Standalone cryosparc installation

Troubleshooting
1

Hi,

I am trying to install Cryosparc on the linux box following the instruction as stated in tutorial. It stop at following step. It seems to me the firewall issue, but would like to confirm with the expert before I contact the IT department at home institution.

cd /home/cryoem/cryosparc_anamika
[cryoem@dhcp240247 cryosparc_anamika]$ export LICENSE_ID="XXXXXXX"
[cryoem@dhcp240247 cryosparc_anamika]$ 
[cryoem@dhcp240247 cryosparc_anamika]$ curl -L https://get.cryosparc.com/download/master-latest/$LICENSE_ID > cryosparc2_master.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
100  555M  100  555M    0     0  36.4M      0  0:00:15  0:00:15 --:--:-- 49.3M
[cryoem@dhcp240247 cryosparc_anamika]$ curl -L https://get.cryosparc.com/download/worker-latest/$LICENSE_ID > cryosparc2_worker.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  624M  100  624M    0     0  36.4M      0  0:00:17  0:00:17 --:--:-- 34.7M
[cryoem@dhcp240247 cryosparc_anamika]$ 
[cryoem@dhcp240247 cryosparc_anamika]$ tar -xf cryosparc2_master.tar.gz
[cryoem@dhcp240247 cryosparc_anamika]$ tar -xf cryosparc2_worker.tar.gz
[cryoem@dhcp240247 cryosparc_anamika]$ 
[cryoem@dhcp240247 cryosparc_anamika]$ cd cryosparc2_master
[cryoem@dhcp240247 cryosparc2_master]$ 
[cryoem@dhcp240247 cryosparc2_master]$ ./install.sh    --standalone \\
Unknown option: \
[cryoem@dhcp240247 cryosparc2_master]$                 --license $LICENSE_ID \\
bash: --license: command not found...
[cryoem@dhcp240247 cryosparc2_master]$                 --worker_path /home/cryoem/cryosparc_anamika/cryosparc_worker \\
bash: --worker_path: command not found...
[cryoem@dhcp240247 cryosparc2_master]$                 --cudapath /usr/local/cuda \\
bash: --cudapath: command not found...
[cryoem@dhcp240247 cryosparc2_master]$                 --ssdpath /home/cryoem/cryosparc_anamika/cryosparc_cache \\
bash: --ssdpath: command not found...
[cryoem@dhcp240247 cryosparc2_master]$                 --initial_email "XXXX" \\
bash: --initial_email: command not found...
[cryoem@dhcp240247 cryosparc2_master]$                 --initial_password XXXX \\
bash: --initial_password: command not found...
[cryoem@dhcp240247 cryosparc2_master]$                 --initial_name "XXXX" \\
bash: --initial_name: command not found...
[cryoem@dhcp240247 cryosparc2_master]$ 
[cryoem@dhcp240247 cryosparc2_master]$ source ~/.bashrc
2

Hi @Anamika,

Sorry, it seems that there is a typo in our guide. The end of each line in the installation command should only have one \, which allows the command to carry over to the next line instead of just running the first one:

cd cryosparc2_master

./install.sh    --standalone \ 
                --license $LICENSE_ID \ 
                --worker_path <worker_path> \ 
                --cudapath <cuda_path> \ 
                --ssdpath <ssd_path> \ 
                --initial_email <user_email> \ 
                --initial_password <user_password> \ 
                --initial_name <user_name> \ 
                [--port <port_number>]

- Suhail

5

Hi Suhail,

Thanks for pointing out typo. I tried again and seems installation works. I did not specify the port as it says in the tutorial that if I do not specify it will take default (Although I also tried with port 39000). However, I cannot access user interface, It says unable to connect. Do I need to specify different port ? I am installing on Linux box with CetOS operating system. Just to be sure I also checked if the port is enabled and it is.

7

Hi Suhail,

This what I see after I run correct script:
Still cannot access web access , please let me what I am doing wrong here. Even when I check the status using cryosparcm status command , this is what I see “bash: cryosparcm: command not found…”

Thanks

Installation Settings:
License ID : XXXX
Root Directory : /XXXXX/cryosparc2_master
Master Hostname : XXX
Database Directory : /XXXX/cryosparc2_database
Base HTTP Port Number : 39000
Developer Install : false
Operating System : Linux
Insecure Install : false
Standalone Install : true
Worker Root Directory : /XXX/cryosparc_worker
Initial User Email : XXXX
Initial User Password : XXX
Initial User Name : XXX
CUDA Path : /usr/local/cuda
SSD : true
SSD Path : /XXX/cryosparc_cache
Version : v2.15.0

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
    #? Yes
8

Hi @Anamika,

Did you source ~/.bashrc after installing? Please do so and see if you can run cryosparcm after that.

Thanks,
Suhail

9

Yes, I did and still see the same.

[cryoem@dhcp240247 cryosparc2_master]$ source ~/.bashrc
[cryoem@dhcp240247 cryosparc2_master]$ cryosparcm status
bash: cryosparcm: command not found…
[cryoem@dhcp240247 cryosparc2_master]$

10

What type of settings do I use for .bashrc script? It seems to me that is not running properly.

11

Hi @Anamika,

From the cryosparc2_master directory, are you able to run:

./bin/cryosparcm status