it fails on slurm

[wisekh6]

Hi Sahil,

According to https://github.com/sahilseth/flowr, flowr should support slurm, but my test failed. Would you help me with this issue?

Thanks in advance,

flowr run x=sleep_pipe platform=slurm execute=TRUE

.....(skipped)
--> checking if required columns are present...
--> checking if resources columns are present...
--> checking if dependency column has valid names...
--> checking if submission column has valid names...
--> checking for missing rows in def...
--> checking for extra rows in def...
--> checking submission and dependency types...
plotting a pdffile...
  |                                                                      |   0%sbatch: error: invalid partition specified: short
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: short
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: short
sbatch: error: Batch job submission failed: Invalid partition name specified
  |=======================                                               |  33%sbatch: error: invalid partition specified: short
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: short
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: short
sbatch: error: Batch job submission failed: Invalid partition name specified
  |===============================================                       |  67%sbatch: error: invalid partition specified: short
sbatch: error: Batch job submission failed: Invalid partition name specified
  |======================================================================| 100%sbatch: error: invalid partition specified: short
sbatch: error: Batch job submission failed: Invalid partition name specified

--> checking if required columns are present...
--> checking if resources columns are present...
--> checking if dependency column has valid names...
--> checking if submission column has valid names...
--> checking for missing rows in def...
--> checking for extra rows in def...
--> checking submission and dependency types...
plotting a pdffile...
There were 16 warnings (use warnings() to see them)

[sahilseth]

Sorry I missed this issue earlier. It is assuming you have a queue named short, if you don't it fails.

Could you try this:

customize this file and supply it: https://github.com/sahilseth/flowr/blob/master/inst/pipelines/sleep_pipe.def

flowr::run(x="sleep_pipe", def = "sleep_pipe_custom.def", platform = "slurm", execute=TRUE)

Also, can you give me an example slurm script you use. Here is the template flowr uses: https://github.com/sahilseth/flowr/blob/master/inst/conf/slurm.sh