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!
