ipython-cluster-helper

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hackdna

slurm 19.05 sinfo data parsing broken

1

xref https://github.com/bcbio/bcbio-nextgen/issues/3097 Slurm 19.05 outputs an additional header, breaking the `sinfo` parsing. Cheers M

matthdsm

"Looking for ipcluster_config" never continue

13

H roryk, I try to use scheduler to schedule our own pipeline. I try to make a view and create a simple test function to run subprocess shell cmd like...

MIAOKUI

Modules in PYTHONPATH cannot be loaded because of -E python option in cluster.py

7

Hi, I first of all would like to congratulate you for this excelent module. It makes very easy to use ipython-parallel, and also it is much easier than other parallelilzation...

ofajardo

PBS with headnode

4

Hi, I would like to use ipython-cluster-helper on a cluster running PBS. The problem is that I have to ssh to the head node to be able to use qsub...

matthias-k

CalledProcessError

3

with cluster_view(scheduler="slurm", queue="hsph", num_jobs=20) as view: view.map(time_waster, range(20)) --------------------------------------------------------------------------- CalledProcessError Traceback (most recent call last) in () ----> 1 with cluster_view(scheduler="slurm", queue=None, num_jobs=20) as view: 2 view.map(time_waster, range(20)) /share/PI/rondror/software/miniconda/lib/python2.7/contextlib.pyc in...

thomasklau

If I have the following code: def run(): with cluster_view(scheduler=None, queue=None, num_jobs=5, direct=True, extra_params={"run_local": True}) as view: a = 1 view.push({'a':a}) test = view.map(some_function, range(20)) When I call run from...

GarrettBeatty

Batch and log file destination

3

Is there any way to direct where the batch submission and log files get placed? If I specify a large number of jobs, my working directory gets filled with a...

nspies