cryoSPRAC v2 standalone installation problem

Install, Configure and Update
1

Hi

I have been trying to install cryoSPARC v2 into our Linux workstation (Ubuntu 16). I was simply following the script provided. However, something is wrong.
"
root@DELL:/home/cryosparc_user/cryosparc/cryosparc2_master# export LICENSE_ID="*"
root@DELL:/home/cryosparc_user/cryosparc/cryosparc2_master# ./install.sh --standalone --license $LICENSE_ID --worker_path /home/cryosparc_user/cryosparc/cryosparc2_worker --cudapath /usr/local/cuda-9.0 --ssdpath /scratch/cryosparc_cache --initial_email @ --initial_password * --initial_name * --port 36600
************ CRYOSPARC SYSTEM: MASTER INSTALLER **************

You are the root user. Are you sure you want to install as root?
This is really not recommended and may introduce security holes.
Proceed at your own risk. Are you sure?

  1. Yes
  2. No
    #? 1
    Continuing.
    Installation Settings:
    License ID : *
    Root Directory : /home/cryosparc_user/cryosparc/cryosparc2_master
    Master Hostname : DELL
    Database Directory : /home/cryosparc_user/cryosparc/cryosparc2_database
    Base HTTP Port Number : 36600
    Developer Install : false
    Operating System : Linux
    Insecure Install : false
    Standalone Install : true
    Worker Root Directory : /home/cryosparc_user/cryosparc/cryosparc2_worker
    Initial User Email : *
    Initial User Password : *
    Initial User Name : guolu
    CUDA Path : /usr/local/cuda-9.0
    SSD : true
    SSD Path : /scratch/cryosparc_cache
    Version : v2.4.6

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.

Checking dependencies…
Dependencies for python have changed - reinstalling…

Installing anaconda python…

PREFIX=/home/cryosparc_user/cryosparc/cryosparc2_master/deps/anaconda
installing: python-2.7.14-h1571d57_29 …
Python 2.7.14 :: Anaconda, Inc.
installing: ca-certificates-2017.08.26-h1d4fec5_0 …
installing: conda-env-2.6.0-h36134e3_1 …
installing: libgcc-ng-7.2.0-h7cc24e2_2 …
installing: libstdcxx-ng-7.2.0-h7a57d05_2 …
installing: libffi-3.2.1-hd88cf55_4 …
installing: ncurses-6.0-h9df7e31_2 …
installing: openssl-1.0.2n-hb7f436b_0 …
installing: tk-8.6.7-hc745277_3 …
installing: yaml-0.1.7-had09818_2 …
installing: zlib-1.2.11-ha838bed_2 …
installing: libedit-3.1-heed3624_0 …
installing: readline-7.0-ha6073c6_4 …
installing: sqlite-3.20.1-hb898158_2 …
installing: asn1crypto-0.23.0-py27h7b0c810_0 …
installing: certifi-2017.11.5-py27h71e7faf_0 …
installing: chardet-3.0.4-py27hfa10054_1 …
installing: enum34-1.1.6-py27h99a27e9_1 …
installing: idna-2.6-py27h5722d68_1 …
installing: ipaddress-1.0.18-py27h337fd85_0 …
installing: pycosat-0.6.3-py27ha4109ae_0 …
installing: pycparser-2.18-py27hefa08c5_1 …
installing: pysocks-1.6.7-py27he2db6d2_1 …
installing: ruamel_yaml-0.11.14-py27h672d447_2 …
installing: six-1.11.0-py27h5f960f1_1 …
installing: cffi-1.11.2-py27ha7929c6_0 …
installing: setuptools-36.5.0-py27h68b189e_0 …
installing: cryptography-2.1.4-py27h6697b16_0 …
installing: wheel-0.30.0-py27h2bc6bb2_1 …
installing: pip-9.0.1-py27ha730c48_4 …
installing: pyopenssl-17.5.0-py27hcee3be0_0 …
installing: urllib3-1.22-py27ha55213b_0 …
installing: requests-2.18.4-py27hc5b0589_1 …
installing: conda-4.3.31-py27_0 …
installation finished.

Done.
anaconda python installation successful.

Preparing to install all conda packages…

Done.
conda packages installation successful.

Preparing to install all pip packages…

Processing ./deps_bundle/python/python_packages/pip_packages/Flask-JSONRPC-0.3.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-PyMongo-0.5.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/libtiff-0.4.2.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File “”, line 1, in
File “/tmp/pip-jTBDeD-build/setup.py”, line 77, in
from numpy.distutils.core import setup, Extension
ImportError: No module named numpy.distutils.core

----------------------------------------

Command “python setup.py egg_info” failed with error code 1 in /tmp/pip-jTBDeD-build/
You are using pip version 9.0.1, however version 18.1 is available.
You should consider upgrading via the ‘pip install --upgrade pip’ command.

Done.
pip packages installation successful.

Main dependency installation completed. Continuing…

Completed.
Currently checking hash for mongodb
Dependencies for mongodb have changed - reinstalling…

mongodb 3.4.10 installation successful.

Completed.
Completed dependency check.

************ 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=/home/cryosparc_user/cryosparc/cryosparc2_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 guolu with email: guolu@im.ac.cn password: 19850902
Traceback (most recent call last):
File “/home/cryosparc_user/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py”, line 174, in _run_module_as_main
“main”, fname, loader, pkg_name)
File “/home/cryosparc_user/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py”, line 72, in _run_code
exec code in run_globals
File “/home/cryosparc_user/cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 56, in
cli = CommandClient(host, int(port))
File “/home/cryosparc_user/cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 17, in init
self._reload()
File “/home/cryosparc_user/cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 35, in _reload
system = self._get_callable(‘system.describe’)()
File “/home/cryosparc_user/cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 28, in func
r = requests.post(self.url, json = data, headers = header, timeout=self.timeout)
File “/home/cryosparc_user/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/api.py”, line 112, in post
return request(‘post’, url, data=data, json=json, **kwargs)
File “/home/cryosparc_user/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/api.py”, line 58, in request
return session.request(method=method, url=url, **kwargs)
File “/home/cryosparc_user/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/sessions.py”, line 508, in request
resp = self.send(prep, **send_kwargs)
File “/home/cryosparc_user/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/sessions.py”, line 618, in send
r = adapter.send(request, **kwargs)
File “/home/cryosparc_user/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/adapters.py”, line 508, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPConnectionPool(host=‘dell’, port=36602): Max retries exceeded with url: /api (Caused by NewConnectionError(’<urllib3.connection.HTTPConnection object at 0x7fe33911d290>: Failed to establish a new connection: [Errno 111] Connection refused’,))
root@DELL:/home/cryosparc_user/cryosparc/cryosparc2_master# cryosparcm status

CryoSPARC System master node installed at
/home/cryosparc_user/cryosparc/cryosparc2_master
Current cryoSPARC version: v2.4.6

cryosparcm process status:

command_core STOPPED Not started
command_proxy STOPPED Not started
command_vis STOPPED Not started
database FATAL Exited too quickly (process log may have details)
watchdog_dev STOPPED Not started
webapp STOPPED Not started
webapp_dev STOPPED Not started

global config variables:

export CRYOSPARC_LICENSE_ID=“2cad5260-fa43-11e8-9939-438569e38fd5”
export CRYOSPARC_MASTER_HOSTNAME=“DELL”
export CRYOSPARC_DB_PATH="/home/cryosparc_user/cryosparc/cryosparc2_database"
export CRYOSPARC_BASE_PORT=36600
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false

"
I would appreciate if someone let me know how to solve this problem - so I can install version 2

Thanks for your help

GL

2

Hi @guolu,

The following error might be caused by running the installation as the root user. It’s possible that running these commands as root uses the system’s python and not the Anaconda python that we’ve included in our dependency bundle. Is it possible if you can remove this installation (simply delete cryosparc2_master and cryosparc2_worker folders) and reinstall as the cryosparc_user account?

Also, the error quoted below may indicate another cryosparc process was running before you started the installation. Please follow steps to ensure any other cryosparc processes are terminated before running an installation/update.

3

Thank you very much!@stephan
I reinstall as the user account and master installation complete.
But something is wrong.
"
************ 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=/home/guolu/crysparc/cryosparc2_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 not already running.
database: started
command_core: started
/home/guolu/crysparc/cryosparc2_master/bin/cryosparcm: 行 393: curl: not found command
/home/guolu/crysparc/cryosparc2_master/bin/cryosparcm: 行 393: curl: not found command
/home/guolu/crysparc/cryosparc2_master/bin/cryosparcm: 行 393: curl: not found command
…
"
What can I do?

Thanks for your help

GL

4

@stephan
I have solved this problem by installing curl.
Thank you.
Then, I browser to http://localhost:39800 to access the cryoSPARC user interface and enter my email account and password. I know the email account and password is correct, but web shows User not found.
What can I do?

Thanks for your help

"
Starting cryoSPARC System master process…
CryoSPARC is not already running.
database: started
command_core: started
cryosparc command core startup complete.
command_vis: started
command_proxy: started
webapp: started

CryoSPARC master started.
From this machine, access the webapp at
http://localhost:39800
From other machines on the network, access at
http://DELL:39800

Startup can take several minutes. Point your browser to the address
and refresh until you see the cryoSPARC web interface.
"

GL

5

Hi @guolu,

Glad the initial problem is fixed!
Is it possible if you can try creating a new user account using cryosparcm and try logging in with that account?
Or, if you have important data on the user account that you can’t access, you can also try resetting your password.

https://cryosparc.com/docs/reference/install/#management--monitoring

6

Hi @stephan
After I create a new user account by using cryosparcm createuser,the problem is fixed and I access my account.
Thank you very much again!