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Posted to issues@arrow.apache.org by "Bramtimm (via GitHub)" <gi...@apache.org> on 2023/03/05 18:10:42 UTC
[GitHub] [arrow] Bramtimm opened a new issue, #34459: Segmentation fault when trying to connect to AWS S3 Storage on CentOS 7 – Amazon Linux 2
Bramtimm opened a new issue, #34459:
URL: https://github.com/apache/arrow/issues/34459
### Describe the bug, including details regarding any error messages, version, and platform.
Hi there,
Since Arrow 11.0.2 we run into a segmentation fault when trying to connect to our AWS S3 storage with the R library of Arrow (see below). When reading the file locally first, the package tends to work fine.
```
arrow::s3_bucket('<bucketname>')
*** caught segfault ***
address 0x28, cause 'memory not mapped'
Traceback:
1: fs___FileSystemFromUri(uri)
2: FileSystem$from_uri(bucket)
3: arrow::s3_bucket("<bucketname>")
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
```
On closer inspection with C++ debugger it seems that the segmentation fault might be related to OpenSSL. We now use `
OpenSSL 1.1.1o 3 May 2022` version, but seem to be stuck on the same error on earlier builds.
```
Thread 1 "R" received signal SIGSEGV, Segmentation fault.
0x00007fffeb5900d9 in evp_md_init_internal () from /usr/local/lib64/libcrypto.so.3
```
As noted in the installation guide we are aware of setting C++ 17 compiler and devtoolsset-11 for centOS, and use a custom image to build our environment wich sets the makevars etc.
We are kind of running out of ideas, so any help is much appreciated!
I’ve added the output of `arrow::arrow_info()` and `sessionInfo()` below.
```
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Amazon Linux 2
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.2
> R
Error: object 'R' not found
> arrow::arrow_info()
Arrow package version: 11.0.0.2
Capabilities:
dataset TRUE
substrait FALSE
parquet TRUE
json TRUE
s3 TRUE
gcs TRUE
utf8proc TRUE
re2 TRUE
snappy TRUE
gzip TRUE
brotli TRUE
zstd TRUE
lz4 TRUE
lz4_frame TRUE
lzo FALSE
bz2 TRUE
jemalloc TRUE
mimalloc TRUE
Memory:
Allocator jemalloc
Current 0 bytes
Max 0 bytes
Runtime:
SIMD Level avx
Detected SIMD Level avx
Build:
C++ Library Version 11.0.0
C++ Compiler GNU
C++ Compiler Version 8.3.1
```
### Component(s)
R
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[GitHub] [arrow] westonpace commented on issue #34459: [R] Segmentation fault when trying to connect to AWS S3 Storage on CentOS 7 – Amazon Linux 2
Posted by "westonpace (via GitHub)" <gi...@apache.org>.
westonpace commented on issue #34459:
URL: https://github.com/apache/arrow/issues/34459#issuecomment-1456933841
Just to verify, is this a segmentation fault on shutdown? In other words, does this happen as one of the last things you do? And, if so, does it still happen if you put a sleep before you exit? There is a known issue with S3 shutdown.
If that's not it do you think there is any chance we could get a full backtrace from reproducing the issue with gdb attached. Something like...
```
R -d gdb
...
gdb prompt> run
...
R prompt> source("my_script.R")
...
SEGFAULT
gdb prompt> bt
```
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[GitHub] [arrow] Bramtimm commented on issue #34459: [R] Segmentation fault when trying to connect to AWS S3 Storage on CentOS 7 – Amazon Linux 2
Posted by "Bramtimm (via GitHub)" <gi...@apache.org>.
Bramtimm commented on issue #34459:
URL: https://github.com/apache/arrow/issues/34459#issuecomment-1460710945
Thanks for your response, the segmentation fault happened irrelevant of shutdown, but it seems that we have resolved the issue. It looks like it was caused by swapping `openssl-devel` to `openssl11-devel` for python 3.11 (i.e. `yum swap -y openssl-devel openssl11-devel`) in our setup before installing Arrow (R) with `install_arrow()`. This seems to cause the segfault in `libcrypto.so.3` when trying to connect to S3.
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[GitHub] [arrow] westonpace closed issue #34459: [R] Segmentation fault when trying to connect to AWS S3 Storage on CentOS 7 – Amazon Linux 2
Posted by "westonpace (via GitHub)" <gi...@apache.org>.
westonpace closed issue #34459: [R] Segmentation fault when trying to connect to AWS S3 Storage on CentOS 7 – Amazon Linux 2
URL: https://github.com/apache/arrow/issues/34459
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[GitHub] [arrow] westonpace commented on issue #34459: [R] Segmentation fault when trying to connect to AWS S3 Storage on CentOS 7 – Amazon Linux 2
Posted by "westonpace (via GitHub)" <gi...@apache.org>.
westonpace commented on issue #34459:
URL: https://github.com/apache/arrow/issues/34459#issuecomment-1468458509
Thanks for the update. I'm going to close this issue then. Feel free to reopen if you need more investigation or run into further issues.
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