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Trying to run easybuild in a rootless containers gives me a fuse-overlayfs segfault.
fuse-overlayfs-0.7.2-2.module+el8.2.0+5768+3759792f.x86_64
podman-1.6.4-2.module+el8.2.0+5364+301aa566.x86_64
Process 24374 (fuse-overlayfs) of user 1000 dumped core.
Stack trace of thread 24374:
#0 0x000000000040d5c0 hash_get_first (fuse-overlayfs)
#1 0x0000000000405074 count_dir_entries.isra.15 (fuse-overlayfs)
#2 0x000000000040c1cc do_rm (fuse-overlayfs)
#3 0x00007f9de6ef6afa fuse_session_process_buf_int (libfuse3.so.3)
#4 0x00007f9de6ef1f5b fuse_session_loop (libfuse3.so.3)
#5 0x0000000000403835 main (fuse-overlayfs)
#6 0x00007f9de671c6a3 __libc_start_main (libc.so.6)
#7 0x00000000004038ee _start (fuse-overlayfs)
Steps to reproduce (rootless):
$ cat Dockerfile.ohpc-gnu9-easybuild
FROM quay.io/ohpc/ohpc-gnu9:1.9.9
MAINTAINER The OpenHPC Project
RUN useradd -ms /bin/bash openhpc
RUN yum -y install EasyBuild-ohpc && \
yum -y install patch make perl && \
yum clean all
WORKDIR /home/openhpc
USER openhpc
ENV PATH="/opt/ohpc/pub/libs/easybuild/4.1.1/software/EasyBuild/4.1.1/bin:${PATH}"
ENV PYTHONPATH="/opt/ohpc/pub/libs/easybuild/4.1.1/software/EasyBuild/4.1.1/lib/python3.6/site-packages"
# This way all commands passed into the container are executed in a
# login shell which is necessary to get lmod working. Commands
# need to be enclosed in quotes.
ENTRYPOINT ["/bin/bash", "-l", "-c"]
$ podman build . -f Dockerfile.ohpc-gnu9-easybuild --tag=ohpc-gnu9-easybuild:1.9.9
$ podman run ohpc-gnu9-easybuild:1.9.9 'eb --robot lz4-1.9.2-GCCcore-8.3.0.eb'
Now it will abort and the segfault from above can be seen in the logs.
The segfault does not happen when running as root.
Comment 1Giuseppe Scrivano
2020-02-19 21:44:41 UTC
it is fixed upstream with:
commit 214d606084453f0d2831317a9048a3cbc554fcc4
Author: Giuseppe Scrivano <gscrivan>
Date: Wed Jan 15 00:02:43 2020 +0100
main: check if file is whiteout
when doing a lookup, make sure the returned file is not a whiteout for
functions that expect the file to exist.
Close: https://github.com/containers/fuse-overlayfs/issues/169
Signed-off-by: Giuseppe Scrivano <gscrivan>
I had to add bzip2 to the Dockerfile for the command to complete
Verified in fuse-overlayfs-0.7.2-5.module+el8.2.0+6060+9dbc027d.x86_64.
Please also see known bug - fuse-overlayfs: could not find file with easybuild - https://bugzilla.redhat.com/show_bug.cgi?id=1815139
Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.
For information on the advisory, and where to find the updated
files, follow the link below.
If the solution does not work for you, open a new bug report.
https://access.redhat.com/errata/RHSA-2020:1650
Trying to run easybuild in a rootless containers gives me a fuse-overlayfs segfault. fuse-overlayfs-0.7.2-2.module+el8.2.0+5768+3759792f.x86_64 podman-1.6.4-2.module+el8.2.0+5364+301aa566.x86_64 Process 24374 (fuse-overlayfs) of user 1000 dumped core. Stack trace of thread 24374: #0 0x000000000040d5c0 hash_get_first (fuse-overlayfs) #1 0x0000000000405074 count_dir_entries.isra.15 (fuse-overlayfs) #2 0x000000000040c1cc do_rm (fuse-overlayfs) #3 0x00007f9de6ef6afa fuse_session_process_buf_int (libfuse3.so.3) #4 0x00007f9de6ef1f5b fuse_session_loop (libfuse3.so.3) #5 0x0000000000403835 main (fuse-overlayfs) #6 0x00007f9de671c6a3 __libc_start_main (libc.so.6) #7 0x00000000004038ee _start (fuse-overlayfs) Steps to reproduce (rootless): $ cat Dockerfile.ohpc-gnu9-easybuild FROM quay.io/ohpc/ohpc-gnu9:1.9.9 MAINTAINER The OpenHPC Project RUN useradd -ms /bin/bash openhpc RUN yum -y install EasyBuild-ohpc && \ yum -y install patch make perl && \ yum clean all WORKDIR /home/openhpc USER openhpc ENV PATH="/opt/ohpc/pub/libs/easybuild/4.1.1/software/EasyBuild/4.1.1/bin:${PATH}" ENV PYTHONPATH="/opt/ohpc/pub/libs/easybuild/4.1.1/software/EasyBuild/4.1.1/lib/python3.6/site-packages" # This way all commands passed into the container are executed in a # login shell which is necessary to get lmod working. Commands # need to be enclosed in quotes. ENTRYPOINT ["/bin/bash", "-l", "-c"] $ podman build . -f Dockerfile.ohpc-gnu9-easybuild --tag=ohpc-gnu9-easybuild:1.9.9 $ podman run ohpc-gnu9-easybuild:1.9.9 'eb --robot lz4-1.9.2-GCCcore-8.3.0.eb' Now it will abort and the segfault from above can be seen in the logs. The segfault does not happen when running as root.