graph-tool version

[pavelToman]

Hello Dawe!
I am trying to install Schist v0.8.3 on UGent HPC to provide this sw to researchers. We are using EasyBuild to build/install and provide sw - so I like to build from source.
For now I am fighting with the dependency graph-tools. I try to install its latest version v2.68. The installation works fine, but check commands failing:
from graph_tool.all import graph_draw
from graph_tool.all import Graph, BlockState
import graph_tool.inference
All of these return same error:

Traceback (most recent call last):
      File "<stdin>", line 1, in <module>
      File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/graph-tool/2.68-foss-2023a/lib/python3.11/site-packages/graph_tool/all.py", line 34, in <module>
        from graph_tool.draw import *
      File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/graph-tool/2.68-foss-2023a/lib/python3.11/site-packages/graph_tool/draw/__init__.py", line 87, in <module>
        from .. inference import minimize_blockmodel_dl, BlockState, ModularityState
      File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/graph-tool/2.68-foss-2023a/lib/python3.11/site-packages/graph_tool/inference/__init__.py", line 331, in <module>
        from . blockmodel import *
      File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/graph-tool/2.68-foss-2023a/lib/python3.11/site-packages/graph_tool/inference/blockmodel.py", line 119, in <module>
        @entropy_state_signature
         ^^^^^^^^^^^^^^^^^^^^^^^
      File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/graph-tool/2.68-foss-2023a/lib/python3.11/site-packages/graph_tool/inference/base_states.py", line 110, in entropy_state_signature
        warn = "\n".join([" " * (m if j == 0 else m + 4) + l.lstrip() for
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/graph-tool/2.68-foss-2023a/lib/python3.11/site-packages/graph_tool/inference/base_states.py", line 110, in <listcomp>
        warn = "\n".join([" " * (m if j == 0 else m + 4) + l.lstrip() for
                          ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
        TypeError: can't multiply sequence by non-int of type 'generator'

What version of graph-tools is recommended to use with Schist v0.8.3 ?

Some details about sw I use:
GCC v12.3.0 + OpenMPI v4.1.5 + FlexiBLAS v3.3.1 + FFTW v3.3.10 + ScaLAPACK v2.2.0
python v3.11.3
Boost v1.83.0
Numpy v1.25.1
Scipy v1.11.1
Pandas v2.0.3
joblib v1.2.0

[dawe]

Hello @pavelToman, my current working installation still uses graph-tool 2.58. I have tried to install gt-2.68 in a test enviroment and cannot reproduce your error, so I guess it's a question you should post on graph-tool issue tracker. Having said that, gt-2.68 (and FWIW gt-2.67 as well) raises a double free error when working with multimodal data.
Given that I am not (yet) exploiting newest features, I suggest you to install gt-2.58, I will add a dependency check on the installer recipe.

[dawe]

Quick update: a fresh install of gt-2.68 on a linux machine (I was on OS X before) doesn't have the double free issue, so I'm not sure what's going on here

[boegel]

@dawe Which Python are you using? I think that may be important here.
I can trigger the same error with a weird construct like this:

>>> m = (x+1 for x in range(5))
>>> " " * m
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: can't multiply sequence by non-int of type 'generator'

[pavelToman]

I just try to build graph-tool v2.59 and all check commands pass ok.
The piece of code that causing the error is:

def entropy_state_signature(cls):
    def entropy(self, **kwargs):
        return self._entropy(**dict(self.get_entropy_args(), **kwargs))
    entropy.__signature__ = inspect.signature(cls._entropy)
    intro, br, rest = cls._entropy.__doc__.partition("\n\n")
    warn = f"""\
    The default arguments of this function are overriden by those
    obtained from :meth:`~{cls.__name__}.get_entropy_args`. To update the
    defaults in a stateful way, :meth:`~{cls.__name__}.update_entropy_args`
    should be called."""
    warn = textwrap.dedent(warn)
    warn = " ".join(warn.splitlines())
    warn = textwrap.fill(warn, width=60, break_long_words=False,
                         replace_whitespace=False)
    warn = f".. warning::\n{warn}"
    lines = cls._entropy.__doc__.splitlines()
    m = min((len(l) - len(l.lstrip()) for l in lines[1:] if l.lstrip() != "")) \
        if len(lines) > 1 else 0
-> warn = "\n".join([" " * (m if j == 0 else m + 4) + l.lstrip() for
                      j, l in enumerate(warn.splitlines())])
    entropy.__doc__ = intro + "\n\n" + warn
    if len(rest) > 0:
        entropy.__doc__ += "\n\n" + rest
    setattr(cls, "entropy", entropy)
    cls.get_entropy_args.__doc__ = \
        cls.get_entropy_args.__doc__.replace("{entropy}",
                                             f":meth:`~{cls.__name__}.entropy`")
    cls.update_entropy_args.__doc__ = \
        cls.update_entropy_args.__doc__.replace("{entropy}",
                                                f":meth:`~{cls.__name__}.entropy`")
    cls.reset_entropy_args.__doc__ = \
        cls.reset_entropy_args.__doc__.replace("{entropy}",
                                               f":meth:`~{cls.__name__}.entropy`")
    return cls

[dawe]

@boegel I tried with a fresh conda install using python 3.12 on Linux without issues. On OS X I tried both 3.10 and 3.12, always raising malloc error (but I suspect it's a clash between graph-tool and joblib)

[dawe]

@pavelToman TBH I haven't ever built gt from source, I relied on the conda binaries

[pavelToman]

@dawe thank you for your help!
Schist v0.8.3 works now with gt v2.59

[pedrofale]

Sorry for re-surfacing this, but I'm still having trouble with the graph-tool compatibilities. Could you please provide a working environment for OS X? Thanks!

[dawe]

@pedrofale what error do you get? What version of schist and graph-tool do you have? Since v0.8.4 I've forced graph-tool dependency to version 2.59 max, this to avoid issues on OS X.
Currently I'm working on OS X 14.5, python 3.12, schist 0.9.0 and graph-tool 2.59 and everything seems to work.