Workspace not showing

Install, Configure and Update
8

Thanks for your feedback. I hope now everything is visible to all.

The answer to your question is

1.What is the url that you enter in the browser in order to access CryoSPARC?
http://localhost:39000/

2. What is the output of the following command
/home/cryosparc_user/software/cryosparc/cryosparc_master/bin/cryosparcm env | grep -v LICENSE
/cryosparc_master/bin/cryosparcm env | grep -v LICENSE
export “CRYOSPARC_INSECURE=false”
export “CRYOSPARC_MONGO_FCV=3.6”
export “CRYOSPARC_LIVE_ENABLED=true”
export “CRYOSPARC_HTTP_LIVEAPP_LEGACY_PORT=39006”
export “CRYOSPARC_CLICK_WRAP=true”
export “CRYOSPARC_MONGO_PORT=39001”
export “CRYOSPARC_DB_CONNECTION_TIMEOUT_MS=20000”
export “CRYOSPARC_PROJECT_DIR_PREFIX=CS-”
export “CRYOSPARC_DB_ENABLE_AUTH_FLAG=–auth”
export “CRYOSPARC_HTTP_APP_LEGACY_PORT=39007”
export “CRYOSPARC_CLUSTER_JOB_MONITOR_MAX_RETRIES=1000000”
export “CRYOSPARC_DB_ENABLE_AUTH=true”
export “CRYOSPARC_MONGO_CACHE_GB=4”
export “CRYOSPARC_ROOT_DIR=/home/cryosparc_user/software/cryosparc/cryosparc_master”
export “CRYOSPARC_PATH=/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/external/mongodb/bin:/home/cryosparc_user/software/cryosparc/cryosparc_master/bin”
export “CRYOSPARC_DEVELOP=false”
export “CRYOSPARC_FORCE_HOSTNAME=true”
export “CRYOSPARC_CONDA_ENV=cryosparc_master_env”
export “CRYOSPARC_BASE_PORT=39000”
export “CRYOSPARC_FORCE_USER=false”
export “CRYOSPARC_HOSTNAME_CHECK=sn4622125205.ctrc.uthscsa.edu”
export “CRYOSPARC_CLUSTER_JOB_MONITOR_INTERVAL=10”
export “CRYOSPARC_COMMAND_RTP_PORT=39005”
export “CRYOSPARC_COMMAND_VIS_PORT=39003”
export “CRYOSPARC_DB_PATH=/home/cryosparc_user/software/cryosparc/cryosparc_database”
export “CRYOSPARC_HEARTBEAT_SECONDS=60”
export “CRYOSPARC_COMMAND_CORE_PORT=39002”
export “CRYOSPARC_MASTER_HOSTNAME=sn4622125205.ctrc.uthscsa.edu”
export “CRYOSPARC_HTTP_APP_PORT=39000”
export “CRYOSPARC_SUPERVISOR_SOCK_FILE=/tmp/cryosparc-supervisor-206773da3c7c06e952eddaffaea9188d.sock”
export “PATH=/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/external/mongodb/bin:/home/cryosparc_user/software/cryosparc/cryosparc_master/bin:/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin:/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/condabin:/home/cryosparc_user/software/cryosparc/cryosparc_master/bin:/home/cryosparc_user/software/cryosparc/cryosparc_master/bin:/usr/local/relion-4.0/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/cryosparc_user/software/cryosparc/cryosparc_master/bin:/home/cryosparc_user/software/cryosparc/cryosparc_master/bin:/home/cryosparc_user/.local/bin:/home/cryosparc_user/bin:/usr/local/relion-4.0/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/relion-4.0/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.18/bin:/usr/local/ResMap:/usr/local/cistem-1.0.0-beta:/usr/local/anaconda3/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.18/bin:/usr/local/ResMap:/usr/local/cistem-1.0.0-beta:/usr/local/anaconda3/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.18/bin:/usr/local/ResMap:/usr/local/cistem-1.0.0-beta:/usr/local/anaconda3/bin”
export “LD_LIBRARY_PATH=/usr/local/relion-4.0/lib:/usr/local/cuda/lib:/usr/local/cuda/lib64:/usr/local/cuda-11.2/lib:/usr/local/cuda-11.2/lib64:/usr/local/cuda-11.1/lib:/usr/local/cuda-11.1/lib64:/usr/local/cuda-11.0/lib:/usr/local/cuda-11.0/lib64:/usr/local/cuda-10.1/lib:/usr/local/cuda-10.1/lib64:/usr/local/relion-4.0/lib:/usr/local/cuda/lib:/usr/local/cuda/lib64:/usr/local/cuda-11.2/lib:/usr/local/cuda-11.2/lib64:/usr/local/cuda-11.1/lib:/usr/local/cuda-11.1/lib64:/usr/local/cuda-11.0/lib:/usr/local/cuda-11.0/lib64:/usr/local/cuda-10.1/lib:/usr/local/cuda-10.1/lib64:/usr/local/relion-4.0/lib:/usr/local/cuda/lib:/usr/local/cuda/lib64:/usr/local/cuda-11.2/lib:/usr/local/cuda-11.2/lib64:/usr/local/cuda-11.1/lib:/usr/local/cuda-11.1/lib64:/usr/local/cuda-11.0/lib:/usr/local/cuda-11.0/lib64:/usr/local/cuda-10.1/lib:/usr/local/cuda-10.1/lib64:”
export “LD_PRELOAD=/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libpython3.8.so”
export “PYTHONPATH=/home/cryosparc_user/software/cryosparc/cryosparc_master”
export “PYTHONNOUSERSITE=true”
export “CONDA_SHLVL=1”
export “CONDA_EXE=/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/bin/conda”
export “CONDA_PREFIX=/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env”
export “CONDA_PYTHON_EXE=/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/bin/python”
export “CONDA_PROMPT_MODIFIER=(cryosparc_master_env)”
export “CONDA_DEFAULT_ENV=cryosparc_master_env”

3. /home/cryosparc_user/software/cryosparc/cryosparc_master/bin/cryosparcm snaplogs

tar: Removing leading /' from member names /home/cryosparc_user/software/cryosparc/cryosparc_master/run/app_api.log tar: Removing leading /’ from hard link targets
/home/cryosparc_user/software/cryosparc/cryosparc_master/run/app.log
/home/cryosparc_user/software/cryosparc/cryosparc_master/run/command_core.log
/home/cryosparc_user/software/cryosparc/cryosparc_master/run/command_rtp.log
/home/cryosparc_user/software/cryosparc/cryosparc_master/run/command_vis.log
/home/cryosparc_user/software/cryosparc/cryosparc_master/run/database.log
/home/cryosparc_user/software/cryosparc/cryosparc_master/run/supervisord.log
/home/cryosparc_user/software/cryosparc/cryosparc_master/run/update.log
Created log archive in /home/cryosparc_user/software/cryosparc/cryosparc_master/run/cryosparc_logs_20230316183640.tgz.

9

@khajafaisaltarique Please can you email us this file.

10

Hi

I am not able to attach .tgz file or its content in this email. Is there any other way out ?

Thanks

Faisal

11

Please can you post the output of the following command, run under the cryosparc_user account:
ls -al /data/cryosparc_projects/CS-t20s-tutorial-dataset-1/

12

Hi it says
ls: cannot access ‘/data/cryosparc_projects/CS-t20s-tutorial-dataset-1/’: No such file or directory

Maybe it got deleted.

13

Hi

There is no such directory even for cryosparc_projects.

Am I missing something ?

Faisal

14

You may want to ask the admin of that computer if a volume that is supposed to be mounted under /data wasn’t mounted.

15

Well, I am the admin and the data volume is also here but I have not created any directory ‘cryosparc_projects’ in it, rather everything goes directly into it in the created directory as required. I do not remember using the t20s tutorial data set or may have deleted it after testing the cryosparc. And with problem facing now I am not able to create a new project. Maybe I can send something with the other projects I am currently working on. Please advice

16

Deletion of files managed by CryoSPARC by non-CryoSPARC means, such as by the rm command, will disrupt CryoSPARC. CryoSPARC project data that are no longer needed and wanted should be deleted via the CryoSPARC interface so that CryoSPARC can track the deletion.
In case the deletion of CryoSPARC-managed files outside CryoSPARC has occurred, you may try the suggestion in Illegal job id "submitted." when trying to get status - #6 by nwong.

17

The update likely was disrupted before completion.
You may try
cryosparcm update --override
(details).
Does this work?

18

[cryosparc_user@sn4622125205 ~]$ cryosparcm update --override
CryoSPARC current version v4.2.1
update starting on Fri Mar 17 21:24:42 CDT 2023

No version specified - updating to latest version.

=============================
Forcing update to version v4.2.1…

Removing previous downloads…
Downloading master update…
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:–:-- 0:00:02 --:–:-- 0
100 759M 100 759M 0 0 5549k 0 0:02:20 0:02:20 --:–:-- 8273k
Downloading worker update…
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:–:-- --:–:-- --:–:-- 0
100 1796M 100 1796M 0 0 5988k 0 0:05:07 0:05:07 --:–:-- 7037k
Done.

Update will now be applied to the master installation,
followed by worker installations on other nodes.

CryoSPARC is running.
Stopping cryoSPARC
Shut down
Deleting old files…
Extracting…
Done.

===================================================
Installing latest master dependencies.

Checking dependencies…
Forcing dependencies to be reinstalled…

Installing anaconda python…

PREFIX=/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda
Unpacking payload …
Extracting : cffi-1.15.0-py38hd667e15_1.conda: 0%| | 0/39 [00:00<?, ?Extracting : pysocks-1.7.1-py38h06a4308_0.conda: 3%|▎ | 1/39 [00:00<00Extracting : pysocks-1.7.1-py38h06a4308_0.conda: 5%|▌ | 2/39 [00:00<00Extracting : conda-content-trust-0.1.1-pyhd3eb1b0_0.conda: 5%|▌ | 2/39Extracting : sqlite-3.38.2-hc218d9a_0.conda: 8%|▊ | 3/39 [00:00<00:02,Extracting : pip-21.2.4-py38h06a4308_0.conda: 10%|█ | 4/39 [00:00<00:01Extracting : brotlipy-0.7.0-py38h27cfd23_1003.conda: 13%|█▎ | 5/39 [00:0Extracting : ld_impl_linux-64-2.35.1-h7274673_9.conda: 15%|█▌ | 6/39 [00Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda: 18%|█▊ | 7/39 [00:00<00:Extracting : ncurses-6.3-h7f8727e_2.conda: 21%|██ | 8/39 [00:00<00:01, 1Extracting : ruamel_yaml-0.15.100-py38h27cfd23_0.conda: 23%|██▎ | 9/39 [0Extracting : certifi-2021.10.8-py38h06a4308_2.conda: 26%|██▌ | 10/39 [00:Extracting : colorama-0.4.4-pyhd3eb1b0_0.conda: 28%|██▊ | 11/39 [00:00<00Extracting : libgomp-9.3.0-h5101ec6_17.conda: 31%|███ | 12/39 [00:00<00:0Extracting : xz-5.2.5-h7b6447c_0.conda: 33%|███▎ | 13/39 [00:00<00:01, 17.Extracting : setuptools-61.2.0-py38h06a4308_0.conda: 36%|███▌ | 14/39 [00:Extracting : six-1.16.0-pyhd3eb1b0_1.conda: 38%|███▊ | 15/39 [00:00<00:01,Extracting : conda-package-handling-1.8.1-py38h7f8727e_0.conda: 41%|████ |Extracting : pycosat-0.6.3-py38h7b6447c_1.conda: 44%|████▎ | 17/39 [00:00<0Extracting : ca-certificates-2022.3.29-h06a4308_1.conda: 46%|████▌ | 18/39 Extracting : python-3.8.13-h12debd9_0.conda: 49%|████▊ | 19/39 [00:00<00:01Extracting : python-3.8.13-h12debd9_0.conda: 51%|█████▏ | 20/39 [00:00<00:00Extracting : pyopenssl-22.0.0-pyhd3eb1b0_0.conda: 51%|█████▏ | 20/39 [00:00<Extracting : pycparser-2.21-pyhd3eb1b0_0.conda: 54%|█████▍ | 21/39 [00:00<00Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda: 56%|█████▋ | 22/39Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda: 59%|█████▉ | 23/39 [00:00<00:0Extracting : requests-2.27.1-pyhd3eb1b0_0.conda: 62%|██████▏ | 24/39 [00:00<0Extracting : _libgcc_mutex-0.1-main.conda: 64%|██████▍ | 25/39 [00:00<00:00, Extracting : readline-8.1.2-h7f8727e_1.conda: 67%|██████▋ | 26/39 [00:00<00:0Extracting : tk-8.6.11-h1ccaba5_0.conda: 69%|██████▉ | 27/39 [00:00<00:00, 93Extracting : tqdm-4.63.0-pyhd3eb1b0_0.conda: 72%|███████▏ | 28/39 [00:00<00:00Extracting : idna-3.3-pyhd3eb1b0_0.conda: 74%|███████▍ | 29/39 [00:00<00:00, 9Extracting : openssl-1.1.1n-h7f8727e_0.conda: 77%|███████▋ | 30/39 [00:00<00:0Extracting : zlib-1.2.12-h7f8727e_1.conda: 79%|███████▉ | 31/39 [00:00<00:00, Extracting : urllib3-1.26.8-pyhd3eb1b0_0.conda: 82%|████████▏ | 32/39 [00:00<00Extracting : cryptography-36.0.0-py38h9ce1e76_0.conda: 85%|████████▍ | 33/39 [0Extracting : conda-4.12.0-py38h06a4308_0.conda: 87%|████████▋ | 34/39 [00:00<00Extracting : libffi-3.3-he6710b0_2.conda: 90%|████████▉ | 35/39 [00:00<00:00, 9Extracting : libstdcxx-ng-9.3.0-hd4cf53a_17.conda: 92%|█████████▏| 36/39 [00:00Extracting : yaml-0.2.5-h7b6447c_0.conda: 95%|█████████▍| 37/39 [00:00<00:00, 9Extracting : _openmp_mutex-4.5-1_gnu.tar.bz2: 97%|█████████▋| 38/39 [00:00<00:0 Collecting package metadata (current_repodata.json): …working… done
Solving environment: …working… done

Package Plan

environment location: /home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda

added / updated specs:
- _libgcc_mutex==0.1=main
- _openmp_mutex==4.5=1_gnu
- brotlipy==0.7.0=py38h27cfd23_1003
- ca-certificates==2022.3.29=h06a4308_1
- certifi==2021.10.8=py38h06a4308_2
- cffi==1.15.0=py38hd667e15_1
- charset-normalizer==2.0.4=pyhd3eb1b0_0
- colorama==0.4.4=pyhd3eb1b0_0
- conda-content-trust==0.1.1=pyhd3eb1b0_0
- conda-package-handling==1.8.1=py38h7f8727e_0
- conda==4.12.0=py38h06a4308_0
- cryptography==36.0.0=py38h9ce1e76_0
- idna==3.3=pyhd3eb1b0_0
- ld_impl_linux-64==2.35.1=h7274673_9
- libffi==3.3=he6710b0_2
- libgcc-ng==9.3.0=h5101ec6_17
- libgomp==9.3.0=h5101ec6_17
- libstdcxx-ng==9.3.0=hd4cf53a_17
- ncurses==6.3=h7f8727e_2
- openssl==1.1.1n=h7f8727e_0
- pip==21.2.4=py38h06a4308_0
- pycosat==0.6.3=py38h7b6447c_1
- pycparser==2.21=pyhd3eb1b0_0
- pyopenssl==22.0.0=pyhd3eb1b0_0
- pysocks==1.7.1=py38h06a4308_0
- python==3.8.13=h12debd9_0
- readline==8.1.2=h7f8727e_1
- requests==2.27.1=pyhd3eb1b0_0
- ruamel_yaml==0.15.100=py38h27cfd23_0
- setuptools==61.2.0=py38h06a4308_0
- six==1.16.0=pyhd3eb1b0_1
- sqlite==3.38.2=hc218d9a_0
- tk==8.6.11=h1ccaba5_0
- tqdm==4.63.0=pyhd3eb1b0_0
- urllib3==1.26.8=pyhd3eb1b0_0
- wheel==0.37.1=pyhd3eb1b0_0
- xz==5.2.5=h7b6447c_0
- yaml==0.2.5=h7b6447c_0
- zlib==1.2.12=h7f8727e_1

The following NEW packages will be INSTALLED:

_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py38h27cfd23_1003
ca-certificates pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
certifi pkgs/main/linux-64::certifi-2021.10.8-py38h06a4308_2
cffi pkgs/main/linux-64::cffi-1.15.0-py38hd667e15_1
charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
colorama pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
conda pkgs/main/linux-64::conda-4.12.0-py38h06a4308_0
conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.8.1-py38h7f8727e_0
cryptography pkgs/main/linux-64::cryptography-36.0.0-py38h9ce1e76_0
idna pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
libgomp pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
ncurses pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
openssl pkgs/main/linux-64::openssl-1.1.1n-h7f8727e_0
pip pkgs/main/linux-64::pip-21.2.4-py38h06a4308_0
pycosat pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1
pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
pyopenssl pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py38h06a4308_0
python pkgs/main/linux-64::python-3.8.13-h12debd9_0
readline pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
requests pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.100-py38h27cfd23_0
setuptools pkgs/main/linux-64::setuptools-61.2.0-py38h06a4308_0
six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
sqlite pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0
tk pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
tqdm pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
urllib3 pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.12-h7f8727e_1

Preparing transaction: …working… done
Executing transaction: …working… done
installation finished.

Done.
anaconda python installation successful.

Extracting all conda packages…

…

Done.
conda packages installation successful.

Main dependency installation completed. Continuing…

Completed.
Currently checking hash for mongodb
Forcing reinstall for dependency mongodb…

mongodb 3.6.23 installation successful.

Completed.
Completed dependency check.
Generating ‘/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/libtiff/tiff_h_4_4_0.py’ from ‘/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/…/include/tiff.h’

===================================================
Successfully updated master to version v4.2.1.

Starting cryoSPARC System master process…
CryoSPARC is not already running.
Traceback (most recent call last):
File “”, line 1, in
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/cryosparc_compute/database_management.py”, line 48, in configure_mongo
initialize_replica_set()
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/cryosparc_compute/database_management.py”, line 87, in initialize_replica_set
admin_db = try_get_pymongo_admin_db(mongo_client)
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/cryosparc_compute/database_management.py”, line 249, in try_get_pymongo_admin_db
admin_db.command(({‘serverStatus’: 1}))
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/database.py”, line 828, in command
return self._command(
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/database.py”, line 703, in _command
return sock_info.command(
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/pool.py”, line 740, in command
return command(
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/network.py”, line 177, in command
helpers._check_command_response(
File “/home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/helpers.py”, line 180, in _check_command_response
raise OperationFailure(errmsg, code, response, max_wire_version)
pymongo.errors.OperationFailure: there are no users authenticated, full error: {‘operationTime’: Timestamp(1679106761, 1), ‘ok’: 0.0, ‘errmsg’: ‘there are no users authenticated’, ‘code’: 13, ‘codeName’: ‘Unauthorized’, ‘$clusterTime’: {‘clusterTime’: Timestamp(1679106761, 1), ‘signature’: {‘hash’: b’\xe8\x84\xa0$vv\xa9\xa3*S\xf2\xcb\xfe\x002E\xb51\x00\xe4’, ‘keyId’: 7164936057471893506}}}
configuring database
Warning: Could not get database status (attempt 1/3)
Warning: Could not get database status (attempt 2/3)
Warning: Could not get database status (attempt 3/3)
[2023-03-17T21:32:49-05:00] Error configuring database. Most recent database log lines:
2023-03-17T21:32:35.714-0500 I STORAGE [initandlisten] exception in initAndListen: DBPathInUse: Unable to lock the lock file: /home/cryosparc_user/software/cryosparc/cryosparc_database/mongod.lock (Resource temporarily unavailable). Another mongod instance is already running on the /home/cryosparc_user/software/cryosparc/cryosparc_database directory, terminating
2023-03-17T21:32:35.714-0500 I CONTROL [initandlisten] now exiting
2023-03-17T21:32:35.714-0500 I CONTROL [initandlisten] shutting down with code:100
2023-03-17T21:32:38.698-0500 I NETWORK [listener] connection accepted from 127.0.0.1:37004 #2930 (130 connections now open)
2023-03-17T21:32:38.698-0500 I NETWORK [conn2930] received client metadata from 127.0.0.1:37004 conn2930: { driver: { name: “PyMongo”, version: “3.13.0” }, os: { type: “Linux”, name: “Linux”, architecture: “x86_64”, version: “4.18.0-372.32.1.el8_6.x86_64” }, platform: “CPython 3.8.15.final.0” }
2023-03-17T21:32:38.699-0500 I NETWORK [listener] connection accepted from 127.0.0.1:37008 #2931 (131 connections now open)
2023-03-17T21:32:38.699-0500 I NETWORK [conn2931] received client metadata from 127.0.0.1:37008 conn2931: { driver: { name: “PyMongo”, version: “3.13.0” }, os: { type: “Linux”, name: “Linux”, architecture: “x86_64”, version: “4.18.0-372.32.1.el8_6.x86_64” }, platform: “CPython 3.8.15.final.0” }
2023-03-17T21:32:48.717-0500 I ACCESS [conn2931] Unauthorized: not authorized on admin to execute command { endSessions: [ { id: UUID(“0c21e721-054f-4b27-a2c4-281813c21cbc”) } ], $clusterTime: { clusterTime: Timestamp(1679106761, 1), signature: { hash: BinData(0, E884A0247676A9A32A53F2CBFE003245B53100E4), keyId: 7164936057471893506 } }, $db: “admin”, readPreference: { mode: "primaryPreferred" } } 2023-03-17T21:32:48.717-0500 I NETWORK [conn2931] end connection 127.0.0.1:37008 (130 connections now open) 2023-03-17T21:32:48.717-0500 I NETWORK [conn2930] end connection 127.0.0.1:37004 (129 connections now open) [cryosparc_user@sn4622125205 ~]

This is what I got after doing cryosparcm update --override
There is some warning: could not get database status
Error configuring database. Most recent database log lines:

Looks like there is some problem in installation in the final step

Faisal

19

Thanks for trying that @khajafaisaltarique.
It is possible that an orphaned mongod database process prevented
cryosparcm update from succeeding.
Please can you post the output of the command:
ps xww | grep -e mongo -e cryosparc

20 
[cryosparc_user@sn4622125205 ~]$ ps xww | grep -e mongo -e cryosparc
 417081 ?        Ss    36:34 python /home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /home/cryosparc_user/software/cryosparc/cryosparc_master/supervisord.conf
 417195 ?        Sl   1797:42 mongod --auth --dbpath /home/cryosparc_user/software/cryosparc/cryosparc_database --port 39001 --oplogSize 64 --replSet meteor --nojournal --wiredTigerCacheSizeGB 4 --bind_ip_all
 417306 ?        Sl   321:19 python -c import cryosparc_command.command_core as serv; serv.start(port=39002)
 417340 ?        Sl   291:16 python -c import cryosparc_command.command_vis as serv; serv.start(port=39003)
 417346 ?        Sl   455:06 python -c import cryosparc_command.command_rtp as serv; serv.start(port=39005)
 417389 ?        Sl    19:39 /home/cryosparc_user/software/cryosparc/cryosparc_master/cryosparc_app/custom-server/nodejs/bin/node dist/server/index.js
 417408 ?        Sl   389:48 /home/cryosparc_user/software/cryosparc/cryosparc_master/cryosparc_app/api/nodejs/bin/node ./bundle/main.js
1731232 ?        Sl    45:52 python -c import cryosparc_compute.run as run; run.run() --project P11 --job J22 --master_hostname sn4622125205.ctrc.uthscsa.edu --master_command_core_port 39002
2915559 tty3     Sl+    0:00 file-roller /home/cryosparc_user/Downloads/viruses-14-02206-s001(1).zip
3238582 ?        Ss     0:29 python /home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /home/cryosparc_user/software/cryosparc/cryosparc_master/supervisord.conf
3406594 pts/0    S+     0:00 grep --color=auto -e mongo -e cryosparc
[cryosparc_user@sn4622125205 ~]$

This is what I got

Faisal

22

Thanks @khajafaisaltarique for this info, which indicates that old CryoSPARC-related processes were not terminated during the update as expected. May I suggest, if it is okay to terminate all currently running CryoSPARC jobs:

  1. Run
    cryosparcm stop
  2. Run these commands:
    kill 417081
kill 3238582 
kill 417195
kill 1731232
  3. Wait 10 seconds.
  4. Ensure that the command
    ps xww | grep -e mongo -e cryosparc_master
    does not show any more mongod or python processes.
  5. Try
    cryosparcm start
  6. If the previous command worked without error, proceed to updating cryosparc_worker according to the Manual Cluster Updates instructions here.
23

Thanks Wtempel

We are almost there. My cryosparc has been updated to 4.2.1. And now workspace from the previous projects are displayed and I am also able to navigate from one projects to other.

But as you mentioned earlier I got the following error while running a new job.

AssertionError: Version mismatch! Worker version (v4.0.3) and Master version (v4.2.1) are not the same. Please update.

I am not able to update cryosparc_worker (maybe due to my limited linux knowledge). I don’t know from where to begin with. Do I need to start from the beginning or the only worker update ? Can you please mention and gudie me with the exact steps and command lines to finish the installation.

Thanks

Faisal

24

@khajafaisaltarique If all the following are true

  • both your cryosparc_master and cryosparc_worker directories are inside
    /home/cryosparc_user/software/cryosparc/
  • /home/cryosparc_user/software/cryosparc/cryosparc_master contains
    files cryosparc_master.tar.gz and cryosparc_worker.tar.gz that where created recently and at approximately the same time

you can try

cd /home/cryosparc_user/software/cryosparc/cryosparc_worker/
ln -s ../cryosparc_master/cryosparc_worker.tar.gz
./bin/cryosparcw update
25

Hi

It is showing the following message. I mean it says that the worker is still v4.0.3

[cryosparc_user@sn4622125205 ~]$ cd /home/cryosparc_user/software/cryosparc/cryosparc_worker/
[cryosparc_user@sn4622125205 cryosparc_worker]$ ln -s ../cryosparc_master/cryosparc_worker.tar.gz
ln: failed to create symbolic link './cryosparc_worker.tar.gz': File exists
[cryosparc_user@sn4622125205 cryosparc_worker]$ ./bin/cryosparcw update
Updating... checking versions
Current version v4.0.3 - New version v4.0.3 
Already up to date
26

So the master is v4.2.1 and the worker is v4.0.3

28

Could it be that the existing file was left over by a previous update? In that case, please delete
/home/cryosparc_user/software/cryosparc/cryosparc_worker/cryosparc_worker.tar.gz and try again the
ln -s and ./bin/cryosparcw update commands.

1 Like
29

You are correct. I did as you recommended and finally everything started working fine.

Thanks a lot. I appreciate

Faisal