libUnderworld/__init__.py in <module>
----> 1 from .libUnderworldPy import *

~/miniconda3/envs/underworld2/lib/python3.7/site-packages/underworld/libUnderworld/libUnderworldPy/__init__.py in <module>
      1 import numpy
      2 from . import StGermain
----> 3 from . import StgDomain
      4 from . import StgFEM
      5 from . import Solvers

~/miniconda3/envs/underworld2/lib/python3.7/site-packages/underworld/libUnderworld/libUnderworldPy/StgDomain.py in <module>
      9     raise RuntimeError("Python 2.7 or later required")
     10 
---> 11 import _StgDomain
     12 
     13 try:

ImportError: libpetsc.so.3.16: cannot open shared object file: No such file or directory

I don't understand if PETSc is really missing, or if it is just a problem related to running Jupyter in WSL and opening the notebook in a browser in Windows.

I guess that what I need is to run proper tests in WSL. Maybe you can suggest some particular test from the test directory?

These are the packages in my environment:

(underworld2) bistek@bwstation:~/model_library/tutorials/ConvectionTutorial$ conda list
# packages in environment at /home/bistek/miniconda3/envs/underworld2:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aiohttp                   3.8.1            py37h540881e_1    conda-forge
aiosignal                 1.2.0              pyhd8ed1ab_0    conda-forge
alsa-lib                  1.2.3.2              h166bdaf_0    conda-forge
anyio                     3.6.1            py37h89c1867_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py37h540881e_2    conda-forge
async-timeout             4.0.2              pyhd8ed1ab_0    conda-forge
asynctest                 0.13.0                     py_0    conda-forge
attr                      2.5.1                h166bdaf_0    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
babel                     2.10.1             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
badlands                  2.0.25           py37h3ffc981_0    geo-down-under
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
bleach                    5.0.0              pyhd8ed1ab_0    conda-forge
bottleneck                1.3.4            py37hda87dfa_1    conda-forge
brotli                    1.0.9                h166bdaf_7    conda-forge
brotli-bin                1.0.9                h166bdaf_7    conda-forge
brotlipy                  0.7.0           py37h540881e_1004    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2021.10.8            ha878542_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2021.10.8        py37h89c1867_2    conda-forge
cffi                      1.15.0           py37h036bc23_0    conda-forge
cftime                    1.6.0            py37hda87dfa_1    conda-forge
charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge
cloudpickle               2.0.0              pyhd8ed1ab_0    conda-forge
cryptography              37.0.1           py37h9ce1e76_0
curl                      7.83.1               h7bff187_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.11.2           py37h540881e_2    conda-forge
dask-core                 1.1.4                    py37_1
dbus                      1.13.6               h5008d03_3    conda-forge
debugpy                   1.6.0            py37hd23a5d3_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
expat                     2.4.8                h27087fc_0    conda-forge
ffmpeg                    4.3.2                h37c90e5_3    conda-forge
fftw                      3.3.10          mpi_openmpi_h36312d9_2    conda-forge
flit-core                 3.7.1              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.0               h8e229c2_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.33.3           py37h540881e_0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
frozenlist                1.3.0            py37h540881e_1    conda-forge
gettext                   0.19.8.1          h73d1719_1008    conda-forge
gflex                     1.1.0              pyh9f0ad1d_1    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
glfw                      3.3.7                h166bdaf_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gnutls                    3.6.13               h85f3911_1    conda-forge
gst-plugins-base          1.20.2               hcf0ee16_0    conda-forge
gstreamer                 1.20.2               hd4edc92_1    conda-forge
h5py                      3.6.0           nompi_py37hd308b1e_100    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.12.1          nompi_h2386368_104    conda-forge
hypre                     2.24.0          mpi_openmpi_h3e9f1a4_0    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
imageio                   2.19.1             pyhcf75d05_0    conda-forge
importlib-metadata        4.11.3           py37h89c1867_1    conda-forge
importlib_metadata        4.11.3               hd8ed1ab_1    conda-forge
importlib_resources       5.7.1              pyhd8ed1ab_0    conda-forge
ipykernel                 6.13.0           py37h25bab4e_0    conda-forge
ipython                   7.33.0           py37h89c1867_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jack                      1.9.18            hfd4fe87_1001    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.1           py37h89c1867_1    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h166bdaf_1    conda-forge
json-c                    0.15                 h98cffda_0    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.5.1              pyhd8ed1ab_0    conda-forge
jupyter-server-proxy      3.2.1              pyhd8ed1ab_0    conda-forge
jupyter_client            7.3.1              pyhd8ed1ab_0    conda-forge
jupyter_core              4.10.0           py37h89c1867_0    conda-forge
jupyter_server            1.17.0             pyhd8ed1ab_0    conda-forge
jupyterlab                3.4.2              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.13.0             pyhd8ed1ab_1    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.2            py37h7cecad7_1    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
lame                      3.100             h7f98852_1001    conda-forge
lavavu                    1.6.7                h3fd9d12_1    geo-down-under
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           14_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_7    conda-forge
libbrotlidec              1.0.9                h166bdaf_7    conda-forge
libbrotlienc              1.0.9                h166bdaf_7    conda-forge
libcap                    2.51                 h166bdaf_1    conda-forge
libcblas                  3.9.0           14_linux64_openblas    conda-forge
libclang                  14.0.3          default_h2e3cab8_0    conda-forge
libclang13                14.0.3          default_h3a83d3e_0    conda-forge
libcups                   2.3.3                hf5a7f15_1    conda-forge
libcurl                   7.83.1               h7bff187_0    conda-forge
libdb                     6.2.32               h9c3ff4c_0    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.3.4                h27087fc_0    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
libglib                   2.70.2               h174f98d_4    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           14_linux64_openblas    conda-forge
libllvm14                 14.0.3               he0ac6c6_0    conda-forge
libnetcdf                 4.8.1           nompi_h329d8a1_102    conda-forge
libnghttp2                1.47.0               h727a467_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.20          pthreads_h78a6416_0    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     14.3                 hd77ab85_0    conda-forge
libsndfile                1.0.31               h9c3ff4c_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libtiff                   4.3.0                h542a066_3    conda-forge
libtool                   2.4.6             h9c3ff4c_1008    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libuv                     1.43.0               h7f98852_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp                   1.2.2                h3452ae3_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.14               h22db469_0    conda-forge
libzip                    1.8.0                h4de3113_1    conda-forge
libzlib                   1.2.11            h166bdaf_1014    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
markupsafe                2.1.1            py37h540881e_1    conda-forge
matplotlib                3.5.2            py37h89c1867_0    conda-forge
matplotlib-base           3.5.2            py37hc347a89_0    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
meshio                    4.4.6              pyhd8ed1ab_0    conda-forge
meshplex                  0.15.14            pyhd8ed1ab_0    conda-forge
metis                     5.1.0             h58526e2_1006    conda-forge
mistune                   0.8.4           py37h5e8e339_1005    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
mpi                       1.0                     openmpi    conda-forge
mpi4py                    3.1.3            py37h910e6d8_1    conda-forge
multidict                 6.0.2            py37h540881e_1    conda-forge
mumps-include             5.2.1               ha770c72_11    conda-forge
mumps-mpi                 5.2.1               hfb3545b_11    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              8.0.29               haf5c9bc_0    conda-forge
mysql-libs                8.0.29               h28c427c_0    conda-forge
nbclassic                 0.3.7              pyhd8ed1ab_0    conda-forge
nbclient                  0.6.3              pyhd8ed1ab_0    conda-forge
nbconvert                 6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          6.5.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.4.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nest-asyncio              1.5.5              pyhd8ed1ab_0    conda-forge
netcdf4                   1.5.8           nompi_py37hf784469_101    conda-forge
nettle                    3.6                  he412f7d_0    conda-forge
networkx                  2.3                        py_0    conda-forge
nodejs                    17.9.0               h96d913c_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
notebook                  6.4.11             pyha770c72_0    conda-forge
notebook-shim             0.1.0              pyhd8ed1ab_0    conda-forge
nspr                      4.32                 h9c3ff4c_1    conda-forge
nss                       3.77                 h2350873_0    conda-forge
numexpr                   2.8.0           py37h85a3170_102    conda-forge
numpy                     1.21.6           py37h976b520_0    conda-forge
openh264                  2.1.1                h780b84a_0    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openmpi                   4.1.3              h846660c_103    conda-forge
openssl                   1.1.1o               h166bdaf_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.3.5            py37h8c16a72_0
pandoc                    2.18                 ha770c72_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parmetis                  4.0.3             he9a3056_1005    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
petsc                     3.17.1          real_ha0799d6_100    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.1.0            py37h44f0d7a_2    conda-forge
pint                      0.18               pyhd8ed1ab_0    conda-forge
pip                       22.1               pyhd8ed1ab_0    conda-forge
prometheus_client         0.14.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.29             pyha770c72_0    conda-forge
psutil                    5.9.0            py37h540881e_1    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptscotch                  6.0.9                h0a9c416_2    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulseaudio                14.0                 hb166930_4    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.12.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.4           py37hd23a5d3_0    conda-forge
pyqt5-sip                 12.9.0           py37hd23a5d3_0    conda-forge
pyrsistent                0.18.1           py37h540881e_1    conda-forge
pysocks                   1.7.1            py37h89c1867_5    conda-forge
python                    3.7.12          hb7a2778_100_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.15.3             pyhd8ed1ab_0    conda-forge
python_abi                3.7                     2_cp37m    conda-forge
pytriangle                20200424         py37h39e3cac_0    geo-down-under
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
pywavelets                1.3.0            py37hda87dfa_1    conda-forge
pyzmq                     22.3.0           py37h0c0c2a8_2    conda-forge
qt-main                   5.15.3               hf97cb25_1    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.27.1             pyhd8ed1ab_0    conda-forge
scalapack                 2.2.0                h67de57e_1    conda-forge
scikit-image              0.15.0           py37hb3f55d8_2    conda-forge
scipy                     1.7.3            py37hf2a6cf1_0    conda-forge
scotch                    6.0.9                hb2e6521_2    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                62.2.0           py37h89c1867_0    conda-forge
simpervisor               0.4                pyhd8ed1ab_0    conda-forge
sip                       6.5.1            py37hcd2ae1e_2    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.2.0            py37h89c1867_3    conda-forge
soupsieve                 2.3.1              pyhd8ed1ab_0    conda-forge
sqlite                    3.38.5               h4ff8645_0    conda-forge
suitesparse               5.10.1               h9e50725_1    conda-forge
superlu                   5.2.2                h16cfea0_0    conda-forge
superlu_dist              7.2.0                h34f6f4d_0    conda-forge
tbb                       2021.5.0             h924138e_1    conda-forge
terminado                 0.13.3           py37h89c1867_1    conda-forge
tinycss2                  1.1.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
toolz                     0.11.2             pyhd8ed1ab_0    conda-forge
tornado                   6.1              py37h540881e_3    conda-forge
traitlets                 5.2.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.2.0                hd8ed1ab_1    conda-forge
typing_extensions         4.2.0              pyha770c72_1    conda-forge
ucx                       1.12.1               h954bc8d_1    conda-forge
underworld2               2.10.0b          py37h2ccf34e_0    geo-down-under
unicodedata2              14.0.0           py37h540881e_1    conda-forge
urllib3                   1.26.9             pyhd8ed1ab_0    conda-forge
uwgeodynamics             2.10.0b                  py37_0    geo-down-under
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.3.2              pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
x264                      1!161.3030           h7f98852_1    conda-forge
xorg-fixesproto           5.0               h7f98852_1002    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxcursor           1.2.0                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxinerama          1.1.4             h9c3ff4c_1001    conda-forge
xorg-libxrandr            1.5.2                h7f98852_1    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-randrproto           1.5.0             h7f98852_1001    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yarl                      1.7.2            py37h540881e_2    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.8.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h166bdaf_1014    conda-forge
zstd                      1.5.2                ha95c52a_0    conda-forge

It looks like I have PETSc 3.17 while underword needs 3.16?

Thank you very much!

andrea-bistacchi commented 2 years ago

Maybe tomorrow I can try with conda install petsc=3.16?

rbeucher commented 2 years ago

OK.Petsc has moved to 3.17 recently. The conda builds need to be updated. You can force petsc 3.16 yes. Let me know if solves the issue.

jmansour commented 2 years ago

@andrea-bistacchi I probably wouldn't expect much performance difference, Docker vs native. Actually, WSL these days is virtualised too, so either way it's virtualisation.

andrea-bistacchi commented 2 years ago

Hello, PETSc seems OK now with conda install petsc=3.16, but it cannot find glucifer. Is it on a particular channel?

andrea-bistacchi commented 2 years ago

Hi, I've seen that in the changes for release 2.9.0 you write:

glucifermodule moved inside underworldand renamed visualisation

Access as import underworld.visualisation

I tested this and it works, then I get more errors further on in the examples. I'll go through all the changes and update the examples.

In any case the conda installation is very easy in the end. This is the complete code:

wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.11.0-Linux-x86_64.sh
sh ./Miniconda3-py39_4.11.0-Linux-x86_64.sh
conda update --all
conda create -n underworld2    # do not specify python version since some of them are not compatible with underworld
conda activate underworld2
conda config --add channels conda-forge
conda config --append channels geo-down-under
conda install -c conda-forge -c geo-down-under underworld2 lavavu uwgeodynamics badlands jupyterlab petsc=3.16

Thanks!

rbeucher commented 2 years ago

Good! @julesghub we need to specify the supported version in the conda recipe to avoid this in the future. @andrea-bistacchi We are gonna release a new version in a couple of weeks, with PETSc 3.17 support

rbeucher commented 2 years ago

I am closing this. New version 3.13 has PETSc 3.17 support. should be good now.