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[R] Segfault on flight test #35391

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nealrichardson opened this issue May 2, 2023 · 5 comments
Closed

[R] Segfault on flight test #35391

nealrichardson opened this issue May 2, 2023 · 5 comments
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Component: R Priority: Critical Type: bug

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@nealrichardson
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Describe the bug, including details regarding any error messages, version, and platform.

This is happening pretty regularly on main now in the ubuntu "force tests" job. As a result, I haven't seen #35238 in a while because this segfault happens before we get to that point :/

cc @paleolimbot

...
Start test: flight_get
/arrow/cpp/src/arrow/status.cc:134: Invalid: Signal stop source already set up
  'test-python-flight.R:56:5' [success]
End test: flight_get

Start test: flight_put with RecordBatch
/arrow/cpp/src/arrow/status.cc:134: Invalid: Signal stop source already set up
  'test-python-flight.R:62:5' [success]
End test: flight_put with RecordBatch

Start test: flight_put with overwrite = FALSE
  'test-python-flight.R:66:5' [success]
/arrow/cpp/src/arrow/status.cc:134: Invalid: Signal stop source already set up

 *** caught segfault ***
address 0xb8, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)

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R
@nealrichardson nealrichardson mentioned this issue May 2, 2023
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@h-vetinari
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The flight tests are also segfaulting in python (on osx), see here

@nealrichardson
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ICYMI @lidavidm @jorisvandenbossche

@jorisvandenbossche
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Other potentially related issue:

@nealrichardson
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That sounds like the same thing--didn't realize it had been happening for so long. It does seem more frequent now though, or has re-emerged after being fixed.

@pitrou pitrou mentioned this issue May 10, 2023
Merged
@paleolimbot paleolimbot mentioned this issue May 29, 2023
Merged
paleolimbot added a commit that referenced this issue May 30, 2023
@paleolimbot
GH-34897: [R] Ensure that the RStringViewer helper class does not own…
0adf154 
… any Array references (#35812)

This was identified and 99% debugged by @ lgautier on rpy2/rpy2-arrow#11 . Thank you!

I have no idea why this does anything; however, the `RStringViewer` class *was* holding on to an unnecessary Array reference and this seemed to fix the crash for me. Maybe a circular reference? The reprex I was using (provided by @ lgautier) was:

Install fresh deps:

```bash
pip3 install pandas pyarrow rpy2-arrow
R -e 'install.packages("arrow", repos = "https://cloud.r-project.org/")'
```

Run this python script:

```python
import pandas as pd
import pyarrow
from rpy2.robjects.packages import importr
import rpy2.robjects
import rpy2_arrow.arrow as pyra
base = importr('base')
nanoarrow = importr('nanoarrow')

code = """
    function(df) {
        # df$col1  # no segfault on exit
        # I(df$col1)  # no segfault on exit
        # df$col2  # no segfault on exit
        I(df$col2)  # segfault on exit
    }
"""
rfunction = rpy2.robjects.r(code)

pd_df = pd.DataFrame({
    "col1": range(10),
    "col2":["a" for num in range(10)]
})
pd_tbl = pyarrow.Table.from_pandas(pd_df)
r_tbl = pyra.pyarrow_table_to_r_table(pd_tbl)
r_df = base.as_data_frame(nanoarrow.as_nanoarrow_array_stream(r_tbl))

output = rfunction(r_df)
print(output)
```

Before this PR (installing R/arrow from main) I get:

```
(.venv) dewey@ Deweys-Mac-mini 2023-05-29_rpy % python reprex-arrow.py
 [1] "a" "a" "a" "a" "a" "a" "a" "a" "a" "a"

zsh: segmentation fault  python reprex-arrow.py
```

After this PR I get:

```
(.venv) dewey@ Deweys-Mac-mini 2023-05-29_rpy % python reprex-arrow.py
 [1] "a" "a" "a" "a" "a" "a" "a" "a" "a" "a"
```

(with no segfault)

I wonder if this also will help with #35391 since it's also a segfault involving the Python <-> R bridge.
* Closes: #34897

Authored-by: Dewey Dunnington <[email protected]>
Signed-off-by: Dewey Dunnington <[email protected]>
thisisnic pushed a commit to thisisnic/arrow that referenced this issue Jun 6, 2023
@paleolimbot @thisisnic
apacheGH-34897: [R] Ensure that the RStringViewer helper class does n…
bcd8e9a 
…ot own any Array references (apache#35812)

This was identified and 99% debugged by @ lgautier on rpy2/rpy2-arrow#11 . Thank you!

I have no idea why this does anything; however, the `RStringViewer` class *was* holding on to an unnecessary Array reference and this seemed to fix the crash for me. Maybe a circular reference? The reprex I was using (provided by @ lgautier) was:

Install fresh deps:

```bash
pip3 install pandas pyarrow rpy2-arrow
R -e 'install.packages("arrow", repos = "https://cloud.r-project.org/")'
```

Run this python script:

```python
import pandas as pd
import pyarrow
from rpy2.robjects.packages import importr
import rpy2.robjects
import rpy2_arrow.arrow as pyra
base = importr('base')
nanoarrow = importr('nanoarrow')

code = """
    function(df) {
        # df$col1  # no segfault on exit
        # I(df$col1)  # no segfault on exit
        # df$col2  # no segfault on exit
        I(df$col2)  # segfault on exit
    }
"""
rfunction = rpy2.robjects.r(code)

pd_df = pd.DataFrame({
    "col1": range(10),
    "col2":["a" for num in range(10)]
})
pd_tbl = pyarrow.Table.from_pandas(pd_df)
r_tbl = pyra.pyarrow_table_to_r_table(pd_tbl)
r_df = base.as_data_frame(nanoarrow.as_nanoarrow_array_stream(r_tbl))

output = rfunction(r_df)
print(output)
```

Before this PR (installing R/arrow from main) I get:

```
(.venv) dewey@ Deweys-Mac-mini 2023-05-29_rpy % python reprex-arrow.py
 [1] "a" "a" "a" "a" "a" "a" "a" "a" "a" "a"

zsh: segmentation fault  python reprex-arrow.py
```

After this PR I get:

```
(.venv) dewey@ Deweys-Mac-mini 2023-05-29_rpy % python reprex-arrow.py
 [1] "a" "a" "a" "a" "a" "a" "a" "a" "a" "a"
```

(with no segfault)

I wonder if this also will help with apache#35391 since it's also a segfault involving the Python <-> R bridge.
* Closes: apache#34897

Authored-by: Dewey Dunnington <[email protected]>
Signed-off-by: Dewey Dunnington <[email protected]>
thisisnic pushed a commit to thisisnic/arrow that referenced this issue Jun 13, 2023
@paleolimbot @thisisnic
apacheGH-34897: [R] Ensure that the RStringViewer helper class does n…
91b885e 
…ot own any Array references (apache#35812)

This was identified and 99% debugged by @ lgautier on rpy2/rpy2-arrow#11 . Thank you!

I have no idea why this does anything; however, the `RStringViewer` class *was* holding on to an unnecessary Array reference and this seemed to fix the crash for me. Maybe a circular reference? The reprex I was using (provided by @ lgautier) was:

Install fresh deps:

```bash
pip3 install pandas pyarrow rpy2-arrow
R -e 'install.packages("arrow", repos = "https://cloud.r-project.org/")'
```

Run this python script:

```python
import pandas as pd
import pyarrow
from rpy2.robjects.packages import importr
import rpy2.robjects
import rpy2_arrow.arrow as pyra
base = importr('base')
nanoarrow = importr('nanoarrow')

code = """
    function(df) {
        # df$col1  # no segfault on exit
        # I(df$col1)  # no segfault on exit
        # df$col2  # no segfault on exit
        I(df$col2)  # segfault on exit
    }
"""
rfunction = rpy2.robjects.r(code)

pd_df = pd.DataFrame({
    "col1": range(10),
    "col2":["a" for num in range(10)]
})
pd_tbl = pyarrow.Table.from_pandas(pd_df)
r_tbl = pyra.pyarrow_table_to_r_table(pd_tbl)
r_df = base.as_data_frame(nanoarrow.as_nanoarrow_array_stream(r_tbl))

output = rfunction(r_df)
print(output)
```

Before this PR (installing R/arrow from main) I get:

```
(.venv) dewey@ Deweys-Mac-mini 2023-05-29_rpy % python reprex-arrow.py
 [1] "a" "a" "a" "a" "a" "a" "a" "a" "a" "a"

zsh: segmentation fault  python reprex-arrow.py
```

After this PR I get:

```
(.venv) dewey@ Deweys-Mac-mini 2023-05-29_rpy % python reprex-arrow.py
 [1] "a" "a" "a" "a" "a" "a" "a" "a" "a" "a"
```

(with no segfault)

I wonder if this also will help with apache#35391 since it's also a segfault involving the Python <-> R bridge.
* Closes: apache#34897

Authored-by: Dewey Dunnington <[email protected]>
Signed-off-by: Dewey Dunnington <[email protected]>
@thisisnic
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I believe this has been fixed by #35812 but feel free to reopen if not

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@jorisvandenbossche @nealrichardson @thisisnic @h-vetinari