Comments (11)
Can I install it via the Conda environment somehow?
Hi @qmpotential
These issues should be caused by environmental dependence. Personally, I would recommend using the Intel MPI suite to compile PETSc and using Conda to manage the Python environment and its dependencies. I do not recommend using OpenMPI or MPICH and PETSc installed by Conda as their performance may be poor.
N.
from underworld2.
@qmpotential
Congratulations! The installation seemed smooth this time. But one thing worth noting is that h5py is automatically installed as a dependency of underworld2 and is usually only serial. It can be detected through the following code, True
means parallel support:
conda activate xxx
import h5py
h5py.get_config().mpi
You can refer here to install h5py that supports parallel IO.
CC=mpicc HDF5_MPI="ON" HDF5_DIR=/path/to/your/hdf5/install/ pip install --no-binary=h5py h5py
from underworld2.
Hi Oleg,
Now you're missing the development header for an MPI implementation.
Try something like
sudo yum install openmpi
to install it.
All Underworld2 build dependencies packages are listed here.
https://github.com/underworldcode/underworld2/blob/master/Installation.rst#build-environment
Also there is this guide to installing most of those dependencies under Ubuntu. Although you're on RHEL it will still be helpful. https://www.underworldcode.org/setting-up-underworld-dependencies/
from underworld2.
I'm not familiar with RHEL8 packages unfortunately.
What openmpi
or mpich
development packages can you install with RHEL8?
E.g. sudo yum search openmpi
from underworld2.
Hi @qmpotential,
I can't make out the error from this log, is there more output information available. If so, please send it through.
Also what version of the code are you installing from source? Which git revision?
Another strategy to overcome this is to use the Underworld2's container images. You could use podman
(preferred container software) or docker
to quickly spin up an Underworld2 instance.
See - https://hub.docker.com/r/underworldcode/underworld2/tags for the available versions. Note the podman
/ docker
commands can be used interchangeably for Underworld usage.
Hope this help.
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Thanks for letting us know pip install underworld
command isn't working.
Underworld can't build on platforms like Colab because our dependency code, PETSc doesn't build on colab.
Hence why we have the container solution which works well on other cloud platforms.
Are you wanting to build the code on a local machine? How are you wanting to use it?
Make sure you have petsc installed and the environment variable PETSC_DIR
pointing to the installation.
Here's some general information about it https://www.underworldcode.org/setting-up-underworld-dependencies/
Note: The PETSc version is old in the link. The latest underworld runs on petsc-3.19.
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Try install the python development header.
Something like
yum -y install python-devel
That will include "Python.h"
from underworld2.
Hi @qmpotential,
Would it be convenient for you to provide complete compilation error information? Sending all installation results to a file instead of a screen may better solve the problem.
N.
from underworld2.
The python package ninja
is not being found
CMake Error at CMakeLists.txt:7 (project):
Running
'/home/olegsupp/.local/bin/ninja' '--version'
failed with:
Traceback (most recent call last):
File "/home/olegsupp/.local/bin/ninja", line 5, in <module>
from ninja import ninja
ModuleNotFoundError: No module named 'ninja'
Run
pip install ninja
For a complete list of build requirements, both programs and python packages, for the current docker image see here.
I'll update the code to ensure ninja
is a requirement in the build phase.
We are getting close to an install.
from underworld2.
What is the new error exactly? A log file would be useful.
You can check if you've installed ninja and mpi as follows
ninja --version
mpicc --show
Did you have any luck using the docker solution?
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That is great! Thank you so much for the notice. I will try that and get back to you!
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Related Issues (20)
- RuntimeError: There were left over keyword arguments. kwargs = [{'_fn_fssa': None}]
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- Uncoupled temperature and compositional field in UW Geodynamics HOT 2
- Adding two plasticities to one material HOT 3
- SystemError: <built-in function SystemLinearEquations_UpdateSolutionOntoNodes> returned a result with an exception set HOT 1
- Parallel computing and An installation problem (MpiRun) HOT 4
- 'surface' integration HOT 2
- Model.mesh.deform_mesh() error with mpirun. Possibly two nodes are in an identical location.
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- May I ask how is the second-order invariant of strain rate(function: fn.tensor.second_invariant)in underworld2.13 calculated?
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- Converging issue for 3D subduction model with oblique trench shape. HOT 1
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- issue with surface processes
- To find the example to generate collision_wedge.gif HOT 2
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