RStudio error after ~1h while executing long running jobs

[fBedecarrats]

I am using a RStudio session on SSP Cloud to run a shiny app that launches long lasting python/scikit-learn jobs through reticulate. Tasks that take less than 1 hour get performed correctly. However, the jobs seem to fail after 1h with the message error below. Rstudio still runs, the session still appear as active, but the jobs never end after this.

Error message

2021-12-11T13:54:25.089754Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:25.090243Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:25.090374Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:25.090451Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:25.290752Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:25.290863Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:25.491031Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:25.491110Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:25.691297Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:25.691480Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:25.891635Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:25.891722Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:26.091886Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:26.091969Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:26.292344Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:26.292413Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:26.492549Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:26.492607Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:26.692727Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:26.692782Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:26.892915Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:26.892991Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:27.093138Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:27.093222Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:27.293365Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:27.293432Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:27.493573Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:27.493644Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:27.693783Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:27.693847Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:27.893973Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:27.894034Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:28.094161Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:28.094225Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:28.294354Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:28.294423Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:28.494552Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:28.494602Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:28.694751Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:28.694820Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:28.895268Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:28.895339Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:29.095489Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:29.095573Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:29.295710Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:29.295772Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:29.495906Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:29.495973Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:29.696119Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:29.696198Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:29.896337Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:29.896414Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140 2021-12-11T13:54:29.896553Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83 2021-12-11T13:54:29.896571Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140

[avouacr]

Hi @fBedecarrats,

Looks like a pretty low-level error, I don't think it's related to Onyxia. I can find only two related issues on RStudio's channels (here and here) but it doesn't help much.

Maybe you could try again with another version of the RStudio image in the ones we provide ("Service" configuration when initialising the service), to check whether it's related to a specific version.

[fBedecarrats]

Thank you for the hints. I don't think it is related to Onyxia per se, but I thought it might be a problem related to the configuration of the container/helm chart used for RStudio... I'll try to solve it locally and report back if some config modification might troubleshoot this. Thanks!