diff options
Diffstat (limited to 'issues/genenetwork')
11 files changed, 598 insertions, 89 deletions
diff --git a/issues/genenetwork/cannot-connect-to-mariadb.gmi b/issues/genenetwork/cannot-connect-to-mariadb.gmi new file mode 100644 index 0000000..3dfe1bc --- /dev/null +++ b/issues/genenetwork/cannot-connect-to-mariadb.gmi @@ -0,0 +1,121 @@ +# Cannot Connect to MariaDB + + +## Description + +GeneNetwork3 is failing to connect to mariadb with the error: + +``` +⋮ +2024-11-05 14:49:00 Traceback (most recent call last): +2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/flask/app.py", line 1523, in full_dispatch_request +2024-11-05 14:49:00 rv = self.dispatch_request() +2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/flask/app.py", line 1509, in dispatch_request +2024-11-05 14:49:00 return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args) +2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/gn3/api/menu.py", line 13, in generate_json +2024-11-05 14:49:00 with database_connection(current_app.config["SQL_URI"], logger=current_app.logger) as conn: +2024-11-05 14:49:00 File "/gnu/store/lzw93sik90d780n09svjx5la1bb8g3df-python-3.10.7/lib/python3.10/contextlib.py", line 135, in __enter__ +2024-11-05 14:49:00 return next(self.gen) +2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/gn3/db_utils.py", line 34, in database_connection +2024-11-05 14:49:00 connection = mdb.connect(db=db_name, +2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/MySQLdb/__init__.py", line 121, in Connect +2024-11-05 14:49:00 return Connection(*args, **kwargs) +2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/MySQLdb/connections.py", line 195, in __init__ +2024-11-05 14:49:00 super().__init__(*args, **kwargs2) +2024-11-05 14:49:00 MySQLdb.OperationalError: (2002, "Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)") +``` + +We have previously defined the default socket file[^1][^2] as "/run/mysqld/mysqld.sock". + +## Troubleshooting Logs + +### 2024-11-05 + +I attempted to just bind `/run/mysqld/mysqld.sock` to `/tmp/mysql.sock` by adding the following mapping in GN3's `gunicorn-app` definition: + +``` +(file-system-mapping + (source "/run/mysqld/mysqld.sock") + (target "/tmp/mysql.sock") + (writable? #t)) +``` + +but that does not fix things. + +I had tried to change the mysql URI to use IP addresses, i.e. + +``` +SQL_URI="mysql://webqtlout:webqtlout@128.169.5.119:3306/db_webqtl" +``` + +but that simply changes the error from the above to the one below: + +``` +2024-11-05 15:27:12 MySQLdb.OperationalError: (2002, "Can't connect to MySQL server on '128.169.5.119' (115)") +``` + +I tried with both `127.0.0.1` and `128.169.5.119`. + +My hail-mary was to attempt to expose the `my.cnf` file generated by the `mysql-service-type` definition to the "pola-wrapper", but that is proving tricky, seeing as the file is generated elsewhere[^4] and we do not have a way of figuring out the actual final path of the file. + +I tried: + +``` +(file-system-mapping + (source (mixed-text-file "my.cnf" + (string-append "[client]\n" + "socket=/run/mysqld/mysqld.sock"))) + (target "/etc/mysql/my.cnf")) +``` + +but that did not work either. + +### 2024-11-07 + +Start digging into how GNU Guix services are defined[^5] to try and understand why the file mapping attempt did not work. + +=> http://git.savannah.gnu.org/cgit/guix.git/tree/gnu/system/file-systems.scm?id=2394a7f5fbf60dd6adc0a870366adb57166b6d8b#n575 +Looking at the code linked above specifically at lines 575 to 588, and 166, it seems, to me, that the mappings attempt should have worked. + +Try it again, taking care to verify that the paths are correct, with: + +``` +(file-system-mapping + (source (mixed-text-file "my.cnf" + (string-append "[client-server]\n" + "socket=/run/mysqld/mysqld.sock"))) + (target "/etc/my.cnf")) +``` + +Try rebuilding on tux04: started getting `Segmentation fault` errors out of the blue for many guix commands 🤦🏿. +Try building container on local dev machine: this took a long time - quit and continue later. + +### 2024-11-08 + +After guix broke, causing the `Segmentation fault` errors above, I did some troubleshooting and was able to finally fix that by pinning guix to version b0b988c41c9e0e591274495a1b2d6f27fcdae15a as shown in the troubleshooting transcript[^6]. + +Now the fixes I did to make python requests work with the newer guix (defined in guix-bioinformatics[^7]) seem to be leading to failures in the older guix version. + +Let me attempt rebasing to reorder the commits, to make the python requests commit come last, to more easily do a `git reset` before rebuilding the container — not successful. +=> https://git.genenetwork.org/gn-machines/commit/?h=production-container&id=610049b2bfa32cae5d3f992b95aac711290efa2a Manually "undo" the changes in a new commit, + +then rebuild the container. This exposes a bug in gn-auth. + +=> https://git.genenetwork.org/gn-auth/commit/?id=4c21d0e43cf0de1084d0e0a243e441c6e72236eb Fix that. + +and update the `public-jwks-uri` value for the client in the admin dashboard, and voila!!! Now the system works. + +Attempt pulling guix "2394a7f5fbf60dd6adc0a870366adb57166b6d8b" into a profile locally: went through without a hitch + +Upgrade guix daemon, and restart it. Delete profile and run `guix gc`, then try pulling guix "2394a7f5fbf60dd6adc0a870366adb57166b6d8b" again. It also went through without a problem. This eliminates the daemon being the culprit: Running `sudo -i guix pull --list-generations` on both tux04 and my local dev machine gives both daemon commits as `2a6d96425eea57dc6dd48a2bec16743046e32e06`. + + +### Footnotes + +=> https://git.genenetwork.org/gn-machines/tree/production.scm?id=46a1c4c8d01198799e6ac3b99998dca40d2c7094#n47 [^1] Lines 47 to 49 of production.scm +=> https://guix.gnu.org/manual/en/html_node/Database-Services.html#index-mysql_002dconfiguration [^2] Guix's mysql-service-type configurations +=> https://mariadb.com/kb/en/server-system-variables/#socket [^3] MariaDB configuration variables: socket +=> https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/services/databases.scm?id=4c56d0cccdc44e12484b26332715f54768738c5f#n576 [^4] Guix: mysql-service-type configuration code +=> https://guix.gnu.org/manual/en/html_node/Defining-Services.html [^5] Guix documentation: Defining Services +=> https://github.com/genenetwork/gn-gemtext-threads/blob/d785b06643b5e5a2470fd0da075dcf77bda82d16/miscellaneous/broken-guix-on-tux04-20241108.org [^6] Broken guix on tux04: Troubleshooting transcript +=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=eb7beb340a9731775e8ad177e47b70dba2f2a84f [^7] guix-bioinformatics: Upgrade guix channel to 2394a7f diff --git a/issues/genenetwork/containerising-production-issues.gmi b/issues/genenetwork/containerising-production-issues.gmi new file mode 100644 index 0000000..ed5702a --- /dev/null +++ b/issues/genenetwork/containerising-production-issues.gmi @@ -0,0 +1,33 @@ +# Containerising Production: Issues + +## Tags + +* type: bug +* assigned: fredm +* priority: critical +* status: closed, completed +* keywords: production, container, tux04 +* interested: alexk, aruni, bonfacem, fredm, pjotrp, soloshelby, zsloan, jnduli + +## Description + +We have recently got production into a container and deployed it: It has come up, however, that there are services that are useful to get a full-featured GeneNetwork system running that are not part of the container. + +This is, therefore, a meta-issue, tracking all issues that relate to the deployment of the disparate services that make up GeneNetwork. + +## Documentation + +=> https://issues.genenetwork.org/topics/genenetwork/genenetwork-services + +The link above documents the various services that make up the GeneNetwork service. + +## Issues + +* [x] Move user directories to a large partition +=> ./handle-tmp-dirs-in-container [x] Link TMPDIR in container to a directory on a large partition +=> ./markdown-editing-service-not-deployed [ ] Define and deploy Markdown Editing service +=> ./umhet3-samples-timing-slow [ ] Figure out and fix UM-HET3 Samples mappings on Tux04 +=> ./setup-mailing-on-tux04 [x] Setting up email service on Tux04 +=> ./virtuoso-shutdown-clears-data [x] Virtuoso seems to lose data on restart +=> ./python-requests-error-in-container [x] Fix python's requests library certificates error +=> ./cannot-connect-to-mariadb [ ] GN3 cannot connect to mariadb server diff --git a/issues/genenetwork/genenetwork2_configurations.gmi b/issues/genenetwork/genenetwork2_configurations.gmi deleted file mode 100644 index 7d08db0..0000000 --- a/issues/genenetwork/genenetwork2_configurations.gmi +++ /dev/null @@ -1,74 +0,0 @@ -# Genenetwork2 Configurations - -## Tags - -* assigned: fredm -* priority: normal -* status: open -* keywords: configuration, config, gn2, genenetwork, genenetwork2 -* type: bug - -## Description - -The current way the configuration in Genenetwork2 works is as follows: - -* The configuration setup begins in `bin/genenetwork` script in the genenetwork2 repository. This script sets up the `GN2_PROFILE` environment variable, and all other environment variables depending on it: see the "`GN2_PROFILE`-Dependent Environment Variables" section below. -* In `wqflask/wqflask/__init__.py` the settings in the file pointed to by `GN2_SETTINGS` environment variable are then loaded. If there is no such file, then it defaults to loading the settings in the `etc/default_settings.py` within the genenetwork2 repository. -* In `wqflask/utility/tools.py` in the genenetwork2 repository, the settings loaded thus far, can then have their values overriden by values set in the environment variables. There is an "OVERRIDES" value that is currently not in use and can be ignored. -* Some other minor configurations are updated/overriden in `wqflask/utility/startup_config.py` - -From these, `GN2_PROFILE` is the only environment variable that needs to be set up. All the other variables can be set in the settings file. - -The file `wqflask/base/webqtlConfig.py` also has some configurations that need to be handled. - -The sub-sections that follow will contain more information on variables and what needs to be done - -### `GN2_PROFILE`-Dependent Environment Variables - -* `PATH`: Exposes the binaries within the profile -* `PYTHONPATH`: Exposes the Python modules within the profile -* `R_LIBS_SITE`: Exposes the R module within the profile -* `JS_GUIX_PATH`: Exposes the Javascript modules within the profile -* `GUIX_GTK3_PATH`: Exposes the GTK modules within the profile -* `GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0" -* `XDG_DATA_DIRS`: Exposes the "share" directories within the profile -* `GIO_EXTRA_MODULES`: Expose the GIO modules -* `GUIX_GENENETWORK_FILES`: Expose the Genenetwork shared files -* `PLINK_COMMAND`: Point to the "PLINK" binary -* `GEMMA_COMMAND`: Point to the "GEMMA" binary -* `GEMMA_WRAPPER_COMMAND`: Point to the `GEMMA` wrapper binary - -### `wqflask/utility/tools.py` - -This is our biggest pain-point. The following are some actions that can be taken to reduce the pain in this module: - -* Refactor functions in to take the "application object" as one of their arguments, to decouple the module from the module where the application is declared -* Remove all settings from this module, instead, override any of the variables that need it at the application creation step, possibly within the `wqflask/wqflask/__init__.py` module. -* Replace all uses of variables from this module with configurations from `flask.current_app.config` as appropriate -* Get rid of this module entirely if possible, moving the functions elsewhere. - -### Modules with Routes but no Blueprints - -These modules are: - -* `wqflask/run_gunicorn.py` -* `wqflask/wqflask/user_session.py` -* `wqflask/wqflask/collect.py` -* `wqflask/wqflask/views.py` -* `wqflask/wqflask/partial_correlations_views.py` -* `wqflask/wqflask/user_login.py` -* `wqflask/wqflask/api/router.py` -* `wqflask/base/trait.py` - -Except for `wqflask/run_gunicorn.py`, each module will have its own Blueprint and then we'll have some top-level Blueprint that import all the others and sets them up. The top-level blueprint will then be registered with the app at the application-creation time. - -For `wqflask/run_gunicorn.py`, the route can remain as is, since this is an entry-point module. - -### `wqflask/wqflask/__init__.py` - -* Move application initialisation into an application factory function -* Replace all uses of `wqflask.app` variable with `flask.current_app` or `create_app()` as necessary - -### Non-Executable Configuration Files - -Eschew executable formats (*.py) for configuration files and prefer non-executable formats e.g. *.cfg, *.json, *.conf etc diff --git a/issues/genenetwork/genenetwork3_configuration.gmi b/issues/genenetwork/genenetwork3_configuration.gmi deleted file mode 100644 index fcab572..0000000 --- a/issues/genenetwork/genenetwork3_configuration.gmi +++ /dev/null @@ -1,15 +0,0 @@ -# Genenetwork2 Configurations - -## Tags - -* assigned: fredm -* priority: normal -* status: open -* keywords: configuration, config, gn2, genenetwork, genenetwork2 -* type: bug - -## Description - -The configuration file should only ever contain settings, and no code. Remove all code from the default settings file. - -Eschew executable formats (*.py) for configuration files and prefer non-executable formats e.g. *.cfg, *.json, *.conf etc diff --git a/issues/genenetwork/guix-bioinformatics-remove-guix-rust-past-crates-channel.gmi b/issues/genenetwork/guix-bioinformatics-remove-guix-rust-past-crates-channel.gmi new file mode 100644 index 0000000..b804e10 --- /dev/null +++ b/issues/genenetwork/guix-bioinformatics-remove-guix-rust-past-crates-channel.gmi @@ -0,0 +1,23 @@ +# guix-bioinformatics: Remove `guix-rust-past-crates` channel + +## Tags + +* assigned: alexm, bonfacem +* interested: fredm +* priority: normal +* status: open +* type: bug +* keywords: guix-bioinformatics, guix-rust-past-crates, guix, rust, crates + +## Description + +GNU Guix recently changed[1] the way it handles packaging of rust packages. + +The old rust packages got moved to the "guix-rust-past-crates" to help avoid huge breakages for systems depending on the older packaging system. "guix-bioinformatics" used a number of rust packages, defined in the old form, and we needed a quick fix, thus the introduction of the "guix-rust-past-crates" channel as a dependency. + +We need to move away from depending on this channel, by updating all the rust crates we use to the new packaging model. + + +## Footnotes + +=> https://guix.gnu.org/en/blog/2025/a-new-rust-packaging-model/ [1] diff --git a/issues/genenetwork/handle-tmp-dirs-in-container.gmi b/issues/genenetwork/handle-tmp-dirs-in-container.gmi new file mode 100644 index 0000000..5f6eb92 --- /dev/null +++ b/issues/genenetwork/handle-tmp-dirs-in-container.gmi @@ -0,0 +1,22 @@ +# Handle Temporary Directories in the Container + +## Tags + +* type: feature +* assigned: fredm +* priority: critical +* status: closed, completed +* keywords: production, container, tux04 +* interested: alexk, aruni, bonfacem, pjotrp, zsloan + +## Description + +The container's temporary directories should be in a large partition on the host to avoid a scenario where the writes fill up one of the smaller drives. + +Currently, we use the `/tmp` directory by default, but we should look into transitioning away from that — `/tmp` is world readable and world writable and therefore needs careful consideration to keep safe. + +Thankfully, we are running our systems within a container, and can bind the container's `/tmp` directory to a non-world-accessible directory, keeping things at least contained. + +### Fixes + +=> https://git.genenetwork.org/gn-machines/commit/?id=7306f1127df9d4193adfbfa51295615f13d32b55 diff --git a/issues/genenetwork/markdown-editing-service-not-deployed.gmi b/issues/genenetwork/markdown-editing-service-not-deployed.gmi new file mode 100644 index 0000000..9d72e4e --- /dev/null +++ b/issues/genenetwork/markdown-editing-service-not-deployed.gmi @@ -0,0 +1,39 @@ +# Markdown Editing Service: Not Deployed + +## Tags + +* type: bug +* status: closed, completed, fixed +* assigned: fredm +* priority: critical +* keywords: production, container, tux04 +* interested: alexk, aruni, bonfacem, fredm, pjotrp, zsloan + +## Description + +The Markdown Editing service is not working on production. + +* Link: https://genenetwork.org/facilities/ +* Repository: https://git.genenetwork.org/gn-guile + +Currently, the code is being run directly on the host, rather than inside the container. + +Some important things to note: + +* The service requires access to a checkout of https://github.com/genenetwork/gn-docs +* Currently, the service is hard-coded to use a specific port: we should probably fix that. + +## Reopened: 2024-11-01 + +While the service was deployed, the edit functionality is not working right, specifically, pushing the edits upstream to the remote seems to fail. + +If you do an edit and refresh the page, it will show up in the system, but it will not proceed to be pushed up to the remote. + +Set `CGIT_REPO_PATH="https://git.genenetwork.org/gn-guile"` which seems to allow the commit to work, but we do not actually get the changes pushed to the remote in any useful sense. + +It seems to me, that we need to configure the environment in such a way that it will be able to push the changes to remote. + + +## Close as Completed + +The markdown editing service is deployed and configured correctly. diff --git a/issues/genenetwork/python-requests-error-in-container.gmi b/issues/genenetwork/python-requests-error-in-container.gmi new file mode 100644 index 0000000..0289762 --- /dev/null +++ b/issues/genenetwork/python-requests-error-in-container.gmi @@ -0,0 +1,174 @@ +# Python Requests Error in Container + +## Tags + +* type: bug +* assigned: fredm +* priority: critical +* status: closed, completed, fixed +* interested: alexk, aruni, bonfacem, pjotrp, zsloan +* keywords: production, container, tux04, python, requests + +## Description + +Building the container with the +=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=eb7beb340a9731775e8ad177e47b70dba2f2a84f upgraded guix definition +leads to python's requests library failing. + +``` +2024-10-30 16:04:13 OSError: Could not find a suitable TLS CA certificate bundle, invalid path: /etc/ssl/certs/ca-certificates.crt +``` + +If you login to the container itself, however, you find that the file `/etc/ssl/certs/ca-certificates.crt` actually exists and has content. + +Possible fixes suggested are to set up correct envvars for the requests library, such as `REQUESTS_CA_BUNDLE` + +See +=> https://requests.readthedocs.io/en/latest/user/advanced/#ssl-cert-verification + +### Troubleshooting Logs + +Try reproducing the issue locally: + +``` +$ guix --version +hint: Consider installing the `glibc-locales' package and defining `GUIX_LOCPATH', along these lines: + + guix install glibc-locales + export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale" + +See the "Application Setup" section in the manual, for more info. + +guix (GNU Guix) 2394a7f5fbf60dd6adc0a870366adb57166b6d8b +Copyright (C) 2024 the Guix authors +License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> +This is free software: you are free to change and redistribute it. +There is NO WARRANTY, to the extent permitted by law. +$ +$ guix shell --container --network python python-requests coreutils +[env]$ ls "${GUIX_ENVIRONMENT}/etc" +ld.so.cache profile +``` + +We see from the above that there are no certificates in the environment with just python and python-requests. + +Okay. Now let's write a simple python script to test things out with: + +``` +import requests + +resp = requests.get("https://github.com") +print(resp) +``` + +and run it! + +``` +$ guix shell --container --network python python-requests coreutils -- python3 test.py +Traceback (most recent call last): + File "/tmp/test.py", line 1, in <module> + import requests + File "/gnu/store/b6ny4p29f32rrnnvgx7zz1nhsms2zmqk-profile/lib/python3.10/site-packages/requests/__init__.py", line 164, in <module> + from .api import delete, get, head, options, patch, post, put, request + File "/gnu/store/b6ny4p29f32rrnnvgx7zz1nhsms2zmqk-profile/lib/python3.10/site-packages/requests/api.py", line 11, in <module> + from . import sessions + File "/gnu/store/b6ny4p29f32rrnnvgx7zz1nhsms2zmqk-profile/lib/python3.10/site-packages/requests/sessions.py", line 15, in <module> + from .adapters import HTTPAdapter + File "/gnu/store/b6ny4p29f32rrnnvgx7zz1nhsms2zmqk-profile/lib/python3.10/site-packages/requests/adapters.py", line 81, in <module> + _preloaded_ssl_context.load_verify_locations( +FileNotFoundError: [Errno 2] No such file or directory +``` + +Uhmm, what is this new error? + +Add `nss-certs` and try again. + +``` +$ guix shell --container --network python python-requests nss-certs coreutils +[env]$ ls ${GUIX_ENVIRONMENT}/etc/ssl/ +certs +[env]$ python3 test.py +Traceback (most recent call last): + File "/tmp/test.py", line 1, in <module> + import requests + File "/gnu/store/17dw8qczqqz9fmj2kxzsbfqn730frqd7-profile/lib/python3.10/site-packages/requests/__init__.py", line 164, in <module> + from .api import delete, get, head, options, patch, post, put, request + File "/gnu/store/17dw8qczqqz9fmj2kxzsbfqn730frqd7-profile/lib/python3.10/site-packages/requests/api.py", line 11, in <module> + from . import sessions + File "/gnu/store/17dw8qczqqz9fmj2kxzsbfqn730frqd7-profile/lib/python3.10/site-packages/requests/sessions.py", line 15, in <module> + from .adapters import HTTPAdapter + File "/gnu/store/17dw8qczqqz9fmj2kxzsbfqn730frqd7-profile/lib/python3.10/site-packages/requests/adapters.py", line 81, in <module> + _preloaded_ssl_context.load_verify_locations( +FileNotFoundError: [Errno 2] No such file or directory +[env]$ +[env]$ export REQUESTS_CA_BUNDLE="${GUIX_ENVIRONMENT}/etc/ssl/certs/ca-certificates.crt" +[env]$ $ python3 test.py +Traceback (most recent call last): + File "/tmp/test.py", line 1, in <module> + import requests + File "/gnu/store/17dw8qczqqz9fmj2kxzsbfqn730frqd7-profile/lib/python3.10/site-packages/requests/__init__.py", line 164, in <module> + from .api import delete, get, head, options, patch, post, put, request + File "/gnu/store/17dw8qczqqz9fmj2kxzsbfqn730frqd7-profile/lib/python3.10/site-packages/requests/api.py", line 11, in <module> + from . import sessions + File "/gnu/store/17dw8qczqqz9fmj2kxzsbfqn730frqd7-profile/lib/python3.10/site-packages/requests/sessions.py", line 15, in <module> + from .adapters import HTTPAdapter + File "/gnu/store/17dw8qczqqz9fmj2kxzsbfqn730frqd7-profile/lib/python3.10/site-packages/requests/adapters.py", line 81, in <module> + _preloaded_ssl_context.load_verify_locations( +FileNotFoundError: [Errno 2] No such file or directory +``` + +Welp! Looks like this error is a whole different thing. + +Let us try with the genenetwork2 package. + +``` +$ guix shell --container --network genenetwork2 coreutils +[env]$ ls "${GUIX_ENVIRONMENT}/etc" +bash_completion.d jupyter ld.so.cache profile +``` + +This does not seem to have the certificates in place either, so let's add nss-certs + +``` +$ guix shell --container --network genenetwork2 coreutils nss-certs +[env]$ ls "${GUIX_ENVIRONMENT}/etc" +bash_completion.d jupyter ld.so.cache profile ssl +[env]$ python3 test.py +Traceback (most recent call last): + File "/tmp/test.py", line 3, in <module> + resp = requests.get("https://github.com") + File "/gnu/store/qigjz4i0dckbsjbd2has0md2dxwsa7ry-profile/lib/python3.10/site-packages/requests/api.py", line 73, in get + return request("get", url, params=params, **kwargs) + File "/gnu/store/qigjz4i0dckbsjbd2has0md2dxwsa7ry-profile/lib/python3.10/site-packages/requests/api.py", line 59, in request + return session.request(method=method, url=url, **kwargs) + File "/gnu/store/qigjz4i0dckbsjbd2has0md2dxwsa7ry-profile/lib/python3.10/site-packages/requests/sessions.py", line 587, in request + resp = self.send(prep, **send_kwargs) + File "/gnu/store/qigjz4i0dckbsjbd2has0md2dxwsa7ry-profile/lib/python3.10/site-packages/requests/sessions.py", line 701, in send + r = adapter.send(request, **kwargs) + File "/gnu/store/qigjz4i0dckbsjbd2has0md2dxwsa7ry-profile/lib/python3.10/site-packages/requests/adapters.py", line 460, in send + self.cert_verify(conn, request.url, verify, cert) + File "/gnu/store/qigjz4i0dckbsjbd2has0md2dxwsa7ry-profile/lib/python3.10/site-packages/requests/adapters.py", line 263, in cert_verify + raise OSError( +OSError: Could not find a suitable TLS CA certificate bundle, invalid path: /etc/ssl/certs/ca-certificates.crt +``` + +We get the expected certificates error! This is good. Now define the envvar and try again. + +``` +[env]$ export REQUESTS_CA_BUNDLE="${GUIX_ENVIRONMENT}/etc/ssl/certs/ca-certificates.crt" +[env]$ python3 test.py +<Response [200]> +``` + +Success!!! + +Adding nss-certs and setting the `REQUESTS_CA_BUNDLE` fixes things. We'll need to do the same for the container, for both the genenetwork2 and genenetwork3 packages (and any other packages that use requests library). + +### Fixes + +=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=fec68c4ca87eeca4eb9e69e71fc27e0eae4dd728 +=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=c3bb784c8c70857904ef97ecd7d36ec98772413d +The two commits above add nss-certs package to all the flask apps, which make use of the python-requests library, which requires a valid CA certificates bundle in each application's environment. + +=> https://git.genenetwork.org/gn-machines/commit/?h=production-container&id=04506c4496e5ca8b3bc38e28ed70945a145fb036 +The commit above defines the "REQUESTS_CA_BUNDLE" environment variable for all the flask applications that make use of python's requests library. diff --git a/issues/genenetwork/setup-mailing-on-tux04.gmi b/issues/genenetwork/setup-mailing-on-tux04.gmi new file mode 100644 index 0000000..45605d9 --- /dev/null +++ b/issues/genenetwork/setup-mailing-on-tux04.gmi @@ -0,0 +1,16 @@ +# Setup Mailing on Tux04 + +## Tags + +* type: bug +* status: closed +* assigned: fredm +* priority: critical +* interested: pjotrp, zsloan +* keywords: production, container, tux04 + +## Description + +We use emails to verify user accounts and allow changing of user passwords. We therefore need to setup a way to send emails from the system. + +I updated the configurations to use UTHSC's mail server diff --git a/issues/genenetwork/umhet3-samples-timing-slow.gmi b/issues/genenetwork/umhet3-samples-timing-slow.gmi new file mode 100644 index 0000000..a3a33a7 --- /dev/null +++ b/issues/genenetwork/umhet3-samples-timing-slow.gmi @@ -0,0 +1,72 @@ +# UM-HET3 Timing: Slow + +## Tags + +* type: bug +* status: open +* assigned: fredm +* priority: critical +* interested: fredm, pjotrp, zsloan +* keywords: production, container, tux04, UM-HET3 + +## Description + +In email from @robw: + +``` +> > Not sure why. Am I testing the wrong way? +> > Are we using memory and RAM in the same way on the two machines? +> > Here are data on the loading time improvement for Tux2: +> > I tested this using a "worst case" trait that we know when—the 25,000 +> > UM-HET3 samples: +> > [1]https://genenetwork.org/show_trait?trait_id=10004&dataset=HET3-ITPPu +> > blish +> > Tux02: 15.6, 15.6, 15.3 sec +> > Fallback: 37.8, 38.7, 38.5 sec +> > Here are data on Gemma speed/latency performance: +> > Also tested "worst case" performance using three large BXD data sets +> > tested in this order: +> > [2]https://genenetwork.org/show_trait?trait_id=10004&dataset=BXD-Longev +> > ityPublish +> > [3]https://genenetwork.org/show_trait?trait_id=10003&dataset=BXD-Longev +> > ityPublish +> > [4]https://genenetwork.org/show_trait?trait_id=10002&dataset=BXD-Longev +> > ityPublish +> > Tux02: 107.2, 329.9 (ouch), 360.0 sec (double ouch) for 1004, 1003, and +> > 1002 respectively. On recompute (from cache) 19.9, 19.9 and 20.0—still +> > too slow. +> > Fallback: 154.1, 115.9 for the first two traits (trait 10002 already in +> > the cache) +> > On recompute (from cache) 59.6, 59.0 and 59.7. Too slow from cache. +> > PROBLEM 2: Tux02 is unable to map UM-HET3. I still get an nginx 413 +> > error: Entity Too Large. +> +> Yeah, Fred should fix that one. It is an nginx setting - we run 2x +> nginx. It was reported earlier. +> +> > I need this to work asap. Now mapping our amazing UM-HET3 data. I can +> > use Fallback, but it is painfully slow and takes about 214 sec. I hope +> > Tux02 gets that down to a still intolerable slow 86 sec. +> > Can we please fix and confirm by testing. The Trait is above for your +> > testing pleasure. +> > Even 86 secs is really too slow and should motivate us (or users like +> > me) to think about how we are using all of those 24 ultra-fast cores on +> > the AMD 9274F. Why not put them all to use for us and users. It is not +> > good enough just to have "it work". It has to work in about 5–10 +> > seconds. +> > Here are my questions for you guys: Are we able to use all 24 cores +> > for any one user? How does each user interact with the CPU? Can we +> > handle a class of 24 students with 24 cores, or is it "complicated"? +> > PROBLEM 3: Zach, Fred. Are we computing render time or transport +> > latency correctly? Ideally the printout at the bottom of mapping pages +> > would be true latency as experienced by the user. As far as I can tell +> > with a stop watch our estimates of time are incorrect by as much as 3 +> > secs. And note that the link +> > to [5]http://joss.theoj.org/papers/10.21105/joss.00025 is not working +> > correctly in the footer (see image below). Oddly enough it works fine +> > on Tux02 +> +> Fred, take a note. +``` + +Figure out what this is about and fix it. diff --git a/issues/genenetwork/virtuoso-shutdown-clears-data.gmi b/issues/genenetwork/virtuoso-shutdown-clears-data.gmi new file mode 100644 index 0000000..2e01238 --- /dev/null +++ b/issues/genenetwork/virtuoso-shutdown-clears-data.gmi @@ -0,0 +1,98 @@ +# Virtuoso: Shutdown Clears Data + +## Tags + +* type: bug +* assigned: fredm +* priority: critical +* status: closed, completed +* interested: bonfacem, pjotrp, zsloan +* keywords: production, container, tux04, virtuoso + +## Description + +It seems that virtuoso has the bad habit of clearing data whenever it is stopped/restarted. + +This issue will track the work necessary to get the service behaving correctly. + +According to the documentation on +=> https://vos.openlinksw.com/owiki/wiki/VOS/VirtBulkRDFLoader the bulk loading process + +``` +The bulk loader also disables checkpointing and the scheduler, which also need to be re-enabled post bulk load +``` + +That needs to be handled. + +### Notes + +After having a look at +=> https://docs.openlinksw.com/virtuoso/ch-server/#databaseadmsrv the configuration documentation +it occurs to me that the reason virtuoso supposedly clears the data is that the `DatabaseFile` value is not set, so it defaults to a new database file every time the server is restarted (See also the `Striping` setting). + +### Troubleshooting + +Reproduce locally: + +We begin by getting a look at the settings for the remote virtuoso +``` +$ ssh tux04 +fredm@tux04:~$ cat /gnu/store/bg6i4x96nm32gjp4qhphqmxqc5vggk3h-virtuoso.ini +[Parameters] +ServerPort = localhost:8981 +DirsAllowed = /var/lib/data +NumberOfBuffers = 4000000 +MaxDirtyBuffers = 3000000 +[HTTPServer] +ServerPort = localhost:8982 +``` + +Copy these into a file locally, and adjust the `NumberOfBuffers` and `MaxDirtyBuffers` for smaller local dev environment. Also update `DirsAllowed`. + +We end up with our local configuration in `~/tmp/virtuoso/etc/virtuoso.ini` with the content: + +``` +[Parameters] +ServerPort = localhost:8981 +DirsAllowed = /var/lib/data +NumberOfBuffers = 10000 +MaxDirtyBuffers = 6000 +[HTTPServer] +ServerPort = localhost:8982 +``` + +Run virtuoso! +``` +$ cd ~/tmp/virtuoso/var/lib/virtuoso/ +$ ls +$ ~/opt/virtuoso/bin/virtuoso-t +foreground +configfile ~/tmp/virtuoso/etc/virtuoso.ini +``` + +Here we start by changing into the `~/tmp/virtuoso/var/lib/virtuoso/` directory which will be where virtuoso will put its state. Now in a different terminal list the files created int the state directory: + +``` +$ ls ~/tmp/virtuoso/var/lib/virtuoso +virtuoso.db virtuoso.lck virtuoso.log virtuoso.pxa virtuoso.tdb virtuoso.trx +``` + +That creates the database file (and other files) with the documented default values, i.e. `virtuoso.*`. + +We cannot quite reproduce the issue locally, since every reboot will have exactly the same value for the files locally. + +Checking the state directory for virtuoso on tux04, however: + +``` +fredm@tux04:~$ sudo ls -al /export2/guix-containers/genenetwork/var/lib/virtuoso/ | grep '\.db$' +-rw-r--r-- 1 986 980 3787456512 Oct 28 14:16 js1b7qjpimdhfj870kg5b2dml640hryx-virtuoso.db +-rw-r--r-- 1 986 980 4152360960 Oct 28 17:11 rf8v0c6m6kn5yhf00zlrklhp5lmgpr4x-virtuoso.db +``` + +We see that there are multiple db files, each created when virtuoso was restarted. There is an extra (possibly) random string prepended to the `virtuoso.db` part. This happens for our service if we do not actually provide the `DatabaseFile` configuration. + + +## Fixes + +=> https://github.com/genenetwork/gn-gemtext-threads/commit/8211c1e49498ba2f3b578ed5b11b15c52299aa08 Document how to restart checkpointing and the scheduler after bulk loading +=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=2dc335ca84ea7f26c6977e6b432f3420b113f0aa Add configs for scheduler and checkpointing +=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=7d793603189f9d41c8ee87f8bb4c876440a1fce2 Set up virtuoso database configurations +=> https://git.genenetwork.org/gn-machines/commit/?id=46a1c4c8d01198799e6ac3b99998dca40d2c7094 Explicitly name virtuoso database files. |