Database error after v4.1.0 update

Hi,

I upgraded CS from 3.3.4 to v4.1.0 and I got this error:

(base) [victor@c105627 ~]$ cryosparcm update --version=v4.1.0
CryoSPARC current version v3.4.0
          update starting on Mon Dec 12 18:11:10 EST 2022

=============================
Updating to version v4.1.0.
=============================
CryoSPARC is running.
Stopping cryoSPARC 
app: stopped
command_core: stopped
command_rtp: stopped
webapp: stopped
command_vis: stopped
database: stopped
Shut down
  Removing previous downloads...
  Downloading master update...
  % 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  842M  100  842M    0     0  60.8M      0  0:00:13  0:00:13 --:--:-- 62.2M
  Downloading worker update...
  % 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 1876M  100 1876M    0     0  60.4M      0  0:00:31  0:00:31 --:--:-- 65.7M
  Done.

 Update will now be applied to the master installation, 
 followed by worker installations on other nodes.

  Deleting old files...
  Extracting...
  Done.
 
===================================================
Installing latest master dependencies.
===================================================
 
  Checking dependencies... 
  Dependencies for python have changed - reinstalling...
  ------------------------------------------------------------------------
  Installing anaconda python...
  ------------------------------------------------------------------------
PREFIX=/home/victor/cryosparc/cryosparc_master/deps/anaconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): done                                                      
Solving environment: done

## Package Plan ##

  environment location: /home/victor/cryosparc/cryosparc_master/deps/anaconda

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py37h27cfd23_1003
    - ca-certificates==2022.3.29=h06a4308_1
    - certifi==2021.10.8=py37h06a4308_2
    - cffi==1.15.0=py37hd667e15_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=py37h7f8727e_0
    - conda==4.12.0=py37h06a4308_0
    - cryptography==36.0.0=py37h9ce1e76_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==21.2.2=py37h06a4308_0
    - pycosat==0.6.3=py37h27cfd23_0
    - pycparser==2.21=pyhd3eb1b0_0
    - pyopenssl==22.0.0=pyhd3eb1b0_0
    - pysocks==1.7.1=py37_1
    - python==3.7.13=h12debd9_0
    - readline==8.1.2=h7f8727e_1
    - requests==2.27.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py37h27cfd23_0
    - setuptools==61.2.0=py37h06a4308_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-py37h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py37h06a4308_2
  cffi               pkgs/main/linux-64::cffi-1.15.0-py37hd667e15_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-py37h06a4308_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-py37h7f8727e_0
  cryptography       pkgs/main/linux-64::cryptography-36.0.0-py37h9ce1e76_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-21.2.2-py37h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h27cfd23_0
  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-py37_1
  python             pkgs/main/linux-64::python-3.7.13-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-py37h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-61.2.0-py37h06a4308_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 not changed.
  Completed dependency check. 
Generating '/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/libtiff/tiff_h_4_4_0.py' from '/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/../include/tiff.h'
 
===================================================
Successfully updated master to version v4.1.0.
===================================================
 
Starting cryoSPARC System master process..
CryoSPARC is not already running.
configuring database
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/victor/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 41, in configure_mongo
    initializeReplicaSet()
  File "/home/victor/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 83, in initializeReplicaSet
    admin_db.command(({'serverStatus': 1}))
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/database.py", line 758, in command
    read_preference, session) as (sock_info, secondary_ok):
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1387, in _socket_for_reads
    server = self._select_server(read_preference, session)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1346, in _select_server
    server = topology.select_server(server_selector)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 246, in select_server
    address))
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 203, in select_servers
    selector, server_timeout, address)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 220, in _select_servers_loop
    (self._error_message(selector), timeout, self.description))
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: timed out, Timeout: 20.0s, Topology Description: <TopologyDescription id: 6397b569e1aba78fbdbbd388, topology_type: Single, servers: [<ServerDescription ('localhost', 39001) server_type: Unknown, rtt: None, error=NetworkTimeout('localhost:39001: timed out')>]>

Downgrading back to 3.4.0 bring CS back again and everything work well.

Any advice?

Does the same error happen if updating to 4.0.3?

Same problem for us on one workstation.
We were trying to update from 4.0.3
Thanks

Hi,

I have the same error when downgrading to 4.0.3:

(base) [victor@c105627 ~]$ cryosparcm update --version=v4.0.3
CryoSPARC current version v4.1.0
          update starting on Tue Dec 13 11:49:47 EST 2022

=============================
Updating to version v4.0.3.
=============================
  Removing previous downloads...
  Downloading master update...
  % 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  792M  100  792M    0     0  21.9M      0  0:00:36  0:00:36 --:--:-- 46.2M
  Downloading worker update...
  % 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 1831M  100 1831M    0     0  45.9M      0  0:00:39  0:00:39 --:--:-- 51.7M
  Done.

 Update will now be applied to the master installation, 
 followed by worker installations on other nodes.

CryoSPARC is running.
Stopping cryoSPARC 
Shut down
  Deleting old files...
  Extracting...
  Done.
 
===================================================
Installing latest master dependencies.
===================================================
 
  Checking dependencies... 
  Dependencies for python have changed - reinstalling...
  ------------------------------------------------------------------------
  Installing anaconda python...
  ------------------------------------------------------------------------
PREFIX=/home/victor/cryosparc/cryosparc_master/deps/anaconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): ...working... done                                       
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/victor/cryosparc/cryosparc_master/deps/anaconda

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py37h27cfd23_1003
    - ca-certificates==2022.3.29=h06a4308_1
    - certifi==2021.10.8=py37h06a4308_2
    - cffi==1.15.0=py37hd667e15_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=py37h7f8727e_0
    - conda==4.12.0=py37h06a4308_0
    - cryptography==36.0.0=py37h9ce1e76_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==21.2.2=py37h06a4308_0
    - pycosat==0.6.3=py37h27cfd23_0
    - pycparser==2.21=pyhd3eb1b0_0
    - pyopenssl==22.0.0=pyhd3eb1b0_0
    - pysocks==1.7.1=py37_1
    - python==3.7.13=h12debd9_0
    - readline==8.1.2=h7f8727e_1
    - requests==2.27.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py37h27cfd23_0
    - setuptools==61.2.0=py37h06a4308_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-py37h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py37h06a4308_2
  cffi               pkgs/main/linux-64::cffi-1.15.0-py37hd667e15_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-py37h06a4308_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-py37h7f8727e_0
  cryptography       pkgs/main/linux-64::cryptography-36.0.0-py37h9ce1e76_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-21.2.2-py37h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h27cfd23_0
  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-py37_1
  python             pkgs/main/linux-64::python-3.7.13-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-py37h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-61.2.0-py37h06a4308_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: ...working... done
Executing transaction: ...working... 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 not changed.
  Completed dependency check. 
Generating '/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/libtiff/tiff_h_4_4_0.py' from '/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/../include/tiff.h'
 
===================================================
Successfully updated master to version v4.0.3.
===================================================
 
Starting cryoSPARC System master process..
CryoSPARC is not already running.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/victor/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 41, in configure_mongo
    initializeReplicaSet()
  File "/home/victor/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 82, in initializeReplicaSet
    admin_db.command(({'serverStatus': 1}))
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/database.py", line 758, in command
    read_preference, session) as (sock_info, secondary_ok):
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1387, in _socket_for_reads
    server = self._select_server(read_preference, session)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1346, in _select_server
    server = topology.select_server(server_selector)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 246, in select_server
    address))
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 203, in select_servers
    selector, server_timeout, address)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 220, in _select_servers_loop
    (self._error_message(selector), timeout, self.description))
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: timed out, Timeout: 20.0s, Topology Description: <TopologyDescription id: 6398ada174bf15b4cdac4738, topology_type: Single, servers: [<ServerDescription ('localhost', 39001) server_type: Unknown, rtt: None, error=NetworkTimeout('localhost:39001: timed out')>]>
configuring database

Can you exit the conda environment you’re in before running any cryoSPARC commands? Since cryoSPARC has its own conda environment, everything might be getting confused.

1 Like

I deactivate the conda environment by: conda deactivate then try to force update to 4.0.4:

[victor@c105627 ~]$ cryosparcm update --version=v4.0.4
CryoSPARC current version v4.1.0
          update starting on Wed Dec 14 11:27:28 EST 2022

=============================
Updating to version v4.0.4.
=============================
  Removing previous downloads...
  Downloading master update...
  % 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  731M  100  731M    0     0  34.9M      0  0:00:20  0:00:20 --:--:-- 29.5M
  Downloading worker update...
  % 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 1831M  100 1831M    0     0  18.3M      0  0:01:39  0:01:39 --:--:-- 27.7M
  Done.

 Update will now be applied to the master installation, 
 followed by worker installations on other nodes.

CryoSPARC is not already running.
If you would like to restart, use cryosparcm restart
  Deleting old files...
  Extracting...
  Done.
 
===================================================
Installing latest master dependencies.
===================================================
 
  Checking dependencies... 
  Dependencies for python have changed - reinstalling...
  ------------------------------------------------------------------------
  Installing anaconda python...
  ------------------------------------------------------------------------
PREFIX=/home/victor/cryosparc/cryosparc_master/deps/anaconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): ...working... done                                       
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/victor/cryosparc/cryosparc_master/deps/anaconda

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py37h27cfd23_1003
    - ca-certificates==2022.3.29=h06a4308_1
    - certifi==2021.10.8=py37h06a4308_2
    - cffi==1.15.0=py37hd667e15_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=py37h7f8727e_0
    - conda==4.12.0=py37h06a4308_0
    - cryptography==36.0.0=py37h9ce1e76_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==21.2.2=py37h06a4308_0
    - pycosat==0.6.3=py37h27cfd23_0
    - pycparser==2.21=pyhd3eb1b0_0
    - pyopenssl==22.0.0=pyhd3eb1b0_0
    - pysocks==1.7.1=py37_1
    - python==3.7.13=h12debd9_0
    - readline==8.1.2=h7f8727e_1
    - requests==2.27.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py37h27cfd23_0
    - setuptools==61.2.0=py37h06a4308_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-py37h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py37h06a4308_2
  cffi               pkgs/main/linux-64::cffi-1.15.0-py37hd667e15_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-py37h06a4308_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-py37h7f8727e_0
  cryptography       pkgs/main/linux-64::cryptography-36.0.0-py37h9ce1e76_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-21.2.2-py37h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h27cfd23_0
  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-py37_1
  python             pkgs/main/linux-64::python-3.7.13-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-py37h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-61.2.0-py37h06a4308_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: ...working... done
Executing transaction: ...working... 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 not changed.
  Completed dependency check. 
Generating '/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/libtiff/tiff_h_4_4_0.py' from '/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/../include/tiff.h'
 
===================================================
Successfully updated master to version v4.0.4.
===================================================
 
Starting cryoSPARC System master process..
CryoSPARC is not already running.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/victor/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 41, in configure_mongo
    initializeReplicaSet()
  File "/home/victor/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 82, in initializeReplicaSet
    admin_db.command(({'serverStatus': 1}))
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/database.py", line 758, in command
    read_preference, session) as (sock_info, secondary_ok):
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1387, in _socket_for_reads
    server = self._select_server(read_preference, session)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1346, in _select_server
    server = topology.select_server(server_selector)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 246, in select_server
    address))
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 203, in select_servers
    selector, server_timeout, address)
  File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 220, in _select_servers_loop
    (self._error_message(selector), timeout, self.description))
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: timed out, Timeout: 20.0s, Topology Description: <TopologyDescription id: 6399fa0f9235511f155d943b, topology_type: Single, servers: [<ServerDescription ('localhost', 39001) server_type: Unknown, rtt: None, error=NetworkTimeout('localhost:39001: timed out')>]>
configuring database

Since localhost:39001 is timing out, check your firewall settings?

Please can you check for any “zombie” CryoSPARC-related process(es):

  1. cryosparcm stop
  2. ps xww | grep -e mongod -e cryosparc

Did you find any?
Does the output of
cryosparcm log database
include any error messages?

After stopping cryosparc I check for zombie processes:

[victor@c105627 ~]$ ps xww | grep -e mongod -e cryosparc
 35990 pts/0    S+     0:00 grep --color=auto -e mongod -e cryosparc

log database:

[victor@c105627 ~]$ cryosparcm log database

n: "3.11.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "3.10.0-1160.24.1.el7.x86_64" }, platform: "CPython 3.7.8.final.0" }
2022-12-13T15:14:28.406-0500 I NETWORK  [listener] connection accepted from 129.112.162.193:52142 #23 (17 connections now open)
2022-12-13T15:14:30.883-0500 I NETWORK  [listener] connection accepted from 129.112.162.193:52156 #24 (18 connections now open)
2022-12-13T15:14:30.884-0500 I NETWORK  [conn24] received client metadata from 129.112.162.193:52156 conn24: { driver: { name: "nodejs", version: "3.3.5" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.24.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE" }
2022-12-13T15:14:30.929-0500 I NETWORK  [listener] connection accepted from 129.112.162.193:52158 #25 (19 connections now open)
2022-12-13T15:14:30.930-0500 I NETWORK  [conn25] received client metadata from 129.112.162.193:52158 conn25: { driver: { name: "nodejs", version: "3.3.5" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.24.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE" }
2022-12-13T15:14:30.950-0500 I NETWORK  [listener] connection accepted from 129.112.162.193:52160 #26 (20 connections now open)
2022-12-13T15:14:30.953-0500 I NETWORK  [conn26] received client metadata from 129.112.162.193:52160 conn26: { driver: { name: "nodejs", version: "3.3.5" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.24.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE" }
2022-12-13T15:14:30.957-0500 I NETWORK  [listener] connection accepted from 129.112.162.193:52162 #27 (21 connections now open)
2022-12-13T15:14:30.958-0500 I NETWORK  [conn27] received client metadata from 129.112.162.193:52162 conn27: { driver: { name: "nodejs", version: "3.3.5" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.24.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE" }
2022-12-13T15:14:40.684-0500 I NETWORK  [listener] connection accepted from 129.112.162.193:52168 #28 (22 connections now open)
2022-12-13T15:14:40.687-0500 I NETWORK  [listener] connection accepted from 129.112.162.193:52170 #29 (23 connections now open)
2022-12-13T15:14:40.689-0500 I NETWORK  [listener] connection accepted from 129.112.162.193:52172 #30 (24 connections now open)
2022-12-13T15:15:35.332-0500 I CONTROL  [signalProcessingThread] got signal 15 (Terminated), will terminate after current cmd ends
2022-12-13T15:15:35.332-0500 I NETWORK  [signalProcessingThread] shutdown: going to close listening sockets...
2022-12-13T15:15:35.332-0500 I NETWORK  [signalProcessingThread] removing socket file: /tmp/mongodb-39001.sock
2022-12-13T15:15:35.333-0500 I REPL     [signalProcessingThread] shutting down replication subsystems
2022-12-13T15:15:35.333-0500 I REPL     [signalProcessingThread] Stopping replication reporter thread
2022-12-13T15:15:35.333-0500 I REPL     [signalProcessingThread] Stopping replication fetcher thread
2022-12-13T15:15:35.333-0500 I REPL     [signalProcessingThread] Stopping replication applier thread
2022-12-13T15:15:35.352-0500 I NETWORK  [conn16] end connection 129.112.162.193:52110 (23 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK  [conn18] end connection 129.112.162.193:52114 (22 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK  [conn19] end connection 129.112.162.193:52116 (21 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK  [conn20] end connection 129.112.162.193:52118 (20 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK  [conn12] end connection 129.112.162.193:52102 (19 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK  [conn28] end connection 129.112.162.193:52168 (17 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK  [conn23] end connection 129.112.162.193:52142 (15 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK  [conn15] end connection 129.112.162.193:52108 (18 connections now open)
2022-12-13T15:15:35.353-0500 I NETWORK  [conn27] end connection 129.112.162.193:52162 (10 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK  [conn24] end connection 129.112.162.193:52156 (13 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK  [conn30] end connection 129.112.162.193:52172 (14 connections now open)
2022-12-13T15:15:35.353-0500 I NETWORK  [conn25] end connection 129.112.162.193:52158 (12 connections now open)
2022-12-13T15:15:35.353-0500 I NETWORK  [conn26] end connection 129.112.162.193:52160 (11 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK  [conn14] end connection 129.112.162.193:52106 (16 connections now open)
2022-12-13T15:15:35.353-0500 I NETWORK  [conn29] end connection 129.112.162.193:52170 (9 connections now open)
2022-12-13T15:15:35.386-0500 I NETWORK  [conn7] end connection 129.112.162.193:52052 (8 connections now open)
2022-12-13T15:15:35.386-0500 I NETWORK  [conn9] end connection 129.112.162.193:52056 (7 connections now open)
2022-12-13T15:15:35.386-0500 I NETWORK  [conn8] end connection 129.112.162.193:52054 (6 connections now open)
2022-12-13T15:15:35.394-0500 I NETWORK  [conn10] end connection 129.112.162.193:52066 (5 connections now open)
2022-12-13T15:15:35.394-0500 I NETWORK  [conn21] end connection 129.112.162.193:52128 (4 connections now open)
2022-12-13T15:15:35.394-0500 I NETWORK  [conn22] end connection 129.112.162.193:52130 (3 connections now open)
2022-12-13T15:15:35.397-0500 I NETWORK  [conn11] end connection 129.112.162.193:52100 (2 connections now open)
2022-12-13T15:15:35.414-0500 I REPL     [signalProcessingThread] Stopping replication storage threads
2022-12-13T15:15:35.415-0500 I FTDC     [signalProcessingThread] Shutting down full-time diagnostic data capture
2022-12-13T15:15:35.428-0500 I STORAGE  [WTOplogJournalThread] oplog journal thread loop shutting down
2022-12-13T15:15:35.428-0500 I STORAGE  [signalProcessingThread] WiredTigerKVEngine shutting down
2022-12-13T15:15:35.441-0500 I STORAGE  [signalProcessingThread] shutdown: removing fs lock...
2022-12-13T15:15:35.442-0500 I CONTROL  [signalProcessingThread] now exiting
2022-12-13T15:15:35.442-0500 I CONTROL  [signalProcessingThread] shutting down with code:0
Waiting for data... (interrupt to abort)

Since proxy has been always a problem setting up our gpu under the institutional network, should I setup proxy settings again for CS v4? I have no problems downgrading to v3.4?

Please can you describe your current proxy settings?

My proxy settings on ~/bash_profile are:


#load proxy environments

export HTTP_PROXY="http://proxy.swmed.edu:3128"
export HTTPS_PROXY="http://proxy.swmed.edu:3128"
export ftp_proxy="proxy.swmed.edu:3128"

Do you really mean ~/bash_profile or ~/.bash_profile?

@Vruiz @rfronzes Please can you post the output of the command
env | grep -i http
run under the Linux account that also runs the CryoSPARC master processes.

Sorry, I meant:

~/.bash_profile

The output of env | grep -i http is:

[victor@c105627 ~]$ env | grep -i http
HTTPS_PROXY=http://proxy.swmed.edu:3128
HTTP_PROXY=http://proxy.swmed.edu:3128

victor is the account that runs cryosparc

@Vruiz Please can you confirm that

  • these settings were already in place when CryoSPARC v3.4.0 was running
  • CryoSPARC v3.4.0 functioned properly with these proxy variables defined
  • CryoSPARC v < 4 did not function without these proxy variables defined
  • these settings were already in place when CryoSPARC v3.4.0 was running
    Yes

  • CryoSPARC v3.4.0 functioned properly with these proxy variables defined

  • CryoSPARC v < 4 did not function without these proxy variables defined
    CS 3.4.0 works with and without these proxy settings

If CryoSPARC failed to start with a pymongo error after an update to CryoSPARC v4.1.0 or v4.1.1, you may try the following:

  1. ensure that cryosparc_master software is at either v4.1.0 or v4.1.1
  2. download cryosparc_master_patch.tar.gz
  3. confirm file integrity. Output of
    md5sum cryosparc_master_patch.tar.gz
    should match: 8df9953103829632756b809f3c637d2f
  4. cryosparcm stop
  5. confirm no more CryoSPARC processes:
    ps xww | grep -e cryosparc -e mongod
  6. kill, but not kill -9, any CryoSPARC-related processes that may still exist
  7. # substitute correct paths
    mv cryosparc_master_patch.tar.gz /path/to/cryosparc_master
    cd /path/to/cryosparc_master
    tar -xzf cryosparc_master_patch.tar.gz --overwrite --strip-components=1 --directory ./
    
  8. if cryosparcm start
    still fails, please post error messages on the forum. Otherwise:
  9. update worker(s)
    # substitute correct paths
    cp /path/to/cryosparc_master/cryosparc_worker.tar.gz /path/to/cryosparc_worker/
    cd /path/to/cryosparc_worker/
    ./bin/cryosparcw update
    

Hi,

Finally, I could install CS v.4.3.1 by stopping CS, killing all processes, and removing mongod.lock:

rm /home/victor/cryosparc/cryosparc_database/mongod.lock

Then cryosparcm update worked well, however, now I can´t access the web interface, I check the CS status and everything looks normal to me:

[victor@c105627 ~]$ cryosparcm start
Starting cryoSPARC System master process..
CryoSPARC is not already running.
configuring database
    configuration complete
database: started
checkdb success
command_core: started
    command_core connection succeeded
    command_core startup successful
command_vis: started
command_rtp: started
    command_rtp connection succeeded
    command_rtp startup successful
app: started
app_api: started
-----------------------------------------------------

CryoSPARC master started. 
 From this machine, access cryoSPARC and cryoSPARC Live at
    http://localhost:39000

 From other machines on the network, access cryoSPARC and cryoSPARC Live at
    http://c105627.dhcp.swmed.org:39000


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

However I´m unable to connect to the web interface through the LAN network, and it worked well before running CS v3.4. This made me suspect that the port 39000 was closed but it´s not since I didn´t change any settings but somehow I can´t connect to this port:
telnet c105627.dhcp.swmed.org 39000
Trying 129.112.162.193…
telnet: connect to address 129.112.162.193: Connection refused
telnet: Unable to connect to remote host

But I can access to 39001:
telnet c105627.dhcp.swmed.org 39001
Trying 129.112.162.193…
Connected to c105627.dhcp.swmed.org.
Escape character is ‘^]’.

I´m really confused and don´t know how to tackle the problem, I would appreciate your help.

Please ensure not to use kill -9 or kill -KILL when shutting down CryoSPARC processes (see this warning).

On the CryoSPARC master computer, please can you run:

ip addr
cryosparcm status | grep ^app
curl 127.0.0.1:39000

and post the commands’ outputs.

Hi wtempel,

I used

kill #process

The output are:

[victor@c105627 ~]$ ip addr
1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default qlen 1000
    link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
    inet 127.0.0.1/8 scope host lo
       valid_lft forever preferred_lft forever
    inet6 ::1/128 scope host 
       valid_lft forever preferred_lft forever
2: enp1s0f0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc mq state UP group default qlen 1000
    link/ether a0:42:3f:3a:4e:90 brd ff:ff:ff:ff:ff:ff
    inet 129.112.162.193/24 brd 129.112.162.255 scope global noprefixroute dynamic enp1s0f0
       valid_lft 218378sec preferred_lft 218378sec
    inet6 fe80::fc51:4f1e:63be:c539/64 scope link noprefixroute 
       valid_lft forever preferred_lft forever
3: enp1s0f1: <NO-CARRIER,BROADCAST,MULTICAST,UP> mtu 1500 qdisc mq state DOWN group default qlen 1000
    link/ether a0:42:3f:3a:4e:91 brd ff:ff:ff:ff:ff:ff
4: virbr0: <NO-CARRIER,BROADCAST,MULTICAST,UP> mtu 1500 qdisc noqueue state DOWN group default qlen 1000
    link/ether 52:54:00:6c:7d:75 brd ff:ff:ff:ff:ff:ff
    inet 192.168.122.1/24 brd 192.168.122.255 scope global virbr0
       valid_lft forever preferred_lft forever
5: virbr0-nic: <BROADCAST,MULTICAST> mtu 1500 qdisc pfifo_fast master virbr0 state DOWN group default qlen 1000
    link/ether 52:54:00:6c:7d:75 brd ff:ff:ff:ff:ff:ff

[victor@c105627 ~]$ cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/home/victor/cryosparc/cryosparc_master
Current cryoSPARC version: v4.2.1
----------------------------------------------------------------------------

CryoSPARC process status:

app                              EXITED    Apr 29 05:22 PM
app_api                          RUNNING   pid 47405, uptime 0:00:16
app_api_dev                      STOPPED   Not started
app_legacy                       STOPPED   Not started
app_legacy_dev                   STOPPED   Not started
command_core                     RUNNING   pid 122490, uptime 1 day, 17:08:30
command_rtp                      RUNNING   pid 122562, uptime 1 day, 17:08:23
command_vis                      RUNNING   pid 122520, uptime 1 day, 17:08:24
database                         RUNNING   pid 122383, uptime 1 day, 17:08:34

----------------------------------------------------------------------------
License is valid
----------------------------------------------------------------------------

global config variables:
export CRYOSPARC_LICENSE_ID="redacted"
export CRYOSPARC_MASTER_HOSTNAME="c105627.dhcp.swmed.org"
export CRYOSPARC_DB_PATH="/home/victor/cryosparc/cryosparc_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false
export CRYOSPARC_CLICK_WRAP=true
export no_proxy=localhost,127.0.0.1,localaddress,.localdomain.com,swmed.org,swmed.edu,*.swmed.org,*.swmed.edu,swlxnexpose.swmed.org,129.112.7.*
export NO_PROXY=localhost,127.0.0.1,localaddress,.localdomain.com,swmed.org,swmed.edu,*.swmed.org,*.swmed.edu,swlxnexpose.swmed.org,129.112.7.*
[victor@c105627 ~]$ curl 127.0.0.1:39000
curl: (7) Failed connect to 127.0.0.1:39000; Connection refused