patchelf fails to --set-interpreter for executable with section headers near start

[ttuegel]

The following command fails on an executable I am trying to patch to run on NixOS:

$ patchelf --set-interpreter /nix/store/ywxpkmy9kagcsvbjjhi46pr4xwpd6sfm-glibc-2.19/lib/ld-linux-x86-64.so.2 --debug server 
patching ELF file `server'
replacing section `.interp' with size 80
this is an executable
using replaced section `.interp'
last replaced is 1
looking at section `.interp'
first reserved offset/addr is 0xc00/0x400c00
first page is 0x400000
patchelf: patchelf.cc:693: void ElfFile<Elf_Ehdr, Elf_Phdr, Elf_Shdr, Elf_Addr, Elf_Off, Elf_Dyn, Elf_Sym>::rewriteSectionsExecutable() [with Elf_Ehdr = Elf64_Ehdr; Elf_Phdr = Elf64_Phdr; Elf_Shdr = Elf64_Shdr; Elf_Addr = long unsigned int; Elf_Off = long unsigned int; Elf_Dyn = Elf64_Dyn; Elf_Sym = Elf64_Sym]: Assertion `(off_t) rdi(hdr->e_shoff) >= startOffset' failed.

I think the assertion is here.

Here are the headers:

$ readelf -e server                                                               
ELF Header:
  Magic:   7f 45 4c 46 02 01 01 00 00 00 00 00 00 00 00 00 
  Class:                             ELF64
  Data:                              2's complement, little endian
  Version:                           1 (current)
  OS/ABI:                            UNIX - System V
  ABI Version:                       0
  Type:                              EXEC (Executable file)
  Machine:                           Advanced Micro Devices X86-64
  Version:                           0x1
  Entry point address:               0x41c9f6
  Start of program headers:          64 (bytes into file)
  Start of section headers:          456 (bytes into file)
  Flags:                             0x0
  Size of this header:               64 (bytes)
  Size of program headers:           56 (bytes)
  Number of program headers:         7
  Size of section headers:           64 (bytes)
  Number of section headers:         22
  Section header string table index: 13

Section Headers:
  [Nr] Name              Type             Address           Offset
       Size              EntSize          Flags  Link  Info  Align
  [ 0]                   NULL             0000000000000000  00000000
       0000000000000000  0000000000000000           0     0     0
  [ 1] .interp           PROGBITS         0000000000400be4  00000be4
       000000000000001c  0000000000000000   A       0     0     1
  [ 2] .got              PROGBITS         0000000000707000  00307000
       0000000000000008  0000000000000008  WA       0     0     8
  [ 3] .got.plt          PROGBITS         0000000000707008  00307008
       0000000000000098  0000000000000008  WA       0     0     8
  [ 4] .dynsym           DYNSYM           0000000000705f50  00305f50
       00000000000001f8  0000000000000018   A       5     0     8
  [ 5] .dynstr           STRTAB           0000000000705c90  00305c90
       0000000000000140  0000000000000000   A       0     0     1
  [ 6] .gnu.version      VERSYM           00000000007059d8  003059d8
       000000000000002a  0000000000000002   A       4     0     2
  [ 7] .gnu.version_r    VERNEED          0000000000705a08  00305a08
       0000000000000040  0000000000000000   A       5     2     8
  [ 8] .rela.plt         RELA             0000000000705dd0  00305dd0
       0000000000000180  0000000000000018   A       4     9     8
  [ 9] .plt              PROGBITS         0000000000705b80  00305b80
       0000000000000110  0000000000000010  AX       0     0     4
  [10] .hash             HASH             0000000000705a48  00305a48
       0000000000000074  0000000000000004   A       4     0     8
  [11] .rela             RELA             00000000007059c0  003059c0
       0000000000000018  0000000000000018   A       4     0     8
  [12] .dynamic          DYNAMIC          00000000007070a0  003070a0
       0000000000000130  0000000000000010  WA       5     0     8
  [13] .shstrtab         STRTAB           0000000000000000  00305ac0
       00000000000000bd  0000000000000000           0     0     1
  [14] .text             PROGBITS         0000000000400c00  00000c00
       0000000000189780  0000000000000000  AX       0     0     8
  [15] .rodata           PROGBITS         000000000058a380  0018a380
       000000000017b640  0000000000000000   A       0     0     8
  [16] .gosymtab         PROGBITS         00000000007059c0  003059c0
       0000000000000000  0000000000000000   A       0     0     8
  [17] .gopclntab        PROGBITS         00000000007059c0  003059c0
       0000000000000000  0000000000000000   A       0     0     8
  [18] .noptrdata        PROGBITS         00000000007071d0  003071d0
       000000000000fd38  0000000000000000  WA       0     0     8
  [19] .data             PROGBITS         0000000000716f08  00316f08
       0000000000007888  0000000000000000  WA       0     0     8
  [20] .bss              NOBITS           000000000071e790  0031e790
       0000000000012bb0  0000000000000000  WA       0     0     8
  [21] .noptrbss         NOBITS           0000000000731340  00331340
       0000000002009e00  0000000000000000  WA       0     0     8
Key to Flags:
  W (write), A (alloc), X (execute), M (merge), S (strings), l (large)
  I (info), L (link order), G (group), T (TLS), E (exclude), x (unknown)
  O (extra OS processing required) o (OS specific), p (processor specific)

Program Headers:
  Type           Offset             VirtAddr           PhysAddr
                 FileSiz            MemSiz              Flags  Align
  PHDR           0x0000000000000040 0x0000000000400040 0x0000000000400040
                 0x0000000000000188 0x0000000000000188  R E    1000
  INTERP         0x0000000000000be4 0x0000000000400be4 0x0000000000400be4
                 0x000000000000001c 0x000000000000001c  R      1
      [Requesting program interpreter: /lib64/ld-linux-x86-64.so.2]
  LOAD           0x0000000000000040 0x0000000000400040 0x0000000000400040
                 0x0000000000306108 0x0000000000306108  R E    1000
  LOAD           0x0000000000307000 0x0000000000707000 0x0000000000707000
                 0x0000000000017790 0x0000000002034140  RW     1000
  DYNAMIC        0x00000000003070a0 0x00000000007070a0 0x00000000007070a0
                 0x0000000000000130 0x0000000000000130  RW     8
  TLS            0x0000000000000000 0x0000000000000000 0x0000000000000000
                 0x0000000000000000 0x0000000000000010  R      8
  GNU_STACK      0x0000000000000000 0x0000000000000000 0x0000000000000000
                 0x0000000000000000 0x0000000000000000  RW     8

 Section to Segment mapping:
  Segment Sections...
   00     
   01     .interp 
   02     .interp .dynsym .dynstr .gnu.version .gnu.version_r .rela.plt .plt .hash .rela .shstrtab .text .rodata .gosymtab .gopclntab 
   03     .got .got.plt .dynamic .noptrdata .data .bss .noptrbss 
   04     .dynamic 
   05     
   06

Has anyone encountered this before? Is there a workaround? Please let me know if there's anything else I need to do to debug the issue.