Troubleshooting
Overview of common issues and advice on how to resolve them.
Last updated
Overview of common issues and advice on how to resolve them.
Last updated
Problems with the steps are indicated with the some of the following error messages:
"Couldn't connect to host" "Could not resolve host" {"success": false} "tar: This does not look like a tar archive" "Version mismatch! Worker and master versions are not the same. Please update." "An unexpected error has occurred."
Steps
If you have installed, .
Check that your LICENSE_ID environment variable is set correctly with this command
Ensure the output exactly matches the CryoSPARC License ID issued to you over email.
Check your machine's connection to CryoSPARC's license servers at get.cryosparc.com with this curl command:
You should see the message {"success": true}. If instead you see {"success": false}, your license is not valid, so please check it has been entered correctly.
If you see an error message like "Couldn't connect to host" or "Could not resolve host" check your Internet connection, firewall or ensure your IT department has the get.cryosparc.com license server domain whitelisted.
Steps
This can happen following a fresh install or recent update.
Steps
In a command line, run cryosparcm status
Check that the output looks like this
Check that all items under "CryoSPARC process status" that do not end in _dev or _legacy are RUNNING. If any are not, run cryosparcm restart
If any non-_dev /non-_legacy components have a status other than RUNNING (such as STOPPED or EXITED), check their log for errors. For example, this command checks for errors on the database process:
(Press control C, then q to stop logging)
If at any point you see No command 'cryosparcm' found or command not found: cryosparcm:
Check that you are on the master node or workstation where cryosparc_master is installed
Run echo $PATH and check that it contains <installation directory>/cryosparc_master/bin
This error message occurs if the email address field does not match any existing users in your CryoSPARC instance. Use the CryoSPARC command-line to verify the details of your user account and change the email address or password if needed.
Run the following command in your terminal: cryosparcm listusers
If an email address is incorrect (e.g., mispelled or with an extra space at the beginning or end), modify it in the database. Run the following commands:
Log into the MongoDB shell: cryosparcm mongo
Once in the MongoDB shell, enter the following (replace the incorrect/correct email):
Exit the MongoDB shell with exit
If you don't remember your password, reset it with the following command (replace with your email address and new password):
An incomplete shutdown of CryoSPARC is likely to interfere with subsequent attempts to start CryoSPARC and/or CryoSPARC software updates. Incomplete shutdowns can occur for various reasons, including, but not limited to:
unclean shutdown of the computer that runs cryosparc_master processes
failed coordination of services by cryosparc_master's supervisord process
Follow this sequence to ensure a complete shutdown of CryoSPARC
For CryoSPARC instances that were not configured as a systemd service, run the command
Do not use
for CryoSPARC instances that are controlled by systemd. For such instances, use the appropriate systemctl stop command.
Confirm that the basic shutdown did not "leave behind" any CryoSPARC-related processes. If the basic shutdown was successful, a suitable ps command should not show any processes for the CryoSPARC instance in question, but processes may be shown if
a glitch occurred during the basic shutdown or
the computer hosts multiple CryoSPARC instances.
To illustrate what kind of processes one might encounter, here is an example command and its output for a running CryoSPARC v4.4 instance:
The ps output may include processes that belong to non-CryoSPARC applications or to CryoSPARC instances other than the CryoSPARC instance that you wish to shutdown. Parent process identifiers and port numbers in the listed commands can help in attributing processes to a common parent supervisord process. Carefully confirm the purpose and identity of any process before termination.
For the example above, it should be sufficient to kill the supervisord process using the process identifier shown by the ps command
and wait a few seconds for the supervisord process' children to be terminated automatically.
Finally, using another ps command with suitable options, re-confirm that all relevant processes have in fact been terminated
An intact CryoSPARC instance manages the creation and deletion of socket files for mongod and supervisord, like
Filenames differ between CryoSPARC instances, for example based on $CRYOSPARC_DB_PORT.
Never delete socket files before confirming that associated processes have been terminated as described in the previous step.
The computer may store socket files that belong to non-CryoSPARC applications or to CryoSPARC instances other than the CryoSPARC instance that you wish to shutdown. Such socket files may have names similar to the files you wish to delete. Carefully confirm the purpose and identity of each file before any deletion.
Follow the steps in this section when you see error messages that look like this:
"License is invalid." "License signature invalid." "Could not find local license file. Please re-establish your connection to the license servers." "Local license file is expired. Please re-establish your connection to the license servers." "Token is invalid. Another CryoSPARC instance is running with the same license ID."
Steps
Run cryosparcm licensestatus. This should result in "License is valid". If you see this error:
Your license ID is not entered configured correctly. Check the CRYOSPARC_LICENSE_ID entry in cryosparc_master/config.sh .
If you see this error:
This includes a list of checks, the last of which will indicate a failure. Depending on which check failed, do one of the following:
Check your Internet connection
Check your machine's connection to CryoSPARC's license servers at get.cryosparc.com with this curl command (substitute <license> with your unique license ID):
Look for the message message {"success": true}
If instead you see {"success": false}, your license is not valid so please check it has been entered correctly.
If you see an error message like "Couldn't connect to host" or "Could not resolve host" check your Internet connection, firewall or ensure your IT department has the get.cryosparc.com license server domain whitelisted.
If you see a license ID conflict such as
"Another cryoSPARC instance is running with the same license ID."
Follow these steps when the CryoSPARC web interface is up and running normally and jobs may be created but do not run. These error messages may indicate this issue:
"list index out of range" "Could not resolve hostname ... Name or service not known"
A job that never changes from Queued or Launched status may also indicate this.
Steps
(For master/worker setups) check that SSH is configured between the master and worker machines.
Check the log for the command_core log to find any application error messages
(press Control + C on the keyboard followed by q to exit when finished)
Refresh job types and reload CryoSPARC:
On worker nodes run:
Restart CryoSPARC:
Clear the job and re-run it.
This indicates that CryoSPARC started the job process but the job encountered an internal error immediately after.
or from the command line with
Substituting PX and JY for the project and job IDs, respectively.
When a job fails, its job card in the interface turns red and the bottom of the job log includes an error message with the text Traceback (most recent call last)
Common failure reasons include:
Invalid or unspecified input slots
Invalid or unspecified required parameters, including file/folder paths
Another process taking up memory on a GPU
Cache not set up correctly for a worker
Lost connection to cryosparc_master
Common job failure error messages:
"AssertionError: Child process with PID ... has terminated unexpectedly!" Job is unresponsive - no heartbeat received in 30 seconds.
Common error messages that indicate incorrectly configured GPU drivers:
"cuInit failed: unknown error" "no CUDA-capable device is detected" "cuMemHostAlloc failed: OS call failed or operation not supported on this OS" "cuCtxCreate failed: invalid device ordinal kernel.cu ... error: identifier "__shfl_down_sync" is undefined
Common error messages that indicate not enough GPU memory:
"cuMemAlloc failed: out of memory" "cuArrayCreate failed: out of memory" "cufftAllocFailed"
Steps
Check the GPU configuration on the workstation or node where the job runs on. Log into that machine and navigate to the CryoSPARC installation directory. Run the cryosparcw gpulist command:
Run nvidia-smi to check that no other processes are using GPU memory. CryoSPARC-related process appear with process name "python"
If you don't recognize the processes using GPU memory, run kill <PID>, substituting <PID> with the value under the Processes PID column
Clear the job and select the "Build" status badge on the job card to enter the Job Builder
Check the job parameters: To learn about setting specific parameters, hover over or touch the parameter names in the Job Builder to see a description of what they do
Refresh job types and reload CryoSPARC:
Check the network connection from the worker machine to the master
Due to their large sizes, cryo-EM datasets can take a long time to process with sub-optimal hardware or parameters. Here are some facilities that CryoSPARC provides for increasing speed/performance.
Some jobs (motion correction, ctf estimation, 2D classification) can run on multiple GPUs. If your hardware supports it, increase the number of GPUs to parallelize over
Extracted particles with large box sizes (relative to their pixel size) take a long time to process. Consider Fourier-cropping (or "binning") the extracted particle blobs with the Downsample Particles job
Minimize the number of processes using system resources on the workstation or worker nodes
Cancel the job, clear and re-queue
cudaErrorInsufficientDriver or CUDA_ERROR_UNSUPPORTED_PTX_VERSIONA job fails with errors similar to the following when the Nvidia driver is out-of-date or incompatible with the target GPU or CUDA Toolkit Version that ships with CryoSPARC:
undefined symbol: _ZSt28__throw_bad_array_new_lengthvA job may fail with the following error when running GPU jobs (Patch Motion Correction, 2D Classification) with CryoSPARC v3.3.2 or v3.4.0 on Ubuntu 22+.
To fix, set environment variables CFLAGS="-static-libstdc++" and CXXFLAGS="-static-libstdc++" to the environment before recompiling the PyCUDA module with cryosparcw newcuda:
In some circumstances, jobs with "Cache particle images on SSD" enabled will not complete with one of the following errors in the job log:
SSD cache needs additional B but drive can only be filled up to B
SSD cache needs additional B but drive has B free. CryoSPARC can only free a maximum of B. This may indicate that programs other than CryoSPARC are using the SSD.
Cannot allocate space on the SSD to cache /path/to/particles.mrc; other non-CryoSPARC processes are using the cache.
Cannot finish transfer; other programs may be accessing the SSD.
FileNotFoundError: [Errno 2] No such file or directory: '…/…/store-v2/...' → '/scratch/instance_cryosparc:39001/links/...’
You may also observe some of the following symptoms:
Slower than expected SSD copy speeds
Jobs that use the SSD cache take much longer than they should
Jobs spend a very long time waiting on cache files locked by other jobs or waiting for additional space to free up
These issues may occur in long-active CryoSPARC instances with many projects and files on the SSD, and many jobs or other non-CryoSPARC processes running simultaneously. There are several strategies to address these or reduce their likelihood.
CryoSPARC automatically removes files from the SSD that have not been accessed in a while (more than 30 days by default) each time the SSD cache system runs. If the SSD is very heavily used in particle processing jobs or by other external tools, leaving more free space available may extend its lifetime. This is possible with one or both of these strategies:
CryoSPARC assumes that it has exclusive access to the SSD cache path. If other programs are accessing the cache path at the same time as CryoSPARC, the cache step may fail with a file system-related or OS-level error.
Option 3: Increase or Reduce the SSD Quota
The SSD Quota is the maximum amount of SSD space that CryoSPARC jobs use on a connected worker. CryoSPARC will never use more than this amount of SSD space. A job that requires caching will delete enough older cache files to ensure the quota is not exceeded.
If the quota is significantly lower than the total size of the SSD and jobs frequently wait for cache space to free up, consider increasing the quota.
If other programs regularly share the SSD with CryoSPARC and jobs fail because the cache drive runs out of space, consider decreasing the quota to reduce the likelihood of this.
The SSD Reserve is the minimum amount of free space that CryoSPARC leaves on the SSD, also considering potential use of the the cache device by other applications even if CryoSPARC has not reached its SSD quota. CryoSPARC jobs will delete, if possible, unused files from its cache until this much space is free again. CryoSPARC jobs will not copy files to the SSD until at least this amount of space is free. This setting is intended to preserve SSD health.
If CryoSPARC reports slower cache write speeds than expected, or jobs that use the SSD cache take longer than they should, consider increasing the reserve.
If jobs frequently wait for cache space to free up, consider decreasing the reserve.
By default, CryoSPARC jobs use a file-system level POSIX lock to ensure mutual exclusion between multiple jobs that access the SSD cache simultaneously. These locks can be unreliable on network file systems such as NFS, GPFS, BeeGFS or Lustre. This may lead to errors during the SSD caching step, particularly during copy or symbolic link operations. Error messages with the following format are key symptoms of this:
FileNotFoundError: [Errno 2] No such file or directory: '…/…/store-v2/...' → '/scratch/instance_cryosparc:39001/links/...’
cryosparc_master uses its MongoDB database to coordinate SSD caching between multiple workers running in parallel. If a job fails unexpectedly during the SSD caching step, this could lead to database inconsistencies which prevent other jobs from proceeding.
To address these, try the following steps:
Ensure no jobs are running in CryoSPARC
In a terminal, enter cryosparcm mongo to enter the interactive database prompt
Enter the following command to check how many records are in an inconsistent state:
If the result is not 0 (zero), enter the following command to fix them
Exit from the database prompt with Ctrl + D
Try re-running the problematic jobs
Fully reset the caching system with the following steps:
Ensure no jobs are running in CryoSPARC
For each connected worker machine:
Navigate to the SSD cache directory containing CryoSPARC's cache files (e.g., /scratch/). This path was configured during installation time
Look for a directory named instance_<master hostname>:<master port + 1> e.g., instance_localhost:39001
Delete this directory and all its contents
The following additional reset instructions are required for CryoSPARC v4.4 or older.
In a terminal, enter cryosparcm mongo to enter the interactive database prompt
Enter the following command to clear out the cache records
Exit from the database prompt with Ctrl + D
Try re-running the problematic jobs
If the issue persists after trying any of the above options, consider disabling the "Cache particle images on SSD" parameter for the affected job.
If you encounter a problem with the user interface in your web browser, e.g., one or more elements of a page are not loading, etc., you can use the following steps to obtain debugging information.
Open the browser console
In Chrome, Firefox, Edge, and Safari this can be done by right clicking the page to open the browser context menu and selecting the Inspect option (Inspect Element in Safari) .
This will open up a “DevTools” panel used for inspecting and debugging in the browser. This panel includes a number of tabs at the top used to display different views. When opened using the context menu the current view will be the Elements tab. Click on the Console tab directly beside the Elements tab in order to view the web console. This is where errors, warnings, and general information about the page’s javascript code can be observed.
In order to keep the console clean in production we disable our development logs. Enable these logs by pasting the command
window.localStorage.setItem('cryosparc_debug', true); into the browser console and then pressing the enter key on your keyboard. undefined will be logged below this command if it was submitted correctly.
Now reload the page and all of the development console logs and errors will be visible.
Save Console Output
Please save console output as a .log file, including the type of browser (Chrome, Firefox, Edge, Safari, etc.) in the file name. The filename should be formatted as such: console_{browser}.log , eg. console_chrome.log . Before saving the file, try to reproduce the issue you encountered.
Chrome or Edge: Right click anywhere in the console panel to open the context menu and select the Save As... option. This will allow you to save the entire output as a .log file.
Firefox: Right click on a console message to open the context menu and select the Save all Messages to File option. This will allow you to save the entire output as a .txt file as default (or .log file optionally).
Safari: Click and drag the cursor over all items in the console output so that the items are all highlighted blue. You can then right click on any of the highlighted items to open the context menu and select the Save Selected option to to save the entire output as a .txt file as default (or .log file optionally).
Save Network Output
Navigate to the Network tab in the DevTools by selecting it from the tabs in the top bar of the panel. If the Network tab is not shown then it is likely hidden in the overflow menu (this appears when there is not enough space to display all of the tab options in the DevTools). Click the overflow menu button represented by two right chevrons (>>) and select the Network option.
Please include the type of web browser (Chrome, Firefox, Edge, or Safari) in the name of the .har file you are saving. The filename should be formatted as such: network_{browser}.har , eg. network_chrome.har .
Chrome or Edge: Click the "Export HAR" button on the panel header.
Firefox: Right click on any of the items in the network request table and then select Save All As HAR from the context menu.
Safari: Right click on any of the items in the network request table and then select Export HAR from the context menu.
For topics not covered above, get additional help through the CryoSPARC Discussion Forum:
If no related discussions exist, please create a new post. Review our Troubleshooting Guidelines for items to include in your post:
, following the steps from the section
If the web interface is inaccessible, check firewall settings to ensure (default 39000) is exposed for network access
Any error messages here could indicate specific configuration issues and may require .
if the above did not restore the the cryosparcm command
use the kill -9 option for mongod processes.
Ensure you entered the license correctly during the .
Follow the before running
Ensure at least one worker is connected to the master. See the page for details. Visit Manage > Resources to see what lanes are available
Check that all non-development CryoSPARC processes are running with the command
If applicable, check that the is correct
Force-reinstall and dependencies. This can help when a worker was not correctly installed. On the workstation or master node run:
Check the job's Event Log for errors. If there are none, check the standard out log either from the interface under Job > Metadata > Job Log
Typically the errors here occur when the worker process cannot connect back to the master. Ensure there is a stable network connection between all machines involved. Ensure CryoSPARC was installed correctly and if necessary.
Incorrectly set up GPU (e.g., running a job on a node without enough GPUs or drivers not installed)
Ensure a of the toolkit is installed and running on the workstation or each worker node
Check the Event log: Select the Job card in the CryoSPARC interface and press the Spacebar on your keyboard to see the log. Scroll down to the bottom and look for the failure reasons in red
If the job failed with a GPU-related error and multiple GPUs are available, try running the job on a different GPU. Press Queue, switch to the "Run on specific GPU" Queue type and select one or more GPUs
If the job failed with AssertionError: Non-optional inputs from the following input groups and their slots are not connected then clear the job, enter the Builder and expand any input groups connected to the job. Missing required slots appear with text "Empty" and "Required"
Find the target job type in this guide's Job Reference for more detailed descriptions of expected input slots and parameters: .
Reduce the box-size of extracted particles. Some jobs need to fit thousands of particles in GPU memory at a time, and larger box sizes exceed GPU memory limits. Either extract with a smaller box size or with the .
Look for extended error information with the (press Ctrl + C on the keyboard to exit when finished)
On occasion, a job fails due to an error in the CryoSPARC code (bug). The CryoSPARC team regularly releases updates and patches with bug fixes. and or . If you find a new bug, see the section for advice.
. This speeds up processing for extracted particles during 2D Classification, ab-initio reconstruction, refinement and more. Ensure the "Cache particle images on SSD" parameter is enabled under "Compute settings" for the target particle-processing job
Check for zombie processes on worker machines. The process is similar to the steps under "Another CryoSPARC instance is running with the same license ID" under the section
To fix this, update the Nvidia driver to the minimum driver version noted in . Please follow instructions specific to the worker's Linux distribution to install the Nvidia driver. The latest Nvidia driver is available to download on .
SSDs naturally degrade over time, the likelihood of failure increasing with heavy usage. Use a tool such as to check the SSD. If enough errors have accumulated, the SSD may have to be replaced.
with the --ssdreserve flag set (default 10GB or 10000MB) to ensure CryoSPARC always leaves the given amount of free space on the SSD (will clean out old files to stay above the threshold)
Set the in cryosparc_master/config.sh to clean up unused files on the SSD more frequently. The default value is 30 days
Change the quota by with --ssdquota <amount in MB> and --update arguments.
Change the reserve by with --ssdreserve <amount in MB> (default 10000) and --update arguments.
Add the following line to to use the CryoSPARC master to broker cache access instead:
