gcc-runtime: remove libz.so from libgfortran.so if present (#47812)

lib/spack/spack/util/elf.py

@@ -7,7 +7,7 @@
 import re
 import struct
 from struct import calcsize, unpack, unpack_from
-from typing import BinaryIO, Dict, List, NamedTuple, Optional, Pattern, Tuple
+from typing import BinaryIO, Callable, Dict, List, NamedTuple, Optional, Pattern, Tuple
 
 
 class ElfHeader(NamedTuple):
@@ -476,6 +476,31 @@ def get_interpreter(path: str) -> Optional[str]:
         return None
 
 
+def _delete_dynamic_array_entry(
+    f: BinaryIO, elf: ElfFile, should_delete: Callable[[int, int], bool]
+) -> None:
+    f.seek(elf.pt_dynamic_p_offset)
+    dynamic_array_fmt = elf.byte_order + ("qQ" if elf.is_64_bit else "lL")
+    dynamic_array_size = calcsize(dynamic_array_fmt)
+    new_offset = elf.pt_dynamic_p_offset  # points to the new dynamic array
+    old_offset = elf.pt_dynamic_p_offset  # points to the current dynamic array
+    for _ in range(elf.pt_dynamic_p_filesz // dynamic_array_size):
+        data = read_exactly(f, dynamic_array_size, "Malformed dynamic array entry")
+        tag, val = unpack(dynamic_array_fmt, data)
+
+        if tag == ELF_CONSTANTS.DT_NULL or not should_delete(tag, val):
+            if new_offset != old_offset:
+                f.seek(new_offset)
+                f.write(data)
+                f.seek(old_offset + dynamic_array_size)
+            new_offset += dynamic_array_size
+
+        if tag == ELF_CONSTANTS.DT_NULL:
+            break
+
+        old_offset += dynamic_array_size
+
+
 def delete_rpath(path: str) -> None:
     """Modifies a binary to remove the rpath. It zeros out the rpath string and also drops the
     DT_R(UN)PATH entry from the dynamic section, so it doesn't show up in 'readelf -d file', nor
@@ -492,29 +517,22 @@ def delete_rpath(path: str) -> None:
         f.seek(rpath_offset)
         f.write(new_rpath_string)
 
-        # Next update the dynamic array
-        f.seek(elf.pt_dynamic_p_offset)
-        dynamic_array_fmt = elf.byte_order + ("qQ" if elf.is_64_bit else "lL")
-        dynamic_array_size = calcsize(dynamic_array_fmt)
-        new_offset = elf.pt_dynamic_p_offset  # points to the new dynamic array
-        old_offset = elf.pt_dynamic_p_offset  # points to the current dynamic array
-        for _ in range(elf.pt_dynamic_p_filesz // dynamic_array_size):
-            data = read_exactly(f, dynamic_array_size, "Malformed dynamic array entry")
-            tag, _ = unpack(dynamic_array_fmt, data)
+        # Delete DT_RPATH / DT_RUNPATH entries from the dynamic section
+        _delete_dynamic_array_entry(
+            f, elf, lambda tag, _: tag == ELF_CONSTANTS.DT_RPATH or tag == ELF_CONSTANTS.DT_RUNPATH
+        )
 
-            # Overwrite any entry that is not DT_RPATH or DT_RUNPATH, including DT_NULL
-            if tag != ELF_CONSTANTS.DT_RPATH and tag != ELF_CONSTANTS.DT_RUNPATH:
-                if new_offset != old_offset:
-                    f.seek(new_offset)
-                    f.write(data)
-                    f.seek(old_offset + dynamic_array_size)
-                new_offset += dynamic_array_size
 
-            # End of the dynamic array
-            if tag == ELF_CONSTANTS.DT_NULL:
-                break
+def delete_needed_from_elf(f: BinaryIO, elf: ElfFile, needed: bytes) -> None:
+    """Delete a needed library from the dynamic section of an ELF file"""
+    if not elf.has_needed or needed not in elf.dt_needed_strs:
+        return
 
-            old_offset += dynamic_array_size
+    offset = elf.dt_needed_strtab_offsets[elf.dt_needed_strs.index(needed)]
+
+    _delete_dynamic_array_entry(
+        f, elf, lambda tag, val: tag == ELF_CONSTANTS.DT_NEEDED and val == offset
+    )
 
 
 class CStringType:

var/spack/repos/builtin/packages/gcc-runtime/package.py

@@ -3,6 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import glob
 import os
 import re
 
@@ -11,7 +12,7 @@
 from llnl.util import tty
 
 from spack.package import *
-from spack.util.elf import parse_elf
+from spack.util.elf import delete_needed_from_elf, parse_elf
 
 
 class GccRuntime(Package):
@@ -72,6 +73,9 @@ def install(self, spec, prefix):
         for path, name in libraries:
             install(path, os.path.join(prefix.lib, name))
 
+        if spec.platform in ("linux", "freebsd"):
+            _drop_libgfortran_zlib(prefix.lib)
+
     def _get_libraries_macho(self):
         """Same as _get_libraries_elf but for Mach-O binaries"""
         cc = Executable(self.compiler.cc)
@@ -124,6 +128,22 @@ def headers(self):
         return HeaderList([])
 
 
+def _drop_libgfortran_zlib(lib_dir: str) -> None:
+    """Due to a bug in GCC's autotools setup (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=87182),
+    libz sometimes appears as a redundant system dependency of libgfortran. Delete it."""
+    libraries = glob.glob(os.path.join(lib_dir, "libgfortran*.so*"))
+    if len(libraries) == 0:
+        return
+    with open(libraries[0], "rb+") as f:
+        elf = parse_elf(f, dynamic_section=True)
+        if not elf.has_needed:
+            return
+        libz = next((x for x in elf.dt_needed_strs if x.startswith(b"libz.so")), None)
+        if libz is None:
+            return
+        delete_needed_from_elf(f, elf, libz)
+
+
 def get_elf_libraries(compiler, libraries):
     """Get the GCC runtime libraries for ELF binaries"""
     cc = Executable(compiler.cc)