> For the complete documentation index, see [llms.txt](https://guide.cryosparc.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure/downloading-and-installing-cryosparc.md). # Downloading and Installing CryoSPARC Downloading and installing the cryosparc\_master and cryosparc\_worker packages. ## Overview Once you've reviewed the CryoSPARC Installation Prerequisites and have decided on an architecture suitable for your situation, the installation process can be distilled to a few main steps which are further detailed below: 1. Download the `cryosparc_master` package 2. Download the `cryosparc_worker` package (the x86-64 package, or the ARM64 (aarch64) package for ARM64 workers) 3. Install the `cryosparc_master` package on the master node 4. Start cryoSPARC for the first time 5. Create the first administrator user 6. \[Optional but recommended] Set up recurring backup of the CryoSPARC database 7. **If you chose to install CryoSPARC via the single-workstation method, at this point, you are finished installing CryoSPARC. Otherwise, continue.** 8. Log onto a worker node and install the `cryosparc_worker` package (installing the `cryosparc_worker` package requires an Nvidia GPU and Nvidia Driver 570.26 or newer on x86-64 workers, or 580.65.06 or newer on ARM64 (aarch64) workers) 9. Depending on whether you're installing CryoSPARC on a cluster or on a standalone worker machine, connect the worker node to CryoSPARC via `cryosparcm cluster connect` or `cryosparcw connect` 10. **CryoSPARC is now fully installed.** You may also choose to add more standalone worker machines at any time by using the `cryosparcw connect` utility. {% hint style="warning" %} You will need at least 15 GB of space to download and install the `cryosparc_master` and `cryosparc_worker`packages {% endhint %} ## Prepare for Installation ### **Log into the workstation** where you would like to install and run CryoSPARC ``` ssh @ ``` {% hint style="info" %} ` = cryosparcuser` * The username of the account that cryoSPARC is to be installed by. ` = uoft` * The hostname of the server where cryoSPARC will be installed on. {% endhint %} ### Select a suitable directory for installation `cryosparc_master/`and/or `cryosparc_worker/`directories will be created inside the selected directory during a subsequent step. Select the directory carefully because the `cryosparc_master/`and `cryosparc_worker/` directories cannot be moved following installation. The absolute path to the installation directory must not exceed 83 characters (after dereferencing sybolic links in the path, if applicable). Suppose one selected and, if necessary, created the `/sw/cryosparc/`directory for this purpose: ```bash # enter the selected directory cd /sw/cryosparc # confirm the max path length is not exceeded echo -n $(pwd -P) | wc -c ``` ## **Download and Extract the `cryosparc_master` and `cryosparc_worker` Packages** Into Your Installation Directory {% hint style="info" %} The `cryosparc_master` package, and therefore single-workstation installation, is available for x86-64 only. The `cryosparc_worker` package is available for x86-64 and ARM64 (aarch64). Each worker must use the package that matches its own CPU architecture; run `uname -m` on the worker, which prints `x86_64` or `aarch64`. A master node can manage workers of both architectures. {% endhint %} ### **Define your License ID** as an environment variable: ```bash LICENSE_ID="your-unique-license-id" ``` {% hint style="info" %} Your unique CryoSPARC license ID * should be included in an e-mail we sent to you * should look similar to the example `682437fb-d6ae-47b8-870b-b530c587da94` * can be used for the installation and operation of a single CryoSPARC master instance and all CryoSPARC workers associated with that single master instance {% endhint %} {% hint style="warning" %} CryoSPARC download or installation commands that include or refer to `$LICENSE_ID` will fail if the `LICENSE_ID` variable is not defined in the current shell's environment. {% endhint %} ### Use `curl` to **download the two files** into tarball archives You can download the latest public CryoSPARC version, or you can specify a particular version to install. For the latest version, use the below commands. To specify a version, replace `VERSION="latest"` with `VERSION="vX.Y.Z"` (for example, `VERSION="v4.7.1"` ). See the [changelog ](https://cryosparc.com/updates)for all available versions. ``` VERSION="latest" curl -L https://get.cryosparc.com/download/master-$VERSION/$LICENSE_ID -o cryosparc_master.tar.gz curl -L https://get.cryosparc.com/download/worker-$VERSION/$LICENSE_ID -o cryosparc_worker.tar.gz ``` The commands above download the x86-64 packages. To download the worker package for an ARM64 (aarch64) worker (available from CryoSPARC v5.1.0), add `?os=linux&arch=aarch64` to the worker URL. Keep the quotation marks, because the URL contains `&`: ``` VERSION="latest" curl -L "https://get.cryosparc.com/download/worker-$VERSION/$LICENSE_ID?os=linux&arch=aarch64" -o cryosparc_worker.tar.gz ``` If you use the ARM64 worker package on an x86-64 machine, or the reverse, `install.sh` stops with an error such as `This CryoSPARC package requires a aarch64 system, but the current system is x86_64.` ### **Extract the downloaded files**: ``` tar -xf cryosparc_master.tar.gz cryosparc_master tar -xf cryosparc_worker.tar.gz cryosparc_worker ``` **Note:** After extracting the worker package, you may see a second folder called `cryosparc2_worker` (note the `2`) containing a single `version` file. This is here for backward compatibility when upgrading from older versions of CryoSPARC and is not applicable for new installations. You may safely delete the `cryosparc2_worker` directory. ## **Install The `cryosparc_master` Package** Follow these instructions to install the master package on the master node. If you are following the Single Workstation setup, once you run the installation command, CryoSPARC will be ready to use. {% hint style="danger" %} After installation and startup, the `cryosparc_master` software [CryoSPARC Installation Prerequisites](/setup-configuration-and-management/cryosparc-installation-prerequisites.md) for connections from other computers, such as CryoSPARC worker nodes and computers from which users browse the CryoSPARC user interface. You must ensure that these ports cannot be accessed *directly* from the internet. The CryoSPARC guide contains [suggestions](/setup-configuration-and-management/how-to-download-install-and-configure/accessing-cryosparc.md) on implementing access to the user interface. {% endhint %} {% hint style="warning" %} If you are installing CryoSPARC on a single workstation, you can use the **Single Workstation** instructions below that simplify installation to a single command. Otherwise, use the **Master Node Only** instructions here, and then continue with the further steps to install on worker nodes separately. {% endhint %} {% hint style="warning" %} Select and monitor the filesystem that hosts the `$CRYOSPARC_DB_PATH` directory carefully. The CryoSPARC instance will fail if the filesystem is allowed to fill up completely. Recovery from such a failure may take significant time for large instance. The directory can be specified during installation with the "--`dbpath"` parameter of the `install.sh` command. Otherwise, the default is a directory named `cryosparc_database` inside the directory where the software tar packages were unpacked. The CryoSPARC database holds metadata, images, plots and logs of jobs that have run. If the database becomes corrupt or lost due to to user error or filesystem issues, the instance must be recovered. A CryoSPARC instance can be recovered as follows: 1. For CryoSPARC versions up to v4.7: In a new/fresh CryoSPARC instance, import the **project directories** of projects from the original instance. This should resurrect all jobs, outputs, inputs, metadata, etc. **Please note:** user and instance level settings and configuration will be lost. Users, worker lanes, and scheduler configurations will need to be re-created in the new instance. 2. For CryoSPARC v5.0+: The new `cryosparcm recover` command can be used to automatically recover an instance if the database is lost. See [Instance Recovery](/setup-configuration-and-management/software-system-guides/guide-instance-recovery-v5.0.md) for more details. {% endhint %} {% tabs %} {% tab title="Single Workstation (Master and Worker combined)" %} ### **Single Workstation** CryoSPARC Installation ``` cd cryosparc_master ./install.sh --standalone \ --license $LICENSE_ID \ --worker_path \ --ssdpath \ --initial_email \ --initial_username "" \ --initial_firstname "" \ --initial_lastname "" \ [--port ] \ [--initial_password ] ``` **Example command execution** ``` ./install.sh --standalone \ --license $LICENSE_ID \ --worker_path /u/cryosparc_user/cryosparc/cryosparc_worker \ --ssdpath /scratch/cryosparc_cache \ --initial_email "someone@structura.bio" \ --initial_password "Password123" \ --initial_username "username" \ --initial_firstname "FirstName" \ --initial_lastname "LastName" \ --port 61000 ``` ### Glossary/Reference ` = /home/cryosparc_user/software/cryosparc/cryosparc_worker` * the **full** path to the worker directory, which was downloaded and extracted in step c) To get the full path, `cd` into the `cryosparc_worker` directory and run the command: `pwd -P` ` = /scratch/cryosparc_cache` * path on the worker node to a writable directory residing on the local SSD (For more information on SSD usage in cryoSPARC, see X) * this is optional, and if omitted, specify the `--nossd` option to indicate that the worker node does not have an SSD ` = someone@structura.bio` * login email address for first CryoSPARC webapp account * this will become an admin account in the user interface ` = "FirstName LastName"` * login username of the initial admin account to be created * ensure the name is quoted ` = "FirstName"` * given name of the initial admin account to be created * ensure the name is quoted ` = "LastName"` * surname of the initial admin account to be created * ensure the name is quoted ` = Password123` * temporary password that will be created for the `` account * Note that if this argument is not specified, a silent input prompt will be provided ` = 61000` * 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. **Choose the base port number carefully to** * avoid conflicts with other applications * avoid conflicts with other CryoSPARC instances that may be running on the same computer {% hint style="info" %} Versions of CryoSPARC prior to v4.4.0 also require `--cudapath ` where \ corresponds to the CUDA installation directory, such as `/opt/cuda-11.8,` that *contains* the `bin/` and `lib64/` subdirectories on the worker node, *not* the `cuda-11.8/bin/` subdirectory. {% endhint %} {% endtab %} {% tab title="Master Node Only" %} ### Master Node CryoSPARC Installation ```bash cd cryosparc_master ./install.sh --license $LICENSE_ID \ --hostname \ --dbpath \ --port \ [--insecure] \ [--allowroot] \ [--yes] ``` **Example command execution** ```bash ./install.sh --license $LICENSE_ID \ --hostname cryoem.cryosparcserver.edu \ --dbpath /u/cryosparcuser/cryosparc/cryosparc_database \ --port 61000 ``` #### Start CryoSPARC ``` ./bin/cryosparcm start ``` #### Create the first user ```bash cryosparcm user create --email "" \ --password "" \ --username "" \ --firstname "" \ --lastname "" \ --role admin ``` In this example, a user with the [*admin* role](/application-guide/admin-panel.md#user-management) is created. See `cryosparcm user` [documentation](/setup-configuration-and-management/management-and-monitoring-v5.0/cryosparcm-reference-v5.0.md#cryosparcm-user-create) for details. {% hint style="info" %} In CryoSPARC v4, use the `cryosparcm createuser` command instead ([syntax](/setup-configuration-and-management/management-and-monitoring-4.7/cryosparcm-4.7.md#cryosparcm-createuser)). {% endhint %} ### Glossary/Reference `--license $LICENSE_ID` * the LICENCE\_ID variable exported in step a) ` = your.cryosparc.hostname.com` * the hostname of the server where the master is to be installed on ` = 61000` * 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. **Choose the base port number carefully to** * avoid conflicts with other applications * avoid conflicts with other CryoSPARC instances that may be running on the same node ` = /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 ` = someone@structura.bio` * login email address for first CryoSPARC webapp account * this will become an admin account in the user interface ` = "FirstName LastName"` * login username of the initial admin account to be created * ensure the name is quoted ` = "FirstName"` * given name of the initial admin account to be created * ensure the name is quoted ` = "LastName"` * surname of the initial admin account to be created * ensure the name is quoted ` = Password123` * temporary password that will be created for the `` 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 {% endtab %} {% endtabs %} ### \[Optional] Re-load your `bashrc`**.** This will allow you to run the `cryosparcm` management script from anywhere in the system: ``` source ~/.bashrc ``` ### **Access the User Interface** After completing the above, navigate your browser to `http://:` to access the CryoSPARC user interface. {% content-ref url="/pages/-M8D1uoTdonr7yVA223d" %} [Accessing the CryoSPARC User Interface](/setup-configuration-and-management/how-to-download-install-and-configure/accessing-cryosparc.md) {% endcontent-ref %} {% hint style="warning" %} If you were following the **Single Workstation** install above, your installation is now complete. {% endhint %} ## Install The **`cryosparc_worker`** Package Log onto the worker node (or a cluster worker node if installing on a cluster) as the `cryosparcuser`, and run the installation command. {% hint style="info" %} Installing `cryosparc_worker` requires a Nvidia GPU and Nvidia Driver version 570.26 or newer (x86-64 workers) or 580.65.06 or newer (ARM64/aarch64 workers) {% endhint %} ### GPU Worker Node CryoSPARC Installation ``` cd cryosparc_worker ./install.sh --license $LICENSE_ID [--yes] ``` ### Worker Installation Glossary/Reference `--license $LICENSE_ID` * The LICENCE\_ID exported in the "Export your License ID as an environment variable" step `--yes` * *\[optional]* do not ask for any user input confirmations {% hint style="info" %} Versions of CryoSPARC prior to v4.4.0 also require `--cudapath ` such as ``` ./install.sh --license $LICENSE_ID --cudapath /opt/cuda-11.8 ``` * Path to the CUDA installation directory on the worker node * **Note**: this path should not be the `cuda/bin/` sub directory, but the CUDA directory that contains both `bin/` and `lib64/` subdirectories {% endhint %} ## Connecting A Worker Node Ensure cryoSPARC is running when connecting a worker node. Log into the worker node and run the `cryosparcw connect` command, substituting the placeholders with your own configuration parameters: ``` cd /path/to/cryosparc_worker ./bin/cryosparcw connect --master \ [--worker ] \ [--port ] \ [--ssdpath ] \ [--sshstr ] \ [--gpus | --no-gpu ] \ [--cpus ] \ [--rams ] \ [--ssdquota ] \ [--ssdreserve ] \ [--lane ] ``` In this concrete CryoSPARC v5 example * CryoSPARC master services are listening on port 31000 and subsequent ports of the `master.mydomain` computer * one logs into the worker1.mydomain computer * and lists the (four) available GPUs * and chooses to *not* use in CryoSPARC the GPU with index 1 ```bash /path/to/cryosparc_worker/bin/cryosparcw gpulist /path/to/cryosparc_worker/bin/cryosparcw connect \ --worker worker1.mydomain \ --master master.mydomain \ --port 31000 \ --ssdpath /scratch/cryosparc_cache \ --gpus 0,2,3 \ --lane lane2 ``` See also `cryosparcw` documentation for CryoSPARC version [4](/setup-configuration-and-management/management-and-monitoring-4.7/cryosparcw-4.7.md#cryosparcw-connect-less-than-options-greater-than) or [5](/setup-configuration-and-management/management-and-monitoring-v5.0/cryosparcw-reference-v5.0.md#cryosparcw-connect). {% hint style="info" %} If a worker that matches the `cryosparcw connect --worker` parameter is already connected to the CryoSPARC instance, the connection will be *updated*. {% endhint %} {% hint style="info" %} In CryoSPARC v4, the `cryosparcw connect --update` parameter is required to update an existing worker connection. In CryoSPARC v5, `--update` is not needed. {% endhint %} ## Connect a Cluster to CryoSPARC CryoSPARC is designed to interface with HPC cluster systems so that jobs can be launched on shared resources that may be used for multiple purposes and by multiple users. CryoSPARC supports most cluster schedulers, including SLURM, SGE and PBS. CryoSPARC architecture when connecting to a cluster is described [here](https://guide.cryosparc.com/setup-configuration-and-management/hardware-and-system-requirements#clusters). We provide examples of [cluster integration scripts](https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure/cryosparc-cluster-integration-script-examples) which can be adapted as required for the specific needs of a particular cluster system.It is also possible to use [custom values in cluster submission scripts](/setup-configuration-and-management/software-system-guides/guide-configuring-custom-variables-for-cluster-job-submission-scripts.md), before a job is queued. ### Connecting CryoSPARC to a cluster during installation Once the `cryosparc_worker` package is installed, the cluster must be registered in the CryoSPARC database. Registration is performed by first creating two files, `cluster_info.json` and `cluster_script.sh` in the current working directory, populating those files, and then running the [command](/setup-configuration-and-management/management-and-monitoring-v5.0/cryosparcm-reference-v5.0.md#cryosparcm-cluster): ``` cryosparcm cluster connect ``` * the cluster information file `cluster_info.json` contains template strings used to construct cluster commands (e.g., qsub, qstat, qdel etc., or their equivalents for your system) * the cluster script template file `cluster_script.sh` contains a [jinja2](https://jinja.palletsprojects.com/en/2.10.x/) template string corresponding to a cluster job script. Examples of the contents of these two files can be found here: {% content-ref url="/pages/-M7DHIJv291IAXg6Tkl\_" %} [CryoSPARC Cluster Integration Script Examples](/setup-configuration-and-management/how-to-download-install-and-configure/cryosparc-cluster-integration-script-examples.md) {% endcontent-ref %} {% hint style="info" %} Creation and/or modification of the `cluster_info.json` and `cluster_script.sh` files is only one step in the configuration of a cluster lane for CryoSPARC jobs. To become effective, information in these files needs to be [registered in the CryoSPARC database](#register-the-cluster-lane-in-the-cryosparc-database) using the `cryosparcm cluster connect` command. {% endhint %} For the submission and managment of CryoSPARC cluster jobs, cluster information and script templates are read from the database, *not* from the `cluster_info.json` and `cluster_script.sh` files. The `jinja2` template engine renders the actual cluster management commands as well as the submission scripts for each CryoSPARC cluster job. ### Variables available in `cluster_info.json` `name`: string, **required** * Unique name for the cluster to be connected (multiple clusters can be connected). * This will be the name of the lane users will see when queuing jobs in CryoSPARC.![](https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2FqW1xyC6W96c0gjf91qda%2Fv4-0-0-installation-section-cluster-queue-0.png?alt=media\&token=6949dca9-a3ca-4d9f-8a98-df05b95115a4) `worker_bin_path`: string, **required** * Absolute path on cluster nodes to the `cryosparcw` script. `cache_path`: string, optional * Absolute path on cluster nodes that is a writable location on the local SSD on each cluster node. This might be `/scratch` or similar. * This path **must** be the same on all cluster nodes. See [Guide: Installation Testing with cryosparcm test](/setup-configuration-and-management/software-system-guides/guide-installation-testing-with-cryosparcm-test.md#cryosparcm-test-workers) for instructions on how to verify that CryoSPARC is able to successfully write to the cache path. * If you plan to use the cluster nodes without an SSD, you can omit this field. `cache_reserve_mb`:, integer, optional * The size (in MB) to initially reserve for the cache on the SSD. This value is 10GB by default, which means CryoSPARC will always leave at least 10GB of free space on the SSD. `cache_quota_mb`: integer, optional * The maximum size (in MB) to use for the cache on the SSD. `send_cmd_tpl`: string, **required** * Used to send a cluster management command to be executed by a cluster node (in case the cryosparc master is not able to directly use cluster management commands). * If your cryosparc master node is able to directly use cluster management commands (e.g., `qsub`, etc.,) then this string can be just `"{{ command }}"`. `qsub_cmd_tpl`: string, **required** * The cluster management 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 in cluster\_script.sh that are available when the job is scheduled (e.g., `cryosparc_username`, `project_uid`, etc.,). * CryoSPARC attempts to extract the cluster job ID from the output of the command assigned to `qsub_cmd_tpl` and subsequently uses the extracted job ID for monitoring and controlling the cluster job, as a parameter for the commands assigned to `qstat_cmd_tpl` or `qdel_cmd_tpl` . {% hint style="info" %} In some cluster configurations where the cluster manager's "native" cluster job submission command generates complex output, CryoSPARC's built-in logic may fail to correctly extract the cluster job ID. In such cases, one can * wrap the native cluster job submission command in an executable shell script * then assign the path of that shell script to `qsub_cmd_tpl`. Aside from running the native cluster job submission command, that shell script should preprocess and simplify the native command's output such that the CryoSPARC built-in logic can correctly extract the cluster job ID from the shell script's output. {% endhint %} `qstat_cmd_tpl`: string, **required** * The cluster management command that will report back the status of cluster job with its ID `{{ cluster_job_id }}`. `qdel_cmd_tpl`: string, **required** * The cluster management command that will kill and remove the cluster job (using `{{ cluster_job_id }}`) from the queue. `qinfo_cmd_tpl`: string, **required** * The cluster management command to retrieve general cluster information. Along with the configuration variables above, a complete cluster configuration requires a template cluster submission script that needs to be prepared in a file named `cluster_script.sh`. The script must send jobs into your cluster scheduler queue and mark them with the appropriate hardware requirements. The CryoSPARC internal scheduler submits jobs with this script as their inputs become ready. The following variables are available for use used within a cluster submission script template. When starting out, example templates may be generated with the commands explained below. ### The Basic Set of Variables Available in `cluster_script.sh` ``` {{ script_path_abs }} # absolute path to the generated submission script {{ run_cmd }} # complete command-line string to run the job {{ num_cpu }} # number of CPUs needed {{ num_gpu }} # number of GPUs needed. {{ ram_gb }} # 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) {{ job_type }} # CryoSPARC job type ``` {% hint style="info" %} The CryoSPARC scheduler does not control GPU allocation when spawning jobs on a cluster. The number of GPUs required is provided as a template variable. Either your submission script or your cluster scheduler is responsible for assigning GPU device indices to each job spawned based on the provided variable. The CryoSPARC worker processes that use one or more GPUs on a cluster simply use device 0, then 1, then 2, etc. {% endhint %} The cluster script template can be further customized with additional variables, as described in {% content-ref url="/pages/5zikU1RIs7uHyIpgV96G" %} [Guide: Configuring Custom Variables for Cluster Job Submission Scripts](/setup-configuration-and-management/software-system-guides/guide-configuring-custom-variables-for-cluster-job-submission-scripts.md) {% endcontent-ref %} ### Register the Cluster Lane in the CryoSPARC Database The `cryosparcm cluster connect` command activates a new or modified cluster lane configuration by uploading information from the files `cluster_info.json` and `cluster_script.sh` to the CryoSPARC database. {% hint style="info" %} The`cryosparcm cluster connect` command attempts reading `cluster_info.json` and `cluster_script.sh` from the current working directory. {% endhint %} {% hint style="warning" %} The `cryosparcm cluster connect` command will overwrite an existing database record if the existing record's `name` matches the `"name"` value inside `cluster_info.json`. {% endhint %} ```bash cryosparcm cluster example # 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 cryosparcm cluster dump # dumps out existing config and script to current working directory 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 cryosparcm cluster remove # removes a cluster configuration from the scheduler ``` ### Test the Registered Cluster Lane The success of the cluster lane's registration may be tested by queuing a CryoSPARC job to the cluster. For example, one may for this purpose: * clone an existing job that was previously completed while the CryoSPARC instance ran on the current CryoSPARC version and queue the clone * create an [Extensive Validation](/setup-configuration-and-management/software-system-guides/tutorial-verify-cryosparc-installation-with-the-extensive-workflow-sysadmin-guide.md) job and queue it to the newly connected cluster lane ### Update a Cluster Lane Configuration To update an existing cluster integration, call the `cryosparcm cluster connect` command with the updated `cluster_info.json` and `cluster_script.sh` in the current working directory. {% hint style="info" %} Note that the `name` field from `cluster_info.json` must be the same in the cluster configuration to update {% endhint %} If you don't already have the `cluster_info.json` and `cluster_script.sh` files in your current working directory, you can get them by running the command `cryosparcm cluster dump ` ### Add Additional Cluster Lanes Additional lanes for a cluster can be added to increase options for submission parameters when submitting jobs to the cluster. The following steps can be followed to create a new lane from an existing cluster configuration: Prerequisites: * a folder containing the cluster setup files - `cluster_folder` * cluster configuration files - `cluster_folder/cluster_info.json` and `cluster_folder/cluster_script.sh` Steps: 1. create a new directory `cluster_folder_new_lane` parallel to `cluster_folder` 2. copy the cluster configuration files `cluster_folder/cluster_info.json` and `cluster_folder/cluster_script.sh` to `cluster_folder_new_lane` 3. change the `name` field in `cluster_folder_new_lane/cluster_info.json` to the desired name of the new lane 4. edit `cluster_folder_new_lane/cluster_info.json` and `cluster_folder_new_lane/cluster_script.sh` with any lane configuration changes 5. set `cluster_folder_new_lane` as the current working directory 6. connect the new cluster lane with `cryosparcm cluster connect` (this must be run with `cluster_folder_new_lane` as the working directory) Note: The folder names `cluster_folder` and `cluster_folder_new_lane` can be changed to more descriptive names if desired, such as the name of the lane.