Error for "create_user" with params

Dear all,
I am trying to install the latest version cryoSPARC(v4.2.1), but i cant create the initial cryoSPARC user.

Error for "create_user" with params ('initial', 'email', 'password', 'username', 'firstname', 'lastname'):
OtherError: [Errno 32] Broken pipe

There was no error reported before this step.

Besides, when i run “cryosparcm status”

CryoSPARC System master node installed at
Current cryoSPARC version: v4.2.1

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                     FATAL     unknown error making dispatchers for 'command_core': ENOENT
command_rtp                      STOPPED   Not started
command_vis                      STOPPED   Not started
database                         EXITED    May 05 10:48 PM

An error ocurred while checking license status
Could not get license verification status. Are all CryoSPARC processes RUNNING?

This workstation has had other users download cryoSPARC through different licenses before, but now I am using a brand new license with the same port number(39000) , does this have anything to do with it?
(I can open the User Interface by firefox but i cant log in, it shows internal sever error )

Do you have any ideas to solve this problem?

Welcome to the forum @Yue

If with download you also mean install, it must be ensured that each CryoSPARC installation has its respective

  • unique license id
  • unique database patch
  • unique and non-overlapping port range. Did you ensure before installation of CryoSPARC that the chosen port number (and the next 9 port numbers) would not interfere with any CryoSPARC instance that may already be installed on that computer?

Thank you for your answer! :sob:
I’ve unloaded the cryoSPARC (old version) others had installed before. The previous attempt to update was unsuccessful, so I reapplied for a new license to install the new version.

Please can you post the output of these two commands:

ps axww | grep -e cryosparc -e mongo
ls -l /tmp/[cm]*.sock
ps axww | grep -e cryosparc -e mongo
 3370 pts/0    S+     0:00 grep --color=auto -e cryosparc -e mongo
11220 ?        Sl   230:33 python -c import cryosparc_command.command_core as serv; serv.start(port=39002)
11255 ?        Sl    71:00 python -c import cryosparc_command.command_vis as serv; serv.start(port=39003)
11274 ?        Sl   145:31 python -c import cryosparc_command.command_rtp as serv; serv.start(port=39005)
11329 ?        Sl   334:05 /software/cryosparc/cryosparc_master/cryosparc_webapp/nodejs/bin/node ./bundle/main.js
11372 ?        Sl   867:39 /software/cryosparc/cryosparc_master/cryosparc_liveapp/nodejs/bin/node ./bundle/main.js
11955 ?        Ss     7:43 python /software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /software/cryosparc/cryosparc_master/supervisord.conf
12729 ?        Ss     0:51 python /software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /software/cryosparc/cryosparc_master/supervisord.conf
36131 ?        Ss     4:18 python /software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /software/cryosparc/cryosparc_master/supervisord.conf
ls -l /tmp/[cm]*.sock
srwx------. 1 xiaoxiao xiaoxiao 0 May  6 14:16 /tmp/cryosparc-supervisor-92da9dd0c09d89200e8222c248ebb24c.sock
srwx------. 1 xiaoxiao xiaoxiao 0 May  6 14:16 /tmp/mongodb-39001.sock
cryosparc_master]$ ./    --standalone \
>                 --license $LICENSE_ID \
>                 --worker_path /software/cryosparc/cryosparc_worker \
>                 --cudapath /usr/local/cuda-10.2 \
>                 --ssdpath /data/cryosparc_cache \
>                 --initial_email - \
>                 --initial_password "-" \
>                 --initial_username "-" \
>                 --initial_firstname "-" \
>                 --initial_lastname "-" \
>                 --port 39000


 Installation Settings:
   License ID              : -
   Root Directory          : /software/cryosparc/cryosparc_master
   Master Hostname         : -
   Database Directory      : /software/cryosparc/cryosparc_database
   Base HTTP Port Number   : 39000
   Developer Install       : false
   Operating System        : Linux
   Insecure Install        : false
   Standalone Install      : true
   Worker Root Directory   : /software/cryosparc/cryosparc_worker
   Initial User Email      : -
   Initial User Name       : -
   Initial First Name      : -
   Initial Last Name       : -
   CUDA Path               : /usr/local/cuda-10.2
   SSD                     : true
   SSD Path                : /data/cryosparc_cache
   Version                 : v4.2.1


The cryoSPARC System master installation will host a database,
web application, and command layer for cryoSPARC, but will not
perform processing jobs.

Please read and confirm the above settings. The cryoSPARC database
will be stored at the database directory which is relative to the
root directory, unless provided as an absolute path.
You can change the database directory now by passing the --dbapth
parameter to this installer, or later via the command line.

Are the above settings correct?
1) Yes
2) No
#? 1


 Setting up hard-coded environment variables


 Installing all dependencies.

Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress
  Checking dependencies...
  Dependencies for python have changed - reinstalling...
  Installing anaconda python...
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /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: done
Executing transaction: done
installation finished.
    anaconda python installation successful.
  Extracting all conda packages...
    conda packages installation successful.
  Main dependency installation completed. Continuing...
  Currently checking hash for mongodb
  Dependencies for mongodb have changed - reinstalling...
  mongodb 3.6.23 installation successful.
  Completed dependency check.
Generating '/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/libtiff/' from '/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/../include/tiff.h'


 CryoSPARC System master has now been installed.
 Add bin directory to your ~/.bashrc ?
1) Yes
2) No
#? 1

 The following lines were appended to your ~/.bashrc:
  export PATH=/software/cryosparc/cryosparc_master/bin:$PATH


  The installer will now download, install and connect the worker
  package on this machine. The worker package will allow cryoSPARC
  to run compute jobs.


 Starting cryoSPARC...

Starting cryoSPARC System master process..
CryoSPARC is already running.
If you would like to restart, use cryosparcm restart


 Creating the initial cryoSPARC user...

Creating user - with email: - and name: -
Error for "create_user" with params ('initial', '-', '-', '-', '-', '-'):
OtherError: [Errno 32] Broken pipe

By the way, this is the whole installation process.
Even if I reinstall(rm -rf the folder and clean the .bashrc), every time I get to the create the initial user step, I get an error.

The simultaneous presence of multiple supervisord processes with identical command paths processes and the apparent absence of a mongos process are unexpected in v4.2.1.
You may try the following (under the Linux account that runs CryoSPARC):

  1. cryosparcm stop
  2. ps xww | grep supervisord.
    Post the output. If any supervisord processes are still present, you may use kill -TERM <process id> to terminate them.
  3. Wait 10 seconds, then run (and post the output):
    ps -eouname,pid,ppid,cmd | grep -e mongo -e cryosparc
    ls -l /tmp/[cm]*.sock
  4. Inspect
    for errors and post if you find any.