Linking works, but ldd does not show linked libraries and runtime fails - linux

I'm trying to compile a library from this repo. Running make test in the root folder produces an executable file tests that depends on libpcreposix and libpcre. The linking line looks like this:
gfortran -std=f2008 -fall-intrinsics -ffree-line-length-none -Wall -Wextra -Wpedantic -Wno-target-lifetime -Wno-compare-reals -Jbuild.gnu.debug -g -Og -fcheck=bounds,do,mem,pointer,recursion -Isrc -Itests -DUSE_PCRE tests/tests.F90 build.gnu.debug/*.o -lpcreposix -lpcre -o build.gnu.debug/tests
As you can see, the required libraries are linked via -lpcreposix -lpcre and this line executes successfully, producing executable tests, which, however, crashes at runtime. I strongly suspect that this crash has something to do with these libraries, so I ran ldd tests, which showed the following output:
$ ldd build.gnu.debug/tests
linux-vdso.so.1 (0x00007ffe5b481000)
libgfortran.so.5 => /usr/lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007fd307a59000)
libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007fd30790a000)
libgcc_s.so.1 => /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fd3078ef000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007fd3078a5000)
libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007fd3076b3000)
/lib64/ld-linux-x86-64.so.2 (0x00007fd307e24000)
As you can see, libpcreposix and libpcre and not even on this list. The libraries were installed via sudo apt install libpcre3 libpcre3-dev and I can see them in /usr/lib/x86_64-linux-gnu/libpcreposix.so.3.13 and /usr/lib/x86_64-linux-gnu/libpcre.so.3.13.3. I have added this path to LD_LIBRARY_PATH (which did not even exist before that), but it did not change anything.
$ echo $LD_LIBRARY_PATH
/usr/lib/x86_64-linux-gnu
The executable tests definitely depends on these libraries, but just in case I have also tried to add -Wl,--no-as-needed to the linking line, which also did not change anything. I have tried the exact same sequence of actions on another machine and it worked without issues (and I was able to see the required libraries in the output of ldd), so it has to be related with the setup of my machine. The machine where I have issues is a recently created virtual machine (Ubuntu 20), so I might have forgotten to install of set up something here.
Edit:
Output of linking with -Wl,--verbose:
$ gfortran -std=f2008 -fall-intrinsics -ffree-line-length-none -Wall -Wextra -Wpedantic -Wno-target-lifetime -Wno-compare-reals -Jbuild.gnu.debug -g -Og -fcheck=bounds,do,mem,pointer,recursion -Isrc -Itests -DUSE_PCRE tests/tests.F90 build.gnu.debug/*.o -lpcreposix -lpcre -o build.gnu.debug/tests -Wl,--verbose
GNU ld (GNU Binutils for Ubuntu) 2.34
Supported emulations:
elf_x86_64
elf32_x86_64
elf_i386
elf_iamcu
elf_l1om
elf_k1om
i386pep
i386pe
using internal linker script:
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/lib/x86_64-linux-gnu/libc.so.6
attempt to open /usr/lib/x86_64-linux-gnu/libc_nonshared.a succeeded
/usr/lib/x86_64-linux-gnu/libc_nonshared.a
(/usr/lib/x86_64-linux-gnu/libc_nonshared.a)elf-init.oS
attempt to open /lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 succeeded
/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
/usr/lib/x86_64-linux-gnu/libc_nonshared.a
/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
attempt to open /usr/lib/gcc/x86_64-linux-gnu/9/libgcc_s.so succeeded
opened script file /usr/lib/gcc/x86_64-linux-gnu/9/libgcc_s.so
/usr/lib/gcc/x86_64-linux-gnu/9/libgcc_s.so
opened script file /usr/lib/gcc/x86_64-linux-gnu/9/libgcc_s.so
attempt to open libgcc_s.so.1 failed
attempt to open /usr/lib/gcc/x86_64-linux-gnu/9/libgcc_s.so.1 failed
attempt to open /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libgcc_s.so.1 succeeded
/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libgcc_s.so.1
attempt to open /usr/lib/gcc/x86_64-linux-gnu/9/libgcc.so failed
attempt to open /usr/lib/gcc/x86_64-linux-gnu/9/libgcc.a succeeded
/usr/lib/gcc/x86_64-linux-gnu/9/libgcc.a
attempt to open /usr/lib/gcc/x86_64-linux-gnu/9/libgcc.so failed
attempt to open /usr/lib/gcc/x86_64-linux-gnu/9/libgcc.a succeeded
/usr/lib/gcc/x86_64-linux-gnu/9/libgcc.a
attempt to open /usr/lib/gcc/x86_64-linux-gnu/9/crtendS.o succeeded
/usr/lib/gcc/x86_64-linux-gnu/9/crtendS.o
attempt to open /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crtn.o succeeded
/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crtn.o
libquadmath.so.0 needed by /usr/lib/gcc/x86_64-linux-gnu/9/libgfortran.so
found libquadmath.so at /usr/lib/gcc/x86_64-linux-gnu/9/libquadmath.so
libgcc_s.so.1 needed by /usr/lib/gcc/x86_64-linux-gnu/9/libgfortran.so
found libgcc_s.so.1 at /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libgcc_s.so.1
ld-linux-x86-64.so.2 needed by /usr/lib/gcc/x86_64-linux-gnu/9/libgfortran.so
found ld-linux-x86-64.so.2 at /lib/x86_64-linux-gnu/ld-linux-x86-64.so.2

Related

Gold: reorder sections using a linker script?

I'm trying to write a linker script that will put the .tdata and .tbss sections beside each other. I'm trying to do this by passing a ld file with the following contents:
SECTIONS
{
.tdata : { *(.tdata .tdata.* .gnu.linkonce.td.*) }
.tbss : { *(.tbss .tbss.* .gnu.linkonce.tb.*) *(.tcommon) }
}
This linker script doesn't appear to have the desired effect. The .tdata and .tbss sections aren't beside each other in the outputted shared library.

`.note.gnu.property' referenced in section `.text' of defined in discarded section `.note.gnu.property'

I have the files port.cpp and port.h.
The code isn't relevant for this question. The problem, I believe, is the linker script.
The linker script contains the following code:
ENTRY(loader)
OUTPUT_FORMAT(elf32-i386)
OUTPUT_ARCH(i386:i386)
SECTIONS
{
. = 0x0100000;
.text :
{
*(.multiboot)
*(.text*)
*(.rodata)
}
.data :
{
start_ctors = .;
KEEP(*( .init_array ));
KEEP(*(SORT_BY_INIT_PRIORITY( .init_array.* )));
end_ctors = .;
*(.data)
}
.bss :
{
*(.bss)
}
/DISCARD/ :
{
*(.fini_array*)
*(.comment)
}
}
And when I run ld with the only flag being -melf_i386 I get this error:
`.note.gnu.property' referenced in section `.text' of port.o: defined in discarded section `.note.gnu.property' of port.o
I believe the problem is the linker, but even after reading ld documentation, looking at the assembly code being generated and adding KEEP(*( .note.gnu.property )); I could not fix it.

Is there a way to remove segment GNU_STACK

I am trying to create a minimum executable using gcc/binutils.
My ld scripts is as below:
OUTPUT_FORMAT("elf64-x86-64", "elf64-x86-64",
"elf64-x86-64")
OUTPUT_ARCH(i386:x86-64)
ENTRY(_start)
SEARCH_DIR("/usr/x86_64-pc-linux-gnu/lib64"); SEARCH_DIR("/usr/lib64/binutils/x86_64-pc-linux-gnu/2.35.164"); SEARCH_DIR("/usr/local/lib64"); SEARCH_DIR("/lib64"); SEARCH_DIR("/usr/lib64"); SEARCH_DIR("/usr/x86_64-pc-linux-gnu/lib"); SEARCH_DIR("/usr/lib64/binutils/x86_64-pc-linux-gnu/2.35.1"); SEARCH_DIR("/usr/local/lib"); SEARCH_DIR("/lib"); SEARCH_DIR("/usr/lib");
SECTIONS
{
PROVIDE (__executable_start = SEGMENT_START("text-segment", 0x400000)); . = SEGMENT_START("text-segment", 0x400000) + SIZEOF_HEADERS;
.text :
{
*(.text.unlikely .text.*_unlikely .text.unlikely.*)
*(.text.exit .text.exit.*)
*(.text.startup .text.startup.*)
*(.text.hot .text.hot.*)
*(SORT(.text.sorted.*))
*(.text .stub .text.* .gnu.linkonce.t.*)
/* .gnu.warning sections are handled specially by elf.em. */
*(.gnu.warning)
}
.data :
{
*(.data .data.* .gnu.linkonce.d.*)
SORT(CONSTRUCTORS)
}
.bss :
{
*(.dynbss)
*(.bss .bss.* .gnu.linkonce.b.*)
*(COMMON)
}
}
Everything is OK for me, except that I see a extra segment header named "GNU_STACK" with size 0.
The header increases 56 bytes of course. Does anyone know how to remove it? Creating elf by hand is crazy, I want to use gcc/binutils to do it.
Looks like no way to do it. Finally I modified binutils source to remove it.
Note: the GNU_STACK ELF program header entry is required to mark the stack as not executable on legacy systems (32-bits x86, arm and powerpc, for example). If you remove it, the stack will be automatically marked as executable by the kernel:
linux-5.17/arch/arm/kernel.elf.c#n80
In modern architectures GNU_STACK is not needed, so your linker script should be modified with the following:
OUTPUT_FORMAT("elf64-x86-64", "elf64-x86-64",
"elf64-x86-64")
OUTPUT_ARCH(i386:x86-64)
ENTRY(_start)
SEARCH_DIR("/usr/x86_64-pc-linux-gnu/lib64"); SEARCH_DIR("/usr/lib64/binutils/x86_64-pc-linux-gnu/2.35.164"); SEARCH_DIR("/usr/local/lib64"); SEARCH_DIR("/lib64"); SEARCH_DIR("/usr/lib64"); SEARCH_DIR("/usr/x86_64-pc-linux-gnu/lib"); SEARCH_DIR("/usr/lib64/binutils/x86_64-pc-linux-gnu/2.35.1"); SEARCH_DIR("/usr/local/lib"); SEARCH_DIR("/lib"); SEARCH_DIR("/usr/lib");
PHDRS
{
READONLY PT_LOAD FILEHDR PHDRS;
READWRITE PT_LOAD;
}
SECTIONS
{
PROVIDE (__executable_start = SEGMENT_START("text-segment", 0x400000)); . = SEGMENT_START("text-segment", 0x400000) + SIZEOF_HEADERS;
.text :
{
*(.text.unlikely .text.*_unlikely .text.unlikely.*)
*(.text.exit .text.exit.*)
*(.text.startup .text.startup.*)
*(.text.hot .text.hot.*)
*(SORT(.text.sorted.*))
*(.text .stub .text.* .gnu.linkonce.t.*)
/* .gnu.warning sections are handled specially by elf.em. */
*(.gnu.warning)
} : READONLY
. = ALIGN(0x1000);
.data :
{
*(.data .data.* .gnu.linkonce.d.*)
SORT(CONSTRUCTORS)
} : READWRITE
.bss :
{
*(.dynbss)
*(.bss .bss.* .gnu.linkonce.b.*)
*(COMMON)
}
}
Change the PHDRS configuration as you prefer.
If you remove the GNU_STACK entry, you should probably use the -Wtrampoline or -fno-trampolines compiler flags:
3.8 Options to Request or Suppress Warnings
3.17 Options for Code Generation Conventions

Why is there unused, empty space between ELF sections?

It seems that binaries created with gcc 4.9.2 on Linux (Ubuntu 15.04, 32-bit) have a couple of thousand unused bytes between sections .eh_frame and .init_array. Example output from objdump -h for a simple executable:
Sections:
Idx Name Size VMA LMA File off Algn
[...]
16 .eh_frame 000000c0 080484ac 080484ac 000004ac 2**2
CONTENTS, ALLOC, LOAD, READONLY, DATA
17 .init_array 00000004 08049f08 08049f08 00000f08 2**2
CONTENTS, ALLOC, LOAD, DATA
[...]
.eh_frame ends at file offset 0x56c but .init_array starts at 0xf08 leaving a hole of 0x99c = 2460 bytes. All other sections start immediately after the end of the previous section.
The size of the unused space varies, making it hard to observe how certain changes affect code size.
Where does this hole come from? Is there a way to avoid it?
Update: Output of ld --verbose:
$ cat so.c
int main() {
return 0;
}
$ gcc so.c -Wl,--verbose -o so
GNU ld (GNU Binutils for Ubuntu) 2.25
Supported emulations:
elf_i386
i386linux
elf32_x86_64
elf_x86_64
elf_l1om
elf_k1om
i386pep
i386pe
using internal linker script:
==================================================
/* Script for -z combreloc: combine and sort reloc sections */
/* Copyright (C) 2014 Free Software Foundation, Inc.
Copying and distribution of this script, with or without modification,
are permitted in any medium without royalty provided the copyright
notice and this notice are preserved. */
OUTPUT_FORMAT("elf32-i386", "elf32-i386",
"elf32-i386")
OUTPUT_ARCH(i386)
ENTRY(_start)
SEARCH_DIR("=/usr/i686-linux-gnu/lib32"); SEARCH_DIR("=/usr/local/lib32"); SEARCH_DIR("=/lib32"); SEARCH_DIR("=/usr/lib32"); SEARCH_DIR("=/usr/i686-linux-gnu/lib"); SEARCH_DIR("=/usr/local/lib/i386-linux-gnu"); SEARCH_DIR("=/usr/local/lib"); SEARCH_DIR("=/lib/i386-linux-gnu"); SEARCH_DIR("=/lib"); SEARCH_DIR("=/usr/lib/i386-linux-gnu"); SEARCH_DIR("=/usr/lib");
SECTIONS
{
/* Read-only sections, merged into text segment: */
PROVIDE (__executable_start = SEGMENT_START("text-segment", 0x08048000)); . = SEGMENT_START("text-segment", 0x08048000) + SIZEOF_HEADERS;
.interp : { *(.interp) }
.note.gnu.build-id : { *(.note.gnu.build-id) }
.hash : { *(.hash) }
.gnu.hash : { *(.gnu.hash) }
.dynsym : { *(.dynsym) }
.dynstr : { *(.dynstr) }
.gnu.version : { *(.gnu.version) }
.gnu.version_d : { *(.gnu.version_d) }
.gnu.version_r : { *(.gnu.version_r) }
.rel.dyn :
{
*(.rel.init)
*(.rel.text .rel.text.* .rel.gnu.linkonce.t.*)
*(.rel.fini)
*(.rel.rodata .rel.rodata.* .rel.gnu.linkonce.r.*)
*(.rel.data.rel.ro .rel.data.rel.ro.* .rel.gnu.linkonce.d.rel.ro.*)
*(.rel.data .rel.data.* .rel.gnu.linkonce.d.*)
*(.rel.tdata .rel.tdata.* .rel.gnu.linkonce.td.*)
*(.rel.tbss .rel.tbss.* .rel.gnu.linkonce.tb.*)
*(.rel.ctors)
*(.rel.dtors)
*(.rel.got)
*(.rel.bss .rel.bss.* .rel.gnu.linkonce.b.*)
*(.rel.ifunc)
}
.rel.plt :
{
*(.rel.plt)
PROVIDE_HIDDEN (__rel_iplt_start = .);
*(.rel.iplt)
PROVIDE_HIDDEN (__rel_iplt_end = .);
}
.init :
{
KEEP (*(SORT_NONE(.init)))
}
.plt : { *(.plt) *(.iplt) }
.text :
{
*(.text.unlikely .text.*_unlikely .text.unlikely.*)
*(.text.exit .text.exit.*)
*(.text.startup .text.startup.*)
*(.text.hot .text.hot.*)
*(.text .stub .text.* .gnu.linkonce.t.*)
/* .gnu.warning sections are handled specially by elf32.em. */
*(.gnu.warning)
}
.fini :
{
KEEP (*(SORT_NONE(.fini)))
}
PROVIDE (__etext = .);
PROVIDE (_etext = .);
PROVIDE (etext = .);
.rodata : { *(.rodata .rodata.* .gnu.linkonce.r.*) }
.rodata1 : { *(.rodata1) }
.eh_frame_hdr : { *(.eh_frame_hdr) }
.eh_frame : ONLY_IF_RO { KEEP (*(.eh_frame)) }
.gcc_except_table : ONLY_IF_RO { *(.gcc_except_table
.gcc_except_table.*) }
/* These sections are generated by the Sun/Oracle C++ compiler. */
.exception_ranges : ONLY_IF_RO { *(.exception_ranges
.exception_ranges*) }
/* Adjust the address for the data segment. We want to adjust up to
the same address within the page on the next page up. */
. = ALIGN (CONSTANT (MAXPAGESIZE)) - ((CONSTANT (MAXPAGESIZE) - .) & (CONSTANT (MAXPAGESIZE) - 1)); . = DATA_SEGMENT_ALIGN (CONSTANT (MAXPAGESIZE), CONSTANT (COMMONPAGESIZE));
/* Exception handling */
.eh_frame : ONLY_IF_RW { KEEP (*(.eh_frame)) }
.gcc_except_table : ONLY_IF_RW { *(.gcc_except_table .gcc_except_table.*) }
.exception_ranges : ONLY_IF_RW { *(.exception_ranges .exception_ranges*) }
/* Thread Local Storage sections */
.tdata : { *(.tdata .tdata.* .gnu.linkonce.td.*) }
.tbss : { *(.tbss .tbss.* .gnu.linkonce.tb.*) *(.tcommon) }
.preinit_array :
{
PROVIDE_HIDDEN (__preinit_array_start = .);
KEEP (*(.preinit_array))
PROVIDE_HIDDEN (__preinit_array_end = .);
}
.init_array :
{
PROVIDE_HIDDEN (__init_array_start = .);
KEEP (*(SORT_BY_INIT_PRIORITY(.init_array.*) SORT_BY_INIT_PRIORITY(.ctors.*)))
KEEP (*(.init_array EXCLUDE_FILE (*crtbegin.o *crtbegin?.o *crtend.o *crtend?.o ) .ctors))
PROVIDE_HIDDEN (__init_array_end = .);
}
.fini_array :
{
PROVIDE_HIDDEN (__fini_array_start = .);
KEEP (*(SORT_BY_INIT_PRIORITY(.fini_array.*) SORT_BY_INIT_PRIORITY(.dtors.*)))
KEEP (*(.fini_array EXCLUDE_FILE (*crtbegin.o *crtbegin?.o *crtend.o *crtend?.o ) .dtors))
PROVIDE_HIDDEN (__fini_array_end = .);
}
.ctors :
{
/* gcc uses crtbegin.o to find the start of
the constructors, so we make sure it is
first. Because this is a wildcard, it
doesn't matter if the user does not
actually link against crtbegin.o; the
linker won't look for a file to match a
wildcard. The wildcard also means that it
doesn't matter which directory crtbegin.o
is in. */
KEEP (*crtbegin.o(.ctors))
KEEP (*crtbegin?.o(.ctors))
/* We don't want to include the .ctor section from
the crtend.o file until after the sorted ctors.
The .ctor section from the crtend file contains the
end of ctors marker and it must be last */
KEEP (*(EXCLUDE_FILE (*crtend.o *crtend?.o ) .ctors))
KEEP (*(SORT(.ctors.*)))
KEEP (*(.ctors))
}
.dtors :
{
KEEP (*crtbegin.o(.dtors))
KEEP (*crtbegin?.o(.dtors))
KEEP (*(EXCLUDE_FILE (*crtend.o *crtend?.o ) .dtors))
KEEP (*(SORT(.dtors.*)))
KEEP (*(.dtors))
}
.jcr : { KEEP (*(.jcr)) }
.data.rel.ro : { *(.data.rel.ro.local* .gnu.linkonce.d.rel.ro.local.*) *(.data.rel.ro .data.rel.ro.* .gnu.linkonce.d.rel.ro.*) }
.dynamic : { *(.dynamic) }
.got : { *(.got) *(.igot) }
. = DATA_SEGMENT_RELRO_END (SIZEOF (.got.plt) >= 12 ? 12 : 0, .);
.got.plt : { *(.got.plt) *(.igot.plt) }
.data :
{
*(.data .data.* .gnu.linkonce.d.*)
SORT(CONSTRUCTORS)
}
.data1 : { *(.data1) }
_edata = .; PROVIDE (edata = .);
. = .;
__bss_start = .;
.bss :
{
*(.dynbss)
*(.bss .bss.* .gnu.linkonce.b.*)
*(COMMON)
/* Align here to ensure that the .bss section occupies space up to
_end. Align after .bss to ensure correct alignment even if the
.bss section disappears because there are no input sections.
FIXME: Why do we need it? When there is no .bss section, we don't
pad the .data section. */
. = ALIGN(. != 0 ? 32 / 8 : 1);
}
. = ALIGN(32 / 8);
. = SEGMENT_START("ldata-segment", .);
. = ALIGN(32 / 8);
_end = .; PROVIDE (end = .);
. = DATA_SEGMENT_END (.);
/* Stabs debugging sections. */
.stab 0 : { *(.stab) }
.stabstr 0 : { *(.stabstr) }
.stab.excl 0 : { *(.stab.excl) }
.stab.exclstr 0 : { *(.stab.exclstr) }
.stab.index 0 : { *(.stab.index) }
.stab.indexstr 0 : { *(.stab.indexstr) }
.comment 0 : { *(.comment) }
/* DWARF debug sections.
Symbols in the DWARF debugging sections are relative to the beginning
of the section so we begin them at 0. */
/* DWARF 1 */
.debug 0 : { *(.debug) }
.line 0 : { *(.line) }
/* GNU DWARF 1 extensions */
.debug_srcinfo 0 : { *(.debug_srcinfo) }
.debug_sfnames 0 : { *(.debug_sfnames) }
/* DWARF 1.1 and DWARF 2 */
.debug_aranges 0 : { *(.debug_aranges) }
.debug_pubnames 0 : { *(.debug_pubnames) }
/* DWARF 2 */
.debug_info 0 : { *(.debug_info .gnu.linkonce.wi.*) }
.debug_abbrev 0 : { *(.debug_abbrev) }
.debug_line 0 : { *(.debug_line .debug_line.* .debug_line_end ) }
.debug_frame 0 : { *(.debug_frame) }
.debug_str 0 : { *(.debug_str) }
.debug_loc 0 : { *(.debug_loc) }
.debug_macinfo 0 : { *(.debug_macinfo) }
/* SGI/MIPS DWARF 2 extensions */
.debug_weaknames 0 : { *(.debug_weaknames) }
.debug_funcnames 0 : { *(.debug_funcnames) }
.debug_typenames 0 : { *(.debug_typenames) }
.debug_varnames 0 : { *(.debug_varnames) }
/* DWARF 3 */
.debug_pubtypes 0 : { *(.debug_pubtypes) }
.debug_ranges 0 : { *(.debug_ranges) }
/* DWARF Extension. */
.debug_macro 0 : { *(.debug_macro) }
.gnu.attributes 0 : { KEEP (*(.gnu.attributes)) }
/DISCARD/ : { *(.note.GNU-stack) *(.gnu_debuglink) *(.gnu.lto_*) }
}
==================================================
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/../../../i386-linux-gnu/crt1.o succeeded
/usr/lib/gcc/i686-linux-gnu/4.9/../../../i386-linux-gnu/crt1.o
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/../../../i386-linux-gnu/crti.o succeeded
/usr/lib/gcc/i686-linux-gnu/4.9/../../../i386-linux-gnu/crti.o
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/crtbegin.o succeeded
/usr/lib/gcc/i686-linux-gnu/4.9/crtbegin.o
attempt to open /tmp/ccQ0fTTK.o succeeded
/tmp/ccQ0fTTK.o
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/libgcc.so failed
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/libgcc.a succeeded
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/libgcc_s.so succeeded
-lgcc_s (/usr/lib/gcc/i686-linux-gnu/4.9/libgcc_s.so)
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/libc.so failed
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/libc.a failed
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/../../../i386-linux-gnu/libc.so succeeded
opened script file /usr/lib/gcc/i686-linux-gnu/4.9/../../../i386-linux-gnu/libc.so
opened script file /usr/lib/gcc/i686-linux-gnu/4.9/../../../i386-linux-gnu/libc.so
attempt to open /lib/i386-linux-gnu/libc.so.6 succeeded
/lib/i386-linux-gnu/libc.so.6
attempt to open /usr/lib/i386-linux-gnu/libc_nonshared.a succeeded
(/usr/lib/i386-linux-gnu/libc_nonshared.a)elf-init.oS
attempt to open /lib/i386-linux-gnu/ld-linux.so.2 succeeded
/lib/i386-linux-gnu/ld-linux.so.2
/lib/i386-linux-gnu/ld-linux.so.2
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/libgcc.so failed
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/libgcc.a succeeded
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/libgcc_s.so succeeded
-lgcc_s (/usr/lib/gcc/i686-linux-gnu/4.9/libgcc_s.so)
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/crtend.o succeeded
/usr/lib/gcc/i686-linux-gnu/4.9/crtend.o
attempt to open /usr/lib/gcc/i686-linux-gnu/4.9/../../../i386-linux-gnu/crtn.o succeeded
/usr/lib/gcc/i686-linux-gnu/4.9/../../../i386-linux-gnu/crtn.o
ld-linux.so.2 needed by /lib/i386-linux-gnu/libc.so.6
found ld-linux.so.2 at /lib/i386-linux-gnu/ld-linux.so.2
There are three regions of memory to consider there:
Read-only data.
Non-lazy relocations that can be fixed up at load time.
Data.
Now, the .eh_frame section is marked READONLY, so it goes into the first section.
.init_array is an array of function pointers to initialization functions, which can be resolved to their absolute addresses when loading the program/library, and then marked read-only (writing to function pointers is a common way to exploit vulnerabilities), so it goes into the second region.
The relevant parts of the linker script are:
[...]
.eh_frame : ONLY_IF_RO { KEEP (*(.eh_frame)) }
[...]
/* Adjust the address for the data segment. We want to adjust up to
the same address within the page on the next page up. */
. = ALIGN (CONSTANT (MAXPAGESIZE)) - ((CONSTANT (MAXPAGESIZE) - .) & (CONSTANT (MAXPAGESIZE) - 1));
. = DATA_SEGMENT_ALIGN (CONSTANT (MAXPAGESIZE), CONSTANT (COMMONPAGESIZE));
[...]
.init_array :
[...]
.got : { *(.got) *(.igot) }
. = DATA_SEGMENT_RELRO_END (SIZEOF (.got.plt) >= 12 ? 12 : 0, .);
.got.plt : { *(.got.plt) *(.igot.plt) }
.data :
[...]
. = DATA_SEGMENT_END (.);
You can consult the documentation for builtin functions for GNU ld linker scripts at https://sourceware.org/binutils/docs/ld/Builtin-Functions.html. But beware that DATA_SEGMENT_ALIGN documentation is incorrect, as reported by Stephen Kell at binutils bug #19203: "DATA_SEGMENT_ALIGN documentation is not consistent with behaviour", apparently since Jakub Jelinek's [PATCH] Fix DATA_SEGMENT_ALIGN. DATA_SEGMENT_ALIGN itself was introduced at a binutils' mailing list thread called [RFC PATCH] Smarter aligning of data segment.
Somehow, the following:
. = ALIGN (CONSTANT (MAXPAGESIZE)) - ((CONSTANT (MAXPAGESIZE) - .) & (CONSTANT (MAXPAGESIZE) - 1));
. = DATA_SEGMENT_ALIGN (CONSTANT (MAXPAGESIZE), CONSTANT (COMMONPAGESIZE));
causes a 1-page jump, which in your example would move you from 0x0804856c to 0x0804956c.
When the linker option -z relro is used, requesting relocations fixed up at load time to be marked read-only, DATA_SEGMENT_RELRO_END causes the previous DATA_SEGMENT_ALIGN to add enough padding to cause the sum of the two arguments of DATA_SEGMENT_RELRO_END to be aligned to a new page.
So, assuming .got.plt has at least three pointers, those first three pointers (which are used right away by the loader) will be in the second region, and the rest of .got.plt on the third.
The padding added by DATA_SEGMENT_ALIGN moves you from 0x0804956c to 0x08049f08. When everything that can be mprotected read-only after fix-ups is emitted, you'll be at 0x0804a000, in a new page, which will be kept read-write.

Bonescript Unable to find devicetree fragment

I'm working with a BeagleBone Black and trying to get bonescript running. I'm running Debian Wheezy with the latest updates and the latest versions of node v0.10.21 and bonescript 0.2.4. I'm able to blink the internal LED, so I'm fairly certain my installation is working fine. My problem is that I'm unable to control any of the P8 or P9 gpios. Using the examples on the bonescript website I'm running the following script. I'm not sure exactly what this error means so even if someone can point me into the right direction I would appreciate it.
Thank you
Scottt
=============================================
var b = require('bonescript');
var led = "P8_3";
var state = 0;
b.pinMode(led, b.output);
toggleLED = function() {
state = state ? 0 : 1;
b.digitalWrite(led, state);
};
timer = setInterval(toggleLED, 100);
stopTimer = function() {
clearInterval(timer);
};
setTimeout(stopTimer, 30000);
=====================================================
I turned on bonescript debugging and get the following output regarding being unable to find the devicetree fragment.
root#debian-armhf:/usr/lib/node_modules/bonescript# nodejs blinkext.js
debug: cpuinfo = processor : 0
model name : ARMv7 Processor rev 2 (v7l)
BogoMIPS : 660.76
Features : swp half thumb fastmult vfp edsp thumbee neon vfpv3 tls
CPU implementer : 0x41
CPU architecture: 7
CPU variant : 0x3
CPU part : 0xc08
CPU revision : 2
Hardware : Generic AM33XX (Flattened Device Tree)
Revision : 0000
Serial : 0000000000000000
debug: index.js loaded
debug: pinMode(P8_3,,,,);
debug: templateFilename = /usr/lib/node_modules/bonescript/bspm_template.dts
debug: fragment = bspm_P8_3_2f
debug: command = dtc -O dtb -o /lib/firmware/bspm_P8_3_2f-00A0.dtbo -b 0 -# /lib/firmware/bspm_P8_3_2f-00A0.dts
error: Failed to find devicetree fragment: bspm_P8_3_2f
info: 0: 54:PF---
1: 55:PF---
2: 56:PF---
3: 57:PF---
4: ff:P-O-L Bone-LT-eMMC-2G,00A0,Texas Instrument,BB-BONE-EMMC-2G
5: ff:P-O-L Bone-Black-HDMI,00A0,Texas Instrument,BB-BONELT-HDMI
debug: Unable to configure mux for pin [object Object]: Error loading devicetree overlay for P8_3 using template bspm
debug: getPinMode(P8_3);
debug: getPinMode(P8_3): Error: ENOENT, no such file or directory '/sys/kernel/debug/pinctrl/44e10800.pinmux/pins'
debug: pinMode: mode = {"pin":"P8_3","name":"GPIO1_6","options":["gpmc_ad6","mmc1_dat6","NA","NA","NA","NA","NA","gpio1_6"],"gpio":{"allocated":false}}
debug: getPinMode(P8_3);
debug: getPinMode(P8_3): Error: ENOENT, no such file or directory '/sys/kernel/debug/pinctrl/44e10800.pinmux/pins'
info: Error loading devicetree overlay for P8_3 using template bspm
=======================================================
Here is what I believe is the overlay template bonescript creates.
/*
* This is a template-generated file from BoneScript
*/
/dts-v1/;
/plugin/;
/{
compatible = "ti,beaglebone", "ti,beaglebone-black";
part_number = "BS_PINMODE_P8_3_0x2f";
version = "00A0";
exclusive-use =
"P8.3",
"gpio1_6";
fragment#0 {
target = <&am33xx_pinmux>;
__overlay__ {
bs_pinmode_P8_3_0x2f: pinmux_bs_pinmode_P8_3_0x2f {
pinctrl-single,pins = <0x018 0x2f>;
};
};
};
fragment#1 {
target = <&ocp>;
__overlay__ {
bs_pinmode_P8_3_0x2f_pinmux {
compatible = "bone-pinmux-helper";
status = "okay";
pinctrl-names = "default";
pinctrl-0 = <&bs_pinmode_P8_3_0x2f>;
target = <&am33xx_pinmux>;
__overlay__ {
bs_pinmode_P8_3_0x2f: pinmux_bs_pinmode_P8_3_0x2f {
pinctrl-single,pins = <0x018 0x2f>;
};
};
};
fragment#1 {
target = <&ocp>;
__overlay__ {
bs_pinmode_P8_3_0x2f_pinmux {
compatible = "bone-pinmux-helper";
status = "okay";
pinctrl-names = "default";
pinctrl-0 = <&bs_pinmode_P8_3_0x2f>;
};
};
};
};
We have forked bonescript and released new package. We faced same error and now solved everything by re-writing lot of code in original bonescript. You can install and use in your projects. https://www.npmjs.org/package/octalbonescript

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