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trouble with snakemake having glpk-utils installed

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  trouble with snakemake having glpk-utils installed Patrice Duroux <patrice.duroux@gmail.com> - 2021-03-22 18:50 +0100
    Re: trouble with snakemake having glpk-utils installed patrice.duroux@gmail.com - 2021-03-23 14:10 +0100

#13289 — trouble with snakemake having glpk-utils installed

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Hi,

With a very simple Snakefile test case like this:

rule test:
    shell:
         'echo "Hello world!"'

here is the output got with glpk-utils installed (sagemath requires it on
this system):

$ snakemake -j1
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job counts:
    count    jobs
    1    test
    1
GLPSOL--GLPK LP/MIP Solver 5.0
Parameter(s) specified in the command line:
 --cpxlp /tmp/1245235-pulp.lp -o /tmp/1245235-pulp.sol
Reading problem data from '/tmp/1245235-pulp.lp'...
/tmp/1245235-pulp.lp:5: missing constraint sense
CPLEX LP file processing error
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/snakemake/__init__.py", line 643, in
snakemake
    success = workflow.execute(
  File "/usr/lib/python3/dist-packages/snakemake/workflow.py", line 961, in
execute
    success = scheduler.schedule()
  File "/usr/lib/python3/dist-packages/snakemake/scheduler.py", line 406,
in schedule
    else self.job_selector_ilp(needrun)
  File "/usr/lib/python3/dist-packages/snakemake/scheduler.py", line 624,
in job_selector_ilp
    prob.solve()
  File "/usr/lib/python3/dist-packages/pulp/pulp.py", line 1643, in solve
    status = solver.actualSolve(self, **kwargs)
  File "/usr/lib/python3/dist-packages/pulp/solvers.py", line 380, in
actualSolve
    raise PulpSolverError("PuLP: Error while executing "+self.path)
pulp.solvers.PulpSolverError: PuLP: Error while executing glpsol

And here is the output once this package removed:

$ snakemake -j1
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job counts:
    count    jobs
    1    test
    1

[Mon Mar 22 18:22:40 2021]
rule test:
    jobid: 0

Hello world!
[Mon Mar 22 18:22:40 2021]
Finished job 0.
1 of 1 steps (100%) done
Complete log:
/home/patrice/tmp/toto/.snakemake/log/2021-03-22T182240.369114.snakemake.log

I do not know if there is a bug behind the scene and which package is
involved.

Thanks!

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#13290

Hi,

I found that it is python3-pulp that calls glpsol provided by glpk-
utils:
https://sources.debian.org/src/python-pulp/1.6.0+dfsg1-5/src/pulp/solvers.py/?hl=100#L100

It's strange that the python3-pulp package didn't at least suggest some
of these tools because tracking my issue using apt rdepends didn't help
that much.

$ apt show python3-pulp
Package: python3-pulp
Version: 1.6.0+dfsg1-5
Priority: optional
Section: python
Source: python-pulp
Maintainer: Debian OpenStack <team+openstack@tracker.debian.org>
Installed-Size: 301 kB
Depends: coinor-cbc, python3-pyparsing, python3:any
Homepage: https://github.com/coin-or/pulp
Tag: implemented-in::python

$ apt rdepends glpk-utils
glpk-utils
Reverse Depends:
  Dépend: sagemath

Should this be an issue on python3-pulp?

Thanks,
Patrice

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