Compilation of pybind11 drivers fails with compiler crash on Ubuntu 18.04 with gcc 7.5.0

[ThomasGWilson]

I am trying to install celerite2 using pip (version=20.2.3) with python3.7 on an Ubuntu18.04 machine, however I get the following error when pip is trying to build wheels for celerite2:

ERROR: Failed building wheel for celerite2 Failed to build celerite2 ERROR: Could not build wheels for celerite2 which use PEP 517 and cannot be installed directly

Thanks, Tom

[dfm]

Hi! This package hasn't really been officially released yet so expect some rough edges (isn't that always true)!

Can you give me some more details?

• I expect that you're installing from source (by cloning from GitHub), but can you give the specific steps you're executing.
• Also: can you add the -v argument to the pip call and share the output in a gist or something? The current error is not sufficient to diagnose.

[ThomasGWilson]

Hi,

Completely understandable :)

Of course, I'm installing from the GitHub clone: pip install git+https://github.com/dfm/celerite2.git

Here's the gist: https://gist.github.com/ThomasGWilson/4a4821a28b6ed6739284d6d1a19c44d4

Cheers, Tom

[dfm]

That gist doesn't seem to be complete (it doesn't have the error!), but I can see an issue. It won't be possible to install from source like that. Instead you should follow the steps here: https://celerite2.readthedocs.io/en/latest/user/install/#from-source With the added note that you'll need to include --recursive in the git clone step. Give that a try and send along the error if it fails again.

[ThomasGWilson]

Hi,

That gist is >3000 lines so the error was beyond the truncation point. Here is the full previous report (https://gist.githubusercontent.com/ThomasGWilson/4a4821a28b6ed6739284d6d1a19c44d4/raw/fe433cb75589e2c980b30ab829fc3bc764dc31c3/gistfile1.txt)

Thanks! I've installed via the steps you recommended, however I'm getting a similar error. Here is the full report (https://gist.githubusercontent.com/ThomasGWilson/29b1399905ff8e8ef4779a4733ba836c/raw/86575a1a70b0033aceff0bba77e74189211bbd34/gistfile1.txt)

The common error here seems to be an issue with one of the gcc arguments:

gcc -pthread -B /home/tom/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic++/include -Ic++/vendor/eigen -Ipython/celerite2 -I/tmp/pip-build-env-2mpwi2p9/overlay/lib/python3.7/site-packages/numpy/core/include -I/tmp/pip-build-env-2mpwi2p9/overlay/lib/python3.7/site-packages/pybind11/include -I/tmp/pip-build-env-2mpwi2p9/overlay/lib/python3.7/site-packages/pybind11/include -I/home/tom/anaconda3/include/python3.7m -c python/celerite2/driver.cpp -o build/temp.linux-x86_64-3.7/python/celerite2/driver.o -DVERSION_INFO="0.0.1rc2.dev18+gfabb85c" -std=c++17 -fvisibility=hidden
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.
error: command 'gcc' failed with exit status 4

For completeness I have gcc version 7.5.0 installed.

[dfm]

Good thanks. That suggests to me that your compiler is running out of RAM or something. Compiling these extensions can be pretty heavy! I'm not sure that I can do too much to diagnose this from here, but we can keep this open to re-investigate later.

In your case, I'd probably recommend trying the pre-compiled binaries unless you have a good argument for avoiding them (or if you're running into issues with them):

python -m pip install celerite2==0.0.1rc1

Nothing has changed (except documentation) since that release candidate.

[ThomasGWilson]

Hi Dan,

Thanks, that has worked!

Cheers,

Tom