Re: [HTCondor-users] [External] - Re: Conda env with workstation pool

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Hi Matt,

Singularity can accept dockerfiles to run the application. Your application may very well be more complex than I am thinking, but if it is just a standalone simple python executable, I doubt the dockerfile will be more than 10 lines. Sure now you have to install another piece of software, but now you have gotten around wrapping your jobs in a runner script (bash or python). I have found that scientists, who just want “to get work done” (not that I blame them, that’s a good goal) are receptive to when changes to their workflow make that goal easier.

You could probably write a template dockerfile and just comment above the lines telling your users which lines to change to what to do what they need. Either that or you could write a pretty simple python program that they run at the command line that builds and submits jobs for them. Or you could get fancier if that would help.

IDK if you have a researcher you could use as a “beta-tester” who would be willing to help get an ergonomic workflow going (usually a friend in the office or team mate), and then you could just demo that to the rest of the researchers. As soon as they hear how much faster results come back, they will be on board.

Just my two cents

-Wes

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From: HTCondor-users <htcondor-users-bounces@xxxxxxxxxxx> On Behalf Of West Matthew
Sent: Monday, July 27, 2020 11:42 AM
To: HTCondor-Users Mail List <htcondor-users@xxxxxxxxxxx>
Subject: [External] - Re: [HTCondor-users] Conda env with workstation pool

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Hi All,

I want to stress something that I might not have made clear in previous messages.

I work with a lots of folks who have little experience with running software outside of a single machine. They have a need to scale up their computing effort in order to do a quality analysis but HTC is not why they got interested in the work. This is not to say a biologist or civil engineer cannot learn the tools to containerize their own software, but often incentives prioritizing immediate results make researchers hesitant to try new tools.

- Why do I need all these other skills just to run software like it does on my laptop?

For mature projects and more experienced developers, I believe using containers is an easy sell. But I hope y'all can understand the predicament of lowering the barrier to entry to working in an HTC framework for beginners.

Cheers,
Matt

From: HTCondor-users <htcondor-users-bounces@xxxxxxxxxxx> on behalf of Michael Pelletier via HTCondor-users <htcondor-users@xxxxxxxxxxx>
Sent: Monday, July 27, 2020 1:11:19 AM
To: HTCondor-Users Mail List
Cc: Michael Pelletier
Subject: Re: [HTCondor-users] Conda env with workstation pool

I set up a Singularity container to auto-activate a specified environment at startup, which works pretty well for my users. You might also be able to use the OS-native python to write a python-language wrapper that pulls in all the activation environment variables to its own environment, and then invokes the target Python script.

Michael V Pelletier

Principal Engineer

Raytheon Technologies

Information Technology

Digital Transormation & Innovation

From: HTCondor-users <htcondor-users-bounces@xxxxxxxxxxx> On Behalf Of West Matthew
Sent: Friday, July 24, 2020 7:48 AM
To: HTCondor-Users Mail List <htcondor-users@xxxxxxxxxxx>
Subject: [External] Re: [HTCondor-users] Conda env with workstation pool

Hi Josh,

I am working from the CHTC recommendation using conda pack. I am curious if you know a way to activate the conda environment from within a python script? Having to wrap my python executable with a bash script is rather frustrating when I am trying to get away from multi-language situation.

I can create the directory and extract the contents of the tarball. I just need to activate the env.

Cheers,

Matt

From: HTCondor-users <htcondor-users-bounces@xxxxxxxxxxx> on behalf of Josh Karpel via HTCondor-users <htcondor-users@xxxxxxxxxxx>
Sent: Thursday, July 23, 2020 4:41:59 PM
To: HTCondor-Users Mail List
Cc: Josh Karpel
Subject: Re: [HTCondor-users] Conda env with workstation pool

That pretty much lines up with what we tell people to do at CHTC: http://chtc.cs.wisc.edu/conda-installation.shtml

Josh Karpel

karpel@xxxxxxxx

On Thu, Jul 23, 2020 at 8:25 AM Michael Pelletier via HTCondor-users <htcondor-users@xxxxxxxxxxx> wrote:

I’ve built a Singularity definition file that installs Miniconda and creates an environment YAML file, then builds the environment, and then configures the container so that the environment is activated automatically at the startup of the Singularity container. With Miniconda a CUDA 10.2 and 18.04 Ubuntu Singularity container file is about 850 megabytes in size.

Singularity doesn’t necessarily have an extra infrastructure layer, as it doesn’t require any services from the host – I bet it would be possible to input-transfer the Singularity executable and run it on an input-transferred container.

Alternatively, you could build out the full virtualenv in a directory with Miniconda, and then input-transfer that whole directory and activate it when the job starts up, which would eliminate the need for modules to be available on the exec node.

Michael V Pelletier
Principal Engineer

Raytheon Technologies
Information Technology
Digital Transormation & Innovation

From: HTCondor-users <htcondor-users-bounces@xxxxxxxxxxx> On Behalf Of West Matthew
Sent: Thursday, July 23, 2020 7:03 AM
To: htcondor-users@xxxxxxxxxxx
Subject: [External] [HTCondor-users] Conda env with workstation pool

I am trying to run an analysis on my local workstation pool that relies on software in a conda virtual environment. When the job runs on a remote machine, it does not have access to the libraries in that env back on the submit machine.

Given that virtual environments are common practice when running locally, I an hoping there is some means of making python libraries accessible without resorting to an extra infrastructure layer like Docker.

Cheers,
Matt
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Re: [HTCondor-users] [External] - Re: Conda env with workstation pool