Fresh install on Mac OS X segfaults or produces a Fortran Runtime error

[appetrosyan]

MWE:

from pypolychord.settings import PolyChordSettings
import matplotlib.pyplot as plt
import pypolychord as ppc
from pypolychord.priors import UniformPrior

def quantile(cube):
    return UniformPrior(-10, 10)(cube)


def lnL(theta):
    return theta**2


settings = PolyChordSettings(2, 0)
ppc.run_polychord(lnL, 2, 0, settings, quantile)

produces

[app-mbp:02918] *** Process received signal ***
[app-mbp:02918] Signal: Segmentation fault: 11 (11)
[app-mbp:02918] Signal code: Address not mapped (1)
[app-mbp:02918] Failing at address: 0x5
[app-mbp:02918] [ 0] 0   libsystem_platform.dylib            0x00007fff6eb4a5fd _sigtramp + 29
[app-mbp:02918] [ 1] 0   ???                                 0x000000011242f53d 0x0 + 4601345341
[app-mbp:02918] *** End of error message ***
fish: 'python3 0.0\ simple\ run.py' terminated by signal SIGSEGV (Address boundary error)

[williamjameshandley]

Could you give a bit more detail about what a 'fresh' install is on OSX? The script you provide runs on my machine, so it likely that this is an OSX-issue, possibly specific to your compilers/MPI setup.

The travis setup shows that there are indeed some unresolved issues associated with OSX + MPI, which look very similar to your own. Lacking an OSX machine testing this is difficult (particularly as the travis spin-up time is 15 minutes for OSX).

Does your code run successfully without MPI?

[appetrosyan]

I can’t run anything PolyChord. The shortest error message I get is

FORTRAN RUNTIME ERRROR: array rank of PUT is not 1.

And that’s what I get without MPI. With MPI it segfaults.

[appetrosyan]

A fresh install is a clear venv, brew MPI, brew GFortran. Pip install every dependency.

[williamjameshandley]

If you run the equivalent commands encoded in the .travis.yml (if MPI=0), do you still get this error?

[appetrosyan]

Exactly the same error messages.

Running with mpirun just wraps the segfaults into MPI warnings.

[williamjameshandley]

Did you install polychord and its dependencies in the same manner as travis? (I ask, because we know that it can work on OSX without segfaults if you do that, and we can then try to isolate what in your setup is causing the segfault on your machine).

[appetrosyan]

Nope. It fails with the following.

[app-mbp:07451] *** Process received signal ***
[app-mbp:07451] Signal: Segmentation fault: 11 (11)
[app-mbp:07451] Signal code: Address not mapped (1)
[app-mbp:07451] Failing at address: 0x1
[app-mbp:07451] [ 0] 0   libsystem_platform.dylib            0x00007fff6eb4a5fd _sigtramp + 29
[app-mbp:07451] *** End of error message ***
[app-mbp:07452] *** Process received signal ***
[app-mbp:07452] Signal: Segmentation fault: 11 (11)
[app-mbp:07452] Signal code: Address not mapped (1)
[app-mbp:07452] Failing at address: 0x1
[app-mbp:07452] [ 0] 0   libsystem_platform.dylib            0x00007fff6eb4a5fd _sigtramp + 29
[app-mbp:07452] *** End of error message ***
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 0 on node app-mbp exited on signal 11 (Segmentation fault: 11).
--------------------------------------------------------------------------

[williamjameshandley]

1. Do the fortran versions work on your machine?

make gaussian
./bin/gaussian ini/gaussian.ini

2. Does compiling with debug flags give us any further detail:

make veryclean
make DEBUG=1 MPI=0 libchord.so
python setup.py install 
python <my script>

[appetrosyan]

1. Fortran works like a charm.

2. Nope. Same bare info:

[app-mbp:07995] *** Process received signal ***
[app-mbp:07995] Signal: Segmentation fault: 11 (11)
[app-mbp:07995] Signal code: Address not mapped (1)
[app-mbp:07995] Failing at address: 0x129e97000
[app-mbp:07995] [ 0] 0   libsystem_platform.dylib            0x00007fff6eb4a5fd _sigtramp + 29
[app-mbp:07995] [ 1] 0   ???                                 0x000000000000000f 0x0 + 15
[app-mbp:07995] *** End of error message ***
fish: 'python3 run_pypolychord.py' terminated by signal SIGSEGV (Address boundary error)

[williamjameshandley]

How far through does it get. Can you do python -c 'import pypolychord' OK?

[williamjameshandley]

Would you be able to paste the stdout during this procedure:

make veryclean
make DEBUG=1 MPI=0 libchord.so
python setup.py install 
python <my script>

[appetrosyan]

On my system python is python2.7, so here's the output of the same with python3.

[appetrosyan]

This is not too critical, as Cobaya still uses PolyChord v1.16, which runs OK on my machine.

[williamjameshandley]

ah -- it's still using mpicc for the pypolychord compilation. Does

CC=gcc CXX=g++ python setup.py install

fix that?

Alternatively, you could try

python setup.py install --no-mpi

[williamjameshandley]

pypolychord 1.17.1 is already the active version in easy-install.pth

You should also make sure that there aren't any other installations of pypolychord on the system (python virtual environments are not completely failsafe)