ModuleNotFoundError: No module named 'cryosparc_compute'

Hello, I am having the following problem when trying to start cryosparc after uploading to version 4.0.3 from version 4.0.1. cryosparc restart gives the same problem

Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'cryosparc_compute'

cryoSPARC instance information

  • Type: single workstation
  • Software version from cryosparcm status
Current cryoSPARC version: v4.0.3
----------------------------------------------------------------------------

CryoSPARC process status:

app                              STOPPED   Not started
app_api                          STOPPED   Not started
app_api_dev                      STOPPED   Not started
app_legacy                       STOPPED   Not started
app_legacy_dev                   STOPPED   Not started
command_core                     STOPPED   Not started
command_rtp                      STOPPED   Not started
command_vis                      STOPPED   Not started
database                         STOPPED   Not started

----------------------------------------------------------------------------
An error ocurred while checking license status
Could not get license verification status. Are all CryoSPARC processes RUNNING?
  • Output of uname -a && free -g on master node
Linux "localhost" 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
              total        used        free      shared  buff/cache   available
Mem:            251           4         239           0           7         246
Swap:             3           0           3

CUDA toolkit path: /usr/local/cuda

CUDA toolkit version:

nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2020 NVIDIA Corporation
Built on Tue_Sep_15_19:10:02_PDT_2020
Cuda compilation tools, release 11.1, V11.1.74
Build cuda_11.1.TC455_06.29069683_0

pycuda information: (11, 1, 0)

output of uname -a && free -g && nvidia-smi

Linux "localhost" 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
              total        used        free      shared  buff/cache   available
Mem:            251           4         239           0           7         246
Swap:             3           0           3
Wed Nov 16 15:00:44 2022       
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 460.84       Driver Version: 460.84       CUDA Version: 11.2     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|                               |                      |               MIG M. |
|===============================+======================+======================|
|   0  GeForce RTX 3090    Off  | 00000000:01:00.0 Off |                  N/A |
| 34%   27C    P8    32W / 350W |     60MiB / 24260MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
|   1  GeForce RTX 3090    Off  | 00000000:21:00.0 Off |                  N/A |
| 33%   25C    P8    19W / 350W |      1MiB / 24268MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
|   2  GeForce RTX 3090    Off  | 00000000:4D:00.0 Off |                  N/A |
| 30%   24C    P8    25W / 350W |      1MiB / 24268MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
|   3  GeForce RTX 3090    Off  | 00000000:4E:00.0 Off |                  N/A |
| 30%   26C    P8    23W / 350W |      1MiB / 24268MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
                                                                               
+-----------------------------------------------------------------------------+
| Processes:                                                                  |
|  GPU   GI   CI        PID   Type   Process name                  GPU Memory |
|        ID   ID                                                   Usage      |
|=============================================================================|
|    0   N/A  N/A      2893      G   /usr/bin/X                         39MiB |
|    0   N/A  N/A      2970      G   /usr/bin/gnome-shell               18MiB |

When doing: cryosparcm licensestatus
It says: An error ocurred while checking license status
Could not get license verification status. Are all CryoSPARC processes RUNNING?

So cryoSPARC isn’t running? Do cryosparcm stop and cryosparcm start throw any errors?

Can you ping out? If the network has issues, the license check will fail.

If I run cryosparcm status with cryoSPARC stopped, it does not report license status in the output (v4.0.3).

cryosparcm start
Traceback (most recent call last):
File “”, line 1, in
ModuleNotFoundError: No module named ‘cryosparc_compute’
Traceback (most recent call last):
File “”, line 1, in
ModuleNotFoundError: No module named ‘cryosparc_compute’
Starting cryoSPARC System master process…
CryoSPARC is not already running.
Traceback (most recent call last):
File “”, line 1, in
ModuleNotFoundError: No module named ‘cryosparc_compute’

cryosparcm stop
CryoSPARC is running.
Stopping cryoSPARC
Shut down

Network is OK, I can connect to internet

ping -c 3 activate.cryosparc.com
PING activate.cryosparc.com (52.222.144.28) 56(84) bytes of data.

activate.cryosparc.com ping statistics —
3 packets transmitted, 0 received, 100% packet loss, time 1999ms

You may want to try the following:

  1. open a shell under the Linux account that usually runs the master processes and run the following commands under that account.
  2. cryosparcm stop
  3. ps axuww | grep supervisord
    (Because under some circumstances, cryosparcm stop fails to terminate all relevant processes.) This process list may include master-related processes that were erroneously started under the wrong Linux account, but also legitimate master-related processes belonging to other users. If supervisord for the relevant CryoSPARC instance is still running, kill the process and wait 10 seconds.
  4. ps axuww | grep mongod
    This process list may include master-related processes that were erroneously started under the wrong Linux account, but also legitimate master-related processes belonging to other users. kill, but not kill -9 the relevant CryoSPARC-related mongod process, if there is any (there shouldn’t be).
  5. confirm there are no more CryoSPARC-related mongod processes by again running
    ps axuww | grep mongod
  6. remove any /tmp/cryosparc-supervisor-*.sock and /tmp/mongodb-*.sock belonging to the relevant CryoSPARC instance that may still be present.
  7. run another update, recording the output:
    cryosparcm update --override 2>&1 | tee update_override.log

I recognize that it is unlikely that there are multiple CryoSPARC instances intended to run on a single workstation, but nevertheless included cautions for that (edge) case. Please update this topic about your progress.

1 Like

There were not any process running.
But the command cryosparcm update --override 2>&1 worked.
Thank you very much.