Implicit rpaths for NAG/GCC mixed toolchain (#14782)

* Implicit rpaths for NAG.

* set up environment when checking for implicit rpaths

lib/spack/spack/compiler.py

@@ -3,6 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import contextlib
 import os
 import platform
 import re
@@ -354,10 +355,11 @@ def _get_compiler_link_paths(self, paths):
             for flag_type in flags:
                 for flag in self.flags.get(flag_type, []):
                     compiler_exe.add_default_arg(flag)
-            output = str(compiler_exe(self.verbose_flag, fin, '-o', fout,
+            with self._compiler_environment():
-                                      output=str, error=str))  # str for py2
+                output = str(compiler_exe(
-
+                    self.verbose_flag, fin, '-o', fout,
-            return _parse_non_system_link_dirs(output)
+                    output=str, error=str))  # str for py2
+                return _parse_non_system_link_dirs(output)
         except spack.util.executable.ProcessError as pe:
             tty.debug('ProcessError: Command exited with non-zero status: ' +
                       pe.long_message)
@@ -468,32 +470,12 @@ def get_real_version(self):
         Use the runtime environment of the compiler (modules and environment
         modifications) to enable the compiler to run properly on any platform.
         """
-        # store environment to replace later
-        backup_env = os.environ.copy()
-
-        # load modules and set env variables
-        for module in self.modules:
-            # On cray, mic-knl module cannot be loaded without cce module
-            # See: https://github.com/spack/spack/issues/3153
-            if os.environ.get("CRAY_CPU_TARGET") == 'mic-knl':
-                spack.util.module_cmd.load_module('cce')
-            spack.util.module_cmd.load_module(module)
-
-        # apply other compiler environment changes
-        env = spack.util.environment.EnvironmentModifications()
-        env.extend(spack.schema.environment.parse(self.environment))
-        env.apply_modifications()
-
         cc = spack.util.executable.Executable(self.cc)
-        output = cc(self.version_argument,
+        with self._compiler_environment():
-                    output=str, error=str,
+            output = cc(self.version_argument,
-                    ignore_errors=tuple(self.ignore_version_errors))
+                        output=str, error=str,
-
+                        ignore_errors=tuple(self.ignore_version_errors))
-        # Restore environment
+            return self.extract_version_from_output(output)
-        os.environ.clear()
-        os.environ.update(backup_env)
-
-        return self.extract_version_from_output(output)
 
     #
     # Compiler classes have methods for querying the version of
@@ -562,6 +544,30 @@ def __str__(self):
                 self.cc, self.cxx, self.f77, self.fc, self.modules,
                 str(self.operating_system)))))
 
+    @contextlib.contextmanager
+    def _compiler_environment(self):
+        # store environment to replace later
+        backup_env = os.environ.copy()
+
+        # load modules and set env variables
+        for module in self.modules:
+            # On cray, mic-knl module cannot be loaded without cce module
+            # See: https://github.com/spack/spack/issues/3153
+            if os.environ.get("CRAY_CPU_TARGET") == 'mic-knl':
+                spack.util.module_cmd.load_module('cce')
+            spack.util.module_cmd.load_module(module)
+
+        # apply other compiler environment changes
+        env = spack.util.environment.EnvironmentModifications()
+        env.extend(spack.schema.environment.parse(self.environment))
+        env.apply_modifications()
+
+        yield
+
+        # Restore environment
+        os.environ.clear()
+        os.environ.update(backup_env)
+
 
 class CompilerAccessError(spack.error.SpackError):
 

lib/spack/spack/compilers/nag.py

@@ -30,6 +30,36 @@ class Nag(spack.compiler.Compiler):
     version_argument = '-V'
     version_regex = r'NAG Fortran Compiler Release ([0-9.]+)'
 
+    @property
+    def verbose_flag(self):
+        # NAG does not support a flag that would enable verbose output and
+        # compilation/linking at the same time (with either '-#' or '-dryrun'
+        # the compiler only prints the commands but does not run them).
+        # Therefore, the only thing we can do is to pass the '-v' argument to
+        # the underlying GCC. In order to get verbose output from the latter
+        # at both compile and linking stages, we need to call NAG with two
+        # additional flags: '-Wc,-v' and '-Wl,-v'. However, we return only
+        # '-Wl,-v' for the following reasons:
+        #   1) the interface of this method does not support multiple flags in
+        #      the return value and, at least currently, verbose output at the
+        #      linking stage has a higher priority for us;
+        #   2) NAG is usually mixed with GCC compiler, which also accepts
+        #      '-Wl,-v' and produces meaningful result with it: '-v' is passed
+        #      to the linker and the latter produces verbose output for the
+        #      linking stage ('-Wc,-v', however, would break the compilation
+        #      with a message from GCC that the flag is not recognized).
+        #
+        # This way, we at least enable the implicit rpath detection, which is
+        # based on compilation of a C file (see method
+        # spack.compiler._get_compiler_link_paths): in the case of a mixed
+        # NAG/GCC toolchain, the flag will be passed to g++ (e.g.
+        # 'g++ -Wl,-v ./main.c'), otherwise, the flag will be passed to nagfor
+        # (e.g. 'nagfor -Wl,-v ./main.c' - note that nagfor recognizes '.c'
+        # extension and treats the file accordingly). The list of detected
+        # rpaths will contain only GCC-related directories and rpaths to
+        # NAG-related directories are injected by nagfor anyway.
+        return "-Wl,-v"
+
     @property
     def openmp_flag(self):
         return "-openmp"

lib/spack/spack/test/compilers.py

@@ -157,13 +157,14 @@ def test_compiler_flags_from_config_are_grouped():
 class MockCompiler(Compiler):
     def __init__(self):
         super(MockCompiler, self).__init__(
-            "badcompiler@1.0.0",
+            cspec="badcompiler@1.0.0",
-            default_compiler_entry['operating_system'],
+            operating_system=default_compiler_entry['operating_system'],
-            None,
+            target=None,
-            [default_compiler_entry['paths']['cc'],
+            paths=[default_compiler_entry['paths']['cc'],
-             default_compiler_entry['paths']['cxx'],
+                   default_compiler_entry['paths']['cxx'],
-             default_compiler_entry['paths']['fc'],
+                   default_compiler_entry['paths']['fc'],
-             default_compiler_entry['paths']['f77']])
+                   default_compiler_entry['paths']['f77']],
+            environment={})
 
     _get_compiler_link_paths = Compiler._get_compiler_link_paths
 
@@ -267,6 +268,32 @@ def test_get_compiler_link_paths_no_verbose_flag():
     assert dirs == []
 
 
+def test_get_compiler_link_paths_load_env(working_env, monkeypatch, tmpdir):
+    gcc = str(tmpdir.join('gcc'))
+    with open(gcc, 'w') as f:
+        f.write("""#!/bin/bash
+if [[ $ENV_SET == "1" && $MODULE_LOADED == "1" ]]; then
+  echo '""" + no_flag_output + """'
+fi
+""")
+    fs.set_executable(gcc)
+
+    # Set module load to turn compiler on
+    def module(*args):
+        if args[0] == 'show':
+            return ''
+        elif args[0] == 'load':
+            os.environ['MODULE_LOADED'] = "1"
+    monkeypatch.setattr(spack.util.module_cmd, 'module', module)
+
+    compiler = MockCompiler()
+    compiler.environment = {'set': {'ENV_SET': '1'}}
+    compiler.modules = ['turn_on']
+
+    dirs = compiler._get_compiler_link_paths([gcc])
+    assert dirs == no_flag_dirs
+
+
 # Get the desired flag from the specified compiler spec.
 def flag_value(flag, spec):
     compiler = None

lib/spack/spack/test/data/compiler_verbose_output/collect2-6.3.0-gnu-ld.txt

@@ -0,0 +1,3 @@
+collect2 version 6.5.0
+/usr/bin/ld -plugin /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/liblto_plugin.so -plugin-opt=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/lto-wrapper -plugin-opt=-fresolution=/tmp/ccbFmewQ.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -rpath /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib64 --eh-frame-hdr -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o output /usr/lib/x86_64-linux-gnu/crt1.o /usr/lib/x86_64-linux-gnu/crti.o /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/crtbegin.o -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0 -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../../../lib64 -L/lib/x86_64-linux-gnu -L/lib/../lib64 -L/usr/lib/x86_64-linux-gnu -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../.. -v /tmp/ccxz6i1I.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/crtend.o /usr/lib/x86_64-linux-gnu/crtn.o
+GNU ld (GNU Binutils for Debian) 2.28

lib/spack/spack/test/data/compiler_verbose_output/nag-6.2-gcc-6.5.0.txt

@@ -0,0 +1,13 @@
+NAG Fortran Compiler Release 6.2(Chiyoda) Build 6223
+Reading specs from /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/specs
+COLLECT_GCC=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/bin/gcc
+COLLECT_LTO_WRAPPER=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/lto-wrapper
+Target: x86_64-pc-linux-gnu
+Configured with: /tmp/m300488/spack-stage/spack-stage-gcc-6.5.0-4sdjgrsboy3lowtq3t7pmp7rx3ogkqtz/spack-src/configure --prefix=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs --with-pkgversion='Spack GCC' --with-bugurl=https://github.com/spack/spack/issues --disable-multilib --enable-languages=c,c++,fortran --disable-nls --with-mpfr=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/mpfr-3.1.6-w63rspk --with-gmp=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gmp-6.1.2-et64cuj --with-system-zlib --with-mpc=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/mpc-1.1.0-en66k4t --with-isl=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/isl-0.18-62v4uyg
+Thread model: posix
+gcc version 6.5.0 (Spack GCC) 
+COMPILER_PATH=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/
+LIBRARY_PATH=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../../../lib64/:/lib/x86_64-linux-gnu/:/lib/../lib64/:/usr/lib/x86_64-linux-gnu/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../../:/lib/:/usr/lib/
+COLLECT_GCC_OPTIONS='-m64' '-o' 'output' '-v' '-mtune=generic' '-march=x86-64'
+ /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/collect2 -plugin /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/liblto_plugin.so -plugin-opt=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/lto-wrapper -plugin-opt=-fresolution=/tmp/ccBpU203.res -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -rpath /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib64 --eh-frame-hdr -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o output /usr/lib/x86_64-linux-gnu/crt1.o /usr/lib/x86_64-linux-gnu/crti.o /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/crtbegin.o -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0 -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../../../lib64 -L/lib/x86_64-linux-gnu -L/lib/../lib64 -L/usr/lib/x86_64-linux-gnu -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../.. /sw/stretch-x64/nag/nag-6.2/lib/NAG_Fortran/f62init.o /sw/stretch-x64/nag/nag-6.2/lib/NAG_Fortran/quickfit.o /tmp/main.000786.o -rpath /sw/stretch-x64/nag/nag-6.2/lib/NAG_Fortran /sw/stretch-x64/nag/nag-6.2/lib/NAG_Fortran/libf62rts.so /sw/stretch-x64/nag/nag-6.2/lib/NAG_Fortran/libf62rts.a -lm -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/crtend.o /usr/lib/x86_64-linux-gnu/crtn.o
+COLLECT_GCC_OPTIONS='-m64' '-o' 'output' '-v' '-mtune=generic' '-march=x86-64'

lib/spack/spack/test/link_paths.py

@@ -32,8 +32,8 @@ def check_link_paths(filename, paths):
 
 def test_icc16_link_paths():
     check_link_paths('icc-16.0.3.txt', [
-        '/usr/tce/packages/intel/intel-16.0.3/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin', # noqa
+        '/usr/tce/packages/intel/intel-16.0.3/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin',  # noqa
-        '/usr/tce/packages/gcc/gcc-4.9.3/lib64/gcc/x86_64-unknown-linux-gnu/4.9.3', # noqa
+        '/usr/tce/packages/gcc/gcc-4.9.3/lib64/gcc/x86_64-unknown-linux-gnu/4.9.3',  # noqa
         '/usr/tce/packages/gcc/gcc-4.9.3/lib64'])
 
 
@@ -82,6 +82,28 @@ def test_clang_apple_ld_link_paths():
         '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/lib'])  # noqa
 
 
+def test_nag_mixed_gcc_gnu_ld_link_paths():
+    # This is a test of a mixed NAG/GCC toolchain, i.e. 'cxx' is set to g++ and
+    # is used for the rpath detection. The reference compiler output is a
+    # result of
+    # '/path/to/gcc/bin/g++ -Wl,-v ./main.c'.
+    check_link_paths('collect2-6.3.0-gnu-ld.txt', [
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0',  # noqa
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib64',  # noqa
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib'])  # noqa
+
+
+def test_nag_link_paths():
+    # This is a test of a NAG-only toolchain, i.e. 'cc' and 'cxx' are empty,
+    # and therefore 'fc' is used for the rpath detection). The reference
+    # compiler output is a result of
+    # 'nagfor -Wc=/path/to/gcc/bin/gcc -Wl,-v ./main.c'.
+    check_link_paths('nag-6.2-gcc-6.5.0.txt', [
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0',  # noqa
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib64',  # noqa
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib'])  # noqa
+
+
 def test_obscure_parsing_rules():
     check_link_paths('obscure-parsing-rules.txt', [
         '/first/path',