Fix double free on Crystal::Loader#close_all

[HertzDevil]

Crystal::Loader#finalize calls #close_all, but the FFI and loader specs call the latter manually, which means that upon a GC cycle all the dynamic library handles are closed once again. This PR prevents this by clearing the list of handles once they are closed.

Resolves #11561. I have also confirmed that #11343 with this patch will turn the LLVM 13 CI green. I managed to reproduce this locally with just:

$ make clean crystal
$ bin/crystal build -o specs spec/compiler/ffi/ffi_spec.cr spec/compiler/loader/unix_spec.cr spec/compiler/semantic/abstract_def_spec.cr
$ ./specs
#Using compiled compiler at .build/crystal
#........................Invalid memory access (signal 11) at address 0x8000
#[0x558b4b517f76] *Exception::CallStack::print_backtrace:Nil +118 in ./specs
#[0x558b4b4f4686] ~procProc(Int32, Pointer(LibC::SiginfoT), Pointer(Void), Nil) +310 in ./specs
#[0x7f84a015e200] ?? +140207598199296 in /lib/x86_64-linux-gnu/libpthread.so.0
#[0x7f84a68daee6] ?? +140207706713830 in /lib64/ld-linux-x86-64.so.2
#[0x7f84a68cdae1] _dl_exception_create +49 in /lib64/ld-linux-x86-64.so.2
#[0x7f84a002f894] _dl_signal_error +52 in /lib/x86_64-linux-gnu/libc.so.6
#[0x7f84a68ccd71] ?? +140207706656113 in /lib64/ld-linux-x86-64.so.2
#[0x7f84a002f940] _dl_catch_exception +128 in /lib/x86_64-linux-gnu/libc.so.6
#[0x7f84a002f9ff] _dl_catch_error +47 in /lib/x86_64-linux-gnu/libc.so.6
#[0x7f84a00eda59] ?? +140207597738585 in /lib/x86_64-linux-gnu/libdl.so.2
#[0x7f84a00ed364] dlclose +36 in /lib/x86_64-linux-gnu/libdl.so.2
#[0x558b4c764742] *Crystal::Loader#close_all:Nil +82 in ./specs
#[0x558b4c7646e6] *Crystal::Loader#finalize:Nil +6 in ./specs
#[0x558b4b4f7606] ~proc15Proc(Pointer(Void), Pointer(Void), Nil) +6 in ./specs
#[0x558b4c7868ae] GC_invoke_finalizers +158 in ./specs
#[0x558b4c7869fe] GC_notify_or_invoke_finalizers +174 in ./specs
#[0x558b4c787e41] GC_generic_malloc +33 in ./specs
#[0x558b4c7880d1] GC_malloc_kind_global +225 in ./specs
#[0x558b4b5cc016] *GC::malloc<UInt64>:Pointer(Void) +6 in ./specs
#[0x558b4b4f4966] ~procProc(UInt64, Pointer(Void)) +6 in ./specs
#[0x7f84a02fcb6d] ?? +140207599897453 in /lib/x86_64-linux-gnu/libpcre.so.3
#[0x7f84a0302962] pcre_study +738 in /lib/x86_64-linux-gnu/libpcre.so.3
#[0x558b4b693dae] *Regex#initialize<String, Regex::Options>:Int32 +302 in ./specs
#[0x558b4b693c6c] *Regex::new<String, Regex::Options>:Regex +92 in ./specs
#[0x558b4b4ecd9f] ~$Regex:2:init +15 in ./specs
#[0x558b4c772a77] *Crystal::OnceState#once<Pointer(Bool), Pointer(Void)>:(Pointer(Bool) | Nil) +183 in ./specs
#[0x558b4b4d3eb5] __crystal_once +37 in ./specs
#[0x558b4b4ecd7e] ~$Regex:2:read +30 in ./specs
#[0x558b4c2aa7fa] *LLVM::default_target_triple:String +106 in ./specs
#[0x558b4c2aa43a] *Crystal::Config::host_target:Crystal::Codegen::Target +42 in ./specs
#[0x558b4b70fb77] *Crystal::Program::new:Crystal::Program +423 in ./specs
#[0x558b4c7725b9] */home/quinton/crystal/crystal/spec/spec_helper.cr::new_program:Crystal::Program +9 in ./specs
#Segmentation fault

However it seems to happen even on earlier LLVM versions; I tried 9 and 11, and both of them produced the same error. I believe calling dlclose more than dlopen on the same handle is undefined behaviour and it is sheer coincidence the other CI jobs didn't break. The following will show that a double free has indeed occurred:

class Crystal::Loader
  def close_all : Nil
    @handles.each do |handle|
      unless LibC.dlclose(handle) == 0
        STDERR.puts String.new(LibC.dlerror)
      end
    end
  end
end

The same spec binary above will print shared object not open a few times. The count varies between runs of the binary for some reason.

[HertzDevil]

A more robust solution would be maintaining our own reference counts for each successful dlopen, to ensure the handles are correctly closed even if they were opened multiple times.

[asterite]

Also as a rule of thumb, if a class defines a finalize method and another public method that ends up doing the same thing, you should use a "closed" flag to prevent double finalize.