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update copyright, vanilla is default, put getenv in main sample
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gweatherby committed Aug 22, 2023
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2 changes: 1 addition & 1 deletion LICENSE
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MIT License

Copyright (c) 2022 NMRbox
Copyright (c) 2023 NMRbox

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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22 changes: 7 additions & 15 deletions README.md
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Expand Up @@ -9,7 +9,7 @@ wedell@uchc.edu
## Background

During this tutorial we will walk through submitting jobs to the HTCondor
workload management system. We will then investigate how the jobs run in the HTCondor
workload management system on NMRbox. We will then investigate how the jobs run in the HTCondor
environment and explore how to manage submitted jobs.

### The submit file
Expand All @@ -25,28 +25,30 @@ Let's look at a simple submit file in detail to see what arguments are necessary


```
universe = vanilla
executable = /bin/ls
arguments = /
log = logs/basic.log
output = logs/basic.out
error = logs/basic.err
getenv=True
queue
```

Going through the lines in order:

* The universe specified which HTCondor universe to run in. These are discussed
in the slides. The most straightforward is the `vanilla` universe. As a beginner this
universe should be suitable for all your jobs.
* The executable specifies which command should actually be ran when the job runs. You
must use an absolute path.
* The arguments line, while technically optional, will almost always be used. It allows you
to specify which command line arguments to provide to the executable.
* The log, output, and error commands specify where HTCondor will log. The output and
error will be populated with whatever the job writes to STDERR and STDOUT while the
log will contain the HTCondor logs related to the scheduling and running of the job.
* This line ensures that the HTCondor job runs with the same shell environment as existed in the shell
where you submitted the job. Without specifying this, your job may fail due to not being able to locate
a called executable in the path, or due to other issues. This is not a very portable option when submitting
to a heterogeneous computing environment, but it works well on production NMRbox machines, and simplifies
your life when developing your first submit files.
* The queue parameter is special. Each time this argument is encountered in the file
HTCondor will submit a job to the queue with whatever arguments were specified prior
in the file. You can specify queue multiple times on different lines, and optionally
Expand Down Expand Up @@ -102,16 +104,6 @@ and rely on the shared file system, which avoids you needing to specify which in
The only thing to be careful of is that you have your job located in your home directory (or a subdirectory)
and not in your scratch directory or other machine-specific temporary directory.

```
getenv=True
```

This line ensures that the HTCondor job runs with the same shell environment as existed in the shell
where you submitted the job. Without specifying this, your job may fail due to not being able to locate
a called executable in the path, or due to other issues. This is not a very portable option when submitting
to a heterogeneous computing environment, but it works well on production NMRbox machines, and simplifies
your life when developing your first submit files.

#### Variables!

It is possible to specify custom variables in your submit file, and have them interpreted in the appropriate
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