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
/software/cryosparc/cryosparc_master
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?
Thanks.
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!
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.
cryosparc_master]$ ./install.sh --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
************ CRYOSPARC SYSTEM: STANDALONE INSTALLER **************
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
Continuing.
******************************************************************
Setting up hard-coded config.sh 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...
------------------------------------------------------------------------
PREFIX=/software/cryosparc/cryosparc_master/deps/anaconda
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.
------------------------------------------------------------------------
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
Dependencies for mongodb have changed - reinstalling...
------------------------------------------------------------------------
mongodb 3.6.23 installation successful.
------------------------------------------------------------------------
Completed.
Completed dependency check.
Generating '/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/libtiff/tiff_h_4_4_0.py' from '/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/../include/tiff.h'
************ CRYOSPARC MASTER INSTALLATION COMPLETE **************
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
************ CRYOSPARC SYSTEM: STANDALONE INSTALLER **************
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):
cryosparcm stop
ps xww | grep supervisord.
Post the output. If any supervisord processes are still present, you may use kill -TERM <process id> to terminate them.
