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Posted to github@arrow.apache.org by GitBox <gi...@apache.org> on 2021/12/21 15:03:34 UTC
[GitHub] [arrow] pitrou opened a new pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
pitrou opened a new pull request #12011:
URL: https://github.com/apache/arrow/pull/12011
Transferring C pointer values between Python and R would involve an intermediate conversion to a double, which might lose precision.
Instead, pass an external pointer from R, which gets converted into a Python capsule.
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[GitHub] [arrow] pitrou commented on pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
pitrou commented on pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#issuecomment-998851074
@paleolimbot
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[GitHub] [arrow] paleolimbot commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
paleolimbot commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773289253
##########
File path: python/pyarrow/types.pxi
##########
@@ -82,6 +84,26 @@ cdef bytes _datatype_to_pep3118(CDataType* type):
return char
+cdef void* _as_c_pointer(v, allow_null=False) except *:
+ """
+ Convert a Python object to a raw C pointer.
+
+ Used mainly for the C data interface.
+ Integers are accepted as well as capsule objects with a NULL name.
+ (the latter for compatibility with raw pointers exported by reticulate)
+ """
+ cdef void* c_ptr
+ if isinstance(v, int):
+ c_ptr = <void*> <uintptr_t > v
+ elif PyCapsule_CheckExact(v):
+ c_ptr = PyCapsule_GetPointer(v, NULL)
+ else:
Review comment:
I think the only good reason to support strings, int64, or raw arrays, is because other language bridges might not be able to convert external pointers and/or pycapsule objects. With reticulate we had a pretty good chance of submitting a PR upstream (although it seems to work out of the box); other language bridges may not be easy or fast to change.
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[GitHub] [arrow] paleolimbot commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
paleolimbot commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773852287
##########
File path: r/src/bridge.cpp
##########
@@ -21,13 +21,6 @@
#include <arrow/c/bridge.h>
-// [[arrow::export]]
Review comment:
Just a note to add this back...I'll take care of it when I do the R ticket handling a potentially old Python version (either remove it and error or use it for an old pyarrow).
##########
File path: r/tests/testthat/test-bridge.R
##########
@@ -25,16 +25,6 @@ test_that("Pointer wrapper accepts external pointers", {
delete_arrow_schema(ptr)
})
-test_that("Pointer wrapper accepts double-casted pointers", {
Review comment:
Same as above (I'll remove this in the R ticket if we're no longer using it).
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[GitHub] [arrow] pitrou commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
pitrou commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773807070
##########
File path: r/R/python.R
##########
@@ -23,11 +23,7 @@ py_to_r.pyarrow.lib.Array <- function(x, ...) {
delete_arrow_array(array_ptr)
})
- x$`_export_to_c`(
- external_pointer_addr_double(array_ptr),
- external_pointer_addr_double(schema_ptr)
- )
-
+ x$`_export_to_c`(array_ptr, schema_ptr)
Review comment:
By the way, in the other direction, if a user has an up-to-date PyArrow but an old R-Arrow, it probably means R will give Python a double?
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[GitHub] [arrow] pitrou commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
pitrou commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773866818
##########
File path: r/R/python.R
##########
@@ -23,11 +23,7 @@ py_to_r.pyarrow.lib.Array <- function(x, ...) {
delete_arrow_array(array_ptr)
})
- x$`_export_to_c`(
- external_pointer_addr_double(array_ptr),
- external_pointer_addr_double(schema_ptr)
- )
-
+ x$`_export_to_c`(array_ptr, schema_ptr)
Review comment:
I did not use that exact wording (in case someone calls it in another context that R), but I added a warning about that.
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[GitHub] [arrow] pitrou commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
pitrou commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773235694
##########
File path: python/pyarrow/types.pxi
##########
@@ -82,6 +84,26 @@ cdef bytes _datatype_to_pep3118(CDataType* type):
return char
+cdef void* _as_c_pointer(v, allow_null=False) except *:
+ """
+ Convert a Python object to a raw C pointer.
+
+ Used mainly for the C data interface.
+ Integers are accepted as well as capsule objects with a NULL name.
+ (the latter for compatibility with raw pointers exported by reticulate)
+ """
+ cdef void* c_ptr
+ if isinstance(v, int):
+ c_ptr = <void*> <uintptr_t > v
+ elif PyCapsule_CheckExact(v):
+ c_ptr = PyCapsule_GetPointer(v, NULL)
+ else:
Review comment:
I don't know, is it actually useful? This is not really a user-facing API. End users will call the higher-level bridge functions.
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[GitHub] [arrow] amol- commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
amol- commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773234552
##########
File path: python/pyarrow/types.pxi
##########
@@ -82,6 +84,26 @@ cdef bytes _datatype_to_pep3118(CDataType* type):
return char
+cdef void* _as_c_pointer(v, allow_null=False) except *:
+ """
+ Convert a Python object to a raw C pointer.
+
+ Used mainly for the C data interface.
+ Integers are accepted as well as capsule objects with a NULL name.
+ (the latter for compatibility with raw pointers exported by reticulate)
+ """
+ cdef void* c_ptr
+ if isinstance(v, int):
+ c_ptr = <void*> <uintptr_t > v
+ elif PyCapsule_CheckExact(v):
+ c_ptr = PyCapsule_GetPointer(v, NULL)
+ else:
Review comment:
Should we also support strings as we did in R? I think there is a value in being consistent
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[GitHub] [arrow] github-actions[bot] commented on pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
github-actions[bot] commented on pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#issuecomment-998851083
https://issues.apache.org/jira/browse/ARROW-15169
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[GitHub] [arrow] pitrou commented on pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
pitrou commented on pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#issuecomment-999576918
@paleolimbot Do you have other concerns here?
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[GitHub] [arrow] ursabot edited a comment on pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
ursabot edited a comment on pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#issuecomment-999688122
Benchmark runs are scheduled for baseline = f904e39ad59bf75da1e74c2a45a9fdfae48d7d62 and contender = 3fc64515275c6515a9a2b7c733a9f8625e9a2978. 3fc64515275c6515a9a2b7c733a9f8625e9a2978 is a master commit associated with this PR. Results will be available as each benchmark for each run completes.
Conbench compare runs links:
[Finished :arrow_down:0.0% :arrow_up:0.0%] [ec2-t3-xlarge-us-east-2](https://conbench.ursa.dev/compare/runs/442b73401d324e43bb67183076424f7e...e29a3bbedaa94129a9e6fe8bcfc4c343/)
[Failed :arrow_down:0.0% :arrow_up:0.0%] [ursa-i9-9960x](https://conbench.ursa.dev/compare/runs/b711e4eed22c4739943ced5bf7611942...741c29075f4f468ab8d51e174c4a308d/)
[Failed :arrow_down:0.45% :arrow_up:0.4%] [ursa-thinkcentre-m75q](https://conbench.ursa.dev/compare/runs/39f46a72af7147ec8700edeb7532852a...9317c081f32a45d3b08afbf16754e82d/)
Supported benchmarks:
ec2-t3-xlarge-us-east-2: Supported benchmark langs: Python. Runs only benchmarks with cloud = True
ursa-i9-9960x: Supported benchmark langs: Python, R, JavaScript
ursa-thinkcentre-m75q: Supported benchmark langs: C++, Java
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[GitHub] [arrow] pitrou commented on pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
pitrou commented on pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#issuecomment-998854912
Also cc @amol-
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[GitHub] [arrow] paleolimbot commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
paleolimbot commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773851085
##########
File path: r/R/python.R
##########
@@ -23,11 +23,7 @@ py_to_r.pyarrow.lib.Array <- function(x, ...) {
delete_arrow_array(array_ptr)
})
- x$`_export_to_c`(
- external_pointer_addr_double(array_ptr),
- external_pointer_addr_double(schema_ptr)
- )
-
+ x$`_export_to_c`(array_ptr, schema_ptr)
Review comment:
True! I forgot about that. As long as the error message is along the lines of "update the R package" it's probably ok! When I do the R version I could do that, too.
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[GitHub] [arrow] ursabot commented on pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
ursabot commented on pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#issuecomment-999688122
Benchmark runs are scheduled for baseline = f904e39ad59bf75da1e74c2a45a9fdfae48d7d62 and contender = 3fc64515275c6515a9a2b7c733a9f8625e9a2978. 3fc64515275c6515a9a2b7c733a9f8625e9a2978 is a master commit associated with this PR. Results will be available as each benchmark for each run completes.
Conbench compare runs links:
[Scheduled] [ec2-t3-xlarge-us-east-2](https://conbench.ursa.dev/compare/runs/442b73401d324e43bb67183076424f7e...e29a3bbedaa94129a9e6fe8bcfc4c343/)
[Scheduled] [ursa-i9-9960x](https://conbench.ursa.dev/compare/runs/b711e4eed22c4739943ced5bf7611942...741c29075f4f468ab8d51e174c4a308d/)
[Scheduled] [ursa-thinkcentre-m75q](https://conbench.ursa.dev/compare/runs/39f46a72af7147ec8700edeb7532852a...9317c081f32a45d3b08afbf16754e82d/)
Supported benchmarks:
ec2-t3-xlarge-us-east-2: Supported benchmark langs: Python. Runs only benchmarks with cloud = True
ursa-i9-9960x: Supported benchmark langs: Python, R, JavaScript
ursa-thinkcentre-m75q: Supported benchmark langs: C++, Java
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[GitHub] [arrow] paleolimbot commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
paleolimbot commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773284257
##########
File path: r/R/python.R
##########
@@ -23,11 +23,7 @@ py_to_r.pyarrow.lib.Array <- function(x, ...) {
delete_arrow_array(array_ptr)
})
- x$`_export_to_c`(
- external_pointer_addr_double(array_ptr),
- external_pointer_addr_double(schema_ptr)
- )
-
+ x$`_export_to_c`(array_ptr, schema_ptr)
Review comment:
Should we provide backward compatibility here? I imagine this will error with `An integer is required` unless a user has an up-to-date pyarrow. I imagine we should do something like this:
``` r
pa <- reticulate::import("pyarrow")
if (package_version(pa$`__version__`) >= "6.0.0.9000") {
# the new code
} else {
# the old code
}
```
...which I'd be happy to do on a separate JIRA ticket if it's not a good fit for this PR.
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[GitHub] [arrow] pitrou commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
pitrou commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773285745
##########
File path: r/R/python.R
##########
@@ -23,11 +23,7 @@ py_to_r.pyarrow.lib.Array <- function(x, ...) {
delete_arrow_array(array_ptr)
})
- x$`_export_to_c`(
- external_pointer_addr_double(array_ptr),
- external_pointer_addr_double(schema_ptr)
- )
-
+ x$`_export_to_c`(array_ptr, schema_ptr)
Review comment:
Ah, you're right. We can do that on a separate JIRA then, IMHO.
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[GitHub] [arrow] paleolimbot commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
paleolimbot commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773292139
##########
File path: r/R/python.R
##########
@@ -23,11 +23,7 @@ py_to_r.pyarrow.lib.Array <- function(x, ...) {
delete_arrow_array(array_ptr)
})
- x$`_export_to_c`(
- external_pointer_addr_double(array_ptr),
- external_pointer_addr_double(schema_ptr)
- )
-
+ x$`_export_to_c`(array_ptr, schema_ptr)
Review comment:
Done! ARROW-15173
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[GitHub] [arrow] amol- commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
amol- commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773241105
##########
File path: python/pyarrow/types.pxi
##########
@@ -82,6 +84,26 @@ cdef bytes _datatype_to_pep3118(CDataType* type):
return char
+cdef void* _as_c_pointer(v, allow_null=False) except *:
+ """
+ Convert a Python object to a raw C pointer.
+
+ Used mainly for the C data interface.
+ Integers are accepted as well as capsule objects with a NULL name.
+ (the latter for compatibility with raw pointers exported by reticulate)
+ """
+ cdef void* c_ptr
+ if isinstance(v, int):
+ c_ptr = <void*> <uintptr_t > v
+ elif PyCapsule_CheckExact(v):
+ c_ptr = PyCapsule_GetPointer(v, NULL)
+ else:
Review comment:
Well if I invoke `export_to_c` and `import_to_c` I end up invoking it. I'm asking just because we supported it in R, so thought it made sense to allow consistent behaviour between the two. In the end it's just one `elif` that doesn't seem to involve much maintenance burden.
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[GitHub] [arrow] paleolimbot commented on pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
paleolimbot commented on pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#issuecomment-999585046
No concerns...looks great!
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[GitHub] [arrow] ursabot edited a comment on pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
ursabot edited a comment on pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#issuecomment-999688122
Benchmark runs are scheduled for baseline = f904e39ad59bf75da1e74c2a45a9fdfae48d7d62 and contender = 3fc64515275c6515a9a2b7c733a9f8625e9a2978. 3fc64515275c6515a9a2b7c733a9f8625e9a2978 is a master commit associated with this PR. Results will be available as each benchmark for each run completes.
Conbench compare runs links:
[Finished :arrow_down:0.0% :arrow_up:0.0%] [ec2-t3-xlarge-us-east-2](https://conbench.ursa.dev/compare/runs/442b73401d324e43bb67183076424f7e...e29a3bbedaa94129a9e6fe8bcfc4c343/)
[Scheduled] [ursa-i9-9960x](https://conbench.ursa.dev/compare/runs/b711e4eed22c4739943ced5bf7611942...741c29075f4f468ab8d51e174c4a308d/)
[Failed :arrow_down:0.45% :arrow_up:0.4%] [ursa-thinkcentre-m75q](https://conbench.ursa.dev/compare/runs/39f46a72af7147ec8700edeb7532852a...9317c081f32a45d3b08afbf16754e82d/)
Supported benchmarks:
ec2-t3-xlarge-us-east-2: Supported benchmark langs: Python. Runs only benchmarks with cloud = True
ursa-i9-9960x: Supported benchmark langs: Python, R, JavaScript
ursa-thinkcentre-m75q: Supported benchmark langs: C++, Java
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[GitHub] [arrow] pitrou commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
pitrou commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773243937
##########
File path: python/pyarrow/types.pxi
##########
@@ -82,6 +84,26 @@ cdef bytes _datatype_to_pep3118(CDataType* type):
return char
+cdef void* _as_c_pointer(v, allow_null=False) except *:
+ """
+ Convert a Python object to a raw C pointer.
+
+ Used mainly for the C data interface.
+ Integers are accepted as well as capsule objects with a NULL name.
+ (the latter for compatibility with raw pointers exported by reticulate)
+ """
+ cdef void* c_ptr
+ if isinstance(v, int):
+ c_ptr = <void*> <uintptr_t > v
+ elif PyCapsule_CheckExact(v):
+ c_ptr = PyCapsule_GetPointer(v, NULL)
+ else:
Review comment:
(in general, accepting more implicit conversions also creates a larger risk of crashes / memory corruption)
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[GitHub] [arrow] pitrou commented on a change in pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
pitrou commented on a change in pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#discussion_r773242898
##########
File path: python/pyarrow/types.pxi
##########
@@ -82,6 +84,26 @@ cdef bytes _datatype_to_pep3118(CDataType* type):
return char
+cdef void* _as_c_pointer(v, allow_null=False) except *:
+ """
+ Convert a Python object to a raw C pointer.
+
+ Used mainly for the C data interface.
+ Integers are accepted as well as capsule objects with a NULL name.
+ (the latter for compatibility with raw pointers exported by reticulate)
+ """
+ cdef void* c_ptr
+ if isinstance(v, int):
+ c_ptr = <void*> <uintptr_t > v
+ elif PyCapsule_CheckExact(v):
+ c_ptr = PyCapsule_GetPointer(v, NULL)
+ else:
Review comment:
But in which situation would you get a string in the first place?
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[GitHub] [arrow] pitrou closed pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
pitrou closed pull request #12011:
URL: https://github.com/apache/arrow/pull/12011
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[GitHub] [arrow] ursabot edited a comment on pull request #12011: ARROW-15169: [Python][R] Avoid unsafe Python-R pointer transfer
Posted by GitBox <gi...@apache.org>.
ursabot edited a comment on pull request #12011:
URL: https://github.com/apache/arrow/pull/12011#issuecomment-999688122
Benchmark runs are scheduled for baseline = f904e39ad59bf75da1e74c2a45a9fdfae48d7d62 and contender = 3fc64515275c6515a9a2b7c733a9f8625e9a2978. 3fc64515275c6515a9a2b7c733a9f8625e9a2978 is a master commit associated with this PR. Results will be available as each benchmark for each run completes.
Conbench compare runs links:
[Finished :arrow_down:0.0% :arrow_up:0.0%] [ec2-t3-xlarge-us-east-2](https://conbench.ursa.dev/compare/runs/442b73401d324e43bb67183076424f7e...e29a3bbedaa94129a9e6fe8bcfc4c343/)
[Scheduled] [ursa-i9-9960x](https://conbench.ursa.dev/compare/runs/b711e4eed22c4739943ced5bf7611942...741c29075f4f468ab8d51e174c4a308d/)
[Scheduled] [ursa-thinkcentre-m75q](https://conbench.ursa.dev/compare/runs/39f46a72af7147ec8700edeb7532852a...9317c081f32a45d3b08afbf16754e82d/)
Supported benchmarks:
ec2-t3-xlarge-us-east-2: Supported benchmark langs: Python. Runs only benchmarks with cloud = True
ursa-i9-9960x: Supported benchmark langs: Python, R, JavaScript
ursa-thinkcentre-m75q: Supported benchmark langs: C++, Java
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