HPC Clusters
vEcoli uses Nextflow and Apptainer containers to run on high-performance computing (HPC) clusters. For users with access to the Covert Lab’s partition on Sherlock, follow the instructions in the Sherlock section. For users looking to run the model on other HPC clusters, follow the instructions in the Other Clusters section.
To speed up HPC workflows, vEcoli supports the HyperQueue executor. See HyperQueue for more information.
Sherlock
On Sherlock, once a workflow is started with runscripts.workflow
,
runscripts/container/build-image.sh
builds an Apptainer image with
a minimal snapshot of your cloned repository. Nextflow starts containers
using this image to run the steps of the workflow. To run or interact
with the model outside of runscripts.workflow
, start an
interactive container by following the steps in Interactive Container.
Setup
Note
The following setup applies to members of the Covert Lab only.
After cloning the model repository to your home directory, add the following
lines to your ~/.bash_profile
, then close and reopen your SSH connection:
# Load newer Git, Java (for nextflow), and Python
module load system git java/21.0.4 python/3.12.1
# Include shared Nextflow and HyperQueue installations on PATH
export PATH=$PATH:$GROUP_HOME/vEcoli_env
Then, run the following to test your setup:
python3 runscripts/workflow.py --config configs/test_sherlock.json
This will run a small workflow that:
Builds an Apptainer image with a snapshot of your cloned repository.
Runs the ParCa.
Runs one simulation.
Runs the mass fraction analysis.
All output files will be saved to a test_sherlock
directory in your
cloned repository. You can modify the workflow output directory by changing
the out_dir
option under emitter_arg
in the config JSON.
See Configuration for a description of the Sherlock-specific
configuration options and Running Workflows for details about running
a workflow on Sherlock.
To run scripts on Sherlock outside a workflow, see Interactive Container. To run scripts on Sherlock through a SLURM batch script, see Non-Interactive Container.
Note
The above setup is sufficient to run workflows on Sherlock. However, if you
have a compelling reason to update the shared Nextflow or HyperQueue binaries,
navigate to $GROUP_HOME/vEcoli_env
and run:
Nextflow:
NXF_EDGE=1 nextflow self-update
HyperQueue: See HyperQueue.
Configuration
To tell vEcoli that you are running on Sherlock, you MUST include the following
keys in your configuration JSON (note the top-level sherlock
key):
{
"sherlock": {
# Boolean, whether to build a fresh Apptainer image. If files that are
# not excluded by .dockerignore did not change since your last build,
# you can set this to false to skip building the image.
"build_image": true,
# Path (relative or absolute, including file name) of Apptainer image to
# build (or use directly, if build_image is false)
"container_image": "",
# Boolean, whether to run using HyperQueue.
"hyperqueue": false,
# Boolean, denotes that a workflow is being run as part of Jenkins
# continuous integration testing. Randomizes the initial seed and
# ensures that all STDOUT and STDERR is piped to the launching process
# so they can be reported by GitHub
"jenkins": false
}
}
In addition to these options, you MUST set the emitter output directory
(see description of emitter_arg
in JSON Config Files) to a path with
enough space to store your workflow outputs. We recommend setting this to
a location in your $SCRATCH
directory (e.g. /scratch/users/{username}/out
).
If using the Parquet emitter and threaded
is not set to false under
emitter_arg
, a warning will be printed suggesting that you set threaded
to false. This ensures that simulations use only a single CPU core, the default
that is allocated per simulation on Sherlock (regardless of whether HyperQueue
is used). On Sherlock, storage speed is not a bottleneck, so performance with
threaded
set to false and 1 core per simulation is comparable to running
with threaded
unset (default: true) and 2 cores per simulation.
If storage speed was a bottleneck, the additional thread would allow
simulation execution to continue while Polars writes Parquet files to disk.
To properly take advantage of this, you would also need to increase the number
of cores per simulation to 2 by modifying the cpus
directive under the
sherlock
and sherlock_hq
profiles in runscripts/nextflow/config.template
.
Warning
~
and environment variables like $SCRATCH
are not expanded in the
configuration JSON. See the warning box at Workflows.
Running Workflows
With these options in the configuration JSON, a workflow can be started by
running python3 runscripts/workflow.py --config {}
, substituting
in the path to your config JSON.
Warning
Remember to use python3
to start workflows instead of python
.
This command should be run on a login node (no need to request a compute node).
If build_image
is true in your config JSON, the terminal will report that
a SLURM job was submitted to build the container image. When the image build
job starts, the terminal will report the build progress.
Note
Files that match the patterns in .dockerignore
are excluded from the image.
Warning
Do not make any changes to your cloned repository or close your SSH connection until the build has finished.
Once the build has finished, the terminal will report that a SLURM job was submitted for the Nextflow workflow orchestrator before exiting back to the shell. At this point, you are free to close your connection, start additional workflows, etc. Unlike workflows run locally, Sherlock’s containerized workflows mean any changes made to the repository after the container image has been built will not affect the running workflow.
Once started, the Nextflow job will stay alive for the duration of the workflow (up to 7 days) and submit new SLURM jobs as needed.
If you are trying to run a workflow that takes longer than 7 days, you can use the resume functionality (see Fault Tolerance). Alternatively, consider running your workflow on Google Cloud, which has no maximum workflow runtime (see Google Cloud).
You can start additional, concurrent workflows that each build a new image
with different modifications to the cloned repository. However, if possible,
we recommend designing your code to accept options through the config JSON
which modify the behavior of your workflow without modifying core code. This
allows you to save time by reusing a previously built image as follows:
set build_image
to false and container_image
to the path of said image.
There is a 4 hour time limit on each job in the workflow, including analyses. This is a generous limit designed to accomodate very slow-dividing cells. Generally, we recommend that users exclude analysis scripts which take more than a few minutes from their workflow configuration. Instead, either run these manually following Interactive Container or create a SLURM batch script to run these analyses following Non-Interactive Container.
Interactive Container
Warning
The following steps should be run on a compute node. See the Sherlock documentation for details.
The maximum resource request for an interactive compute
node is 2 hours, 4 CPU cores, and 8GB RAM/core. Scripts that require more
resources should be submitted as SLURM batch scripts to the mcovert
or owners
partition (see Non-Interactive Container).
To run scripts on Sherlock, you must have either:
Previously run a workflow on Sherlock and have access to the built container image
Built a container image manually using
runscripts/container/build-image.sh
with the-a
flag
Start an interactive container with your full image path (see the warning box at Workflows) by navigating to your cloned repository and running:
runscripts/container/interactive.sh -i container_image -a
Note
Inside the interactive container, you can safely use python
directly
in addition to the usual uv
commands.
The above command launches a container containing a snapshot of your
cloned repository as it was when the image was built. This snapshot
is located at /vEcoli
inside the container and is mostly intended
to guarantee reproducibility for troubleshooting failed workflow jobs.
More specifically, users who wish to debug a failed workflow job should:
Start an interactive container with the image used to run the workflow.
Use
nano
to add breakpoints (import ipdb; ipdb.set_trace()
) to the relevant scripts in/vEcoli
.Navigate to the working directory (see Troubleshooting) for the job that you want to debug.
Invoke
bash .command.sh
to run the failing task and pause upon reaching your breakpoints, allowing you to inspect variables and step through the code.
Warning
~
and environment variables like $SCRATCH
do not work
inside the container. Follow the instructions in the warning box at
Workflows outside the container to get the full path to
use inside the container.
Danger
Any changes that you make to /vEcoli
inside the container are discarded
when the container terminates.
To start an interactive container that reflects the current state of your
cloned repository, navigate to your cloned repository and run the above
command with the -d
flag to start a “development” container:
runscripts/container/interactive.sh -i container_image -a -d
In this mode, instead of editing source files in /vEcoli
, you can
directly edit the source files in your cloned repository and have those
changes immediately reflected when running those scripts inside the
container. Because you are just modifying your cloned repository, any
code changes you make will persist after the container terminates and
can be tracked using Git version control.
Non-Interactive Container
To run any script inside a container without starting an interactive session,
use the same command as Interactive Container but specify a command
using the -c
flag. For example, to run the ParCa process, navigate to
your cloned repository and run the following command, replacing container_image
with the path to your container image and {}
with the path to your
configuration JSON:
runscripts/container/interactive.sh -i container_image -c "python /vEcoli/runscripts/parca.py --config {}"
This feature is intended for use in SLURM batch scripts to manually run analysis scripts with custom resource requests. Make sure to include one of the following directives at the top of your script:
#SBATCH --partition=owners
: This is the largest partition on Sherlock and the most likely to have free resources available for job scheduling. Even so, queue times are variable, and other users may preempt your job at any moment, though this is anecdotally rare for small jobs under an hour long.#SBATCH --partition=mcovert
: Best for high priority scripts (short queue time) that you cannot risk being preempted. The number of available cores is 32 minus whatever is currently being used by other users in themcovert
partition. Importantly, if all 32 cores are in use bymcovert
users, not only will your script have to wait for resources to free up, so will any workflows. As such, treat this partition as a limited resource reserved for high priority jobs.#SBATCH --partition=normal
: Potentially longer queue time than either of the two options above but no risk of preemption.#SBATCH --partition=owners,normal
: Uses either theowners
ornormal
partition. This is the recommended option for the vast majority of scripts.
Just as with interactive containers, to run scripts directly from your
cloned repository and not the snapshot, add the -d
flag and drop the
/vEcoli/
prefix from script names. Note that changing files in your
cloned repository may affect SLURM batch jobs submitted with this flag.
Other Clusters
Nextflow has support for a wide array of HPC schedulers. If your HPC cluster uses a supported scheduler, you can likely run vEcoli on it with fairly minimal modifications.
Prerequisites
The following are required:
Nextflow (requires Java)
Python 3.9+
Git clone vEcoli to a location that is accessible from all nodes in your cluster
out_dir
underemitter_arg
set to a location that is accessible from all nodes in your cluster
If your cluster has Apptainer (formerly known as Singularity) installed,
check to see if it is configured to automatically mount the filesystem of
out_dir
(e.g. $SCRATCH
). If not, you will need to add -B /full/path/to/out_dir
to the containerOptions
directives in runscripts/nextflow/config.template
,
substituting in the absolute path to out_dir
. Additionally, you will need to
manually specify the same paths when running interactive containers
(see Interactive Container) using the -p
option.
If your cluster does not have Apptainer, you can try the following steps:
Completely follow the local setup instructions in the README (install uv, etc).
Delete the following lines from
runscripts/nextflow/config.template
:
process.container = 'IMAGE_NAME'
...
apptainer.enabled = true
Make sure to always set
build_runtime_image
to false in your config JSONs (see Configuration)
Cluster Options
If your HPC cluster uses the SLURM scheduler,
you can use vEcoli on that cluster by changing the queue
option in
runscripts/nextflow/config.template
and runscripts/nextflow/template.nf
and all instances of --partition=QUEUE(S)
in runscripts.workflow
to the right queue(s) for your cluster. Also, remove the --prefer="CPU_GEN...
clusterOptions
in those same files.
If your HPC cluster uses a different scheduler, refer to the Nextflow
executor documentation
for more information on configuring the right executor. Beyond the changes above,
you will at least need to modify the executor
directives for the sherlock
and sherlock_hq
profiles in runscripts/nextflow/config.template
and for the
hqWorker
process in runscripts/nextflow/template.nf
. Additionally, you will
need to replace the SLURM submission directives in runscripts.workflow.main()
with equivalent directives for your scheduler.
HyperQueue
HyperQueue consists of a head server and one or more workers allocated by the underlying HPC scheduler. By configuring the worker jobs to persist for long enough to complete multiple tasks, HyperQueue reduces the amount of time spent waiting in the queue, which is especially important for workflows with numerous shorter tasks like ours. We recommend using HyperQueue for all workflows that span more than a handful of generations.
Internal Logic
If the hyperqueue
option is set to true under the sherlock
key in the
configuration JSON used to run runscripts/workflow.py
, the following steps
will occur in order:
If
build_image
is True, submit a SLURM job to build the container image.Submit a single long-running SLURM job on the dedicated Covert Lab partition to run both Nextflow and the HyperQueue head server.
Start the HyperQueue head server (initially no workers).
Nextflow submits a SLURM job to run the ParCa then another to create variants. Both must finish for Nextflow to calculate the maximum number of concurrent simulations
# seeds * # variants
.Nextflow submits SLURM jobs to start
(# seeds * # variants) // 4
HyperQueue workers, each worker with 4 cores, 16GB RAM, and a 24 hour limit. A proportionally smaller worker is potentially created to handle the remainder (e.g. for 2 leftover, 2 cores, 8GB RAM, and same 24 hour limit).Nextflow submits simulation tasks to the HyperQueue head server, which schedules them on the available workers.
Nextflow submits analysis tasks to SLURM directly as they do not hold up the workflow and can wait for a bit in the queue. This increases simulation throughput by dedicating all HyperQueue worker resources to running simulations.
If any HyperQueue worker job terminates with one of three exit codes (see Fault Tolerance), it is resubmitted by Nextflow to maintain the optimal number of workers for parallelizing the workflow.
As lineages fail and/or complete, the number of concurrent simulations decreases and HyperQueue workers start to go idle. Idle workers automatically terminate after 5 minutes of inactivity.
Upon completion of the Nextflow workflow, the HyperQueue head server terminates any remaining workers and exits.
Monitoring
As long as --server-dir
is given as described below, the hq
command can be
run on any node to monitor the status of the HyperQueue workers and jobs
for a given workflow
(cheatsheet).
# Replace OUTDIR with the output directory and EXPERIMENT_ID with the
# experiment ID from your configuration JSON.
# Get HyperQueue JOB_ID from this list of jobs
hq --server-dir OUTDIR/EXPERIMENT_ID/nextflow/.hq-server job list
# Get more detailed information about a specific job by ID, including
# its work directory, runtime, and node
hq --server-dir OUTDIR/EXPERIMENT_ID/nextflow/.hq-server job info JOB_ID
Updating
HyperQueue is distributed as a pre-built binary on GitHub.
Unfortunately, this binary is built with a newer version of GLIBC than the
one available on Sherlock, necessitating a rebuild from source. A binary built
in this way is available in $GROUP_HOME/vEcoli_env
to users with access to
the Covert Lab’s partition on Sherlock. This is added to PATH
in the
Sherlock setup instructions, so no further action is required.
Users who want or need to build from source should follow these instructions.