Problem with Root (on biodynamo-v1.05.3) following update on macOS 12.6.1

After running a routine update on my macOS Monterey system, I stumbled upon an error running my compiled BioDynaMo code version. Therefore, I had to recompile BioDynaMo (make, make install) once again. The compilation (and local installation) went smooth, as well as the compilation of my code (that uses of course BioDynaMo). Unfortunately, when trying to run the executable I received a fatal error on my terminal :frowning: and the execution cannot run!
Without being sure what’s wrong, first look tells that there is an issue with ROOT. Any advice what to do to overcome this? Pasting below the error message shown on my terminal (I’m sorry it’s that long).
Thanks in advance.
cheers,
V

=============================================
…/…/build/./invitro_neuro input.csv 1234

Project “invitro_neuro” started… [ …/…/build/./invitro_neuro input.csv 1234]
mkdir: results: File exists
mkdir: results/in: File exists
Parameter read complete…
[input file: input.csv; 2 biochemicals; 2 cell phenotypes]
input_line_1:1:2: error: module ‘Darwin’ uses additional module map ‘/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/darwin_posix_pthread.modulemap’ used when the module was built
#include
^
input_line_1:1:2: note: imported by module ‘std’ in ‘/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/std.pcm’
Warning in cling::IncrementalParser::CheckABICompatibility():
Failed to extract C++ standard library version.
Warning in cling::IncrementalParser::CheckABICompatibility():
Possible C++ standard library mismatch, compiled with _LIBCPP_ABI_VERSION ‘1’
Extraction of runtime standard library version was: ‘’
input_line_2:1:2: fatal error: module file ‘/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/std.pcm’ is out of date and needs to be rebuilt
#include “cling/Interpreter/RuntimeUniverse.h”
^
input_line_2:1:2: note: imported by module ‘Cling_Runtime_Extra’ in ‘/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/Cling_Runtime_Extra.pcm’
input_line_2:1:2: note: imported by module ‘Cling_Runtime’ in ‘/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/Cling_Runtime.pcm’
Replaced symbol atexit cannot be found in JIT!
Replaced symbol at_quick_exit cannot be found in JIT!
<<< cling interactive line includer >>>: fatal error: module file ‘/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/Darwin.pcm’ is out of date and needs to be rebuilt
Failed to load module Darwin
Failed to load module std
Failed to load module _Builtin_intrinsics
Failed to load module ROOT_Foundation_C
Failed to load module ROOT_Config
Failed to load module ROOT_Rtypes
Failed to load module ROOT_Foundation_Stage1_NoRTTI
Failed to load module Core
Failed to load module Rint
Failed to load module RIO
Failed to load module MathCore
Failed to load module Hist
Failed to load module Darwin
Failed to load module Unfold
Failed to load module Imt
Failed to load module HistPainter
Failed to load module PyMVA
Failed to load module RHTTPSniff
Failed to load module RHTTP
Failed to load module FitPanel
Failed to load module ROOTVecOps
Failed to load module ProofDraw
Failed to load module Quadp
Failed to load module ROOT_Foundation_Stage1_NoRTTI
Failed to load module GeomPainter
Failed to load module Genetic
Failed to load module Eve
Failed to load module TreeViewer
Failed to load module Physics
Failed to load module EG
Failed to load module Tree
Failed to load module HistFactory
Failed to load module Spectrum
Failed to load module Matrix
Failed to load module Html
Failed to load module Hist
Failed to load module GuiHtml
Failed to load module _Builtin_intrinsics
Failed to load module Gpad
Failed to load module TMVAGui
Failed to load module Fumili
Failed to load module Net
Failed to load module RGL
Failed to load module Geom
Failed to load module Postscript
Failed to load module GCocoa
Failed to load module RCsg
Failed to load module Cling_Runtime
Failed to load module SPlot
Failed to load module RooFit
Failed to load module GeomBuilder
Failed to load module ROOT_Config
Failed to load module RooFitMore
Failed to load module Rint
Failed to load module XMLParser
Failed to load module MultiProc
Failed to load module RooStats
Failed to load module Proof
Failed to load module RooFitRDataFrameHelpers
Failed to load module Ged
Failed to load module Recorder
Failed to load module FFTW
Failed to load module GuiBld
Failed to load module RooFitCore
Failed to load module Gui
Failed to load module SQLIO
Failed to load module XMLIO
Failed to load module ROOT_Rtypes
Failed to load module std
Failed to load module RIO
Failed to load module ProofPlayer
Failed to load module ROOTTMVASofie
Failed to load module ASImage
Failed to load module ROOT_Foundation_C
Failed to load module MathMore
Failed to load module Foam
Failed to load module RSQLite
Failed to load module SpectrumPainter
Failed to load module Minuit2
Failed to load module Core
Failed to load module MLP
Failed to load module ROOTDataFrame
Failed to load module GenVector
Failed to load module NetxNG
Failed to load module Minuit
Failed to load module RootAuth
Failed to load module Graf3d
Failed to load module TMVA
Failed to load module ASImageGui
Failed to load module Graf
Failed to load module Gdml
Failed to load module ProofBench
Failed to load module Cling_Runtime_Extra
Failed to load module MathCore
Failed to load module Gviz3d
Failed to load module ROOTTPython
Failed to load module TreePlayer
Failed to load module Smatrix
Failed to load module SessionViewer
Failed to load module Thread

*** Break *** segmentation violation
[/usr/lib/system/libsystem_platform.dylib] _sigtramp (no debug info)
[] (no debug info)
[/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/libCling.so] ROOT::TMetaUtils::TNormalizedCtxtImpl::TNormalizedCtxtImpl(cling::LookupHelper const&) (no debug info)
[/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/libCling.so] ROOT::TMetaUtils::TNormalizedCtxt::TNormalizedCtxt(cling::LookupHelper const&) (no debug info)
[/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/libCling.so] TCling::TCling(char const*, char const*, char const* const*) (no debug info)
[/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/libCling.so] CreateInterpreter (no debug info)
[/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/libCore.so] TROOT::InitInterpreter() (no debug info)
[/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/libCore.so] ROOT::Internal::GetROOT2() (no debug info)
[/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/libCore.so] TDirectory::~TDirectory() (no debug info)
[/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/third_party/root/lib/libCore.so] TROOT::~TROOT() (no debug info)
[/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/lib/libbiodynamo.dylib] bdm::Simulation::Initialize(bdm::CommandLineOptions*, std::__1::function<void (bdm::Param*)> const&, std::__1::vector<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > > > const&) /Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo/src/core/simulation.cc:316
[/Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo-v1.05.3/lib/libbiodynamo.dylib] bdm::Simulation::Simulation(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::function<void (bdm::Param*)> const&, std::__1::vector<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > > > const&) /Users/vasvav/Work/Bitbucket/invitro_neuro/libs/biodynamo/src/core/simulation.cc:0
[/Users/vasvav/Work/Bitbucket/invitro_neuro/build/libinvitro_neuro.dylib] invitro_neuro(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, int) /Users/vasvav/Work/Bitbucket/invitro_neuro/src/invitro_neuro.h:2907
[/Users/vasvav/Work/Bitbucket/invitro_neuro/build/libinvitro_neuro.dylib] main /Users/vasvav/Work/Bitbucket/invitro_neuro/src/invitro_neuro.cc:49
[/usr/lib/dyld] start (no debug info)
make: *** [run] Error 139

Hi Vas,

I saw it too last night after a fresh install of BioDynaMo. I’m quite sure that it’s due to the new Xcode and compilers released a few days ago. I assumed you upgraded to the new Xcode, right? Alas it seem independent from the macOS version as you are still on 12 and I’m already on 13.

Cheers, Fons.

Hi Fons,
Maybe I checked in for the update on Xcode’s compilers (hence the issue) - usually I am very hesitant upgrading the OS so as to avoid any issues with numerical libraries/platforms, e.g. BioDynaMo.
Ok, I will upgrade to macOS13 now and check again if BioDynaMo compiles successfully :slight_smile: hope it does.
cheers,
Vas