Hi, I am trying to install cryosparc on my desktop using:
./install.sh --standalone --license aaabbbccc --worker_path ../cryosparc_worker --cudapath /usr/local/cuda-11.7 --ssdpath ../cryosparc_cache --initial_email xxx --initial_password xxx --initial_username xxx --initial_firstname xxx --initial_lastname xxx
But I am getting:
************ CRYOSPARC SYSTEM: STANDALONE INSTALLER **************
Installation Settings:
License ID : aaabbbccc
Root Directory : /homes/xinliu/cryosparc/cryosparc_master
Master Hostname : it207dt
Database Directory : /homes/xinliu/cryosparc/cryosparc_database
Base HTTP Port Number : 39000
Developer Install : false
Operating System : Linux
Insecure Install : false
Standalone Install : true
Worker Root Directory : ../cryosparc_worker
Initial User Email : xxx
Initial User Name : xh
Initial First Name : xh
Initial Last Name : Liu
CUDA Path : /usr/local/cuda-11.7
SSD : true
SSD Path : ../cryosparc_cache
Version : v4.3.1
******************************************************************
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) 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=/homes/xinliu/cryosparc/cryosparc_master/deps/anaconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /homes/xinliu/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 '/homes/xinliu/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/libtiff/tiff_h_4_4_0.py' from '/homes/xinliu/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=/homes/xinliu/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 xh with email: liuxh2@shanghaitech.edu.cn and name: xh Liu
*** CommandClient: (http://it207dt:39002/api) URL Error [Errno 111] Connection refused
Traceback (most recent call last):
File "/homes/xinliu/cryosparc/cryosparc_master/cryosparc_tools/cryosparc/command.py", line 105, in func
with make_json_request(self, "/api", data=data) as request:
File "/homes/xinliu/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/contextlib.py", line 113, in __enter__
return next(self.gen)
File "/homes/xinliu/cryosparc/cryosparc_master/cryosparc_tools/cryosparc/command.py", line 192, in make_request
raise CommandClient.Error(client, error_reason, url=url)
cryosparc_tools.cryosparc.command.Error: *** CommandClient: (http://it207dt:39002/api) URL Error [Errno 111] Connection refused
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/homes/xinliu/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 "/homes/xinliu/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/homes/xinliu/cryosparc/cryosparc_master/cryosparc_compute/client.py", line 55, in <module>
cli = CommandClient(host=host, port=int(port))
File "/homes/xinliu/cryosparc/cryosparc_master/cryosparc_compute/client.py", line 36, in __init__
super().__init__(service, host, port, url, timeout, headers, cls=NumpyEncoder)
File "/homes/xinliu/cryosparc/cryosparc_master/cryosparc_tools/cryosparc/command.py", line 92, in __init__
self._reload() # attempt connection immediately to gather methods
File "/homes/xinliu/cryosparc/cryosparc_master/cryosparc_tools/cryosparc/command.py", line 119, in _reload
system = self._get_callable("system.describe")()
File "/homes/xinliu/cryosparc/cryosparc_master/cryosparc_tools/cryosparc/command.py", line 108, in func
raise CommandClient.Error(
cryosparc_tools.cryosparc.command.Error: *** CommandClient: (http://it207dt:39002) Did not receive a JSON response from method "system.describe" with params ()
xinliu@it207dt:~/cryosparc/cryosparc_master$ ^C
xinliu@it207dt:~/cryosparc/cryosparc_master$ ^C
xinliu@it207dt:~/cryosparc/cryosparc_master$ cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/homes/xinliu/cryosparc/cryosparc_master
Current cryoSPARC version: v4.3.1
----------------------------------------------------------------------------
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 STOPPED Not started
command_rtp STOPPED Not started
command_vis STOPPED Not started
database STOPPED Not started
----------------------------------------------------------------------------
*** CommandClient: (http://it207dt:39002/api) URL Error [Errno 111] Connection refused
An error ocurred while checking license status
Could not get license verification status. Are all CryoSPARC processes RUNNING?
xinliu@it207dt:~/cryosparc/cryosparc_master$ ping it207dt
PING it207dt (127.0.1.1) 56(84) bytes of data.
64 bytes from it207dt (127.0.1.1): icmp_seq=1 ttl=64 time=0.014 ms
64 bytes from it207dt (127.0.1.1): icmp_seq=2 ttl=64 time=0.015 ms
^C
--- it207dt ping statistics ---
2 packets transmitted, 2 received, 0% packet loss, time 1005ms
rtt min/avg/max/mdev = 0.014/0.014/0.015/0.000 ms
xinliu@it207dt:~/cryosparc/cryosparc_master$ telnet it207dt 39002
Trying 127.0.1.1...
telnet: Unable to connect to remote host: Connection refused
xinliu@it207dt:~/cryosparc/cryosparc_master$ sudo ufw status
[sudo] password for xinliu:
Status: inactive
xinliu@it207dt:~/cryosparc/cryosparc_master$ cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/homes/xinliu/cryosparc/cryosparc_master
Current cryoSPARC version: v4.3.1
----------------------------------------------------------------------------
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 STOPPED Not started
command_rtp STOPPED Not started
command_vis STOPPED Not started
database STOPPED Not started
----------------------------------------------------------------------------
*** CommandClient: (http://it207dt:39002/api) URL Error [Errno 111] Connection refused
An error ocurred while checking license status
Could not get license verification status. Are all CryoSPARC processes RUNNING?
xinliu@it207dt:~/cryosparc/cryosparc_master$ cryosparcm start
Starting cryoSPARC System master process..
CryoSPARC is already running.
If you would like to restart, use cryosparcm restart
xinliu@it207dt:~/cryosparc/cryosparc_master$ cryosparcm restart
CryoSPARC is running.
Stopping cryoSPARC
Shut down
Starting cryoSPARC System master process..
CryoSPARC is not already running.
configuring database
Warning: Could not get database status (attempt 1/3)
Warning: Could not get database status (attempt 2/3)
Warning: Could not get database status (attempt 3/3)
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/homes/xinliu/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 48, in configure_mongo
initialize_replica_set()
File "/homes/xinliu/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 87, in initialize_replica_set
admin_db = try_get_pymongo_db(mongo_client)
File "/homes/xinliu/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 250, in try_get_pymongo_db
admin_db.command(({'serverStatus': 1}))
File "/homes/xinliu/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/database.py", line 827, in command
with self.__client._socket_for_reads(read_preference, session) as (sock_info, secondary_ok):
File "/homes/xinliu/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/contextlib.py", line 113, in __enter__
return next(self.gen)
File "/homes/xinliu/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/mongo_client.py", line 1478, in _socket_for_reads
server = self._select_server(read_preference, session)
File "/homes/xinliu/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/mongo_client.py", line 1436, in _select_server
server = topology.select_server(server_selector)
File "/homes/xinliu/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/topology.py", line 250, in select_server
return random.choice(self.select_servers(selector, server_selection_timeout, address))
File "/homes/xinliu/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/topology.py", line 211, in select_servers
server_descriptions = self._select_servers_loop(selector, server_timeout, address)
File "/homes/xinliu/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/topology.py", line 226, in _select_servers_loop
raise ServerSelectionTimeoutError(
pymongo.errors.ServerSelectionTimeoutError: Got response id 808465440 but expected 1687926652, Timeout: 20.0s, Topology Description: <TopologyDescription id: 64f0e79ab6b7bf405399ec03, topology_type: Single, servers: [<ServerDescription ('localhost', 39001) server_type: Unknown, rtt: None, error=ProtocolError('Got response id 808465440 but expected 1687926652')>]>
[2023-08-31T15:20:00-04:00] Error configuring database. Most recent database log lines:
2023-08-31T15:18:47.114-0400 I CONTROL [initandlisten] git version: d352e6a4764659e0d0350ce77279de3c1f243e5c
2023-08-31T15:18:47.114-0400 I CONTROL [initandlisten] allocator: tcmalloc
2023-08-31T15:18:47.114-0400 I CONTROL [initandlisten] modules: none
2023-08-31T15:18:47.114-0400 I CONTROL [initandlisten] build environment:
2023-08-31T15:18:47.114-0400 I CONTROL [initandlisten] distarch: x86_64
2023-08-31T15:18:47.114-0400 I CONTROL [initandlisten] target_arch: x86_64
2023-08-31T15:18:47.114-0400 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/homes/xinliu/cryosparc/cryosparc_database", journal: { enabled: false } } }
2023-08-31T15:18:47.114-0400 E STORAGE [initandlisten] Failed to set up listener: SocketException: Address already in use
2023-08-31T15:18:47.114-0400 I CONTROL [initandlisten] now exiting
2023-08-31T15:18:47.114-0400 I CONTROL [initandlisten] shutting down with code:48
Can anyone please offer some help? Thanks!