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Hi cBioPortal developers. I am trying to deploy cBioPortal on a VPS server using Docker. SSD 200GB 3Core memory 2GB Debian12 amd64 Then I get the following message and it will not proceed permanently. I confirmed that cBioPortal works fine on my local macOS and Ubuntu Desktop. So I tried to deploy cBioPortal on the VPS server as well. I can operate the terminal, but I am not a IT engineer and I don't know how web apps work or how to deploy them. I would appreciate it if you could tell me where to start checking. I understand that Discussions is not a support center, but is run by volunteers. Thank you very much. [+] Running 47/13 ✔ cbioportal-session-database 9 layers [⣿⣿⣿⣿⣿⣿⣿⣿⣿] 0B/0B Pulled 40.7s ✔ cbioportal-database 11 layers [⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿] 0B/0B Pulled 51.0s ✔ cbioportal 18 layers [⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿] 0B/0B Pulled 113.5s ✔ cbioportal-session 5 layers [⣿⣿⣿⣿⣿] 0B/0B Pulled 90.2s [+] Running 7/6 ✔ Network cbioportal-docker-compose_cbio-net Created 0.1s ✔ Volume "cbioportal-docker-compose_cbioportal_mysql_data" Created 0.0s ✔ Volume "cbioportal-docker-compose_cbioportal_mongo_data" Created 0.0s ✔ Container cbioportal-database-container Created 0.7s ✔ Container cbioportal-session-database-container Created 0.7s ✔ Container cbioportal-session-container Created 0.1s ✔ Container cbioportal-container Created 0.0s Attaching to cbioportal-container, cbioportal-database-container, cbioportal-session-container, cbioportal-session-database-container cbioportal-database-container | 2023-10-11 00:44:25+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.43-1.el7 started. cbioportal-session-database-container | 2023-10-11T00:44:26.191+0000 I CONTROL [main] Automatically disabling TLS 1.0, to force-enable TLS 1.0 specify --sslDisabledProtocols 'none' cbioportal-session-database-container | 2023-10-11T00:44:26.198+0000 W ASIO [main] No TransportLayer configured during NetworkInterface startup cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] MongoDB starting : pid=1 port=27017 dbpath=/data/db 64-bit host=ece0968527e0 cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] db version v4.2.24 cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] git version: 5e4ec1d24431fcdd28b579a024c5c801b8cde4e2 cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.1.1 11 Sep 2018 cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] allocator: tcmalloc cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] modules: none cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] build environment: cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] distmod: ubuntu1804 cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] distarch: x86_64 cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] target_arch: x86_64 cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] options: { net: { bindIp: "*" } } cbioportal-session-database-container | 2023-10-11T00:44:26.203+0000 I STORAGE [initandlisten] cbioportal-session-database-container | 2023-10-11T00:44:26.203+0000 I STORAGE [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine cbioportal-session-database-container | 2023-10-11T00:44:26.203+0000 I STORAGE [initandlisten] ** See http://dochub.mongodb.org/core/prodnotes-filesystem cbioportal-session-database-container | 2023-10-11T00:44:26.203+0000 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=471M,cache_overflow=(file_max=0M),session_max=33000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager= Check Logs: Look at the logs for each container to see if there are any errors or warnings that might give you a clue about what's going wrong. You can use the following command to view logs: sh Check Resource Allocation: Make sure your VPS has enough resources (CPU, memory) to run all the containers. You mentioned you have 2GB of memory, which might be on the lower side for running multiple containers. Network Configuration: Ensure that your network configuration allows for proper communication between containers and that there are no firewall rules blocking traffic. Permissions: Verify that the Docker daemon has the necessary permissions to access the required directories and files. Consult Documentation: The cBioPortal GitHub repository has a discussion section where you can ask questions and get help from the community. |
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You're encountering some issues deploying cBioPortal on your VPS server. Here are a few steps you can take to troubleshoot the problem: Check Logs: Look at the logs for each container to see if there are any errors or warnings that might give you a clue about what's going wrong. You can use the following command to view logs: sh Check Resource Allocation: Make sure your VPS has enough resources (CPU, memory) to run all the containers. You mentioned you have 2GB of memory, which might be on the lower side for running multiple containers. Network Configuration: Ensure that your network configuration allows for proper communication between containers and that there are no firewall rules blocking traffic. Permissions: Verify that the Docker daemon has the necessary permissions to access the required directories and files. Consult Documentation: The cBioPortal GitHub repository has a discussion section where you can ask questions and get help from the community. If you continue to experience issues, it might be helpful to reach out to the cBioPortal support community or seek assistance from someone with more experience in IT and Docker deployments. |
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Hi there. |
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Hi cBioPortal developers.
I am trying to deploy cBioPortal on a VPS server using Docker.
Then I get the following message and it will not proceed permanently.
I confirmed that cBioPortal works fine on my local macOS and Ubuntu Desktop. So I tried to deploy cBioPortal on the VPS server as well. I can operate the terminal, but I am not a IT engineer and I don't know how web apps work or how to deploy them.
I would appreciate it if you could tell me where to start checking.
I understand that Discussions is not a support center, but is run by volunteers. Thank you very much.
After a while, the following message may appear.
And finally, the following message keeps appearing
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