From 2ca3a518138cb5212cebf47612204d05ff4f0952 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 30 Aug 2023 12:33:36 +0200 Subject: [PATCH] Update faq.md --- bih-cluster/docs/help/faq.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/bih-cluster/docs/help/faq.md b/bih-cluster/docs/help/faq.md index 0376a4f71..09e58154a 100644 --- a/bih-cluster/docs/help/faq.md +++ b/bih-cluster/docs/help/faq.md @@ -597,6 +597,27 @@ slurmstepd: error: task[0] unable to set taskset '0x0' This is a minor failure related to Slurm and cgroups. Your job **should** run through successfully despite this error (that is more of a warning for end-users). +## All of my R jobs crash! + +We are aware of an issue with running `R` from `conda-forge/r-base` when unexpected locales are used. +We have seen users connecting from macOS to report these issues. +You might see the following error: + +``` +Base R During startup - Warning message: +Setting LC_CTYPE failed, using "C" +*** caught segfault *** +address (nil), cause 'memory not mapped' +``` + +You can try using `export LC_ALL=C` before starting R. +If this resolves your problem, you can put the following lines into your `~/.bashrc` to persist this: + +``` +# Force setting "C" locale to prevent issues with locales. +export LC_ALL=C +``` + ## My login stalls / something weird is happening You can try to run `ssh -l USER hpc-login-1.cubi.bihealth.org bash -iv`.