Error building native library in Fedora 28

[bgatessucks]

Notice I edited ~/.Mathematica/Paclets/Repository/PJLink-.0.2/PJLink/MathLinkEnvironment.py:666 to reflect the actual installation root for Mathematica.

running build
running build_ext
building 'PJLinkNativeLibrary' extension
creating build
creating build/temp.linux-x86_64-3.6
gcc -pthread -B /opt/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/Wolfram/Mathematica/11.3/SystemFiles/Links/MathLink/DeveloperKit/Linux-x86-64/CompilerAdditions -I/opt/anaconda/include/python3.6m -c PJLinkNativeLibrary.cpp -o build/temp.linux-x86_64-3.6/PJLinkNativeLibrary.o
g++ -pthread -shared -B /opt/anaconda/compiler_compat -L/opt/anaconda/lib -Wl,-rpath=/opt/anaconda/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/PJLinkNativeLibrary.o -L/opt/Wolfram/Mathematica/11.3/SystemFiles/Links/MathLink/DeveloperKit/Linux-x86-64/CompilerAdditions -lMLi4 -o /home/fsiano/.Mathematica/Paclets/Repository/PJLink-1.0.2/PJLink/PJLinkNativeLibrary/src/PJLinkNativeLibrary.cpython-36m-x86_64-linux-gnu.so
An exception has occurred, use %tb to see the full traceback.

SystemExit: error: command 'g++' failed with exit status 1


/opt/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py:2918: UserWarning: To exit: use 'exit', 'quit', or Ctrl-D.
  warn("To exit: use 'exit', 'quit', or Ctrl-D.", stacklevel=1)

and %tb gives

---------------------------------------------------------------------------
DistutilsExecError                        Traceback (most recent call last)
/opt/anaconda/lib/python3.6/distutils/unixccompiler.py in link(self, target_desc, objects, output_filename, output_dir, libraries, library_dirs, runtime_library_dirs, export_symbols, debug, extra_preargs, extra_postargs, build_temp, target_lang)
    196 
--> 197                 self.spawn(linker + ld_args)
    198             except DistutilsExecError as msg:

/opt/anaconda/lib/python3.6/distutils/ccompiler.py in spawn(self, cmd)
    908     def spawn(self, cmd):
--> 909         spawn(cmd, dry_run=self.dry_run)
    910 

/opt/anaconda/lib/python3.6/distutils/spawn.py in spawn(cmd, search_path, verbose, dry_run)
     35     if os.name == 'posix':
---> 36         _spawn_posix(cmd, search_path, dry_run=dry_run)
     37     elif os.name == 'nt':

/opt/anaconda/lib/python3.6/distutils/spawn.py in _spawn_posix(cmd, search_path, verbose, dry_run)
    158                           "command %r failed with exit status %d"
--> 159                           % (cmd, exit_status))
    160             elif os.WIFSTOPPED(status):

DistutilsExecError: command 'g++' failed with exit status 1

During handling of the above exception, another exception occurred:

LinkError                                 Traceback (most recent call last)
/opt/anaconda/lib/python3.6/distutils/core.py in setup(**attrs)
    147         try:
--> 148             dist.run_commands()
    149         except KeyboardInterrupt:

/opt/anaconda/lib/python3.6/distutils/dist.py in run_commands(self)
    954         for cmd in self.commands:
--> 955             self.run_command(cmd)
    956 

/opt/anaconda/lib/python3.6/distutils/dist.py in run_command(self, command)
    973         cmd_obj.ensure_finalized()
--> 974         cmd_obj.run()
    975         self.have_run[command] = 1

/opt/anaconda/lib/python3.6/distutils/command/build.py in run(self)
    134         for cmd_name in self.get_sub_commands():
--> 135             self.run_command(cmd_name)
    136 

/opt/anaconda/lib/python3.6/distutils/cmd.py in run_command(self, command)
    312         """
--> 313         self.distribution.run_command(command)
    314 

/opt/anaconda/lib/python3.6/distutils/dist.py in run_command(self, command)
    973         cmd_obj.ensure_finalized()
--> 974         cmd_obj.run()
    975         self.have_run[command] = 1

/opt/anaconda/lib/python3.6/distutils/command/build_ext.py in run(self)
    338         # Now actually compile and link everything.
--> 339         self.build_extensions()
    340 

/opt/anaconda/lib/python3.6/distutils/command/build_ext.py in build_extensions(self)
    447         else:
--> 448             self._build_extensions_serial()
    449 

/opt/anaconda/lib/python3.6/distutils/command/build_ext.py in _build_extensions_serial(self)
    472             with self._filter_build_errors(ext):
--> 473                 self.build_extension(ext)
    474 

/opt/anaconda/lib/python3.6/distutils/command/build_ext.py in build_extension(self, ext)
    557             build_temp=self.build_temp,
--> 558             target_lang=language)
    559 

/opt/anaconda/lib/python3.6/distutils/ccompiler.py in link_shared_object(self, objects, output_filename, output_dir, libraries, library_dirs, runtime_library_dirs, export_symbols, debug, extra_preargs, extra_postargs, build_temp, target_lang)
    716                   export_symbols, debug,
--> 717                   extra_preargs, extra_postargs, build_temp, target_lang)
    718 

/opt/anaconda/lib/python3.6/distutils/unixccompiler.py in link(self, target_desc, objects, output_filename, output_dir, libraries, library_dirs, runtime_library_dirs, export_symbols, debug, extra_preargs, extra_postargs, build_temp, target_lang)
    198             except DistutilsExecError as msg:
--> 199                 raise LinkError(msg)
    200         else:

LinkError: command 'g++' failed with exit status 1

During handling of the above exception, another exception occurred:

SystemExit                                Traceback (most recent call last)
<ipython-input-3-a1f503dd0203> in <module>()
----> 1 ker = SubprocessKernel()
      2 def MEval (expr, wait = True, kernel = ker):
      3     """MEval evaluates a Mathematica expression in the Mathematica kernel
      4 
      5     """

~/.Mathematica/Paclets/Repository/PJLink-1.0.2/SubprocessKernel/SubprocessKernel.py in __init__(self, init, debug_level)
     15 
     16     def __init__(self, init = None, debug_level = 0):
---> 17         super().__init__(NativeLink(init=init, debug_level=debug_level))
     18         self.__py_eval_link = None
     19         self.__reader = None

~/.Mathematica/Paclets/Repository/PJLink-1.0.2/PJLink/NativeLink.py in __init__(self, init, debug_level)
     46         self._init = init
     47         self.__errMsgOut = [ "" ]
---> 48         self._loadNativeLibrary(debug_level=debug_level)
     49 
     50         self.__markStack = deque()

~/.Mathematica/Paclets/Repository/PJLink-1.0.2/PJLink/NativeLink.py in _loadNativeLibrary(self, initialize, debug_level, setup, *args)
    127                         argv1 = sys.argv
    128                         sys.argv = [ "-q", "build", "build_ext", "--inplace" ]
--> 129                         import setup as setup
    130                         sys.path.pop(0)
    131                         sys.argv = argv1

~/.Mathematica/Paclets/Repository/PJLink-1.0.2/PJLink/PJLinkNativeLibrary/src/setup.py in <module>()
     54        version = '1.0',
     55        description = 'Implementation of JLinkNativeLibrary for python',
---> 56        ext_modules = [module1]
     57        )
     58 

/opt/anaconda/lib/python3.6/distutils/core.py in setup(**attrs)
    161                 raise
    162             else:
--> 163                 raise SystemExit("error: " + str(msg))
    164 
    165     return dist

SystemExit: error: command 'g++' failed with exit status 1

[b3m2a1]

Thanks for the report. Someone else had issues with an Anaconda distribution of python failing to build because of the #include <cstdint>. That was circumventable with a Mac-specific fix, so I'm guessing g++ is failing because of the same issue (i.e. Anaconda does odd things). I'll google to see if I can find a workaround that I can implement for Fedora too.

Out of curiosity, what did you need to change in MathLinkEnvironment? If more configuration is needed I should allow it to be passed in the initialization.

[b3m2a1]

I'm going to expunge the "-q" from the sys.argv with the hope that it allows things to be cleaner for people with issues in the future. Do you mind testing it without that and letting me know what happens? It might quiet a more particular message.

[bgatessucks]

Using the standard python which comes with Fedora (not anaconda) and PJLink versrion 1.0.3:
Because of #5 I changed (3 instances) in
~/.Mathematica/Paclets/Repository/PJLink-1.0.3/PJLink/MathLinkEnvironment.py

os.path.join(root, "SystemFiles", ...) to os.path.join(root, "11.3", "SystemFiles", ...)

Notice the include has -I/opt/Wolfram/Mathematica/SystemFiles/... (not -I/opt/Wolfram/Mathematica/11.3/SystemFiles/...).

unning build_ext
building 'PJLinkNativeLibrary' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/opt/Wolfram/Mathematica/SystemFiles/Links/MathLink/DeveloperKit/Linux/CompilerAdditions -I/usr/include/python3.6m -c PJLinkNativeLibrary.cpp -o build/temp.linux-x86_64-3.6/PJLinkNativeLibrary.o

An exception has occurred, use %tb to see the full traceback.

SystemExit: error: command 'gcc' failed with exit status 1


/usr/lib/python3.6/site-packages/IPython/core/interactiveshell.py:2971: UserWarning: To exit: use 'exit', 'quit', or Ctrl-D.
  warn("To exit: use 'exit', 'quit', or Ctrl-D.", stacklevel=1)

and %tb:

--------------------------------------------------------------------------
DistutilsExecError                        Traceback (most recent call last)
/usr/lib64/python3.6/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
    126             self.spawn(compiler_so + cc_args + [src, '-o', obj] +
--> 127                        extra_postargs)
    128         except DistutilsExecError as msg:

/usr/lib64/python3.6/distutils/ccompiler.py in spawn(self, cmd)
    908     def spawn(self, cmd):
--> 909         spawn(cmd, dry_run=self.dry_run)
    910 

/usr/lib64/python3.6/distutils/spawn.py in spawn(cmd, search_path, verbose, dry_run)
     35     if os.name == 'posix':
---> 36         _spawn_posix(cmd, search_path, dry_run=dry_run)
     37     elif os.name == 'nt':

/usr/lib64/python3.6/distutils/spawn.py in _spawn_posix(cmd, search_path, verbose, dry_run)
    158                           "command %r failed with exit status %d"
--> 159                           % (cmd, exit_status))
    160             elif os.WIFSTOPPED(status):

DistutilsExecError: command 'gcc' failed with exit status 1

During handling of the above exception, another exception occurred:

CompileError                              Traceback (most recent call last)
/usr/lib64/python3.6/distutils/core.py in setup(**attrs)
    147         try:
--> 148             dist.run_commands()
    149         except KeyboardInterrupt:

/usr/lib64/python3.6/distutils/dist.py in run_commands(self)
    954         for cmd in self.commands:
--> 955             self.run_command(cmd)
    956 

/usr/lib64/python3.6/distutils/dist.py in run_command(self, command)
    973         cmd_obj.ensure_finalized()
--> 974         cmd_obj.run()
    975         self.have_run[command] = 1

/usr/lib64/python3.6/distutils/command/build_ext.py in run(self)
    338         # Now actually compile and link everything.
--> 339         self.build_extensions()
    340 

/usr/lib64/python3.6/distutils/command/build_ext.py in build_extensions(self)
    447         else:
--> 448             self._build_extensions_serial()
    449 

/usr/lib64/python3.6/distutils/command/build_ext.py in _build_extensions_serial(self)
    472             with self._filter_build_errors(ext):
--> 473                 self.build_extension(ext)
    474 

/usr/lib64/python3.6/distutils/command/build_ext.py in build_extension(self, ext)
    532                                          extra_postargs=extra_args,
--> 533                                          depends=ext.depends)
    534 

/usr/lib64/python3.6/distutils/ccompiler.py in compile(self, sources, output_dir, macros, include_dirs, debug, extra_preargs, extra_postargs, depends)
    573                 continue
--> 574             self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
    575 

/usr/lib64/python3.6/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
    128         except DistutilsExecError as msg:
--> 129             raise CompileError(msg)
    130 

CompileError: command 'gcc' failed with exit status 1

During handling of the above exception, another exception occurred:

SystemExit                                Traceback (most recent call last)
<ipython-input-2-46b7fe96b177> in <module>()
----> 1 ker = SubprocessKernel()
      2 def MEval (expr, wait = True, kernel = ker) :
      3     """MEval evaluates a Mathematica expression in the Mathematica kernel
      4 
      5     """

.Mathematica/Paclets/Repository/PJLink-1.0.3/SubprocessKernel/SubprocessKernel.py in __init__(self, init, debug_level)

.Mathematica/Paclets/Repository/PJLink-1.0.3/PJLink/NativeLink.py in __init__(self, init, debug_level)

.Mathematica/Paclets/Repository/PJLink-1.0.3/PJLink/NativeLink.py in _loadNativeLibrary(self, initialize, debug_level, *args)

.Mathematica/Paclets/Repository/PJLink-1.0.3/PJLink/PJLinkNativeLibrary/__init__.py in <module>()

.Mathematica/Paclets/Repository/PJLink-1.0.3/PJLink/PJLinkNativeLibrary/__init__.py in _get_lib_dir_loc()

.Mathematica/Paclets/Repository/PJLink-1.0.3/PJLink/PJLinkNativeLibrary/src/setup.py in <module>()

/usr/lib64/python3.6/distutils/core.py in setup(**attrs)
    161                 raise
    162             else:
--> 163                 raise SystemExit("error: " + str(msg))
    164 
    165     return dist

SystemExit: error: command 'gcc' failed with exit status 1

[b3m2a1]

@bgatessucks I think I got a patch for this path as well as the others. The path finding is a bit more centralized now. Can you give it another try? Hopefully the only issue is just these paths.

[bgatessucks]

Not there yet with 1.0.4:
I have several versions of Mathematica installed at /opt/Wolfram/Mathematica/ver with ver in

10.4.1
11.0.1
11.1
11.1.1
11.2
11.3
7.0.1
8.0.4
9.0.1

and it seems that 10.4.1 gets picked up.
Would it be possible to add an argument for the user to provide the Mathematica root ?

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~/.Mathematica/Paclets/Repository/PJLink-1.0.4/PJLink/MathLinkEnvironment.py in get_Kernel_binary(cls, version, use_default_root)
    723         try:
--> 724             root = cls.get_Mathematica_root(version, use_default_root=use_default_root)
    725         except ValueError:

~/.Mathematica/Paclets/Repository/PJLink-1.0.4/PJLink/MathLinkEnvironment.py in get_Mathematica_root(cls, mname, use_default_root)
    699         if mname is None and cls.CURRENT_MATHEMATICA is None:
--> 700             root = cls.get_Installed_Mathematica(use_default_root=use_default_root)
    701             if plat == "Darwin":

~/.Mathematica/Paclets/Repository/PJLink-1.0.4/PJLink/MathLinkEnvironment.py in get_Installed_Mathematica(cls, use_default_root)
    656                 vers = app
--> 657                 verNum = float(app)
    658                 mathematicas.append((mathematica, verNum, vers))

ValueError: could not convert string to float: '10.4.1'

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
<ipython-input-2-46b7fe96b177> in <module>()
----> 1 ker = SubprocessKernel()
      2 def MEval (expr, wait = True, kernel = ker) :
      3     """MEval evaluates a Mathematica expression in the Mathematica kernel
      4 
      5     """

~/.Mathematica/Paclets/Repository/PJLink-1.0.4/SubprocessKernel/SubprocessKernel.py in __init__(self, init, debug_level)
     15 
     16     def __init__(self, init = None, debug_level = 0):
---> 17         super().__init__(NativeLink(init=init, debug_level=debug_level))
     18         self.__py_eval_link = None
     19         self.__reader = None

~/.Mathematica/Paclets/Repository/PJLink-1.0.4/PJLink/NativeLink.py in __init__(self, init, debug_level)
     35 
     36         if init is None:
---> 37             bin = self.Env.get_Kernel_binary()
     38             init = ["-linkmode", "launch", "-linkname", "'{}' -mathlink".format(bin)]#, "-mathlink", "-wstp"]
     39         elif isinstance(init, str) and os.path.isfile(init):

~/.Mathematica/Paclets/Repository/PJLink-1.0.4/PJLink/MathLinkEnvironment.py in get_Kernel_binary(cls, version, use_default_root)
    725         except ValueError:
    726             if not (isinstance(version, str) and os.path.isfile(version)):
--> 727                 raise ValueError("Don't know how to find the WolframKernel executable on system {}".format(plat))
    728             else:
    729                 mbin = version

ValueError: Don't know how to find the WolframKernel executable on system Linux

[b3m2a1]

@bgatessucks Okay I think I got a fix in place for the bad directory finding. Thanks for all your help with this. I also have a system where you can provide your own $InstallationDirectory. Try :

from PJLink import MathLinkEnvironment as Env
Env.INSTALLATION_DIRECTORY = "mathematica/installation/directory"

I got it to find things properly on Mac for a different Mathematica version, but we'll see how it goes.

[bgatessucks]

Progress, it's just g++ now, with Env.INSTALLATION_DIRECTORY = "/opt/Wolfram/Mathematica/11.3":

running build_ext
building 'PJLinkNativeLibrary' extension
creating build
creating build/temp.linux-x86_64-3.6
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/opt/Wolfram/Mathematica/11.3/SystemFiles/Links/MathLink/DeveloperKit/Linux-x86-64/CompilerAdditions -I/usr/include/python3.6m -c PJLinkNativeLibrary.cpp -o build/temp.linux-x86_64-3.6/PJLinkNativeLibrary.o
g++ -pthread -shared -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -g -flto -fuse-linker-plugin -ffat-lto-objects -flto-partition=none build/temp.linux-x86_64-3.6/PJLinkNativeLibrary.o -L/opt/Wolfram/Mathematica/11.3/SystemFiles/Links/MathLink/DeveloperKit/Linux-x86-64/CompilerAdditions -L/usr/lib64 -lMLi4 -lpython3.6m -o ~/.Mathematica/Paclets/Repository/PJLink-1.0.5/PJLink/PJLinkNativeLibrary/src/PJLinkNativeLibrary.cpython-36m-x86_64-linux-gnu.so

An exception has occurred, use %tb to see the full traceback.

SystemExit: error: command 'g++' failed with exit status 1

DistutilsExecError                        Traceback (most recent call last)
/usr/lib64/python3.6/distutils/unixccompiler.py in link(self, target_desc, objects, output_filename, output_dir, libraries, library_dirs, runtime_library_dirs, export_symbols, debug, extra_preargs, extra_postargs, build_temp, target_lang)
    204 
--> 205                 self.spawn(linker + ld_args)
    206             except DistutilsExecError as msg:

/usr/lib64/python3.6/distutils/ccompiler.py in spawn(self, cmd)
    908     def spawn(self, cmd):
--> 909         spawn(cmd, dry_run=self.dry_run)
    910 

/usr/lib64/python3.6/distutils/spawn.py in spawn(cmd, search_path, verbose, dry_run)
     35     if os.name == 'posix':
---> 36         _spawn_posix(cmd, search_path, dry_run=dry_run)
     37     elif os.name == 'nt':

/usr/lib64/python3.6/distutils/spawn.py in _spawn_posix(cmd, search_path, verbose, dry_run)
    158                           "command %r failed with exit status %d"
--> 159                           % (cmd, exit_status))
    160             elif os.WIFSTOPPED(status):

DistutilsExecError: command 'g++' failed with exit status 1

During handling of the above exception, another exception occurred:

LinkError                                 Traceback (most recent call last)
/usr/lib64/python3.6/distutils/core.py in setup(**attrs)
    147         try:
--> 148             dist.run_commands()
    149         except KeyboardInterrupt:

/usr/lib64/python3.6/distutils/dist.py in run_commands(self)
    954         for cmd in self.commands:
--> 955             self.run_command(cmd)
    956 

/usr/lib64/python3.6/distutils/dist.py in run_command(self, command)
    973         cmd_obj.ensure_finalized()
--> 974         cmd_obj.run()
    975         self.have_run[command] = 1

/usr/lib64/python3.6/distutils/command/build_ext.py in run(self)
    338         # Now actually compile and link everything.
--> 339         self.build_extensions()
    340 

/usr/lib64/python3.6/distutils/command/build_ext.py in build_extensions(self)
    447         else:
--> 448             self._build_extensions_serial()
    449 

/usr/lib64/python3.6/distutils/command/build_ext.py in _build_extensions_serial(self)
    472             with self._filter_build_errors(ext):
--> 473                 self.build_extension(ext)
    474 

/usr/lib64/python3.6/distutils/command/build_ext.py in build_extension(self, ext)
    557             build_temp=self.build_temp,
--> 558             target_lang=language)
    559 

/usr/lib64/python3.6/distutils/ccompiler.py in link_shared_object(self, objects, output_filename, output_dir, libraries, library_dirs, runtime_library_dirs, export_symbols, debug, extra_preargs, extra_postargs, build_temp, target_lang)
    716                   export_symbols, debug,
--> 717                   extra_preargs, extra_postargs, build_temp, target_lang)
    718 

/usr/lib64/python3.6/distutils/unixccompiler.py in link(self, target_desc, objects, output_filename, output_dir, libraries, library_dirs, runtime_library_dirs, export_symbols, debug, extra_preargs, extra_postargs, build_temp, target_lang)
    206             except DistutilsExecError as msg:
--> 207                 raise LinkError(msg)
    208         else:

LinkError: command 'g++' failed with exit status 1

During handling of the above exception, another exception occurred:

SystemExit                                Traceback (most recent call last)
<ipython-input-5-46b7fe96b177> in <module>()
----> 1 ker = SubprocessKernel()
      2 def MEval (expr, wait = True, kernel = ker) :
      3     """MEval evaluates a Mathematica expression in the Mathematica kernel
      4 
      5     """

.Mathematica/Paclets/Repository/PJLink-1.0.5/SubprocessKernel/SubprocessKernel.py in __init__(self, init, debug_level)

.Mathematica/Paclets/Repository/PJLink-1.0.5/PJLink/NativeLink.py in __init__(self, init, debug_level)

.Mathematica/Paclets/Repository/PJLink-1.0.5/PJLink/NativeLink.py in _loadNativeLibrary(self, initialize, debug_level, *args)

.Mathematica/Paclets/Repository/PJLink-1.0.5/PJLink/PJLinkNativeLibrary/__init__.py in <module>()

.Mathematica/Paclets/Repository/PJLink-1.0.5/PJLink/PJLinkNativeLibrary/__init__.py in _get_lib_dir_loc()

.Mathematica/Paclets/Repository/PJLink-1.0.5/PJLink/PJLinkNativeLibrary/src/setup.py in <module>()

/usr/lib64/python3.6/distutils/core.py in setup(**attrs)
    161                 raise
    162             else:
--> 163                 raise SystemExit("error: " + str(msg))
    164 
    165     return dist

SystemExit: error: command 'g++' failed with exit status 1

[b3m2a1]

@bgatessucks do you have a library called MLi4 in /opt/Wolfram/Mathematica/11.3/SystemFiles/Links/MathLink/DeveloperKit/Linux-x86-64/CompilerAdditions? For me it's MLi4.a, but setup.py doesn't care about the extension. The fact that it got through the gcc call suggests it's just a linking issue, now.

[b3m2a1]

I tried to rewrite the dependency finder so that it doesn't require a file called MLi4 but instead looks for the highest-version library files in the directory. Let me know if it worked. If not, can you paste the file names inside /opt/Wolfram/Mathematica/11.3/SystemFiles/Links/MathLink/DeveloperKit/Linux-x86-64/CompilerAdditions? My current guess is I'm selecting that file incorrectly.

[bgatessucks]

ls /opt/Wolfram/Mathematica/11.3/SystemFiles/Links/MathLink/DeveloperKit/Linux-x86-64/CompilerAdditions gives:

libML32i3.a
libML32i3.so
libML32i4.a
libML32i4.so
libML64i3.a
libML64i3.so
libML64i4.a
libML64i4.so
MathLink.cmake
mathlink.h
MathLink-release.cmake
mcc
mprep

[b3m2a1]

Ah that could entirely be the issue then. Any chance the current version (1.0.6) builds? I added more intelligent path-finding so it ought to have found either libML64i4 or libML32i4 but I can't be sure which. It's also possible to specify this directly with Env.MATHLINK_LIBRARY_NAME = "ML64i4". Once again thanks for all your help. I have no access to any Linux or Windows machine so this is super useful.

[bgatessucks]

Progress but not there yet:

Env.INSTALLATION_DIRECTORY = "/opt/Wolfram/Mathematica/11.3"
Env.MATHLINK_LIBRARY_NAME = "ML64i4"

ImportError                               Traceback (most recent call last)
<ipython-input-5-46b7fe96b177> in <module>()
----> 1 ker = SubprocessKernel()
      2 def MEval (expr, wait = True, kernel = ker) :
      3     """MEval evaluates a Mathematica expression in the Mathematica kernel
      4 
      5     """

~/.Mathematica/Paclets/Repository/PJLink-1.0.6/SubprocessKernel/SubprocessKernel.py in __init__(self, init, debug_level)
     15 
     16     def __init__(self, init = None, debug_level = 0):
---> 17         super().__init__(NativeLink(init=init, debug_level=debug_level))
     18         self.__py_eval_link = None
     19         self.__reader = None

~/.Mathematica/Paclets/Repository/PJLink-1.0.6/PJLink/NativeLink.py in __init__(self, init, debug_level)
     46         self._init = init
     47         self.__errMsgOut = [ "" ]
---> 48         self._loadNativeLibrary(debug_level=debug_level)
     49 
     50         self.__markStack = deque()

~/.Mathematica/Paclets/Repository/PJLink-1.0.6/PJLink/NativeLink.py in _loadNativeLibrary(self, initialize, debug_level, *args)
    101             except ImportError as e:
    102                 self.__LIBRARY_LOAD_EXCEPTION = e
--> 103                 raise e
    104             else:
    105                 self.__NATIVE_LIBRARY_LOADED = True

~/.Mathematica/Paclets/Repository/PJLink-1.0.6/PJLink/NativeLink.py in _loadNativeLibrary(self, initialize, debug_level, *args)
     98 
     99             try:
--> 100                 import PJLink.PJLinkNativeLibrary as pj
    101             except ImportError as e:
    102                 self.__LIBRARY_LOAD_EXCEPTION = e

~/.Mathematica/Paclets/Repository/PJLink-1.0.6/PJLink/PJLinkNativeLibrary/__init__.py in <module>()
     50 try:
     51     sys.path.insert(0, _get_lib_dir_loc())
---> 52     from PJLinkNativeLibrary import *
     53 finally:
     54     sys.path.pop(0)

ImportError: libML64i4.so: cannot open shared object file: No such file or directory

[b3m2a1]

That's very odd...so the library compiled but gave that warning? Could you show me the compiler output and what's in ~/.Mathematica/Paclets/Repository/PJLink-1.0.6/PJLink/PJLinkNativeLibrary? I think it must be linking against the .so version of libML64i4 instead of the .a, since it was able to find both. If that's the case I'll need to change how I choose to the link MathLink library in slightly.