Installation
Users can install multiple versions of CryoSPARC. However, each version must have its own separate database. Since version 5, a single CryoSPARC version can also support multiple worker-node architectures simultaneously. For example, the same version can have lanes for x86_64 workers (CPU and A100 nodes on Merlin 7) and aarch64 workers (Grace Hopper nodes on Merlin 7). When submitting a job, the user can then select the appropriate worker architecture.
Mixed Worker Architectures
Currently, a single CryoSPARC installation cannot have both x86_64 and aarch64 workers installed simultaneously on Merlin 7. If you need to use both architectures, separate CryoSPARC installations must be used.
Support for running both architectures under the same CryoSPARC version will soon become available.
Before installing CryoSPARC, obtain a license key from the CryoSPARC download page.
Installation on CPU and A100 nodes¶
The installation can be performed from one of the Merlin 7 login nodes. By default, the CryoSPARC installation path is /data/user/$USER/cryosparc. This path can be changed but you will need to add the flag -d [path to CryoSPARC installation] in the cryosparc-merlin commands when using a non-default path.
To install CryoSPARC version 4.7.1 in the default path (/data/user/$USER/cryosparc):
CryoSPARC base port
The installer also automatically selects a new base port based on availability in the remote node. There is no need to specify one manually during the installation.
Follow the instructions displayed by the installation script.
If an existing installation is overwritten, the installer automatically backs up the previous database.
When the master-node installation starts, the installer will ask:
Are the above settings correct?
Enter 1 and press Enter to proceed.
Later, it will ask:
Add bin directory to your ~/.bashrc ?
Enter 2 and press Enter.
You can then create your CryoSPARC user account. Do not use the same password as your PSI password.
Installation on Grace Hopper nodes¶
Installing CryoSPARC for the Grace Hopper nodes is similar to the standard installation described above. The main differences are:
- The worker-node architecture is
aarch64. - A different CryoSPARC version is used.
- A separate installation path must be specified to avoid conflicts with an existing installation.
In this example, the installation path is /data/user/$USER/cryosparc_beta.
The installation command is:
cryosparc-merlin install complete \
--license [CryoSPARC License] \
--version 5.1.0-privatebeta.2 \
-d /data/user/$USER/cryosparc_beta \
--arch-worker aarch64
Grace Hopper Node Availability
The installation requires an interactive job on a Grace Hopper node to compile the aarch64 worker components. If all Grace Hopper nodes are busy, the job may take some time to start. The installation will continue automatically once a suitable node becomes available.
The master node remains x86_64 because the CryoSPARC instance runs on a node with an x86_64 CPU architecture. Only the worker architecture is changed to aarch64.
As with the standard installation, when the installer asks:
Are the above settings correct?
Enter 1 and press Enter to proceed.
When it asks:
Add bin directory to your ~/.bashrc ?
Enter 2 and press Enter.
Possible Issues¶
The installation may complete without installing the default lanes. If this happens, run:
If CryoSPARC is installed in a location other than /data/user/$USER/cryosparc, specify the installation path with -d: