summit anaconda build error #1524
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@zeneofa anaconda prefers their own gcc/g++ compilers: ContinuumIO/anaconda-issues#6619 it's an anaconda issue. Not sure how Summit admins are handling this issue of mixing the system gcc with anaconda packages. Hope it helps. |
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Thanks for the pointer. I was thinking of going down that route, but remember the nightmare associated with multiple different gcc's and lots of broken environments, so I was hesitant at first. Anaconda has since changed the way it handles these anaconda compilers, which I am so happy about. I have managed to get things compiled using the anaconda gxx and gcc compilers in a test conda environment. I am hoping to turn this into a recipe to be able to install this into our groups main conda environment. At the moment running into cmake FindMPI issues. I will also need to test portability, to see if this works without polluting the main environment with the anaconda compilers. |
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@zeneofa thanks for following up and sharing your plans. My experience with anaconda is that it's great for pre-compiled packages from anaconda cloud, but I ran into similar difficulties when building from source and mixing compilers from system environments. Still, we are having a release at the of the month, we are going to put a release into anaconda cloud, potentially conda-forge but not without issues. |
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I'm not sure this is specific to Conda. I'm building using Spack and getting this, regardless of which version of gcc I choose. It's possible Spack cleans the environment such that it's missing something needed. So I also tried building without Spack and see the same thing. I wouldn't call it completely convincing though, b/c I copied the CMake line for how Spack ran CMake. I have my shell environment in that case, but it is verbatim the same CMake call Spack ran, just actually in the shell. |
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Actually mine is a little different. I'm seeing it after bpls has been build (which might be the last thing?). And it doesn't even look like it's building anything when the error happens. It looks like it might be when something is exiting. |
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Hi @suchyta1 you're correct, it's not conda, but environment specific. I don't know how spack or conda resolve conflicts with the python system libraries and environment. adios2 compiles without conda and spack on Summit as reported above. conda and spack add another degree of freedom on top of Summit modules for your environment. Seems |
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(Spack wipes the environment before starting -- at least in principle.) I attached my whole output log. |
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Oh, I think it's my python library step that's failing. I'm building in parallel, so bpls probably finished while the python part is going. Mine is probably b/c I'm using my own version of Python built with Spack, instead of a system one, but IDK. |
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This isn't an ideal solution, but it works if you do a debug build. I think what's going wrong is using |
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Hi @suchyta1 , thanks for digging deeper and narrowing this down. I think we should file a ticket with Summit. In all honesty, I am not aware how much they support conda/spack environments. Still, if it worked for you in the past they probably would be interested in the issue with |
chuckatkins
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Feb 27, 2020
Code extracted from:
https://github.com/pybind/pybind11.git
at commit 80d452484c5409444b0ec19383faa84bb7a4d351 (v2.4.3).
Upstream Shortlog
-----------------
Ahuva Kroizer (1):
8f5b7fce FAQ addition (ornladios#1606)
Alexander Gagarin (2):
0071a3fe Fix async Python functors invoking from multiple C++ threads (ornladios#1587) (ornladios#1595)
b3bf248e Fix casting of time points with non-system-clock duration with VS (ornladios#1748)
Allan Leal (1):
e76dff77 Fix for Issue ornladios#1258 (ornladios#1298)
Andre Schmeißer (1):
19189b4c Make `overload_cast_impl` available in C++11 mode. (ornladios#1581)
Ansgar Burchardt (1):
a22dd2d1 correct stride in matrix example and test
Antony Lee (6):
a303c6fc Remove spurious quote in error message. (ornladios#1202)
0826b3c1 Add spaces around "=" in signature repr.
8fbb5594 Clarify error_already_set documentation.
55dc1319 Clarify docs for functions taking bytes and not str.
58e551cc Properly report exceptions thrown during module initialization.
baf6b990 Silence GCC8's -Wcast-function-type. (ornladios#1396)
Axel Huebl (9):
4b84bad7 Fix Travis GCC 7 Python 3.6.6 (ornladios#1436)
97b20e53 CMake: Remember Python Version (ornladios#1434)
3a94561c Debug Builds: -DPy_DEBUG (ornladios#1438)
435dbdd1 add_module: allow include as SYSTEM (ornladios#1416)
9424d5d2 type_record: Uninit Member (ornladios#1658)
1c627c9e pybind11_getbuffer: useless safe nullptr check (ornladios#1664)
a2cdd0b9 dict_readonly: member init (ornladios#1661)
000aabb2 Test: Numpy Scalar Creation (ornladios#1530)
38f408fc value_and_holder: uninit members (ornladios#1660)
Baljak (1):
81da9888 Fix Intel C++ compiler warning on Windows (ornladios#1608)
Blake Thompson (1):
30c03523 Added __contains__ to stl bindings for maps (ornladios#1767)
Boris Dalstein (2):
b30734ee Fix typo in doc: build-in -> built-in
96be2c15 Fix version mismatch typos in .travis.yml (ornladios#1948)
Boris Staletic (4):
289e5d9c Implement an enum_ property "name"
f4b4e2e9 Use new Doxygen archive URL - fixes Travis
0ca6867e Avoid Visual Studio 2017 15.9.4 ICE
b3f0b4de new sphinx (ornladios#1786)
Borja Zarco (2):
e2b884c3 Use `PyGILState_GetThisThreadState` when using gil_scoped_acquire. (ornladios#1211)
b2fdfd12 Avoid use of lambda to work around a clang bug. (ornladios#1883)
Bruce Merry (2):
1e6172d4 Fix some minor mistakes in comments on struct instance
3b265787 Document using atexit for module destructors on PyPy (ornladios#1169)
Chris Rusby (1):
22859bb8 Support more natural syntax for vector extend
Christoph Kahl (1):
640b8fe6 fix ornladios#1406 add mingw compatibility (ornladios#1851)
Dan (10):
a175b21e Avoid decoding already-decoded strings from cindex.
4612db54 Try to autodetect the location of the clang standard libraries.
b46bb64d Allow user to override default values of -x and -std=.
a33212df Wrap the main functionality of mkdoc in a function.
ede328a7 Allow writing output to file instead of stdout.
a163f881 Delete partially-written file in the event of an error.
590e7ace Avoid storing global state.
2c8c5c4e Split into seperate functions for easier invocation from python.
e0b8bbbc Use a file-local constant for non-prefixing nodes.
41f29ccd Parse command-line args in a separate function.
Darius Arnold (1):
09330b94 Fix typos in documentation (ornladios#1635)
David Caron (1):
307ea6b7 Typo
Davis E. King (1):
9343e68b Fix cmake scripts so projects using CUDA .cu files build correctly. (ornladios#1441)
Dean Moldovan (3):
c10ac6cf Make it possible to generate constexpr signatures in C++11 mode
56613945 Use semi-constexpr signatures on MSVC
0aef6422 Simplify function signature annotation and parsing
Dennis Luxen (1):
221fb1e1 Untangle cast logic to not implicitly require castability (ornladios#1442)
Dmitry (1):
8f5a8ab4 Don't strip debug symbols in RelWithDebInfo mode (ornladios#1892)
Elliott Sales de Andrade (1):
5e7591c6 Update PyPI URLs.
Eric Cousineau (2):
e9ca89f4 numpy: Add test for explicit dtype checks. At present, int64 + uint64 do not exactly match dtype(...).num
4a3464fd numpy: Provide concrete size aliases
Francesco Biscani (1):
ba33b2fc Add -Wdeprecated to test suite and fix associated warnings (ornladios#1191)
François Becker (1):
ce9d6e2c Fixed typo in classes.rst (ornladios#1388)
Guilhem Saurel (2):
e7ef34f2 compatibility with pytest 4.0, fix ornladios#1670
43a39bc7 ignore numpy.ufunc size warnings
Henry Schreiner (10):
04b41f03 Upgrading to Xcode 9 & fix OSX/Py3 build failure
cf0d0f9d Matching Python 2 int behavior on Python 2 (ornladios#1186)
6c62d279 Fix for conda failures on Windows
ffd56ebe Fix pip issues on AppVeyor CI (ornladios#1369)
3789b4f9 Update C++ macros for C++17 and MSVC Z mode (ornladios#1347)
0f404a5d Allow recursive checkout without https (ornladios#1563)
ae951ca0 CI fixes (ornladios#1744)
73b840dc Fix for issue in latest conda (ornladios#1757)
9bb33131 Fixing warnings about conversions in GCC 7+ (ornladios#1753)
047ce8c4 Fix iostream when used with nogil (ornladios#1368)
Ian Bell (1):
502ffe50 Add docs and tests for unary op on class (ornladios#1814)
Igor Socec (1):
a301c5ad Dtype field ordering for NumPy 1.14 (ornladios#1837)
Ivan Smirnov (1):
d1db2ccf Make register_dtype() accept any field containers (ornladios#1225)
Ivor Wanders (1):
2b045757 Improve documentation related to inheritance. (ornladios#1676)
Jamie Snape (1):
a0b8f70d Ensure PythonLibsNew_FOUND is set in FindPythonLibsNew module (ornladios#1373)
Jason Rhinelander (31):
c6a57c10 Fix dtype string leak
d2757d04 Remove superfluous "requires_numpy"
64a99b92 Specify minimum needed cmake version in test suite
1b08df58 Fix `char &` arguments being non-bindable
7672292e Add informative compilation failure for method_adaptor failures
6a81dbbb Fix 2D Nx1/1xN inputs to eigen dense vector args
a582d6c7 Build /permissive- under VS2017
835fa9bc Miscellaneous travis-ci updates/fixes
32ef69ac Qualify `cast_op_type` to help ICC
5c7a290d Fix new flake8 E741 error from using `l` variable
71178922 __qualname__ and nested class naming fixes (ornladios#1171)
086d53e8 Clean up eigen download code (and bump to 3.3.4)
3be401f2 Silence new MSVC C++17 deprecation warnings
48e1f9aa Fix premature destruction of args/kwargs arguments
367d723a Simplify arg copying
b48d4a01 Added py::args ref counting tests
88efb251 Fixes for numpy 1.14.0 compatibility
507da418 Use a named rather than anon struct in instance
326deef2 Fix segfault when reloading interpreter with external modules (ornladios#1092)
adbc8111 Use stricter brace initialization
657a51e8 Remove unnecessary `detail::`
add56ccd MSVC workaround for broken `using detail::_` warning
431fc0e1 Fix numpy dtypes test on big-endian architectures
1ddfacba Fix for Python3 via brew
e88656ab Improve macro type handling for types with commas
9f41c8ea Fix class name in overload failure message
6d0b4708 Reimplement version check and combine init macros
6862cb9b Add workaround for clang 3.3/3.4
e763f046 Base class destructor should be virtual
f7bc18f5 Fix compatibility with catch v2
177713fa Fix gcc-8 compilation warning
Jeff VanOss (3):
05d379a9 fix return from std::map bindings to __delitem__ (ornladios#1229)
01839dce remove duplicate feature from list (ornladios#1476)
77ef03d5 compile time check that properties have no py:arg values (ornladios#1524)
Jeffrey Quesnelle (1):
f93cd0aa PYBIND11_TLS_REPLACE_VALUE should use macro argument value in Python 3.7+ (ornladios#1683)
Jeremy Maitin-Shepard (1):
a3f4a0e8 Add support for __await__, __aiter__, and __anext__ protocols (ornladios#1842)
Josh Kelley (1):
741576dd Update documentation for initialize_interpreter (ornladios#1584)
Justin Bassett (1):
2cbafb05 fix detail::pythonbuf::overflow()'s return value to return not_eof(c) (ornladios#1479)
Jörg Kreuzberger (1):
69dc380c ornladios#1208 Handle forced unwind exception (e.g. during pthread termination)
Karl Haubenwallner (1):
e9d6e879 Added a debug flag to the PYBIND11_INTERNALS_VERSION (ornladios#1549)
Khachajantc Michael (1):
e3cb2a67 Use std::addressof to obtain holder address instead of operator&
Krzysztof Fornalczyk (1):
5c8746ff check for already existing enum value added; added test (ornladios#1453)
Lori A. Burns (3):
bdbe8d0b Enforces intel icpc >= 2017, fixes ornladios#1121 (ornladios#1363)
868d94fc Apply c++ standard flag only to files of CXX language. (ornladios#1678)
f6c4c104 restores __invert__ to arithmetic-enabled enum, fixes ornladios#1907 (ornladios#1909)
Maciek Starzyk (1):
9b028562 Update PyPI URLs
Manuel Schneider (1):
492da592 another typo (ornladios#1675)
Marc Schlaich (1):
ab003dbd Correct VS version in FAQ
Matthias Geier (1):
7bb1da96 fix copy-paste error: non-const -> const
Michael Goulding (1):
77374a7e VS 15.8.0 Preview 4.0 has a bug with alias templates (ornladios#1462)
Michał Wawrzyniec Urbańczyk (1):
978d439e Add PYBIND11_ prefix to the THROW macro to prevent name collisions. (ornladios#1578)
Naotoshi Seo (1):
5ef1af13 Fix SEGV to create empty shaped numpy array (ornladios#1371)
Nathan (1):
9b3fb053 Allow Windows.h min/max to coexist with pybind11 (ornladios#1847)
Omar Awile (2):
ac6cb91a Fixed small typo (ornladios#1633)
95f750a8 Add optional buffer size to pythonbuf::d_buffer constructor (ornladios#1687)
Patrik Huber (1):
41a4fd8a Fix missing word typo
Pauli Virtanen (1):
c9d32a81 numpy: fix refcount leak to dtype singleton (ornladios#1860)
Roland Dreier (2):
7a24bcf1 Fix malformed reST (ornladios#1802)
1aa8dd17 Fix assertion failure for unions (ornladios#1685) (ornladios#1709)
Rune Paamand (2):
73634b6d Update iostream.h: Changed a local varname 'self' to 'self_' (ornladios#1535)
06d021b6 Issue ornladios#1532: Incompatible config options, /MP vs /Gm for MSVC in DEBUG (ornladios#1533)
Ryota Suzuki (1):
1377fbf7 Fix unintentional escaping of character on Windows (ornladios#1574) (ornladios#1575)
Samuel Debionne (2):
87fa6a43 Detect whether we are running in a Conda environment and adjust get_include() (ornladios#1877)
6ca312b3 Avoid infinite recursion in is_copy_constructible (ornladios#1910)
Saran Tunyasuvunakool (2):
b60fd233 Make sure `detail::get_internals` acquires the GIL before making Python calls. (ornladios#1836)
bdf1a2cc In internals.h, only look at _DEBUG when compiling with MSVC. (ornladios#1855)
Semen Yesylevskyy (1):
ef13fb2e Info about inconsistent detection of Python version between pybind11 … (ornladios#1093)
Sergei Izmailov (3):
979d75de doc: Add note about casting from `None` to `T*` (ornladios#1760)
09f08294 Avoid conversion to `int_` rhs argument of enum eq/ne (ornladios#1912)
6cb584e9 Adapt to python3.8 C API change (ornladios#1950)
Sergei Lebedev (2):
08b0bda4 Added set::contains and generalized dict::contains (ornladios#1884)
046267c6 Added .empty() to all collection types (ornladios#1887)
Stephen Larew (1):
5b4751af Add const to buffer:request() (ornladios#1890)
Steven Johnson (1):
4ddf7c40 Add missing includes for better Bazel compatibility (ornladios#1255)
Tarcísio Fischer (1):
54eb8193 Fix scoped enums comparison for equal/not equal cases (ornladios#1339) (ornladios#1571)
Ted Drain (1):
0a0758ce Added write only property functions for issue ornladios#1142 (ornladios#1144)
Thomas Hrabe (1):
534b756c Minor documentation clarification in numpy.rst (ornladios#1356)
Thomas Peters (1):
dffe869d quiet clang warning by adding default move ctor (ornladios#1821)
Tom de Geus (1):
a7ff616d Simplified example allowing more robust usage, fixed minor spelling issues
Tomas Babej (1):
01fada76 Minor typo
Toru Niina (1):
74d335a5 Replace a usage of C++14 language features with C++11 code (ornladios#1833)
Trevor Laughlin (1):
63c2a972 Enable unique_ptr holder with mixed Deleters between base and derived types (ornladios#1353)
Unknown (1):
0b3f44eb Trivial typos
Vladimír Vondruš (2):
5b0ea77c Fix -Wmissing-prototypes warning on Clang. (ornladios#1863)
04c8f4b5 Expose BufferError among other pybind11 exceptions. (ornladios#1852)
Wenzel Jakob (51):
f94d7598 updated changelog for v2.2.1 release
6d19036c support docstrings in enum::value() (ornladios#1160)
e7d304fb added citation reference (fixes ornladios#767) (ornladios#1189)
15e0e445 Moved section on licensing of contributions (fixes ornladios#1109) (ornladios#1188)
ff6bd092 Fix pybind11 interoperability with Clang trunk (ornladios#1269)
2d0507db added v2.2.2 changelog
060936fe Detect pybind11 header path without depending on pip internals (fixes ornladios#1174) (ornladios#1190)
ed670055 Minor fix for MSVC warning CS4459 (ornladios#1374)
f5f66189 updated changelog for v2.2.3
cbd16a82 stl.h: propagate return value policies to type-specific casters (ornladios#1455)
d4b37a28 added py::ellipsis() method for slicing of multidimensional NumPy arrays
885b5b90 Eigen test suite: don't create a np.matrix
e0f3a766 Fixed flake8 error in test_iostream.py
44e39e0d fix regression reported by @cyfdecyf in ornladios#1454 (ornladios#1517)
35c82c72 changelog for version 2.2.4 & features targeted for 2.3.0
06710020 object_api: support the number protocol
b4b22924 relax operator[] for tuples, lists, and sequences
f4245181 enum_: move most functionality to a non-template implementation
c8e9f3cc quench __setstate__ warnings (fixes ornladios#1522)
c9b8933e flake8 fix
9f73060c std::array<> caster: support arbitrary sequences (ornladios#1602)
adc2cdd5 fixed regression in STL type caster RVPs (fixes ornladios#1561) (ornladios#1603)
e2eca4f8 Support C++17 aligned new statement (ornladios#1582)
cea42467 fix py::cast<void *> (ornladios#1605)
64205140 added std::deque to overview.rst
d1f64fa9 AppVeyor: quench pip deprecation warnings for v2.7
ccbe68b0 added binding delattr() -> PyObject_DelAttr analogous to hasattr()
25abf7ef flake8 fixes
e11e71d8 Make compiler flags for -Werror specific to GNU, Clang, or Intel
51ca6b08 Update docs on std::out_of_range exception mapping (ornladios#1254)
cf36e3d9 updated changelog
64f2a5f8 begin work on v2.3.1
ed39c504 README.md: added several folks who've made repeated contributions
a1b71df1 fix issue ornladios#1804 (warning about redefined macros)
8b90b1da error_already_set: acquire GIL one line earlier (fixes ornladios#1779)
9fd47121 fix test suite (pytest changes in ExceptionInfo class)
b2c4ff60 renamed local gil_scoped_acquire to gil_scoped_acquire_local to avoid ambiguity
c9f5a464 pybind11 internals: separate different compilers
00a0aa99 v2.4.0 release
e825205a begin working on v2.4.1
21d0eb46 Fix Python 3.8 test regression
5fd187eb minor changelog cleanup
31680e6f Implicit conversion from enum to int for Python 3.8 (fix by @sizmailov)
e44fcc3c v2.4.1 release
82cf7935 begin working on next version
f3109d84 future-proof Python version check from commit 31680e6 (@lgritz)
7f5dad7d Remove usage of C++14 constructs (fixes ornladios#1929)
7ec2ddfc v2.4.2 release
2abd7e1e updated release.rst to remove parts that are now automated
34c2281e begin working on next version
80d45248 v2.4.3 release
Yannick Jadoul (4):
b4719a60 Switching deprecated Thread Local Storage (TLS) usage in Python 3.7 to Thread Specific Storage (TSS) (ornladios#1454)
085a2943 Increasing timeout in test_gil_scoped.py to get AppVeyor to succeed
97784dad [BUGFIX] Fixing pybind11::error_already_set.matches to also work with exception subclasses (ornladios#1715)
d23c821b Make static member functions, added with `def_static`, `staticmethod` descriptor instances (ornladios#1732)
Zach DeVito (1):
03874e37 Fix leak in var arg handling
ali-beep (1):
5ef13eb6 Add negative indexing support to stl_bind. (ornladios#1882)
cdyson37 (1):
111b25b2 Mention flake8 and check-style.sh in CONTRIBUTING (ornladios#1567)
kingofpayne (1):
12e8774b Added support for list insertion. (ornladios#1888)
luz.paz (2):
28cb6764 misc. typos
13c08072 Typo
luzpaz (2):
4b874616 Misc. typos (ornladios#1384)
21bf16f5 misc. comment typo (ornladios#1629)
martinRenou (1):
35045eee Add getters for exception type, value and traceback (ornladios#1641)
nstelzen (1):
c2514340 Added note in documentation regarding make install (ornladios#1801)
oremanj (2):
fd9bc8f5 Add basic support for tag-based static polymorphism (ornladios#1326)
e7761e33 Fix potential crash when calling an overloaded function (ornladios#1327)
phil-zxx (1):
c6b699d9 Added ability to convert from datetime.date to system_clock::time_point (ornladios#1848)
sizmailov (1):
21c3911b add signed overload for `py::slice::compute`
voxmea (1):
17983e74 Adds type_caster support for std::deque. (ornladios#1609)
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Google brought me here. When compiling our app (WarpX) on Summit with the default GCC 6.4.0 module I also get an ICE when using LTO. This could be a GCC bug on power... |
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Filed as https://gcc.gnu.org/bugzilla/show_bug.cgi?id=96343. If anyone finds a small reproducer then please share :) |
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@ax3l, Closing this as very old and since it was filed with gcc and rejected there I think it wasn't an ADIOS problem. |
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Hi,
I am having problems trying to build adios2 on summit, using the anaconda environment. I seems that the adios2.cpython-36m-powerpc64le-linux-gnu.so file is not created all. I am building from the github master branch
The modules that I have loaded:
I use the following command to build
After this I run
which then errors with:
I have loaded the output logs on gist here: https://gist.github.com/zeneofa/9c6d8ccb102a8c21f45032dfce29846a
This seems to be anaconda specific, as when I use the standard python module I do not get the lto error.
This is independent of python version, using the anaconda 3.7 version also fails.
Any help would be much appreciated. Thanks in advance.
P
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