[WIP] Adding ROOT_jll #9300

peremato · 2024-08-23T15:27:37Z

This is a new attempt to cross-compile ROOT in order to produce ROOT_jll. It starts from #7666
The current status is:

It builds for the host platform (x86_64-linux-musl) 😄 - not tested the produced binaries
It also builds for gnu platform (x86_64-linux-gnu-cxx11) 😄 and creates the tarball
- There are some errors checking the produced shared libraries (although I have disabled dll opening them). For example:

  ERROR in cling::CIFactory::createCI(): cannot extract standard library include paths!
  Invoking:
    LC_ALL=C x86_64-linux-gnu-g++   -xc++ -E -v /dev/null 2>&1 | sed -n -e '/^.include/,${' -e '/^ \/.*++/p' -e '}'
  Results was:
  With exit code 0
  <built-in>:6:9: warning: '__STDC_LIMIT_MACROS' macro redefined [-Wmacro-redefined]
  #define __STDC_LIMIT_MACROS 1
          ^
  /opt/x86_64-linux-musl/bin/../lib/gcc/x86_64-linux-musl/11.1.0/include/stdint.h:5:11: note: previous definition is here
  #  define __STDC_LIMIT_MACROS
            ^
  <built-in>:7:9: warning: '__STDC_CONSTANT_MACROS' macro redefined [-Wmacro-redefined]
  #define __STDC_CONSTANT_MACROS 1
          ^
  /opt/x86_64-linux-musl/bin/../lib/gcc/x86_64-linux-musl/11.1.0/include/stdint.h:7:11: note: previous definition is here
  #  define __STDC_CONSTANT_MACROS
            ^
  input_line_2:6:18: error: exception specification in declaration does not match previous declaration
  extern "C++" int at_quick_exit(void(*f)())  throw ()  { return __cxa_atexit((void(*)(void*))f, 0, __dso_handle); }
                   ^
  /opt/x86_64-linux-musl/x86_64-linux-musl/sys-root/usr/include/stdlib.h:48:5: note: previous declaration is here
  int at_quick_exit (void (*) (void));
      ^
  Replaced symbol at_quick_exit cannot be found in JIT!
  In file included from input_line_3:38:
  In file included from /../lib/gcc/x86_64-redhat-linux/11/../../../../include/c++/11/cassert:44:
  /usr/include/assert.h:37:28: error: function-like macro '__GNUC_PREREQ' is not defined
  #if defined __cplusplus && __GNUC_PREREQ (2,95)

I can start the root executable once deployed 😄. To reproduce:

julia build_tarballs.jl --verbose --debug   x86_64-linux-gnu-cxx11
julia build_tarballs.jl --deploy=local --skip-build  x86_64-linux-gnu-cxx11

What I get is:

 $ julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.11.0-rc2 (2024-07-29)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

(@v1.11) pkg> dev /build/mato_sftnight/.julia/dev/ROOT_jll
   Resolving package versions...
  No Changes to `~/.julia/environments/v1.11/Project.toml`
  No Changes to `~/.julia/environments/v1.11/Manifest.toml`

julia> using ROOT_jll
Precompiling ROOT_jll...
  1 dependency successfully precompiled in 3 seconds. 67 already precompiled.

julia> run(ROOT_jll.root())
ERROR in cling::CIFactory::createCI(): cannot extract standard library include paths!
Invoking:
  LC_ALL=C x86_64-linux-gnu-g++   -xc++ -E -v /dev/null 2>&1 | sed -n -e '/^.include/,${' -e '/^ \/.*++/p' -e '}'
Results was:
With exit code 0
<built-in>:6:9: warning: '__STDC_LIMIT_MACROS' macro redefined [-Wmacro-redefined]
#define __STDC_LIMIT_MACROS 1
        ^
/opt/x86_64-linux-musl/bin/../lib/gcc/x86_64-linux-musl/11.1.0/include/stdint.h:5:11: note: previous definition is here
#  define __STDC_LIMIT_MACROS
          ^
<built-in>:7:9: warning: '__STDC_CONSTANT_MACROS' macro redefined [-Wmacro-redefined]
#define __STDC_CONSTANT_MACROS 1
        ^
/opt/x86_64-linux-musl/bin/../lib/gcc/x86_64-linux-musl/11.1.0/include/stdint.h:7:11: note: previous definition is here
#  define __STDC_CONSTANT_MACROS
          ^
input_line_2:6:18: error: exception specification in declaration does not match previous declaration
extern "C++" int at_quick_exit(void(*f)())  throw ()  { return __cxa_atexit((void(*)(void*))f, 0, __dso_handle); }
                 ^
/opt/x86_64-linux-musl/x86_64-linux-musl/sys-root/usr/include/stdlib.h:48:5: note: previous declaration is here
int at_quick_exit (void (*) (void));
    ^
Replaced symbol at_quick_exit cannot be found in JIT!
In file included from input_line_3:38:
In file included from /../lib/gcc/x86_64-redhat-linux/11/../../../../include/c++/11/cassert:44:
/usr/include/assert.h:37:28: error: function-like macro '__GNUC_PREREQ' is not defined
#if defined __cplusplus && __GNUC_PREREQ (2,95)
                           ^
   ------------------------------------------------------------------
  | Welcome to ROOT 6.32.02                        https://root.cern |
  | (c) 1995-2024, The ROOT Team; conception: R. Brun, F. Rademakers |
  | Built for linuxx8664gcc on Jan 01 1970, 00:00:00                 |
  | From heads/master@tags/v6-32-02                                  |
  | With                                                             |
  | Try '.help'/'.?', '.demo', '.license', '.credits', '.quit'/'.q'  |
   ------------------------------------------------------------------
root [0] .q

I have not managed yet to fully build for MacOS. 😢
- It fails when compiling the generated dictionaries produced by rootcling because I think the generated code is not compilable by clang.
- To reproduce:

julia build_tarballs.jl --verbose --debug   aarch64-apple-darwin-cxx11

The errors are of this form:

[17:24:51] ninja: job failed: /opt/bin/aarch64-apple-darwin20-libgfortran5-cxx11/aarch64-apple-darwin20-clang++ --sysroot=/opt/aarch64-apple-darwin20/aarch64-apple-darwin20/sys-root -DR__ARC4_STDLIB -D_COMPLEX_H -D__CLANG_STDATOMIC_H -D__COMPLEX_H__ -D__STDC_NO_COMPLEX__ -I/workspace/build/include -I/workspace/build/ginclude -I/workspace/srcdir/root-6.32.02/core/base/inc -I/workspace/srcdir/root-6.32.02/core/base/v7/inc -I/workspace/srcdir/root-6.32.02/core/clib/inc -I/workspace/srcdir/root-6.32.02/core/clingutils/inc -I/workspace/srcdir/root-6.32.02/core/clingutils/res -I/workspace/srcdir/root-6.32.02/core/cont/inc -I/workspace/srcdir/root-6.32.02/core/foundation/inc -I/workspace/srcdir/root-6.32.02/core/foundation/v7/inc -I/workspace/srcdir/root-6.32.02/core/foundation/res -I/workspace/srcdir/root-6.32.02/core/gui/inc -I/workspace/srcdir/root-6.32.02/core/meta/inc -I/workspace/srcdir/root-6.32.02/core/rint/inc -I/workspace/srcdir/root-6.32.02/core/textinput/inc -I/workspace/srcdir/root-6.32.02/core/textinput/src -I/workspace/srcdir/root-6.32.02/core/thread/inc -I/workspace/srcdir/root-6.32.02/core/zip/inc -I/workspace/srcdir/root-6.32.02/core/lzma/inc -I/workspace/srcdir/root-6.32.02/core/lz4/inc -I/workspace/srcdir/root-6.32.02/core/zstd/inc -I/workspace/srcdir/root-6.32.02/core/macosx/inc -I/workspace/srcdir/root-6.32.02/core/unix/inc -I/workspace/srcdir/root-6.32.02/core/unix/../clib/res -fcolor-diagnostics -Wc++11-narrowing -Wsign-compare -Wsometimes-uninitialized -Wconditional-uninitialized -Wheader-guard -Warray-bounds -Wcomment -Wtautological-compare -Wstrncat-size -Wloop-analysis -Wbool-conversion -m64 -pipe -W -Wall -Woverloaded-virtual -fsigned-char -fno-common -Qunused-arguments -pthread -stdlib=libc++ -O3 -DNDEBUG -mmacosx-version-min=11.0 -fPIC -std=c++17 -MD -MT core/CMakeFiles/G__Core.dir/G__Core.cxx.o -MF core/CMakeFiles/G__Core.dir/G__Core.cxx.o.d -o core/CMakeFiles/G__Core.dir/G__Core.cxx.o -c /workspace/build/core/G__Core.cxx
[17:24:51] /workspace/build/core/G__Core.cxx:312:81: error: use of undeclared identifier '__gnu_cxx'
[17:24:51]    static TGenericClassInfo *GenerateInitInstanceLocal(const ::reverse_iterator<__gnu_cxx::__normal_iterator<TString*,vector<TString> > >*)
[17:24:51]                                                                                 ^
[17:24:51] /workspace/build/core/G__Core.cxx:312:110: error: 'TString' does not refer to a value
[17:24:51]    static TGenericClassInfo *GenerateInitInstanceLocal(const ::reverse_iterator<__gnu_cxx::__normal_iterator<TString*,vector<TString> > >*)
[17:24:51]                                                                                                              ^
[17:24:51] /workspace/srcdir/root-6.32.02/core/base/inc/TVirtualX.h:43:7: note: declared here
[17:24:51] class TString;
[17:24:51]       ^
[17:24:51] /workspace/build/core/G__Core.cxx:312:118: error: expected expression
[17:24:51]    static TGenericClassInfo *GenerateInitInstanceLocal(const ::reverse_iterator<__gnu_cxx::__normal_iterator<TString*,vector<TString> > >*)
[17:24:51]                                                                                                                      ^
[17:24:51] /workspace/build/core/G__Core.cxx:312:135: error: expected ')'
[17:24:51]    static TGenericClassInfo *GenerateInitInstanceLocal(const ::reverse_iterator<__gnu_cxx::__normal_iterator<TString*,vector<TString> > >*)
[17:24:51]                                                                                                                                       ^
[17:24:51] /workspace/build/core/G__Core.cxx:312:55: note: to match this '('
[17:24:51]    static TGenericClassInfo *GenerateInitInstanceLocal(const ::reverse_iterator<__gnu_cxx::__normal_iterator<TString*,vector<TString> > >*)
[17:24:51]                                                       ^
[17:24:51] /workspace/build/core/G__Core.cxx:314:26: error: use of undeclared identifier '__gnu_cxx'
[17:24:51]       ::reverse_iterator<__gnu_cxx::__normal_iterator<TString*,vector<TString> > > *ptr = nullptr;
[17:24:51]                          ^
[17:24:51] /workspace/build/core/G__Core.cxx:314:55: error: 'TString' does not refer to a value
[17:24:51]       ::reverse_iterator<__gnu_cxx::__normal_iterator<TString*,vector<TString> > > *ptr = nullptr;
[17:24:51]                                                       ^

vgvassilev · 2024-08-23T16:44:19Z

Cling needs to ask the system compiler about the include paths to libstdc++. Do you have a c++ compiler installed?

giordano · 2024-08-23T20:05:50Z

Do you have a c++ compiler installed?

We have both a compiler for the host platform and a cross-compiler for the target one, which one should we use for this?

vgvassilev · 2024-08-23T20:58:24Z

Do you have a c++ compiler installed?

We have both a compiler for the host platform and a cross-compiler for the target one, which one should we use for this?

I believe the one you compile with. It should be the same as the one you will have on the platform you deploy.

peremato · 2024-08-26T09:13:43Z

@giordano what @vgvassilev is referring is to have the used compiler on the [user] system where you install the ROOT_jll package. This is not going to be easy, unless the compiler itself is a _jll package. If there was a way to set the include path to the libstdc++ then we would not need to have the compiler installed, isn't it?
@vgvassilev, for the problem on MacOS, is there a way to tell rootling to generate code that is compilable with clang? In other words, how to tell rootling the target platform?

vgvassilev · 2024-08-26T09:34:26Z

@vgvassilev, for the problem on MacOS, is there a way to tell rootling to generate code that is compilable with clang? In other words, how to tell rootling the target platform?

I suspect that if we are able to point cling to the right compiler, rootcling will just work. Note that ROOT has been developed for many years without cross-compilation in mind and even if it builds it is not necessarily to run. You can see all of the ifdef X in the codebase. I believe that most of them are harmless but there are a few in cling and rootcling that needs to be rewritten asking about the target triple rather then relying on the compiler macro.

giordano · 2024-08-27T20:25:17Z

This is not going to be easy, unless the compiler itself is a _jll package. If there was a way to set the include path to the libstdc++ then we would not need to have the compiler installed, isn't it?

We do have Clang compilers packaged up in JLLs (Clang_jll), but I don't think we ship libcxx (nor libstdc++) anywhere.

grasph · 2024-09-24T10:10:24Z

Hello,

I had a look at the new version of the recipe. For reminder, the recipe was already working for musl, but the package cannot be used due to this issue. So, I will focus on glibc and limit myself to the simplest case of x86_64.

The error about conflicting atexit and at_quick_exit prototypes, when generating the dictionary in the ROOT build process was solved in this new version, by using the host (x86_64/gcc+musl) headers for the c and c++ standard libraries instead of the target ones (x86_64/gcc+glibc). There are differences in the headers from glibc and musl, which I expect are the source of the error. I'm not sure it is correct to use here the host headers, but at least it compiles as Pere reported.

While building works, we have now a similar error when executing ROOT. The execution is done outside the Alpine container, and we have therefore only the glibc headers available. Note that I've solved the error about the compiler not found by creating a link with the expected name, and the at_quick_exit prototype error is still there.

In addition, I get the error IncrementalExecutor::executeFunction: symbol '_ZN5cling7runtime6gClingE' unresolved while linking [cling interface function]! , when entering commands on the ROOT prompt.

For reminder, in absence of --sysroot option for rootcling, we use the environment variable CPLUS_INCLUDE_PATH to for the PATH list that the compiler returns, when executed by rootcling without this option. Nevertheless, it seems not enough. There is some reminiscence of the include path of the host rootcling or root was compiled. @vgvassilev do you have an idea, where it comes from.

Philippe.

vgvassilev · 2024-09-24T10:47:31Z

In addition, I get the error IncrementalExecutor::executeFunction: symbol '_ZN5cling7runtime6gClingE' unresolved while linking [cling interface function]! , when entering commands on the ROOT prompt.

This very likely means for some reason Cling cannot finds its runtime. There is RuntimeUniverse.h which is supposed to be included at start-up time of Cling. Then the symbol should be provided by libCling.so. Can you find that symbol with nm?

grasph · 2024-09-24T11:17:09Z

The gCling symbol is in the libCling.so, but nm shows it without the cling::runtime:: namespace prefix and with the "U" type (undefined). libCling.so from working installation displays the same (no namespace and with U type.

SimeonEhrig · 2024-10-02T10:00:50Z

This is not going to be easy, unless the compiler itself is a _jll package. If there was a way to set the include path to the libstdc++ then we would not need to have the compiler installed, isn't it?

We do have Clang compilers packaged up in JLLs (Clang_jll), but I don't think we ship libcxx (nor libstdc++) anywhere.

I can confirm, that Clang_jll does not ship it's own STL. It use the system STL. In my case it is the libcxx 14.

peremato added 4 commits August 22, 2024 16:07

Merge branch 'ROOT-1'

b618f30

Added more library products

a503434

Build the global PCH

19cf8bf

typo in patch

4231068

peremato mentioned this pull request Aug 23, 2024

[WIP] add ROOT #7666

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Temporary fix for host local prefix to simplify recipe

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[WIP] Adding ROOT_jll #9300

[WIP] Adding ROOT_jll #9300

peremato commented Aug 23, 2024

vgvassilev commented Aug 23, 2024

giordano commented Aug 23, 2024

vgvassilev commented Aug 23, 2024

peremato commented Aug 26, 2024

vgvassilev commented Aug 26, 2024

giordano commented Aug 27, 2024

grasph commented Sep 24, 2024 •

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vgvassilev commented Sep 24, 2024

grasph commented Sep 24, 2024

SimeonEhrig commented Oct 2, 2024

[WIP] Adding ROOT_jll #9300

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[WIP] Adding ROOT_jll #9300

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peremato commented Aug 23, 2024

vgvassilev commented Aug 23, 2024

giordano commented Aug 23, 2024

vgvassilev commented Aug 23, 2024

peremato commented Aug 26, 2024

vgvassilev commented Aug 26, 2024

giordano commented Aug 27, 2024

grasph commented Sep 24, 2024 • edited Loading

vgvassilev commented Sep 24, 2024

grasph commented Sep 24, 2024

SimeonEhrig commented Oct 2, 2024

grasph commented Sep 24, 2024 •

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