Comments (5)
Update: this appears to be related to a change in the last PR into develop
. Even when importing the results from the completed model, it still thinks the model did not run and looks for OUTPUT.
> restest <- rbabylon::import_result(file.path(MODEL_DIR, "101.yaml"))
> restest %>% model_summary(.wait=0)
/data/rbabylon-example-project/model/pk/101/101.ext file does not look finished but there is also no `101/OUTPUT` file. Your run may have failed.
---
Model is still running. Tail of `101/OUTPUT` file:
---
FALSEError in nonmem_summary(.res, ...) : 101.ctl is not finished and 0 second wait time has elapsed. Check back later or increase `.wait`.
--
|
from bbr.
seth and i discussed that this morning some, I think this model_summary needs an overhaul.
Here is what I am thinking - model_summary() should only work if the model is completed.
-
we need to define how we can reliably detect completion, as quickly as possible. For example scanning the entire ext file for -1000000 lines means reading that entire file, which could be quite large.
-
It should just return either a model result, or print a message saying model not completed, no summary avialable, and return NULL
-
we need to separately provide monitoring functions that can handle whatever waiting the scientist may want
spec %>% submit_model() %>% wait_until_complete() %>% summarize_model()
the reason that waiting should be moved outside of specific submission is this allows composability and other customization. For example, maybe we want to provide a wait function that also has enough logic to know about failures - basically a specific tryCatch
spec %>% submit_model() %>%
wait_until_complete(error = function(e) {
# some details of what to do if error occurs
}) %>%
summarize_model()
from bbr.
that seems like a reasonable expectation to me. if you're pulling out wait_until_complete
, it would also be nice to have a wait_until_starts
. e.g. if I'm shooting off some runs overnight before I leave work, I would run spec %>% submit_model %>% wait_until_starts()
to verify that the run started before I shutdown my workflow
from bbr.
@callistosp this will be closed when the linked PR merges. The fix is that model_summary() just stops with an informative error if it can't get a summary (see tests mentioned below). We are intending to make a better version of check_nonmem_progress()
in a future release, and this will be incorporated into model_summary()
under the hood.
If you have thoughts on how you would like that to work, like some of the ones you put in the comments above, you can open a new issue with the desired functionality and tag it with the milestone roadmap
.
Tests
- tests/testthat/test-summary.R
- model_summary() fails predictably if it can't find some parts (i.e. model isn't finished)
- model_summary() fails predictably if no .lst file present
from bbr.
We're closing this because there is another issue to deal with this:
#31
from bbr.
Related Issues (20)
- Function to run NMTRAN on a model object HOT 7
- Feature request: make `get_data_path` also read in the path from the ctl HOT 3
- test-initial-estimates.R: missing skips for old nmrec
- Point to bbr.bayes in readme HOT 1
- config_log error when model run with multiple NONMEM versions HOT 5
- param_estimates and initial_estimates use different names for THETA records HOT 2
- `model_summary` bug when called via `summary_log()` HOT 2
- Bootstrap: revisit how we sample the input data HOT 2
- dOFV and AIC columns for summary_log() HOT 1
- Bootstrap: mechanism to only include data that entered the original problem
- Bootstrap: function adjustments needed HOT 3
- Address deprecated warning in function `check_grd`
- Bootstrap runs should inherit attached bbi_args HOT 1
- inherit_param_estimates: revisit rounding and use matrix-handling PR HOT 1
- check_nonmem_finished and get_model_status refactor: improve wait times & change functionality HOT 8
- WK files created by bbr - delete by default? HOT 7
- Consider fail-safe for checking on terminated models HOT 4
- bbi package installation failed HOT 7
- Option to start bootstrap runs at final estimates from parent run HOT 1
- No error or warning when trying to overwrite run when `.wait = FALSE` HOT 9
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from bbr.