# test-conda-env-hpc

## Question

Does the conda environment that you have activated on the login node also get used in the compute nodes when submitting a job?

## Methods

* Used conda version 4.6.14
1. Activate a conda env with snakemake installed.
	1. Submit the job & note the job id.
	1. The log file should have snakemake output.
1. Activate a conda env without snakemake.
	1. Submit the job & note the job id.
	1. The log file should have an error message that the snakemake command was not found.

### SLURM
* HPC: `beta-login.stage.arc-ts.umich.edu`
* Script: `submit-slurm.sh`
* Conda environments:
    * With snakemake: `slurm-with-smk.yaml`
    * Without snakemake: `slurm-no-smk.yaml`

### PBS-Torque
* HPC: `flux-login.arc-ts.umich.edu`
* Script: `submit-pbs.sh`
* Conda environments:
    * With snakemake: `pbs-with-smk.yaml`
    * Without snakemake: `pbs-no-smk.yaml`

## Results

### SLURM job with snakemake: 33069

```
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
		1	touch
		1

[Mon Jun  3 14:06:20 2019]
rule touch:
	output: file.txt
	jobid: 0

[Mon Jun  3 14:06:20 2019]
Finished job 0.
1 of 1 steps (100%) done
Complete log: /home/sovacool/test-conda-env/.snakemake/log/2019-06-03T140620.029171.snakemake.log
```

### SLURM job without snakemake: 33070

Conda environment: `slurm-no-smk.yaml`

```
/var/spool/slurmd.spool/job33070/slurm_script: line 49: snakemake: command not found
```

### PBS job with snakemake: 33732423

```
nyx5568
/home/sovacool/test-conda-env-hpc
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	touch
	1

[Wed Jun  5 11:01:27 2019]
rule touch:
    output: file.txt
    jobid: 0

[Wed Jun  5 11:01:27 2019]
Finished job 0.
1 of 1 steps (100%) done
Complete log: /home/sovacool/test-conda-env-hpc/.snakemake/log/2019-06-05T110127.477703.snakemake.log
```

### PBS job without snakemake: 33732416

```
nyx5089
/home/sovacool/test-conda-env-hpc
/var/spool/torque/mom_priv/jobs/33732416.nyx.arc-ts.umich.edu.SC: line 21: snakemake: command not found
```

## Conclusion

Yes!