Strange error when calling a c function using ccall

General Usage
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1

I need to use code in c++, for which I made a c-style function and use ccall. I also have tried CxxWrap. In both cases, I sometimes got the following lengthy message when calling the c function.

free(): invalid pointer

signal (6): Aborted
in expression starting at none:0
unknown function (ip: 0x7fc4346ed64c)
gsignal at /usr/bin/../lib/libc.so.6 (unknown line)
abort at /usr/bin/../lib/libc.so.6 (unknown line)
unknown function (ip: 0x7fc4346e17ed)
unknown function (ip: 0x7fc4346f73db)
unknown function (ip: 0x7fc4346f922b)
__libc_free at /usr/bin/../lib/libc.so.6 (unknown line)
_ZN4llvm9AAResultsD2Ev at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm20AAResultsWrapperPass13runOnFunctionERNS_8FunctionE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
operator() at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:612
_ZN4llvm3orc14IRCompileLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm3orc31BasicIRLayerMaterializationUnit11materializeESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession26materializeOnCurrentThreadESt10unique_ptrINS0_19MaterializationUnitESt14default_deleteIS3_EES2_INS0_29MaterializationResponsibilityES4_IS7_EE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZNSt17_Function_handlerIFvSt10unique_ptrIN4llvm3orc19MaterializationUnitESt14default_deleteIS3_EES0_INS2_29MaterializationResponsibilityES4_IS7_EEEPSA_E9_M_invokeERKSt9_Any_dataOS6_OS9_ at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession22dispatchOutstandingMUsEv at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession17OL_completeLookupESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EESt10shared_ptrINS0_23AsynchronousSymbolQueryEESt8functionIFvRKNS_8DenseMapIPNS0_8JITDylibENS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISF_EEEENSG_ISD_EENS_6detail12DenseMapPairISD_SI_EEEEEE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm3orc25InProgressFullLookupState8completeESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession19OL_applyQueryPhase1ESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EENS_5ErrorE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS0_10LookupKindERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS8_EENS0_15SymbolLookupSetENS0_11SymbolStateENS_15unique_functionIFvNS_8ExpectedINS_8DenseMapINS0_15SymbolStringPtrENS_18JITEvaluatedSymbolENS_12DenseMapInfoISI_EENS_6detail12DenseMapPairISI_SJ_EEEEEEEEESt8functionIFvRKNSH_IS6_NS_8DenseSetISI_SL_EENSK_IS6_EENSN_IS6_SV_EEEEEE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EERKNS0_15SymbolLookupSetENS0_10LookupKindENS0_11SymbolStateESt8functionIFvRKNS_8DenseMapIS5_NS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISK_EEEENSL_IS5_EENS_6detail12DenseMapPairIS5_SN_EEEEEE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EENS0_15SymbolStringPtrENS0_11SymbolStateE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS_8ArrayRefIPNS0_8JITDylibEEENS0_15SymbolStringPtrENS0_11SymbolStateE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS_8ArrayRefIPNS0_8JITDylibEEENS_9StringRefENS0_11SymbolStateE at /usr/bin/../lib/julia/libLLVM-12jl.so (unknown line)
addModule at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:779
jl_add_to_ee at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:1059
jl_add_to_ee at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:1103
jl_add_to_ee at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:1125 [inlined]
_jl_compile_codeinst at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:154
jl_generate_fptr at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:350
jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1980
jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:2246 [inlined]
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2239 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
#43 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:266
jfptr_YY.43_49069.clone_1 at /usr/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
with_repl_linfo at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:510
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
display at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:259
display at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:271
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
display at ./multimedia.jl:328
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
jl_f__call_latest at /buildworker/worker/package_linux64/build/src/builtins.c:757
#invokelatest#2 at ./essentials.jl:716 [inlined]
invokelatest at ./essentials.jl:714 [inlined]
print_response at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:293
#45 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:277
jfptr_YY.45_47416.clone_1 at /usr/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
with_repl_linfo at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:510
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
print_response at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:275
do_respond at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:846
jfptr_do_respond_47228.clone_1 at /usr/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
jl_f__call_latest at /buildworker/worker/package_linux64/build/src/builtins.c:757
#invokelatest#2 at ./essentials.jl:716 [inlined]
invokelatest at ./essentials.jl:714 [inlined]
run_interface at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/LineEdit.jl:2493
jfptr_run_interface_47761.clone_1 at /usr/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
run_frontend at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:1232
#49 at ./task.jl:429
jfptr_YY.49_47185.clone_1 at /usr/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
start_task at /buildworker/worker/package_linux64/build/src/task.c:877
Allocations: 2465718 (Pool: 2464978; Big: 740); GC: 2
Aborted (core dumped)

and it crashes the julia session.

This error seems to happen randomly, but I notice that if it appears and crashes julia, then it is more likely that it appears again immediately after I restart julia and call the same function.

I think it is related to the library I call, but the library has been tested quite long and we do not have this issue when they are used in c++. Maybe related to the way I compiled it? Anyone has ideas about this issue? Thanks.

2

I think this is an memory-related issue. What I need is passing a julia vector to the C function. Currently, I pass Ptr{myVec} to the C function, which has double * as the corresponding type. I guess this causes some problems at the end. What is the recommended way to pass an data array to a C function?

3

Do you mind sharing a minimal example? The error log is not informative.

Currently, I pass Ptr{myVec} to the C function, which has double * as the corresponding type.

This clearly won’t do, as pointer to a Julia object is not a pointer to its data. Maybe Calling C and Fortran Code · The Julia Language will help.

4

Yes, the julia code is the following

const PATH_TO_LIB = ".../path_to_mylib"
function f_GF(xs::Vector{Float64})
    ccall((:GF, PATH_TO_LIB), Cdouble, (Ptr{Cdouble}, Csize_t), xs, length(xs))
end

The c++ code has the following structure:

myClass globalObj(....); 

extern "C" {

double GF(double *array_in, size_t numElm) {
  std::vector<double> xs(numElm);
  for(int i=0; i<numElm; i++) {
    xs[i]=array_in[i];
  }
  std::complex<double> res = globlaObj.someFunc(...);
  return res;
}

By the way, the manual uses Ptr{} and I just follows. Obviously I didn’t really understand its meaning and how to correctly pass an array to the c/c++ library. What should I do? Thank you.

5

The ccall is fine. I would worry more about possible library clashes. What libraries are your C++ code linked with?

6

The “library” is actually a single-file cpp, which uses boost and a library we developed before. That library is well-tested and used for a while without problems. It uses Eigen.

I tried a stupid solution:

 ccall((:GF8, PATH_TO_LIB), Cdouble, (Cdouble, Cdouble, Cdouble, Cdouble, Cdouble, Cdouble, Cdouble, Cdouble, Cdouble),
          xs[1],xs[2],xs[3],xs[4],xs[5],xs[6],xs[7],xs[8],xs[9]
          )

Instead of a function taking an array, I pass values directly. With this most time I can run the program in REPL, but after that exit() causes

signal (11): Segmentation fault
in expression starting at REPL[2]:1

However, if I run the ccall before I really run the program (which calls the library many times) this issue seems to disappear, and the julia session ends normally. Very strange behavior.

7

You can try to explicitly open your library with Libdl.dlopen and see if any RTLD_* flag makes a difference. Cf. loading pytorch causes invalid pointer crash on free() · Issue #973 · JuliaPy/PyCall.jl · GitHub, which has a vaguely similar failure mode.

8

Changed to 1.8.5, and I got this on exit() when passing Ref{}

corrupted size vs. prev_size

signal (6): Aborted
in expression starting at REPL[3]:1

Is there any reference for those RTLD_*?

9

Those are described in manual pages for dlopen, e.g. dlopen(3) - Linux manual page.

1 Like
10

Thank you. Without those RTLD_* parameters, I have

const lib = Libdl.dlopen(PATH_TO_LIB)
const sym = Libdl.dlsym(lib, :GF)  
function f_GF(xs::Vector{Float64})
    ccall(sym, Cdouble, (Ref{Cdouble}, Csize_t), xs, length(xs))
end

This code seems to work quite well. Sometimes I still got segmentation faults when exit(), but overall it seems usable. I tested it on julia 1.6.7 and 1.8.5. Both gave similar behaviors.

Any explanation for the difference, although I think loading a library explicitly seems more reasonable by itself?

11

The problem is probably within your c++ code, here is an example that won’t error:

// lib.cpp
#include <iostream>
extern "C" {
double GF(double *array, size_t num) {
    for (size_t i = 0; i < num; i++) {
        std::cout << array[i];
    }
    return 1.234;
}
}

# CMakeLists.txt
cmake_minimum_required(VERSION 3.12)
project(ccall-playground)
add_library(lib SHARED lib.cpp)
set_target_properties(lib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS ON)

const lib = "build/Debug/lib.dll"
function GF(array)
    @ccall lib.GF(array::Ptr{Cdouble}, length(array)::Csize_t)::Cdouble
end
GF(Float64[1,2,3])

Also note that writing the wrapper is tedious, so you can use Clang.jl or CBinding.jl.

12

Yeah, I really have no idea what’s wrong. Thanks for providing the code including the cmake setup.