Lanes

A standard CryoSPARC complete installation creates a set of default lanes configured for the Merlin 7 cluster.

The lanes available by default are listed below.

Lanes	Memory	CPUs	Time	Queue
cpu-hourly	Set by CryoSPARC	Set by CryoSPARC	1 hour	hourly
cpu-daily	Set by CryoSPARC	Set by CryoSPARC	24 hours (1 day)	daily

a100-hourly	Set by CryoSPARC	16 per GPU	1 hour	a100-hourly
a100-daily-4h	Set by CryoSPARC	16 per GPU	4 hours	a100-daily
a100-daily	Set by CryoSPARC	16 per GPU	24 hours (1 day)	a100-daily
a100-general-2d	Set by CryoSPARC	16 per GPU	48 hours (2 days)	a100-general
a100-general-2d-100Gb	100 Gb	16 per GPU	48 hours (2 days)	a100-general

gh-hourly	Set by CryoSPARC	72 per GPU	1 hour	gh-hourly
gh-daily-4h	Set by CryoSPARC	72 per GPU	4 hours	gh-daily
gh-daily	Set by CryoSPARC	72 per GPU	24 hours (1 day)	gh-daily
gh-general-2d	Set by CryoSPARC	72 per GPU	48 hours (2 days)	gh-general
gh-general-2d-100Gb	100 Gb	72 per GPU	48 hours (2 days)	gh-general

During installation, lanes are created according to the architecture of the available worker nodes.

Default lanes¶

The default lanes can also be installed in an existing CryoSPARC installation using the cryosparc-merlin command.

For x86_64 worker nodes (CPU and A100 nodes on Merlin 7):

Bash

cryosparc-merlin lanes create default --arch-worker x86_64

For aarch64 worker nodes (Grace Hopper nodes on Merlin 7):

Bash

cryosparc-merlin lanes create default --arch-worker aarch64

The -d / --cryosparc-path option

If the CryoSPARC installation is not located in the default directory /data/user/$USER/cryosparc, specify the installation path using the -d option.

The lanes are created in the CryoSPARC installation directory under lanes/. For example, /data/user/$USER/cryosparc/lanes/.

To install all lanes stored in this directory, run:

Bash

cryosparc-merlin lanes install --all

Create lanes¶

You can create custom CryoSPARC lanes using the cryosparc-merlin lanes create command:

Bash

cryosparc-merlin lanes create \
    --name          [Lane name] \
    --cache-path    [Cache directory] \
    --cluster       ['merlin7' or 'gmerlin7'] \
    --memory        [Memory in GB] \
    --time          [dd-hh:mm:ss] \
    --partition     [Partition] \
    --gpus          [Number of GPUs] \
    --cpus-per-task [Number of CPUs] \
    --arch-worker   ['x86_64' or 'aarch64']

The lane configuration is saved in the CryoSPARC installation directory under lanes/.

Node CPU architecture

On Merlin 7, CPU and A100 nodes have a x86_64 CPU architecture while the Grace-Hopper nodes have a aarch64 CPU architecture.

Install lanes¶

To install a previously created lane into the CryoSPARC database, run:

Bash

cryosparc-merlin lanes install --name [Lane name]

Remove lanes¶

To remove a lane from the CryoSPARC database, run:

Bash

cryosparc-merlin lanes remove --name [Lane name]

Note

Removing a lane from the CryoSPARC database does not remove its configuration file from the lanes/ directory.