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push eventRosettaCommons/PyRosetta.notebooks
commit sha 311d20c922aaa7bf1d29a402d35e0d1e08230f1f
Updating references to python3.6 to 3.7 following colab's update Google CoLab updated to python3.7 at least as recently as 2021/02/25 Ahead of the next PyRosetta boot camp, this needed to be updated
commit sha f187158eb065d60f6a3f2284c7ff560e22250129
Updating student-notebooks
commit sha 6dfa37d53631da138a9ae12cfc3bf2e05ade8941
Re-run notebooks to update the embedded .png
commit sha 76b8a8db49d49eaba982293fcf4c91cf438416a8
fix rabd notebook with recent changes.
commit sha baa4175a607a61ecae729ff4a4e060b860b36857
Update 12.02-RosettaAntibodyDesign-RAbD.ipynb Manually put back new python version
commit sha 53c0f59fc054ac68cbb5c80622a6642d437578c3
Added a link to install Google Colab app for first time users in the instructions.
commit sha b10dbb95b0a9a687d58040a40d4fd1f7e9b44195
Merge pull request #64 from branch aleaverfay/update_colab_instructions_to_py37 Updating references to python3.6 to 3.7 following colab's update about a week ago. If you download the 3.6 version, then when you try to run `from pyrosetta import *`, the colab environment throws and error.
commit sha 6e8f8acac93f19e9641cc589a926b7467204428c
Merge pull request #62 from RosettaCommons/sergey adding whell-install and PyMOL-Colab demos
commit sha 3df63f1b3d308d8694aa1f400e6c015d3d703c96
Merge pull request #65 from RosettaCommons/rabd2 Fix rabd notebook with recent changes to master.
commit sha 66cb994635ab635c7d5e4a4f3c8aaa9a36306331
fix issue with block.
commit sha 207d46f935fa69aa1272163cc525d6e11e4ac67c
Merge pull request #66 from RosettaCommons/rabd3 Fix RabD issue with block.
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delete branch RosettaCommons/pybind11
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PR closed RosettaCommons/pybind11
Bumps pre-commit/action from v2.0.0 to v2.0.1. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pre-commit/action/releases">pre-commit/action's releases</a>.</em></p> <blockquote> <h2>pre-commit/action@v2.0.1</h2> <h3>Fixes</h3> <ul> <li>Avoid failures if cache saving fails <ul> <li><a href="https://github-redirect.dependabot.com/pre-commit/action/issues/54">#54</a> PR by <a href="https://github.com/s-weigand"><code>@s-weigand</code></a></li> <li><a href="https://github-redirect.dependabot.com/pre-commit/action/issues/53">#53</a> issue by <a href="https://github.com/s-weigand"><code>@s-weigand</code></a></li> </ul> </li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pre-commit/action/commit/b54880c283dfc80a3fc1baf61807e8ae84471361"><code>b54880c</code></a> v2.0.1</li> <li><a href="https://github.com/pre-commit/action/commit/8ac8946854ea5db3be6a2eb8600ba0ac178ad9de"><code>8ac8946</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/54">#54</a> from s-weigand/fix-53</li> <li><a href="https://github.com/pre-commit/action/commit/d1027a948b51ee71764d270f9cfeeee2715c01c7"><code>d1027a9</code></a> Wrapped saving pre-commit cache to cache, in a try catch block</li> <li><a href="https://github.com/pre-commit/action/commit/0404b969641801ff99d4cecbfabf14304270b4c9"><code>0404b96</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/89">#89</a> from pre-commit/dependabot/npm_and_yarn/y18n-4.0.1</li> <li><a href="https://github.com/pre-commit/action/commit/52ec6e5c9fe15aa1c68925623c0f825e8066e726"><code>52ec6e5</code></a> Bump y18n from 4.0.0 to 4.0.1</li> <li><a href="https://github.com/pre-commit/action/commit/f52f43f850c62e8f2ee58893bf4a7ae42a1e3ece"><code>f52f43f</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/87">#87</a> from pre-commit/pre-commit-ci-update-config</li> <li><a href="https://github.com/pre-commit/action/commit/007c7cde5205c83d2fd0b6d36d3c1d0c68bcdadc"><code>007c7cd</code></a> [pre-commit.ci] pre-commit autoupdate</li> <li><a href="https://github.com/pre-commit/action/commit/1365adcff2d9c8606f13644b56e5a5c52fc393c9"><code>1365adc</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/86">#86</a> from pre-commit/pre-commit-ci-update-config</li> <li><a href="https://github.com/pre-commit/action/commit/5e4d1b7a22f4f47dfe6cb987ca5e37ba053b3fcf"><code>5e4d1b7</code></a> [pre-commit.ci] pre-commit autoupdate</li> <li><a href="https://github.com/pre-commit/action/commit/ec497e5c4a44eaca8283b84d85d4105e30fb6903"><code>ec497e5</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/84">#84</a> from pre-commit/dependabot/npm_and_yarn/elliptic-6.5.4</li> <li>Additional commits viewable in <a href="https://github.com/pre-commit/action/compare/v2.0.0...b54880c283dfc80a3fc1baf61807e8ae84471361">compare view</a></li> </ul> </details> <br />
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PR opened RosettaCommons/pybind11
Bumps pre-commit/action from v2.0.0 to v2.0.2. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pre-commit/action/releases">pre-commit/action's releases</a>.</em></p> <blockquote> <h2>pre-commit/action@v2.0.2</h2> <p>retag of 2.0.1 but on the proper branch</p> <h2>pre-commit/action@v2.0.1</h2> <h3>Fixes</h3> <ul> <li>Avoid failures if cache saving fails <ul> <li><a href="https://github-redirect.dependabot.com/pre-commit/action/issues/54">#54</a> PR by <a href="https://github.com/s-weigand"><code>@s-weigand</code></a></li> <li><a href="https://github-redirect.dependabot.com/pre-commit/action/issues/53">#53</a> issue by <a href="https://github.com/s-weigand"><code>@s-weigand</code></a></li> </ul> </li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pre-commit/action/commit/9cf68dc1ace5504cd0e05b9f3df32e6a0822ad89"><code>9cf68dc</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/12c0cbaee9b37d569632139754759021b4dc2ed7"><code>12c0cba</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/686243b93a269e859b827b37c83af97ad125b407"><code>686243b</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/5b6c59a01a99def46b9fd96111c1533e8df334cf"><code>5b6c59a</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/23933a87f57b9d68d9841cef1ca481eac28c9458"><code>23933a8</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/ba03328ac18694cb521a8fcb053db2f07419862b"><code>ba03328</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/055fa4e7efbddb7cdc641d81a40c4497a3f4e39d"><code>055fa4e</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/2fcbdbb9ddd55fb1f15449c82b3e66ffb1320634"><code>2fcbdbb</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/8ba276b2444e938dfc4a7ec990b590b0be4f11e9"><code>8ba276b</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/34072ce8c47fc47e70ba4d94386763155b3c1f8e"><code>34072ce</code></a> Deployed to github pages</li> <li>See full diff in <a href="https://github.com/pre-commit/action/compare/v2.0.0...9cf68dc1ace5504cd0e05b9f3df32e6a0822ad89">compare view</a></li> </ul> </details> <br />
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pull request commentRosettaCommons/pybind11
chore(deps): bump pre-commit/action from v2.0.0 to v2.0.1
Superseded by #7.
comment created time in 13 days
create barnchRosettaCommons/pybind11
branch : dependabot/github_actions/pre-commit/action-v2.0.2
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PR opened RosettaCommons/pybind11
Bumps pre-commit/action from v2.0.0 to v2.0.1. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pre-commit/action/releases">pre-commit/action's releases</a>.</em></p> <blockquote> <h2>pre-commit/action@v2.0.1</h2> <h3>Fixes</h3> <ul> <li>Avoid failures if cache saving fails <ul> <li><a href="https://github-redirect.dependabot.com/pre-commit/action/issues/54">#54</a> PR by <a href="https://github.com/s-weigand"><code>@s-weigand</code></a></li> <li><a href="https://github-redirect.dependabot.com/pre-commit/action/issues/53">#53</a> issue by <a href="https://github.com/s-weigand"><code>@s-weigand</code></a></li> </ul> </li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pre-commit/action/commit/b54880c283dfc80a3fc1baf61807e8ae84471361"><code>b54880c</code></a> v2.0.1</li> <li><a href="https://github.com/pre-commit/action/commit/8ac8946854ea5db3be6a2eb8600ba0ac178ad9de"><code>8ac8946</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/54">#54</a> from s-weigand/fix-53</li> <li><a href="https://github.com/pre-commit/action/commit/d1027a948b51ee71764d270f9cfeeee2715c01c7"><code>d1027a9</code></a> Wrapped saving pre-commit cache to cache, in a try catch block</li> <li><a href="https://github.com/pre-commit/action/commit/0404b969641801ff99d4cecbfabf14304270b4c9"><code>0404b96</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/89">#89</a> from pre-commit/dependabot/npm_and_yarn/y18n-4.0.1</li> <li><a href="https://github.com/pre-commit/action/commit/52ec6e5c9fe15aa1c68925623c0f825e8066e726"><code>52ec6e5</code></a> Bump y18n from 4.0.0 to 4.0.1</li> <li><a href="https://github.com/pre-commit/action/commit/f52f43f850c62e8f2ee58893bf4a7ae42a1e3ece"><code>f52f43f</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/87">#87</a> from pre-commit/pre-commit-ci-update-config</li> <li><a href="https://github.com/pre-commit/action/commit/007c7cde5205c83d2fd0b6d36d3c1d0c68bcdadc"><code>007c7cd</code></a> [pre-commit.ci] pre-commit autoupdate</li> <li><a href="https://github.com/pre-commit/action/commit/1365adcff2d9c8606f13644b56e5a5c52fc393c9"><code>1365adc</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/86">#86</a> from pre-commit/pre-commit-ci-update-config</li> <li><a href="https://github.com/pre-commit/action/commit/5e4d1b7a22f4f47dfe6cb987ca5e37ba053b3fcf"><code>5e4d1b7</code></a> [pre-commit.ci] pre-commit autoupdate</li> <li><a href="https://github.com/pre-commit/action/commit/ec497e5c4a44eaca8283b84d85d4105e30fb6903"><code>ec497e5</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/84">#84</a> from pre-commit/dependabot/npm_and_yarn/elliptic-6.5.4</li> <li>Additional commits viewable in <a href="https://github.com/pre-commit/action/compare/v2.0.0...b54880c283dfc80a3fc1baf61807e8ae84471361">compare view</a></li> </ul> </details> <br />
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create barnchRosettaCommons/pybind11
branch : dependabot/github_actions/pre-commit/action-v2.0.1
created branch time in 14 days
issue closedRosettaCommons/binder
Issue using generated bindings
Hi, I successfully generated and compiled binding for the esmini simulator by calling binder like this and using the config/headers file in the src directory. The generated bindings for each module are accessible in the separated directories under ./src.
However, I noticed the following two issues:
Issue 1: Memory Corruption
import pyesminilib
pyesminilib.SE_Init( '/home/[...]/esmini-pybind11/esmini/resources/xosc/lane_change.xosc',1,1,0,0)
From the log message I can see SE_Init function is called with the correct arguments but the binding introduces a memory corruption as below:
esmini GIT REV: 06f0360
esmini GIT TAG:
esmini GIT BRANCH: master
esmini BUILD VERSION: N/A - client build
esminiLib.cpp / 104 / ConvertArguments(): Player arguments: viewer --osc /home/[...]/esmini-pybind11/esmini/resources/xosc/lane_change.xosc --window 60 60 800 400 --disable_controllers
python3: malloc.c:2379: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.
Aborted (core dumped)
Issue 2: Missing methods
I noticed that not all methods are included in the generated bindings. As one example one of the constructor methods (ScenarioPlayer(int &argc, char *argv[])) is missing as can be seen in the generated bindings. (note, it is not only the constructors that are missing. SE_InitWithArgs and many other methods are also missing)
closed time in 20 days
ebadiissue commentRosettaCommons/binder
Issue using generated bindings
I narrowed down the problematic methods to these two methods
-- this quite odd... But overall: this issue is clearly outside the scope of Binder (ie Binder done its work: code was wrapped, results was compiled without the errors) and it should be propagated to Pybind11 team.
If/when you going to submit this to Pybind11 team could you please mention me? I am curious to learn of what might have caused this behavior. Thanks,
comment created time in 20 days
issue commentRosettaCommons/binder
Issue using generated bindings
Yes, I didn't push the bindings to the repository. The changes are minor:
~/repositories/esmini-pybind11$ git diff src/playerbase/pyplayerbase.cpp
diff --git a/src/playerbase/pyplayerbase.cpp b/src/playerbase/pyplayerbase.cpp
index d60d314..09fca15 100644
--- a/src/playerbase/pyplayerbase.cpp
+++ b/src/playerbase/pyplayerbase.cpp
@@ -27,9 +27,10 @@ void bind_unknown_unknown(std::function< pybind11::module &(std::string const &n
{
{ // ScenarioPlayer file: line:35
pybind11::class_<ScenarioPlayer, std::shared_ptr<ScenarioPlayer>> cl(M(""), "ScenarioPlayer", "");
+ cl.def( pybind11::init( [](){ return new ScenarioPlayer(); } ) );
cl.def_readwrite("sensor", &ScenarioPlayer::sensor);
- cl.def_readonly("maxStepSize", &ScenarioPlayer::maxStepSize);
- cl.def_readonly("minStepSize", &ScenarioPlayer::minStepSize);
+ cl.def_readwrite("maxStepSize", &ScenarioPlayer::maxStepSize);
+ cl.def_readwrite("minStepSize", &ScenarioPlayer::minStepSize);
cl.def_readwrite("opt", &ScenarioPlayer::opt);
cl.def_readwrite("callback", &ScenarioPlayer::callback);
cl.def_readwrite("exe_path_", &ScenarioPlayer::exe_path_);
check if commenting out anything but constructor bindings for ScenarioPlayer makes any difference by commenting out bindings for all member functions and data members here
As you suggested I removed the extra method and my empty constructor starts working without any memory corruption again! I narrowed down the problematic methods to these two methods :
cl.def("SetParameterValue", (int (ScenarioPlayer::*)(const char *, const void *)) &ScenarioPlayer::SetParameterValue, "C++: ScenarioPlayer::SetParameterValue(const char *, const void *) --> int", pybind11::arg("name"), pybind11::arg("value"));
cl.def("GetParameterValue", (int (ScenarioPlayer::*)(const char *, void *)) &ScenarioPlayer::GetParameterValue, "C++: ScenarioPlayer::GetParameterValue(const char *, void *) --> int", pybind11::arg("name"), pybind11::arg("value"));
This is as far as I could go today.
comment created time in 24 days
push eventRosettaCommons/binder
commit sha 1c98fce9b0f9f2fea810f384d3001d3c8035d3e6
Remove semicolons in module_header to prevent gcc warnings when compiling with -pedantic
commit sha 664499d47a8a96c5a9793337ee405ad61f035c17
Merge pull request #152 from andriish/fix_pedandic_warnings remove semicolons in module_header
push time in 24 days
PR merged RosettaCommons/binder
Hi @lyskov ,
here is a tiny, completely non-urgent pull request.
The idea is to remove semicolons in "module_header" to prevent gcc warnings when compiling with -Wpedantic.
The messages I see look like this:
warning: extra ‘;’ [-Wpedantic]
PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);
^
warning: extra ‘;’ [-Wpedantic]
PYBIND11_DECLARE_HOLDER_TYPE(T, T*);
^
warning: extra ‘;’ [-Wpedantic]
PYBIND11_MAKE_OPAQUE(std::shared_ptr<void>);
^
There are two other warnings:
warning: ISO C++11 requires at least one argument for the "..." in a variadic macro
PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);
^
warning: ISO C++11 requires at least one argument for the "..." in a variadic macro
PYBIND11_DECLARE_HOLDER_TYPE(T, T*);
however these are inside the pybind11
code.
Best regards,
Andrii
pr closed time in 24 days
issue commentRosettaCommons/binder
Issue using generated bindings
@ebadi could you please point me to where source code generated by Binder is located? I found this https://github.com/ebadi/esmini-pybind11/blob/master/src/playerbase/pyplayerbase.cpp but it lack bindings for constructor so i am guessing you might have a newer version?
On issue itself: i looked at the code here https://github.com/ebadi/esmini-pybind11/blob/master/src/playerbase/pyplayerbase.cpp#L28 and everything seems to be in order. I would recommend to investigate the following:
- check if commenting out anything but constructor bindings for ScenarioPlayer makes any difference by commenting out bindings for all member functions and data members here: https://github.com/ebadi/esmini-pybind11/blob/master/src/playerbase/pyplayerbase.cpp#L30
- if above make no difference then check if compiling/linking work as expected by adding dummy struct into you original C++ code (say
struct Dummy {};
) and then running Binder on this code base and trying to importDummy
in python. - if above works then issue have to be in how
ScenarioPlayer
class initiate it members (i see some custom classes in it: https://github.com/ebadi/esmini/commit/6913ab193807ff0fc8004b408938a2e392efa86f#diff-7b24101d5a5cf8ec18012f762c597a8d10d39876a01cf6b40a103a926989addcR109 ). try to create a minimal C++ executable with main function creatingScenarioPlayer
object, - see if that works - if minimal C++ excitable works then propagate this to Pybind11 team
Hope that helps,
comment created time in 24 days
issue commentRosettaCommons/binder
Issue using generated bindings
I created a minimal example and I still get memory corruption errors when I run the this simple test script:
BTW, I dockerized the build process as documented here.
$python3 tests/scenarioplayer.py
malloc(): corrupted top size
Aborted (core dumped)
in gdb :
~/r/esmini-pybind11 (master) [127]> gdb python3
GNU gdb (Ubuntu 9.2-0ubuntu1~20.04) 9.2
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Type "show copying" and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Registered pretty printers for UE4 classes
Reading symbols from python3...
(No debugging symbols found in python3)
(gdb) r tests/scenarioplayer.py
Starting program: /usr/bin/python3 tests/scenarioplayer.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
malloc(): corrupted top size
Program received signal SIGABRT, Aborted.
__GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50
50 ../sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) bt
#0 __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50
#1 0x00007ffff7dd2859 in __GI_abort () at abort.c:79
#2 0x00007ffff7e3d3ee in __libc_message (action=action@entry=do_abort, fmt=fmt@entry=0x7ffff7f67285 "%s\n") at ../sysdeps/posix/libc_fatal.c:155
#3 0x00007ffff7e4547c in malloc_printerr (str=str@entry=0x7ffff7f65556 "malloc(): corrupted top size") at malloc.c:5347
#4 0x00007ffff7e4883a in _int_malloc (av=av@entry=0x7ffff7f98b80 <main_arena>, bytes=bytes@entry=104) at malloc.c:4107
#5 0x00007ffff7e4a2d4 in __GI___libc_malloc (bytes=104) at malloc.c:3058
#6 0x00007ffff512fc29 in operator new(unsigned long) () from /lib/x86_64-linux-gnu/libstdc++.so.6
#7 0x00007ffff6e93694 in ?? () from /home/wave/.local/lib/python3.8/site-packages/pyplayerbase.cpython-38-x86_64-linux-gnu.so
#8 0x00007ffff6ea25ae in ?? () from /home/wave/.local/lib/python3.8/site-packages/pyplayerbase.cpython-38-x86_64-linux-gnu.so
#9 0x00000000005f2fb9 in PyCFunction_Call ()
#10 0x00000000005f3446 in _PyObject_MakeTpCall ()
#11 0x000000000050aa4a in ?? ()
#12 0x00000000005f2b87 in PyObject_Call ()
#13 0x000000000059bc1c in ?? ()
#14 0x00000000005a6867 in ?? ()
#15 0x00007ffff6e9f02d in ?? () from /home/wave/.local/lib/python3.8/site-packages/pyplayerbase.cpython-38-x86_64-linux-gnu.so
#16 0x00000000005f3446 in _PyObject_MakeTpCall ()
#17 0x000000000056f1ca in _PyEval_EvalFrameDefault ()
#18 0x000000000056822a in _PyEval_EvalCodeWithName ()
#19 0x000000000068c1e7 in PyEval_EvalCode ()
#20 0x000000000067d5a1 in ?? ()
#21 0x000000000067d61f in ?? ()
#22 0x000000000067d6db in PyRun_FileExFlags ()
#23 0x000000000067da6e in PyRun_SimpleFileExFlags ()
#24 0x00000000006b6132 in Py_RunMain ()
#25 0x00000000006b64bd in Py_BytesMain ()
#26 0x00007ffff7dd40b3 in __libc_start_main (main=0x4eec80 <main>, argc=2, argv=0x7fffffffdf38, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffdf28)
at ../csu/libc-start.c:308
#27 0x00000000005f927e in _start ()
(gdb)
comment created time in 25 days
PR opened RosettaCommons/binder
Hi @lyskov ,
here is a tiny, completely non-urgent pull request.
The idea is to remove semicolons in "module_header" to prevent gcc warnings when compiling with -Wpedantic.
The messages I see look like this:
warning: extra ‘;’ [-Wpedantic]
PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);
^
warning: extra ‘;’ [-Wpedantic]
PYBIND11_DECLARE_HOLDER_TYPE(T, T*);
^
warning: extra ‘;’ [-Wpedantic]
PYBIND11_MAKE_OPAQUE(std::shared_ptr<void>);
^
There are two other warnings:
warning: ISO C++11 requires at least one argument for the "..." in a variadic macro
PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);
^
warning: ISO C++11 requires at least one argument for the "..." in a variadic macro
PYBIND11_DECLARE_HOLDER_TYPE(T, T*);
however these are inside the pybind11
code.
Best regards,
Andrii
pr created time in a month
issue closedRosettaCommons/binder
Issue using generated bindings
Hi, I successfully generated and compiled binding for the esmini simulator by calling binder like this and using the config/headers file in the src directory. The generated bindings for each module are accessible in the separated directories under ./src.
However, I noticed the following two issues:
Issue 1: Memory Corruption
import pyesminilib
pyesminilib.SE_Init( '/home/[...]/esmini-pybind11/esmini/resources/xosc/lane_change.xosc',1,1,0,0)
From the log message I can see SE_Init function is called with the correct arguments but the binding introduces a memory corruption as below:
esmini GIT REV: 06f0360
esmini GIT TAG:
esmini GIT BRANCH: master
esmini BUILD VERSION: N/A - client build
esminiLib.cpp / 104 / ConvertArguments(): Player arguments: viewer --osc /home/[...]/esmini-pybind11/esmini/resources/xosc/lane_change.xosc --window 60 60 800 400 --disable_controllers
python3: malloc.c:2379: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.
Aborted (core dumped)
Issue 2: Missing methods
I noticed that not all methods are included in the generated bindings. As one example one of the constructor methods (ScenarioPlayer(int &argc, char *argv[])) is missing as can be seen in the generated bindings. (note, it is not only the constructors that are missing. SE_InitWithArgs and many other methods are also missing)
closed time in a month
ebadiissue commentRosettaCommons/binder
Issue using generated bindings
Thanks @lyskov and @eknabevcc Issue 1: I will investigate this further and come back with more details. Issue 2: Right, it makes sense. I only expected to receive a warning message instead of the tool silently skipping/ignoring these methods.
Thanks again, I close this issue for now.
comment created time in a month
push eventRosettaCommons/PyRosetta.notebooks
commit sha 66cb994635ab635c7d5e4a4f3c8aaa9a36306331
fix issue with block.
commit sha 207d46f935fa69aa1272163cc525d6e11e4ac67c
Merge pull request #66 from RosettaCommons/rabd3 Fix RabD issue with block.
push time in a month
PR merged RosettaCommons/PyRosetta.notebooks
pr closed time in a month
PR opened RosettaCommons/PyRosetta.notebooks
pr created time in a month
issue commentRosettaCommons/binder
Issue using generated bindings
Re issue 1: Try initialize esmini without viewer:
pyesminilib.SE_Init( '/home/[...]/esmini-pybind11/esmini/resources/xosc/lane_change.xosc',1,0,0,0)
The viewer is quite complex and it would be interesting to see if the issue is related to it or not - a way to narrow down the scope.
Re issue 2: We've tried to stick with basic C data types to simplify DLL usage. Maybe it would be possible to use C++ std-types as well, but would need some investigation and testing on a few platforms.
comment created time in a month