Problems installing PETSc & Firedrake with CMake/SLEPc - Ubuntu 20.04

[cpjordan]

Hi, I'm trying to install Firedrake following the instructions on the install page with a few slight changes. Machine is a Dell Precision 5820 Tower X-Series (Ubuntu 20.04.6 LTS). I tried to install with CMake because the default system CMake is 3.16.3 and PETSc warned that it needed to be a more recent version. I installed with SLEPc following another discussion in the install FAQ which seemed to suggest it might help (and no harm in doing so I guess!). Default Python3 is 3.8, so installing with 3.11 as follows:

mkdir firedrake_dir
cd firedrake_dir
curl -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-configure

sudo apt install $(python3.11 firedrake-configure --show-system-packages)
git clone --depth 1 --branch $(python3.11 firedrake-configure --show-petsc-version) https://gitlab.com/petsc/petsc.git
export SLEPC_DIR=$PETSC_DIR/$PETSC_ARCH
cd petsc
python3.11 ../firedrake-configure --show-petsc-configure-options | xargs -L1 ./configure --download-cmake --download-slepc
make PETSC_DIR=/home/s1626662/firedrake_dir/petsc PETSC_ARCH=arch-firedrake-default all
make PETSC_DIR=/home/s1626662/firedrake_dir/petsc PETSC_ARCH=arch-firedrake-default check

The check leads to:

Running PETSc check examples to verify correct installation
Using PETSC_DIR=/home/s1626662/firedrake_dir/petsc and PETSC_ARCH=arch-firedrake-default
Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process
See https://petsc.org/release/faq/
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
Number of SNES iterations = 2
Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes
See https://petsc.org/release/faq/
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
Number of SNES iterations = 2
1c1
< lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
---
> keylid velocity = 0.0016, prandtl # = 1., grashof # = 1.
3,4c3,4
<   1 SNES Function norm 4.12227e-06
<   2 SNES Function norm 6.098e-11
---
>   1 SNES Function norm 3.32882e-06
>   2 SNES Function norm < 1.e-11
/home/s1626662/firedrake_dir/petsc/src/snes/tutorials
Possible problem with ex19 running with HYPRE, diffs above
=========================================
1c1
< lid velocity = 0.0625, prandtl # = 1., grashof # = 1.
---
> lid velocity = 0.0625, prandtl # = 1., grashof # = 1.
/home/s1626662/firedrake_dir/petsc/src/snes/tutorials
Possible problem with ex19 running with MUMPS, diffs above
=========================================
1c1
< lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
---
> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
/home/s1626662/firedrake_dir/petsc/src/snes/tutorials
Possible problem with ex19 running with SuiteSparse, diffs above
=========================================
1c1
< lid velocity = 0.0025, prandtl # = 1., grashof # = 1.
---
> lid velocity = 0.0025, prandtl # = 1., grashof # = 1.
/home/s1626662/firedrake_dir/petsc/src/snes/tutorials
Possible problem with ex19 running with SuperLU_DIST, diffs above
=========================================
0a1
> 
\ No newline at end of file
/home/s1626662/firedrake_dir/petsc/src/vec/vec/tests
Possible problem with ex47 running with HDF5, diffs above
=========================================
Running SLEPc check examples to verify correct installation
Using SLEPC_DIR=/home/s1626662/firedrake_dir/petsc/arch-firedrake-default/externalpackages/git.slepc, PETSC_DIR=/home/s1626662/firedrake_dir/petsc, and PETSC_ARCH=arch-firedrake-default
C/C++ example src/eps/tests/test10 run successfully with 1 MPI process
C/C++ example src/eps/tests/test10 run successfully with 2 MPI processes
Completed SLEPc check examples
Completed PETSc check examples
Error while running make check
make[1]: *** [makefile:125: check] Error 1
make: *** [GNUmakefile:17: check] Error 2

I persisted anyway with the Firedrake install just to see if it would work:

cd ..

python3.11 -m venv venv-firedrake
. venv-firedrake/bin/activate
export $(python3.11 firedrake-configure --show-env)
pip cache remove slepc4py
pip cache remove petsc4py
pip install --no-binary h5py "firedrake @ git+https://github.com/firedrakeproject/firedrake.git#[check,slepc]"

This failed because of a HDF5 version issue - I've attached the output to keep this shorter but I assume PETSc needs to be fixed first anyway. PETSc make and configure logs are attached! Help would be much appreciated.

make.log
configure.log
firedrake_error.txt

UPDATE:
I also tried installing on another machine - HP Z6 G5 Workstation Desktop (Ubuntu 22.04.5 LTS) which has Python 3.10 as default Python 3, following the exact instructions on the website and got:

Running PETSc check examples to verify correct installation
Using PETSC_DIR=/home/s1626662/firedrake_dir/petsc and PETSC_ARCH=arch-firedrake-default
C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes
C/C++ example src/snes/tutorials/ex19 run successfully with HYPRE
C/C++ example src/snes/tutorials/ex19 run successfully with MUMPS
3,5c3,4
<   1 SNES Function norm 3.32845e-06
<   2 SNES Function norm < 1.e-11
< Number of SNES iterations = 2
---
>   1 SNES Function norm 0.0404122
> Number of SNES iterations = 1
/home/s1626662/firedrake_dir/petsc/src/snes/tutorials
Possible problem with ex19 running with SuiteSparse, diffs above
=========================================
2c2
< Number of SNES iterations = 2
---
> Number of SNES iterations = 0
/home/s1626662/firedrake_dir/petsc/src/snes/tutorials
Possible problem with ex19 running with SuperLU_DIST, diffs above
=========================================
C/C++ example src/vec/vec/tests/ex47 run successfully with HDF5
Completed PETSc check examples
Error while running make check
make[1]: *** [makefile:125: check] Error 1
make: *** [GNUmakefile:17: check] Error 2

so I'm wondering if it's just a current issue with PETSc? I can upload the relevant PETSc logs for that as well if helpful.

[connorjward]

This could well be an issue with older Ubuntu versions and the latest release of PETSc. We test using the most recent LTS (24.04) so might not have caught regressions.

Since 20.04 is end-of-life in a month I would recommend updating that workstation if possible.

To try and isolate the issue you could try producing a more minimal set of configure options and reporting this to PETSc.

[cpjordan]

Thanks, I'll just have to use Docker for the Ubuntu 20.04 machine - it's stuck there sadly. Updated to Ubuntu 24.04 on my other machine and no problem with installation unsurprisingly.