Using patchelf --add-needed and --remove-needed breaks PIE executable

[gamazeps]

I currently need patchelf to add a dependency to an elf file (in the jarify project if it's of any use). It seems to fail, here is a minimal repro.

I am building a simple C file compiled with -fPIE/-fpie and calling the following commands

$patchelf --remove-needed libpthread.so.0 thread
$ldd thread
Inconsistency detected by ld.so: dl-version.c: 224: _dl_check_map_versions: Assertion `needed != NULL' failed!
$patchelf --add-needed libpthread.so.0 thread
stat: No such file or director

The Makefile used here is:

CC=gcc
CFLAGS=-fPIE
LDFLAGS=-lpthread -fpie 

OBJECTS=thread.o

hello: $(OBJECTS)
	$(CC) $(CFLAGS) $(OBJECTS) -o thread $(LDFLAGS)

all:hello

.PHONY: clean
clean:
	rm -f *~ *.o thread

The c source file thread.c, (simply the wikipedia example of pthread in order to get a dynamic dependency)

#include <pthread.h>
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
 
#define NUM_THREADS     5
 
void* perform_work( void* argument )
{
  int passed_in_value;
 
  passed_in_value = *( ( int* )argument );
  printf( "Hello World! It's me, thread with argument %d!\n", passed_in_value );
 
  /* optionally: insert more useful stuff here */
 
  return NULL;
}
 
int main( int argc, char** argv )
{
  pthread_t threads[ NUM_THREADS ];
  int thread_args[ NUM_THREADS ];
  int result_code;
  unsigned index;
 
  // create all threads one by one
  for( index = 0; index < NUM_THREADS; ++index )
  {
    thread_args[ index ] = index;
    printf("In main: creating thread %d\n", index);
    result_code = pthread_create( &threads[index], NULL, perform_work, &thread_args[index] );
    assert( !result_code );
  }
 
  // wait for each thread to complete
  for( index = 0; index < NUM_THREADS; ++index )
  {
    // block until thread 'index' completes
    result_code = pthread_join( threads[ index ], NULL );
    assert( !result_code );
    printf( "In main: thread %d has completed\n", index );
   }
 
   printf( "In main: All threads completed successfully\n" );
   exit( EXIT_SUCCESS );
}

cc @mboes

[gamazeps]

A colleague on NixOS could not reproduce this.

I am using Ubuntu 16.04 LTS and uname -a gives the following output:
Linux terrier 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

I am also using patchelf on current master version, that is commit hash: 327d80443672c397970738f9e216a7e86cbf3ad7

Sorry if the bug report is not very helpful, I will gladly provide any information that you deem necessary.

[dezgeg]

A probable cause is that --remove-needed doesn't update the symbol versioning table. I have some WIP patches that I might get finished at some point...

[knedlsepp]

Some derivations of my custom nixpkgs-overlay broke on the upgrade to 18.03 with a dl-version.c: 224: _dl_check_map_versions: Assertion needed != NULL' failed`. There hasn't been any patchelf version-bump in the meantime, but it's got something to do with the remove-needed. @dezgeg: Do you have this WIP somewhere on github?

[Knightingales]

I've stumbled upon this and it is still happening. Take a simple "Hello, world!" executable and compile it:
gcc -pie -fPIE -o hello hello.c
and run
patchelf --add-needed libsomething.so ./hello
Running the ELF post edit results in
cannot execute binary file: Exec format error

[domenkozar]

Maybe try with new release? https://nixos.org/releases/patchelf/patchelf-0.10/

[ezyang]

I am able to confirm that --replace-needed did not work with patchelf-0.9 from my distro with this error message, but worked when I used master.

[domenkozar]

This is probably fixed, but needs a regression test.

[ericxsun]

I met the same error while using patchelf-0.11 to remove needed so on ubuntu 18.04

$ patchelf --version
patchelf 0.11

when edit so

$ patchelf --remove-needed libcublas.so.10.0 libonnxruntime.so

the following error would occur

$ ldd libonnxruntime.so
Inconsistency detected by ld.so: dl-version.c: 205: _dl_check_map_versions: Assertion `needed != NULL' failed!

[domenkozar]

@ericxsun could you attach libonnxruntime.so

[ericxsun]

@ericxsun could you attach libonnxruntime.so

@domenkozar pls see the shared file
https://drive.google.com/file/d/1rQZYIkzOu4UGJ4Cczm-FVM2LrxYw1Xc0/view?usp=sharing

[ericxsun]

@domenkozar any progress?

[domenkozar]

I can reproduce.

libonnxruntime.so: ELF 64-bit LSB shared object, x86-64, version 1 (GNU/Linux), statically linked, BuildID[sha1]=bec1cd4af318b6fc16319023d88714328d027886, with debug_info, not stripped

Someone could rebase #166 and check if that PR fixes the problem.

[ericxsun]

I can reproduce.

libonnxruntime.so: ELF 64-bit LSB shared object, x86-64, version 1 (GNU/Linux), statically linked, BuildID[sha1]=bec1cd4af318b6fc16319023d88714328d027886, with debug_info, not stripped

Someone could rebase #166 and check if that PR fixes the problem.

I guess it won't be ok, i.e., will not fix this problem.

the problem here, looks like things in replaceNeeded, updating the .gnu.version_r section