Master Node cryoSPARC Installation

cd cryosparc_master
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./install.sh --license $LICENSE_ID \
             --hostname <master_hostname> \
             --dbpath <db_path> \
             --port <port_number> \
             [--insecure] \
             [--allowroot] \
             [--yes] \

Example command execution

./install.sh --license $LICENSE_ID \
             --hostname cryoem.cryosparcserver.edu \
             --dbpath /u/cryosparcuser/cryosparc/cryosparc_database \
             --port 45000 \

Start cryoSPARC

./bin/cryosparcm start

Create the first user

cryosparcm createuser --email "<user email>" \
                      --password "<user password>" \
                      --username "<login username>" \
                      --firstname "<given name>" \
                      --lastname "<surname>"

Glossary/Reference

--license $LICENSE_ID

• the LICENCE_ID variable exported in step a)

<master_hostname> = your.cryosparc.hostname.com

• the hostname of the server where the master is to be installed on

<port_number> = 39000

• The base port number for this cryoSPARC instance. Do not install cryosparc master on the same machine multiple times with the same port number - this can cause database errors. 39000 is the default, which will be used if you don't specify this option.

<db_path> = /u/cryosparcuser/cryosparc/cryosparc_database

• the absolute path to a folder where the cryoSPARC database is to be installed. Ensure this location is in a readable and writeable location. The folder will be created if it doesn't already exist

<initial_email> = someone@structura.bio

• login email address for first cryoSPARC webapp account

• this will become an admin account in the user interface

<initial_username> = "FirstName LastName"

• login username of the initial admin account to be created

• ensure the name is quoted

<initial_firstname> = "LastName"

• given name of the initial admin account to be created

• ensure the name is quoted

<initial_lastname> = "LastName"

• surname of the initial admin account to be created

• ensure the name is quoted

<user_password> = Password123

• temporary password that will be created for the <user_email> account

--insecure

• [optional] specify this option to ignore SSL certificate errors when connecting to HTTPS endpoints. This is useful if you are behind an enterprise network using SSL injection.

--allowroot

• [optional] if you run the installation function with root privileges, it will fail. Specify this option to force cryoSPARC to be installed as the root user.

--yes

• [optional] do not ask for any user input confirmations

Connecting a Cluster to cryoSPARC

Once the cryosparc_worker package is installed, the cluster must be registered with the master process, including providing template job submission commands and scripts that the master process will use to submit jobs to the cluster scheduler.

To register the cluster, you will need to provide cryoSPARC with two files: cluster_info.json and clusters_script.sh. The first file (cluster_info.json) contains template strings used to construct cluster commands (like qsub, qstat, qdel etc., or their equivalents for your system), and the second file (cluster_script.sh) contains a template string to construct appropriate cluster submission scripts for your system. The jinja2 template engine is used to generate cluster submission/monitoring commands as well as submission scripts for each job.

The following fields are required to be defined as template strings in the configuration of a cluster. Examples for PBS are given here, but you can use any command required for your particular cluster scheduler.

cluster_info.json
name               :  "cluster1"
# A unique name for the cluster to be connected (multiple clusters can be connected)
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worker_bin_path    :   "/path/to/cryosparc_worker/bin/cryosparcw"
# Path on cluster nodes to the cryosparcw entry point for worker process
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cache_path         :   "/path/to/local/SSD/on/cluster/nodes"
# Path on cluster nodes that is a writable location on local SSD on each cluster node. This might be /scratch or similar. This path MUST be the same on all cluster nodes. Note that the installer does not check that this path exists, so make sure it does and is writable. If you plan to use the cluster nodes without SSD, you can leave this blank.
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send_cmd_tpl       :   "ssh loginnode {{ command }}"
# Used to send a command to be executed by a cluster node (in case the cryosparc master is not able to directly use cluster commands). If your cryosparc master node is able to directly use cluster commands (like qsub etc) then this string can be just "{{ command }}"
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qsub_cmd_tpl       :   "qsub {{ script_path_abs }}"
# The exact command used to submit a job to the cluster, where the job is defined in the cluster script located at {{ script_path_abs }}. This string can also use any of the variables defined below that are available inside the cluster script (num_gpus, num_cpus, etc)
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qstat_cmd_tpl      :   "qstat -as {{ cluster_job_id }}"
# Cluster command that will report back the status of cluster job with id {{ cluster_job_id }}.
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qdel_cmd_tpl       :   "qdel {{ cluster_job_id }}"
# Cluter command that will kill and remove {{ cluster_job_id }} from the queue.
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qinfo_cmd_tpl      :   "qstat -q"
# General cluster information command
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transfer_cmd_tpl   :   "scp {{ src_path }} loginnode:{{ dest_path }}"
# Command that can be used to transfer a file {{ src_path }} on the cryosparc master node to {{ dest_path }} on the cluster nodes. This is used when the master node is remotely updating a cluster worker installation. This is optional - if it is incorrect or omitted, you can manually update the cluster worker installation.

Along with the above commands, a complete cluster configuration requires a template cluster submission script. The script should be able to send jobs into your cluster scheduler queue marking them with the appropriate hardware requirements. The cryoSPARC internal scheduler will take care of submitting jobs as their inputs become ready. The following variables are available to be used within a cluster submission script template. Examples of templates, for use as a starting point, can be generated with the commands explained below.

cluster_script.sh
{{ script_path_abs }}    # the absolute path to the generated submission script
{{ run_cmd }}            # the complete command-line string to run the job
{{ num_cpu }}            # the number of CPUs needed
{{ num_gpu }}            # the number of GPUs needed.
{{ ram_gb }}             # the amount of RAM needed in GB
{{ job_dir_abs }}        # absolute path to the job directory
{{ project_dir_abs }}    # absolute path to the project dir
{{ job_log_path_abs }}   # absolute path to the log file for the job
{{ worker_bin_path }}    # absolute path to the cryosparc worker command
{{ run_args }}           # arguments to be passed to cryosparcw run
{{ project_uid }}        # uid of the project
{{ job_uid }}            # uid of the job
{{ job_creator }}        # name of the user that created the job (may contain spaces)
{{ cryosparc_username }} # cryosparc username of the user that created the job (usually an email)

Note: The cryoSPARC scheduler does not assume control over GPU allocation when spawning jobs on a cluster. The number of GPUs required is provided as a template variable, but either your submission script, or your cluster scheduler itself is responsible for assigning GPU device indices to each job spawned. The actual cryoSPARC worker processes that use one or more GPUs on a cluster will simply begin using device 0, then 1, then 2, etc. Therefore, the simplest way to get GPUs correctly allocated is to ensure that your cluster scheduler or submission script sets the CUDA_VISIBLE_DEVICES environment variable, so that device 0 is always the first GPU that the particular spawned job should use. The example script for pbs clusters (generated as below) shows now to check which GPUs are available at runtime, and automatically select the next available device.

To actually create or set a configuration for a cluster in cryoSPARC, use the following commands. the example, dump, and connect commands read two files from the current working directory: cluster_info.json and cluster_script.sh

cryosparcm cluster example <cluster_type>
# dumps out config and script template files to current working directory
# examples are available for pbs and slurm schedulers but others should be very similar
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cryosparcm cluster dump <name>
# dumps out existing config and script to current working directory
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cryosparcm cluster connect
# connects new or updates existing cluster configuration, reading cluster_info.json and cluster_script.sh from the current directory, using the name from cluster_info.json
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cryosparcm cluster remove <name>
# removes a cluster configuration from the scheduler