Installation failure

Install, Configure and Update
1

Hi,
I tried to install the latest version of Cryosparc, and failed at the last step when the program launched itself. The error message is similar to what I got with “cryosparm install test”, pasted below. I can still launch the program with “cryosparm start” afterwards and see the login interface on a web browser, but when I tried to log in, it said user doesn’t exist. I opened the ports 39000:39010 with ufw (the OS is is Ubuntu 20.04) prior to the installation. I also tried to install version 3, which failed and program doesn’t even lanunch, saying something like “failed to spawn”.

Running installation tests…
✓ Running as cryoSPARC owner
✓ Running on master node
✓ CryoSPARC is running
*** CommandClient: (http://OldGPU:39002/api) HTTP Error 403 notresolvable; please check cryosparcm log command_core for additional information.
Response from server: b’\n\n\n\n\n \n \n McAfee Web Gateway - Notification\n \n \n\n\n\n\n\n <table class='bodyTable'>\n \n <td class='bodyData' background='/mwg-internal/de5fs23hu73ds/files/utsw/img/bg_body.gif'>\n\n<table class='logoTable'>\n \n <td class='logoData'>\n <img src='/mwg-internal/de5fs23hu73ds/files/utsw/img/utswLogo.jpg'>\n \n \n\n\n\n\n\n\n<table class='titleTable'>\n \n <td class='titleData'>\n Host Not Resolvable\n \n \n\n\n\n\n\n \n \n \n

\n The Host is not resolvable.
\n This website is down. Please contact the site owner if you believe this is an error.\n
\n\n\n\n\n \n \n \n
\n URL:
\n
\n\n\n\n\n\n<table class='footTable'>\n \n <td class='helpDeskData'>\n For assistance, please contact the IR Service Desk at 214-648-7600.\n \n \n \n <td class='footData'>\n generated 2023-01-09 12:21:21 by McAfee Web Gateway [129.112.115.40/m-proxy1] \n
\n Python-urllib/3.8\n
\n Give Not Resolvable for NXDOMAIN Web Sites\n
\n Client IP [192.168.11.1]\n \n \n\n\n\n \n \n \n\n\n’
Traceback (most recent call last):
File “/home/xuewu_cryosparc/cryosparc/cryosparc_master/cryosparc_tools/cryosparc/command.py”, line 104, in func
with make_json_request(self, “/api”, data=data) as request:
File “/home/xuewu_cryosparc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/contextlib.py”, line 113, in enter
return next(self.gen)
File “/home/xuewu_cryosparc/cryosparc/cryosparc_master/cryosparc_tools/cryosparc/command.py”, line 191, in make_request
raise CommandClient.Error(client, error_reason, url=url)
cryosparc_tools.cryosparc.command.Error: *** CommandClient: (http://OldGPU:39002/api) HTTP Error 403 notresolvable; please check cryosparcm log command_core for additional information.
Response from server: b’\n\n\n\n\n \n \n McAfee Web Gateway - Notification\n \n \n\n\n\n\n\n <table class='bodyTable'>\n \n <td class='bodyData' background='/mwg-internal/de5fs23hu73ds/files/utsw/img/bg_body.gif'>\n\n<table class='logoTable'>\n \n <td class='logoData'>\n <img src='/mwg-internal/de5fs23hu73ds/files/utsw/img/utswLogo.jpg'>\n \n \n\n\n\n\n\n\n<table class='titleTable'>\n \n <td class='titleData'>\n Host Not Resolvable\n \n \n\n\n\n\n\n \n \n \n
\n The Host is not resolvable.
\n This website is down. Please contact the site owner if you believe this is an error.\n
\n\n\n\n\n \n \n \n
\n URL:
\n
\n\n\n\n\n\n<table class='footTable'>\n \n <td class='helpDeskData'>\n For assistance, please contact the IR Service Desk at 214-648-7600.\n \n \n \n <td class='footData'>\n generated 2023-01-09 12:21:21 by McAfee Web Gateway [129.112.115.40/m-proxy1] \n
\n Python-urllib/3.8\n
\n Give Not Resolvable for NXDOMAIN Web Sites\n
\n Client IP [192.168.11.1]\n \n \n\n\n\n \n \n \n\n\n’

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “/home/xuewu_cryosparc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/runpy.py”, line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File “/home/xuewu_cryosparc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/runpy.py”, line 87, in _run_code
exec(code, run_globals)
File “/home/xuewu_cryosparc/cryosparc/cryosparc_master/cryosparc_command/instance_tests/installation_test.py”, line 10, in
import patch
File “/home/xuewu_cryosparc/cryosparc/cryosparc_master/patch.py”, line 34, in
CLI = client.CommandClient(
File “/home/xuewu_cryosparc/cryosparc/cryosparc_master/cryosparc_compute/client.py”, line 36, in init
super().init(service, host, port, url, timeout, headers, cls=NumpyEncoder)
File “/home/xuewu_cryosparc/cryosparc/cryosparc_master/cryosparc_tools/cryosparc/command.py”, line 91, in init
self._reload() # attempt connection immediately to gather methods
File “/home/xuewu_cryosparc/cryosparc/cryosparc_master/cryosparc_tools/cryosparc/command.py”, line 118, in _reload
system = self._get_callable(“system.describe”)()
File “/home/xuewu_cryosparc/cryosparc/cryosparc_master/cryosparc_tools/cryosparc/command.py”, line 107, in func
raise CommandClient.Error(
cryosparc_tools.cryosparc.command.Error: *** CommandClient: (http://OldGPU:39002) Did not receive a JSON response from method “system.describe” with params ()

Xuewu

2

Welcome to the forum @xuewuzhang.
Please can you post the full command lines of the install.sh command(s) that you used for installation of CryoSPARC? Please also post the output of the following commands (run on the computer that is supposed to run CryoSPARC master processes:

  1. hostname -f
  2. host $(hostname -f)
3

The install.sh command:
cd cryosparc_master
./install.sh --standalone
–license $LICENSE_ID
–worker_path /home/xuewu_cryosparc/cryosparc/cryosparc_worker
–cudapath /usr/local/cuda
–ssdpath /home/xuewu_cryosparc/cryosparc_cache
–initial_email “xuewu.zhang@utsouthwestern.edu”
–initial_password “qwerty”
–initial_username “xuewu”
–initial_firstname “xuewu”
–initial_lastname “zhang” \

hostname -f output: OldGPU
OldGPU.dhcp.swmed.org has address 192.168.11.1

Thanks,
Xuewu

4

Hi Xuewu,

It is due to UTSW internet proxy. Try to use the guest wifi to set it up.

5

In addition to the internet proxy, capitalization in your hostname may also cause problems after installation. If you do not plan to connect additional workers to this “standalone” instance, the following configuration may sidestep these problems:

  1. cryosparcm stop

  2. ps xww | grep -e cryosparc -e mongo

  3. kill (but not kill -9) processes related to your CryoSPARC instance

  4. remove the /tmp/cryosparc-supervisor-*.sock of your (not, potentially, someone else’s) CryoSPARC instance, if it still exists

  5. edit /home/xuewu_cryosparc/cryosparc/cryosparc_master/config.sh:
    export CRYOSPARC_MASTER_HOSTNAME="127.0.0.1" (edit existing line)
    export CRYOSPARC_HOSTNAME_CHECK="127.0.0.1" (this variable definition is probably not currently present in the file and should be added to the file

  6. cryosparcm start

  7. /home/xuewu_cryosparc/cryosparc/cryosparc_worker/bin/cryosparcw connect --worker 127.0.0.1 --master 127.0.0.1 --ssdpath /home/xuewu_cryosparc/cryosparc_cache
6

yliucj, I did suspect that, but I have done the installation in the past with the same proxy settings and it worked. Plus, the server doesn’t have a WIFI adaptor, so I can’t test it now.

Wtempel, I tried this, but at the last step, I got:
/home/xuewu_cryosparc/cryosparc/cryosparc_worker/bin/cryosparcw: line 67: config.sh: No such file or directory
It looks like that the cryosparw script cannot find the “config.sh” file. I modified the script to include the full-path of “config.sh”, but that triggered even more errors.

7

I also tried to change the host name to all lower case, that didn’t help.

8

It seems the --standalone installation did not proceed to the worker installation step. You may want to try:

cd /home/xuewu_cryosparc/cryosparc/cryosparc_worker/
./install.sh --cudapath /usr/local/cuda --license "your license id"

before proceeding to the cryosparcw connect step.

9

You are right. I did this and now it is connected. Strangely, it still said that user not found. I used the the command line tool to create the initial user, and could login in finally and see the version 4.0 interface for the first time. There are some additional issues, I will try to figure them out myself. Thanks!

10

After reading some older posts with similar problems, I figure out that the key is to set the “no_proxy” environment variable. It was set to “127.0.0.1, localhost”. I added “oldgpu” (the host name) to it. Now the installation completed without problem. It might be useful to include this in the installation instruction.
Thanks,
Xuewu

11

Hi @xuewuzhang, I’m facing the same issue right now trying to install cryosparc in single workstation. It didn’t proceed to the worker node installation either, so I did the same as @wtempel suggested, but in my case it didn’t solve the issue. The same error is still there. I’m new to this so I’m not sure where to set the “no_proxy” environment variable and add the hostname. Could you tell me where to change this configuration? Do I have to install all over again?

Thanks!!
Alejandro

12

Assuming you are using the bash terminal, you should have a “.bashrc” file in your home directory. Open it with a text editor and add this line to it:
export no_proxy=“127.0.0.1, localhost, XXX”.
Replace the “XXX” with the hostname of your computer. You can find the hostname by using commands “hostname” and “hostname -f”, if the results are different, add them both, separated by comma. Save the file, then use “source .bashrc” to activate it. Stop cryosparcm and do a fresh installation, hopefully it will solve the problem. (Just in case, you should also check in the .bashrc that the http_proxy and https_proxy variables are set correctly).

13

Thank you so much @xuewuzhang, I was able to solve the problem!