Closed barakr closed 11 years ago
drussel
commented
11 years ago Related issues pop up occasionally. But all the errors have tended to be things that pop up every once in a while in long tests and so haven't yielded much info for tracking it down.
barakr
commented
11 years ago well, this one pops out every 1:4 runs of 3 seconds in debug mode :)
On Thu, Aug 29, 2013 at 10:52 AM, drussel notifications@github.com wrote:
Related issues pop up occasionally. But all the errors have tended to be things that pop up every once in a while in long tests and so haven't yielded much info for tracking it down.
— Reply to this email directly or view it on GitHubhttps://github.com/salilab/imp/issues/496#issuecomment-23508922 .
Barak
drussel
commented
11 years ago I think that is better than we have had so far :-)
On Thu, Aug 29, 2013 at 10:59 AM, barakr notifications@github.com wrote:
well, this one pops out every 1:4 runs of 3 seconds in debug mode :)
On Thu, Aug 29, 2013 at 10:52 AM, drussel notifications@github.com wrote:
Related issues pop up occasionally. But all the errors have tended to be things that pop up every once in a while in long tests and so haven't yielded much info for tracking it down.
— Reply to this email directly or view it on GitHub< https://github.com/salilab/imp/issues/496#issuecomment-23508922> .
Barak
— Reply to this email directly or view it on GitHubhttps://github.com/salilab/imp/issues/496#issuecomment-23509556 .
drussel
commented
11 years ago Not a general issue. The container doesn't currently handle the radii changing, as they do during initialization. Probably worth adding for robustness.
barakr
commented
11 years ago ah ok! easy to see why it is a complicated issue to handle. Still, inflating radii is a common technique in molecular modeling, so might run into it in future again. I will document it that fixed particles radii is assumed, for now.
On Fri, Aug 30, 2013 at 1:16 PM, drussel notifications@github.com wrote:
Not a general issue. The container doesn't currently handle the radii changing, as they do during initialization. Probably worth adding for robustness.
— Reply to this email directly or view it on GitHubhttps://github.com/salilab/imp/issues/496#issuecomment-23586664 .
Barak
drussel
commented
11 years ago It is actually quite easy to handle, just wasn't considered when being implemented. A lot of things don't really handle it, I suspect.
On Fri, Aug 30, 2013 at 1:27 PM, barakr notifications@github.com wrote:
ah ok! easy to see why it is a complicated issue to handle. Still, inflating radii is a common technique in molecular modeling, so might run into it in future again. I will document it that fixed particles radii is assumed, for now.
On Fri, Aug 30, 2013 at 1:16 PM, drussel notifications@github.com wrote:
Not a general issue. The container doesn't currently handle the radii changing, as they do during initialization. Probably worth adding for robustness.
— Reply to this email directly or view it on GitHub< https://github.com/salilab/imp/issues/496#issuecomment-23586664> .
Barak
— Reply to this email directly or view it on GitHubhttps://github.com/salilab/imp/issues/496#issuecomment-23587195 .
drussel
commented
11 years ago I don't seem to be able to get it to fail any more.
in npctransport but seems general - When running (with checks on) medium_test_sites_from_simulation_data.py, then once every 4-5 runs, I get an error:
InternalException: Internal check failure: Pair "2" and "5" not found in list with coordinates (25, 25, 25: 25) and (44.2644, -25.9387, 26.439: 25) list is [] File "/piri1/home/barak/imp_git/repository/modules/core/src/internal/CoreCloseBipartitePairContainer.cpp", line 130 Context: BD0::optimize/do_simulate/BipartitePairsStatisticsOptimizerState0::update/BipartitePairsStatisticsOptimizerState0::update_always/CoreCloseBipartitePairContainer::before_evaluate/CoreCloseBipartitePairContainer::do_before_evaluate