I frequently but unpredictably have my rserver sessions hang with the cpu pegged at 100%. There are no errors but rstudio-server becomes unresponsive and I have to kill the process in order to get things working again. This seems to be related to writing to disk as it will often happen when I save a script, a csv (using readr::write_csv, but not utils::write.csv). I can make it happen predictably when I knit an rmarkdown to pdf. It gets to "output file:<>.knit.md" and gets stuck there.
I've tried to look up a way to get the log files for the rsession, but haven't been able to get it to work, maybe because I am on a VM?
I'm connecting to a google compute VM instance running:
Ubuntu 18.04.6 LTS
"Linux"
release
"5.4.0-1080-gcp"
version
"#87~18.04.1-Ubuntu SMP Fri Jun 10 18:50:42 UTC 2022"
Here's the version info:
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
version.string R version 4.2.0 (2022-04-22)
nickname Vigorous Calisthenics
Here's the rstudio-server information:
RStudio 2022.07.0+548 "Spotted Wakerobin" Release (34ea3031089fa4e38738a9256d6fa6d70629c822, 2022-07-06) for Ubuntu Bionic
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/103.0.0.0 Safari/537.36.
I'd be happy to get any additional information that would be useful, and/or direction to some instructions on how to get the appropriate logs.
Thanks!
*** UPDATE ***
When I run perf while the process is hanging I get the following output:
Samples: 33K of event 'cpu-clock:pppH', 4000 Hz, Event count (approx.): 6900362281 lost: 0/0 drop: 0/0
Children Self Command Parent symbol Shared Object Pid:Command
+ 92.23% 33.40% rsession [other] /lib/x86_64-linux-gnu/libc-2.27.so 3918:rsession
+ 38.20% 38.20% rsession [other] /proc/kcore 3918:rsession
+ 23.64% 23.53% rsession [other] /opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin/libiomp5.so 3918:rsession
+ 2.13% 1.91% perf [other] /usr/lib/linux-gcp-5.4-tools-5.4.0-1083/perf 10593:perf
+ 2.07% 0.02% perf [other] /lib/x86_64-linux-gnu/libpthread-2.27.so 10593:perf
+ 2.06% 0.79% perf [other] /lib/x86_64-linux-gnu/libc-2.27.so 10593:perf
1.30% 1.30% perf [other] /proc/kcore 10593:perf
+ 0.91% 0.00% rsession [other] [unknown] 3918:rsession
0.40% 0.40% swapper [other] /proc/kcore 0:swapper
+ 0.15% 0.15% perf do_page_fault /proc/kcore 10593:perf
0.15% 0.10% perf [other] /lib/x86_64-linux-gnu/libc-2.27.so 10581:perf
0.05% 0.04% perf [other] /usr/lib/linux-gcp-5.4-tools-5.4.0-1083/perf 10581:perf
0.03% 0.01% perf-top-UI [other] /usr/lib/linux-gcp-5.4-tools-5.4.0-1083/perf 10594:perf-top-UI
0.02% 0.02% perf-top-UI [other] /lib/x86_64-linux-gnu/libslang.so.2.3.1 10594:perf-top-UI
0.02% 0.02% rcu_sched [other] /proc/kcore 11:rcu_sched
0.01% 0.00% perf [other] [unknown] 10581:perf
0.01% 0.01% rserver [other] /usr/lib/rstudio-server/bin/rserver 1473:rserver
0.01% 0.01% perf do_page_fault /proc/kcore 10581:perf
0.01% 0.01% rsession [other] /proc/kcore 3921:rsession
0.01% 0.01% rserver [other] /usr/lib/rstudio-server/bin/rserver 1472:rserver
0.01% 0.01% perf [other] /proc/kcore 10581:perf
0.01% 0.01% rserver [other] /lib/x86_64-linux-gnu/libc-2.27.so 1473:rserver
0.01% 0.00% perf [other] [unknown] 10593:perf
0.01% 0.00% rserver [other] [unknown] 1472:rserver
0.01% 0.01% rserver [other] /lib/x86_64-linux-gnu/libz.so.1.2.11 1472:rserver
0.01% 0.01% rserver [other] /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25 1472:rserver
0.01% 0.01% rserver [other] /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25 1473:rserver
0.01% 0.01% rsession [other] /usr/lib/rstudio-server/bin/rsession 3921:rsession
0.01% 0.01% perf [other] /usr/lib/x86_64-linux-gnu/libelf-0.170.so 10593:perf
0.01% 0.01% perf-top-UI [other] /lib/x86_64-linux-gnu/libc-2.27.so 10594:perf-top-UI
0.00% 0.00% kworker/5:4-mm_ [other] /proc/kcore 8344:kworker/5:4-mm_
0.00% 0.00% google_guest_ag [other] /usr/bin/google_guest_agent 1805:google_guest_ag
0.00% 0.00% google_guest_ag [other] [unknown] 1805:google_guest_ag
0.00% 0.00% rsession [other] [unknown] 3921:rsession
0.00% 0.00% rsession [other] /lib/x86_64-linux-gnu/libpthread-2.27.so 3921:rsession
0.00% 0.00% cron [other] /proc/kcore 2000:cron
0.00% 0.00% kworker/2:0-eve [other] /proc/kcore 10255:kworker/2:0-eve
0.00% 0.00% snapd [other] /proc/kcore 1758:snapd
0.00% 0.00% sshd [other] /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 9691:sshd
0.00% 0.00% perf [other] /lib/x86_64-linux-gnu/libslang.so.2.3.1 10593:perf
0.00% 0.00% rserver [other] /usr/lib/rstudio-server/bin/rserver 1470:rserver
0.00% 0.00% rserver [other] /lib/x86_64-linux-gnu/libc-2.27.so 1470:rserver
0.00% 0.00% rserver [other] /proc/kcore 1472:rserver
0.00% 0.00% sshd [other] /proc/kcore 9691:sshd