Installation doesn't find configured packages #146
Comments
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What do you have for PETSC_INCLUDE_DIR in build/CMakeCache.txt? Can you send this file? @cameronrutherford @jaelynlitz |
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Of course! I attached the file and also copied out the petsc relevant parts:
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I am a little confused about what's going wrong here. If possible, I would suggest in updating PETSc to a newer version, and running with Since you aren't building with Ipopt, and you are running on a linux box, have you considered using our ghcr package to get started? You can try pulling this version of the ExaGO package for example. Based on our # Build stage with Spack pre-installed and ready to be used
FROM spack/ubuntu-jammy as builder
# Install OS packages needed to build the software
RUN apt-get -yqq update && apt-get -yqq upgrade \
&& apt-get -yqq install autoconf \
&& rm -rf /var/lib/apt/lists/*
# What we want to install and how we want to install it
# is specified in a manifest file (spack.yaml)
RUN mkdir /opt/spack-environment \
&& (echo spack: \
&& echo ' specs:' \
&& echo ' - exago@1.6.0~ipopt+python+mpi' \
&& echo ' ^libffi@3.4.2' \
&& echo ' ^petsc~fortran~hdf5~hypre+metis' \
&& echo ' concretizer:' \
&& echo ' unify: true' \
&& echo ' reuse: true' \
&& echo ' mirrors:' \
&& echo ' spack: https://binaries.spack.io/develop' \
&& echo ' packages:' \
&& echo ' all:' \
&& echo ' providers:' \
&& echo ' mpi:' \
&& echo ' - openmpi' \
&& echo ' zlib-api:' \
&& echo ' - zlib' \
&& echo ' zlib-ng:' \
&& echo ' buildable: false' \
&& echo ' mpich:' \
&& echo ' buildable: false' \
&& echo ' config:' \
&& echo ' install_tree: /opt/software' \
&& echo ' view: /opt/views/view') > /opt/spack-environment/spack.yaml
# Find external packages
RUN cd /opt/spack-environment && spack env activate . && spack external find --all --exclude python
# Do this separate of install to cache keys...
RUN cd /opt/spack-environment && spack env activate . && spack mirror add develop https://binaries.spack.io/develop && spack buildcache keys --install --trust && spack concretize -f && ( spack mirror create -a || true )
# Install buggy linux-uuid package
RUN cd /opt/spack-environment && spack env activate . && spack install --no-checksum --fail-fast util-linux-uuid
# Install PETSc
RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast petsc
# Install the software, remove unnecessary deps
RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y
# Strip all the binaries
RUN find -L /opt/views/view/* -type f -exec readlink -f '{}' \; | \
xargs file -i | \
grep 'charset=binary' | \
grep 'x-executable\|x-archive\|x-sharedlib' | \
awk -F: '{print $1}' | xargs strip
# Modifications to the environment that are necessary to run
RUN cd /opt/spack-environment && \
spack env activate --sh -d . > activate.sh
RUN { \
echo '#!/bin/sh' \
&& echo '.' /opt/spack-environment/activate.sh \
&& echo 'exec "$@"'; \
} > /entrypoint.sh \
&& chmod a+x /entrypoint.sh \
&& ln -s /opt/views/view /opt/view
RUN apt-get -yqq update && apt-get -yqq upgrade \
&& apt-get -yqq install gfortran \
&& rm -rf /var/lib/apt/lists/*
ENTRYPOINT [ "/entrypoint.sh" ]
CMD [ "/bin/bash" ]
# Make sure root user gets spack packages
RUN echo "source /entrypoint.sh" >> /root/.bashrc |
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Hi Cameron, haven't considered but I will try. I have not really used docker before, but probably something that I should do anyway so I will see how far I get with that, thanks! |
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Running the above as a Dockefile fails while installing PETsc and/or Blas: |
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The linked docker image works though.. Is there also an available docker image including GPU support ? And if so, how can I find the available images? Thank you already though to get me started! |
We don't currently have a docker image that we build / publish with GPU support unfortunately. We really need CoinHSL in order to get most of ExaGO's complex applications functioning, so this for a while has blocked us supporting builds for SCOPFLOW / SOPFLOW and GPU builds out of the box. I suppose we could go a ghcr image for CUDA / ROCm as well, but again they wouldn't have SOPFLOW / SCOPFLOW supported... |
That's quite the ugly error... If you add a copy of the line If you can't get anywhere with that, it might be worth reporting a bug with the openblas folk... |
Issue type
Relates to
Summary
I have followed the Manual installation as carefully as possieble, installed all dependencies ( PETSC 3.16.0, CMake 3.22.1, OpenMPI 4.1.2 and blas) and the build call runs, but the make -j call fails.
I installed petsc in a non-standard directory and and it passed the make test all call. The Environment variables $PETSC_DIR and $PETSC_ARCH are set specific to that installation. The pther dependencies are installed in standard locations.
I also tried installation using spacks but it failed also. I have no experience with spacks just gave it a quick try. I tried different petsc versions and installations but never managed to fully run make install.
Exact commands to reproduce, if applicable
The cmake call:
cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALLDIR -DPETSC_DIR=$PETSC_DIR -DPETSC_ARCH="petsc-3-16" -DCMAKE_BUILD_TYPE=Debug
followed by:
make install
or
make -j
which fails.
I am running everything on a virtual linux machine (Ubuntu).
Relevant logs and/or screenshots, if applicable
The successful cmake call specifically finding petsc:
And the error message for make -j:
make install throws a similar message regarding petsc.h
p.s. I am fairly unexperienced, if I can approve on describing the issue please let me know.
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