cryosparcw reference
How to use the cryosparcw utility for managing cryoSPARC workers
Run all commands in this section while logged into the workstation or worker nodes where the
cryosparc_worker package is installed.Verify that
cryosparcw is in the worker's PATH with this command:which cryosparcw
and ensure the output is not empty.
Alternatively navigate to the worker installation directory and in
bin/cryosparcw. Example:cd /path/to/cryosparc_worker
bin/cryosparcw gpulist
Execute a shell command in a transient CryoSPARC worker shell environment. For example,
cryosparcw call which pythonprints the path of the CryoSPARC worker environment’s Python executable.
Run this command from a worker node or workstation to register a worker with the master, or to edit the configuration on an existing worker.
Enter
cryosparcw connect --help to see full usage details.$ cryosparcw connect --help
usage: connect.py [-h] [--worker WORKER] [--master MASTER] [--port PORT]
[--sshstr SSHSTR] [--update] [--nogpu] [--gpus GPUS]
[--nossd] [--ssdpath SSDPATH] [--ssdquota SSDQUOTA]
[--ssdreserve SSDRESERVE] [--lane LANE] [--newlane]
[--rams RAMS] [--cpus CPUS] [--monitor_port MONITOR_PORT]
Connect to cryoSPARC master
optional arguments:
-h, --help show this help message and exit
--worker WORKER
--master MASTER
--port PORT
--sshstr SSHSTR
--update
--nogpu
--gpus GPUS
--nossd
--ssdpath SSDPATH
--ssdquota SSDQUOTA
--ssdreserve SSDRESERVE
--lane LANE
--newlane
--rams RAMS
--cpus CPUS
--monitor_port MONITOR_PORT
Example command to connect a worker in a single-machine workstation on a new resources lane.
cryosparcw connect \
--worker localhost \
--master localhost \
--port 39000 \
--ssdpath /scratch/cryosparc_cache \
--lane default \
--newlane
Overview of available options.
--worker <WORKER>: (Required) Hostname of the worker that the master can use for access the worker. If the master and worker are running on the same machine (e.g., a workstation), specify--worker localhostIf the master and worker are on the same local network and the master has SSH access to the worker, enter--worker $(hostname)--master <MASTER>: (Required) Hostname of the local network machine--port <PORT>: Port on which the master node is running (default39000)--update: Update an existing worker configuration instead of registering a new one--sshstr <SSHSTR>: SSH-login string for the master to use to send commands to the workers (default$(whoami)@<WORKER>)--nogpu: Registers a worker without any GPUs installed or with GPU access disabled--gpus <GPUS>: Comma-separated list of GPU slots indexes that this worker has access to, starting with0. e.g., to only enable the last two GPUs on a 4-GPU machine, enter--gpus 2,3--nossd: If specified, this worker does not have access to a Solid-State Drive (SSD) to use for caching particle data--ssdpath <SSDPATH>: Path to the location of the mounted SSD drive on the file system to use for caching. e.g.,--ssdpath /scratch/cryosparc_cache--ssdquota <SSDQUOTA>: The maximum amount of space on the SSD that cryoSPARC uses on this worker, in megabytes (MB). Workers automatically remove older cache files to remain below this quota--ssdreserve <SSDRESERVE>: The amount of space to initially reserve on the SSD for this worker--lane <LANE>: Which of cryoSPARC's scheduler lanes to add this worker to. Use with--newlaneto automatically create a new lane--newlane: Create a new scheduler lane to use for this worker instead of using an existing one--rams <RAMS>: Comma-separated list of 8GB Random Access Memory (RAM) slots indexes to use for cryoSPARC jobs--cpus <CPUS>: Comma-separated list of CPU core indexes to use for cryoSPARC jobs--monitor_port <MONITOR_PORT>: Not used
Lists which GPUs the CryoSPARC worker processes have access to.
$ cryosparcw gpulist
Detected 4 CUDA devices.
id pci-bus name
---------------------------------------------------------------
0 0000:02:00.0 Quadro GP100
1 0000:84:00.0 Quadro GP100
2 0000:83:00.0 GeForce GTX 1080 Ti
3 0000:03:00.0 GeForce GTX TITAN X
---------------------------------------------------------------
Use this to verify that the worker is installed correctly
Specifies a new path to the CUDA installation to use. Example usage:
cryosparcw newcuda /usr/local/cuda-10.0
Install a patch previously downloaded on the master node with
cryosparcm patch --download that is copied to the worker installation directory.