Undefined reference to function while compiling .c and .cpp files.

[arteevraina]

After this PR got merged in the main branch. I tried to compile stdlib using new build of fpm. I was still getting the same error

test/hash_functions/test_hash_functions.f90 which is giving me this error :
undefined reference to generate_all_c_hash

This issue is not just limited to .cpp files, but .c files also show the same error while compiling. To test that out, I have created a modified version of with_c example for testing. You can check this out here.

FPM VERSION : I am running the executable fpm version of the current main branch.

Logs for Reproducible Example

(env) arteev@pavilion:~/reproducible-example$ fpm build
c_code.c                               done.
with_c.f90                             done.
libwith_c.a                            done.
main.f90                               done.
with_c                                 failed.
[100%] Compiling...
/usr/bin/ld: build/gfortran_2A42023B310FA28D/with_c/libwith_c.a(src_with_c.f90.o): in function `__with_c_MOD_system_isdir':
/home/arteev/reproducible-example/./src/with_c.f90:22: undefined reference to `my_isdir'
collect2: error: ld returned 1 exit status
<ERROR> Compilation failed for object " with_c "
<ERROR>stopping due to failed compilation
STOP 1

Show Model for Reproducible Example

(env) arteev@pavilion:~/reproducible-example$ fpm build --show-model|sed "s/,/,\n/g" -
 fpm_model_t(package_name="with_c",
 packages=[package_t(name="with_c",
 sources=[srcfile_t(file_name="app/c_code.c",
 exe_name="",
 unit_scope=FPM_SCOPE_APP,
 modules_provided=[],
 parent_modules=[],
 unit_type=FPM_UNIT_CSOURCE,
 modules_used=[],
 include_dependencies=[],
 link_libraries=[],
 digest=-4855192256658658792),
 srcfile_t(file_name="app/main.f90",
 exe_name="with_c",
 unit_scope=FPM_SCOPE_APP,
 modules_provided=[],
 parent_modules=[],
 unit_type=FPM_UNIT_PROGRAM,
 modules_used=["with_c"],
 include_dependencies=[],
 link_libraries=[],
 digest=9186979595472880402),
 srcfile_t(file_name="./src/with_c.f90",
 exe_name="",
 unit_scope=FPM_SCOPE_LIB,
 modules_provided=["with_c"],
 parent_modules=[],
 unit_type=FPM_UNIT_MODULE,
 modules_used=[],
 include_dependencies=[],
 link_libraries=[],
 digest=6240126590444891773)])],
 compiler=(fc="gfortran",
 cc="gcc"),
 archiver=(ar="ar -rs "),
 fortran_compile_flags=" -Wall -Wextra -Wimplicit-interface -fPIC -fmax-errors=1 -g -fcheck=bounds -fcheck=array-temps -fbacktrace -fcoarray=single",
 c_compile_flags="",
 cxx_compile_flags="",
 link_flags="",
 build_prefix="build/gfortran",
 link_libraries=[],
 external_modules=[],
 deps=dependency_tree_t(...))

cc: @awvwgk @LKedward @jvdp1 @zoziha

[arteevraina]

@awvwgk I remember in yesterday's meeting, we moved .c and .cpp files out of the src directory to either app directory or test directory (as we can see in reproducible example). Does that mean they are working fine in src directory and we have to fix it for app and test directory only ?

[jvdp1]

Does that mean they are working fine in src directory and we have to fix it for app and test directory only ?

Yes, it works fine when the .c file is in the src directory.
Note that the same case with Fortran files only works fine.

[arteevraina]

When I try to compile the reproducible project with with_c.f90 & c_code.c file in src directory and run fpm build --verbose, the log which shows archive being generated has two object files in command src_c_code.c.o & src_with_c.f90.o, but on the other hand if I try to compile reproducible example as it is. I can only see only one object file src_with_c.f90.o in command line. I think this might also be one of the reasons for linker issue ?

Logs when with_c.f90 && c_code.c are in src directory

 <INFO> BUILD_NAME: build/gfortran
 <INFO> COMPILER:  gfortran
 <INFO> C COMPILER:  gcc
 <INFO> CXX COMPILER: g++
 <INFO> COMPILER OPTIONS:   -Wall -Wextra -Wimplicit-interface -fPIC -fmax-errors=1 -g -fcheck=bounds -fcheck=array-temps -fbacktrace -fcoarray=single
 <INFO> C COMPILER OPTIONS:  
 <INFO> CXX COMPILER OPTIONS: 
 <INFO> LINKER OPTIONS:  
 <INFO> INCLUDE DIRECTORIES:  []
 + mkdir -p build/gfortran_2A42023B310FA28D
 + mkdir -p build/gfortran_00000000811C9DC5
[  0%]                       c_code.c
 + mkdir -p build/gfortran_00000000811C9DC5/with_c/
 + gcc -c ./src/c_code.c  -o build/gfortran_00000000811C9DC5/with_c/src_c_code.c.o
[ 20%]                       c_code.c  done.
[ 20%]                     with_c.f90
 + mkdir -p build/gfortran_2A42023B310FA28D/with_c/
 + gfortran -c ./src/with_c.f90  -Wall -Wextra -Wimplicit-interface -fPIC -fmax-errors=1 -g -fcheck=bounds -fcheck=array-temps -fbacktrace -fcoarray=single -J build/gfortran_2A42023B310FA28D -Ibuild/gfortran_2A42023B310FA28D -o build/gfortran_2A42023B310FA28D/with_c/src_with_c.f90.o
[ 40%]                     with_c.f90  done.
[ 40%]                    libwith_c.a
 + ar -rs build/gfortran_2A42023B310FA28D/with_c/libwith_c.a build/gfortran_00000000811C9DC5/with_c/src_c_code.c.o build/gfortran_2A42023B310FA28D/with_c/src_with_c.f90.o
ar: creating build/gfortran_2A42023B310FA28D/with_c/libwith_c.a
[ 60%]                    libwith_c.a  done.
[ 60%]                       main.f90
 + gfortran -c app/main.f90  -Wall -Wextra -Wimplicit-interface -fPIC -fmax-errors=1 -g -fcheck=bounds -fcheck=array-temps -fbacktrace -fcoarray=single -J build/gfortran_2A42023B310FA28D -Ibuild/gfortran_2A42023B310FA28D -o build/gfortran_2A42023B310FA28D/with_c/app_main.f90.o
[ 80%]                       main.f90  done.
[ 80%]                         with_c
 + mkdir -p build/gfortran_2A42023B310FA28D/app/
 + gfortran  -Wall -Wextra -Wimplicit-interface -fPIC -fmax-errors=1 -g -fcheck=bounds -fcheck=array-temps -fbacktrace -fcoarray=single  build/gfortran_2A42023B310FA28D/with_c/app_main.f90.o build/gfortran_2A42023B310FA28D/with_c/libwith_c.a -o build/gfortran_2A42023B310FA28D/app/with_c
[100%]                         with_c  don

Logs when we run reproducible example as it is.

 <INFO> BUILD_NAME: build/gfortran
 <INFO> COMPILER:  gfortran
 <INFO> C COMPILER:  gcc
 <INFO> CXX COMPILER: g++
 <INFO> COMPILER OPTIONS:   -Wall -Wextra -Wimplicit-interface -fPIC -fmax-errors=1 -g -fcheck=bounds -fcheck=array-temps -fbacktrace -fcoarray=single
 <INFO> C COMPILER OPTIONS:  
 <INFO> CXX COMPILER OPTIONS: 
 <INFO> LINKER OPTIONS:  
 <INFO> INCLUDE DIRECTORIES:  []
 + mkdir -p build/gfortran_2A42023B310FA28D
 + mkdir -p build/gfortran_00000000811C9DC5
[  0%]                       c_code.c
 + mkdir -p build/gfortran_00000000811C9DC5/with_c/
 + gcc -c app/c_code.c  -o build/gfortran_00000000811C9DC5/with_c/app_c_code.c.o
[ 20%]                       c_code.c  done.
[ 20%]                     with_c.f90
 + mkdir -p build/gfortran_2A42023B310FA28D/with_c/
 + gfortran -c ./src/with_c.f90  -Wall -Wextra -Wimplicit-interface -fPIC -fmax-errors=1 -g -fcheck=bounds -fcheck=array-temps -fbacktrace -fcoarray=single -J build/gfortran_2A42023B310FA28D -Ibuild/gfortran_2A42023B310FA28D -o build/gfortran_2A42023B310FA28D/with_c/src_with_c.f90.o
[ 40%]                     with_c.f90  done.
[ 40%]                    libwith_c.a
 + ar -rs build/gfortran_2A42023B310FA28D/with_c/libwith_c.a build/gfortran_2A42023B310FA28D/with_c/src_with_c.f90.o
ar: creating build/gfortran_2A42023B310FA28D/with_c/libwith_c.a
[ 60%]                    libwith_c.a  done.
[ 60%]                       main.f90
 + gfortran -c app/main.f90  -Wall -Wextra -Wimplicit-interface -fPIC -fmax-errors=1 -g -fcheck=bounds -fcheck=array-temps -fbacktrace -fcoarray=single -J build/gfortran_2A42023B310FA28D -Ibuild/gfortran_2A42023B310FA28D -o build/gfortran_2A42023B310FA28D/with_c/app_main.f90.o
[ 80%]                       main.f90  done.
[ 80%]                         with_c
 + mkdir -p build/gfortran_2A42023B310FA28D/app/
 + gfortran  -Wall -Wextra -Wimplicit-interface -fPIC -fmax-errors=1 -g -fcheck=bounds -fcheck=array-temps -fbacktrace -fcoarray=single  build/gfortran_2A42023B310FA28D/with_c/app_main.f90.o build/gfortran_2A42023B310FA28D/with_c/libwith_c.a -o build/gfortran_2A42023B310FA28D/app/with_c
/usr/bin/ld: build/gfortran_2A42023B310FA28D/with_c/libwith_c.a(src_with_c.f90.o): in function `__with_c_MOD_system_isdir':
/home/arteev/reproducible-example/./src/with_c.f90:22: undefined reference to `my_isdir'
collect2: error: ld returned 1 exit status
[100%]                         with_c  done.

/usr/bin/ld: build/gfortran_2A42023B310FA28D/with_c/libwith_c.a(src_with_c.f90.o): in function `__with_c_MOD_system_isdir':
/home/arteev/reproducible-example/./src/with_c.f90:22: undefined reference to `my_isdir'
collect2: error: ld returned 1 exit status
<ERROR> Compilation failed for object " with_c "
<ERROR>stopping due to failed compilation
STOP 1

cc: @awvwgk

[LKedward]

Thanks for looking into this @arteevraina and apologies for the late response from myself. I think this is actually the same problem as #556. fpm currently only links executables to the library and to any module sources in the same directory (or a subdirectory). We can probably now update this to simply link executables with any targets with source files in the same directory (or a subdirectory). The relevant routine to look at is resolve_target_linking and specifically get_link_objects which currently loops over module dependencies of executable targets. This can be changed to loop over all targets and link any non-library targets that have source files in the right location. Hope that makes sense, let me know if not!

[zoziha]

We can probably now update this to simply link executables with any targets with source files in the same directory (or a subdirectory).

We can probably now update this to simply link executables with any targets with C/C++ source files in the same directory (or a subdirectory).

It seems that fpm cannot detect dependencies between Fortran sources and C/C++ sources, and eventually, C/C++ source files under the app/ path are ignored at link time.

(Based on reproducible project, I got a more simplified version repository branch reproducible project.)

[LKedward]

We can probably now update this to simply link executables with any targets with C/C++ source files in the same directory (or a subdirectory).

No, I believe my original statement stands correct because we also need to link to non-module Fortran sources which are also not currently linked with executables (hence #556).

It seems that fpm cannot detect dependencies between Fortran sources and C/C++ sources, and eventually, C/C++ source files under the app/ path are ignored at link time.

There's no hard necessity for fpm to detect this from the source file content - fpm only needs to know about Fortran module dependencies to get the compilation order correct. We infer the link-time dependency based on the presence of the source file in the folder.

[LKedward]

fyi, I'm now working on a patch for this (and #556)