CryoSPARC installation does not complete: Completed dependency check

Mahrad · July 7, 2023, 5:20pm

Hi,

I am new to CryoSPARC and I am running into some trouble installing the program.

The program is being installed on ComputeCanada
I use a windows 11 desktop laptop
I have verified my license
I have tried reinstalling the program and the same problem has reoccurred

PowerShell log:

[mahrad3@cedar5 cryosparc_master]$ ./install.sh --standalone \

–license <MY_LICENSE>
–worker_path /home/mahrad3/projects/def-janehowe/mahrad3/cryoSPARC/cryosparc_worker/bin/cryosparcw
–cudapath /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.2.2
–ssdpath /home/mahrad3/scratch/cryoSPARC
–initial_email “MY_EMAIL”
–initial_username “mahrad3”
–initial_firstname “Mahrad”
–initial_lastname “Nemati”
–port 24000

************ CRYOSPARC SYSTEM: STANDALONE INSTALLER **************

Input initial user password:
Input initial user password (again):

Installation Settings:
License ID : <MY_LICENSE>
Root Directory : /project/6045546/mahrad3/cryoSPARC/cryosparc_master
Master Hostname : cedar5.cedar.computecanada.ca
Database Directory : /project/6045546/mahrad3/cryoSPARC/cryosparc_database
Base HTTP Port Number : 24000
Developer Install : false
Operating System : Linux
Insecure Install : false
Standalone Install : true
Worker Root Directory : /home/mahrad3/projects/def-janehowe/mahrad3/cryoSPARC/cryosparc_worker/bin/cryosparcw
Initial User Email : <MY_EMAIL>
Initial User Name : mahrad3
Initial First Name : Mahrad
Initial Last Name : Nemati
CUDA Path : /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.2.2
SSD : true
SSD Path : /home/mahrad3/scratch/cryoSPARC
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?

Yes
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=/project/6045546/mahrad3/cryoSPARC/cryosparc_master/deps/anaconda
Unpacking payload …
Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /project/6045546/mahrad3/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.

After this output I am unable to type anything. I have spent over 2 hours on this screen and the installation never completes. If I try to open a new window or close this window and log back into ComputeCanada, it’s evident that the installation has not completed:

[mahrad3@cedar1 ~]$ cryosparcm status
-bash: cryosparcm: command not found

How do I fix this problem?

Thanks,
Mahrad

wtempel · July 7, 2023, 6:44pm

Welcome to the forum @Mahrad.

It is possible that your laptop’s connection to the (ComputeCanada) server has been disrupted, which may disrupt installation. If an unstable connection to the server is indeed the problem, you may want to run remote commands inside a remote screen or tmux session. This way, a disrupted connection would allow

remote commands to continue without interruption
you to “re-attach” to the remote session after restoring the connection between laptop and server

This could indicate an incomplete CryoSPARC installation, but could also occur after successful installation if

/project/6045546/mahrad3/cryoSPARC/cryosparc_master/bin

is not in your $PATH.

Mahrad · July 24, 2023, 4:12pm

Thank you so much for the quick response. The problem is resolved, the issue was the limited disk space allocated to the file I was attempting to install the software in.