ModuleNotFoundError: No module named 'cryosparc_compute'

Install, Configure and Update
1

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 |
2

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

3

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).

4

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

5

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
6

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