Aligns TLS section in elf binary to fix termux / ARM64 bionic error message: TLS Segement is underaligned

align_file.py

# copied from https://github.com/Lzhiyong/termux-ndk/blob/master/patches/align_fix.py
# wiht small adjustments

import struct
import sys
import os

if len(sys.argv) < 2:
    print('Usage: ' + os.path.basename(sys.argv[0]) + ' input_file')
    exit(-1)

with open(sys.argv[1], 'r+b') as f:
  f.seek(0)
  hdr = f.read(16)
  if hdr[0] != 0x7f or hdr[1] != ord('E') or hdr[2] != ord('L') or hdr[3] != ord('F'):
    print('Not an elf file')
    exit(-1)

  if hdr[4] == 1:
    # 32 bit code
    # print('32 bit code')
    f.seek(28)
    offset = struct.unpack('<I', f.read(4))[0]
    f.seek(42)
    phsize = struct.unpack('<H', f.read(2))[0]
    phnum = struct.unpack('<H', f.read(2))[0]
    for i in range(0, phnum):
      f.seek(offset + i * phsize)
      t = struct.unpack('<I', f.read(4))[0]
      if t == 7:
        f.seek(28 - 4, 1)
        align = struct.unpack('<I', f.read(4))[0]
        # print('Found TLS segment with align = ' + str(align))
        if (align < 32):
          # print('TLS segment is underaligned, patching')
          f.seek(-4, 1)
          f.write(struct.pack('<I', 32))

  elif hdr[4] == 2:
    f.seek(32)
    offset = struct.unpack('<Q', f.read(8))[0]
    f.seek(54)
    phsize = struct.unpack('<H', f.read(2))[0]
    phnum = struct.unpack('<H', f.read(2))[0]
    print(offset, phsize, phnum)
    for i in range(0, phnum):
        f.seek(offset + i * phsize)
        t = struct.unpack('<I', f.read(4))[0]
        if t == 7:
            f.seek(48 - 4, 1)
            align_pos = f.tell()
            align = struct.unpack('<Q', f.read(8))[0]
            print(f"Found TLS segment with align = {align} at offset {align_pos}")
            if align < 4096:
                print(f"TLS segment is underaligned ({align}), patching to 4096")
                f.seek(-8, 1)
                f.write(struct.pack('<Q', 4096))

  else:
    print('Unknown file class')
    exit(-1)