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ARM-64 / OS-64 issues #20

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allyssonallan opened this issue Jan 12, 2024 · 3 comments
Closed

ARM-64 / OS-64 issues #20

allyssonallan opened this issue Jan 12, 2024 · 3 comments

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@allyssonallan
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allyssonallan commented Jan 12, 2024 •
edited
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Hey Gabriel,

Thanks for your support as always (considering other issues here). I had a same problem from this grenaud/deML#12

I tried a workaround using the osx-64 conda side, unfortunately without success.

conda config --env --set subdir osx-64

Then, I tried to experiment Docker and it worked perfectly inside the dev container:

uname -a
Linux 435bf23243e8 6.5.11-linuxkit #1 SMP PREEMPT Wed Dec  6 17:08:31 UTC 2023 aarch64 GNU/Linux

The src/deamSim smoothly worked in this stake. I hope you consider some advice in the readme to use linux-based Docker for the unwary mac voyagers.

Happy new year! And keep forward, your work is awesome!

Cheers from Brazil,
All

setup:

uname -a
Darwin AllyssonM2pro.local 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:55:06 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6020 arm64

Error:

make
cd bamtools/ && mkdir -p build/  && cd build/ && if cmake ..; then echo ""; else if cmake3 ..; then echo ""; else echo "cmake failed, please install cmake v3"; fi  fi  && make
Found system JsonCpp, not using bundled version
-- Configuring done (0.1s)
-- Generating done (0.1s)
-- Build files have been written to: gargammel/bamtools

[ 66%] Built target BamTools
[ 74%] Built target BamTools-utils
[100%] Built target bamtools_cmd
cp bamtools/build/src/api/bamtools_api_export.h bamtools/src/api && cd ../.. 
make -C libgab
Makefile:72: warning: overriding commands for target `-'
Makefile:68: warning: ignoring old commands for target `-'
bamtools found
Makefile:72: warning: overriding commands for target `-'
Makefile:68: warning: ignoring old commands for target `-'
c++ -Wall  -lm -O3 -I. -Igzstream/ -Igargammel/bamtools/src/ -I/gargammel/bamtools/src/  -c ReconsReferenceBAM.cpp -o ReconsReferenceBAM.o
clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument]
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:281:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy_move_common.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/iterator_operations.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/iter_swap.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__utility/swap.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_nothrow_move_constructible.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/is_nothrow_constructible.h:17:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:41:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:281:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy_move_common.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/iterator_operations.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/ranges_iterator_concept.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/concepts.h:31:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/iter_move.h:15:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:429:13: error: reference to unresolved using declaration
    typedef ptrdiff_t difference_type;
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:281:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy_move_common.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/iterator_operations.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/ranges_iterator_concept.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/concepts.h:34:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/pointer_traits.h:67:29: error: reference to unresolved using declaration
    typedef _LIBCPP_NODEBUG ptrdiff_t type;
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:281:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy_move_common.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/iterator_operations.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/ranges_iterator_concept.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/concepts.h:34:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/pointer_traits.h:141:13: error: reference to unresolved using declaration
    typedef ptrdiff_t difference_type;
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:281:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy_move_common.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/iterator_operations.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/advance.h:27:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/limits:117:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:281:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/copy_move_common.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/iterator_operations.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/advance.h:27:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/limits:827:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:539:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:290:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/construct_at.h:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/new:97:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:92:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:290:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/construct_at.h:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/new:98:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:300:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/reverse_iterator.h:23:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/iterator.h:22:56: error: reference to unresolved using declaration
template<class _Category, class _Tp, class _Distance = ptrdiff_t,
                                                       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:307:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:19:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/stdexcept:48:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iosfwd:101:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:307:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/tuple:254:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:307:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/tuple:259:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/compare:145:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__compare/compare_partial_order_fallback.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__compare/partial_order.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__compare/weak_order.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__compare/strong_order.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:315:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:307:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/tuple:259:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/compare:157:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:307:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/tuple:1860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/utility:260:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:308:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__split_buffer:21:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:96:13: error: reference to unresolved using declaration
    typedef ptrdiff_t   difference_type;
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:308:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__split_buffer:21:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:185:13: error: reference to unresolved using declaration
    typedef ptrdiff_t   difference_type;
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:322:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:3359:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:1711:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:3359:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:1747:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/inplace_merge.h:27:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/temporary_buffer.h:27:12: error: reference to unresolved using declaration
pair<_Tp*, ptrdiff_t>
           ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [ReconsReferenceBAM.o] Error 1
make[1]: *** [gargammel/bamtools/src/-/gargammel/bamtools/src] Error 2
make: *** [libgab/libgab.a] Error 2
@grenaud
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grenaud commented Jan 12, 2024

dear Allysson, Unfortunately, I do not have a mac and cannot replicate this and debug, can you have access to a server running Linux?

@allyssonallan
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Hey Gabriel, Thanks for your support. It perfectly worked in Linux inside the docker. Maybe some clang incompatibility due to the new ARM-64 architecture.

@grenaud
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grenaud commented Jan 16, 2024

ok my apologies if I do not have a mac to fix this issue.

@grenaud grenaud closed this as completed Jan 16, 2024
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