AMBER Archive (2006)

Subject: Re: AMBER: amber7 compiling error

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Sun Apr 16 2006 - 14:30:23 CDT

Hi,

On Sun, 16 Apr 2006, linfu wrote:

> $ uname -a
> Linux ganode002 2.4.21-4-NUMA #1 SMP Thu Jul 15 20:16:43 CST 2004 x86_64 unknown
> $ ln -s -f Machines/Machine.pgf77 MACHINE
> $ make install
> /storage/SCSI/st12/home/user/siocrxw/MD/amber7/src/Machines/standard/sys.a(erfcfun.o)(*ABS*+0x6564006366726570): multiple definition of `no symbol'
> /usr/bin/ld: Warning: size of symbol `' changed from 3832616347984999219 to 26861573295531634 in /storage/SCSI/st12/home/user/siocrxw/MD/amber7/src/Machines/standard/sys.a(erfcfun.o)
> /usr/bin/ld: Warning: type of symbol `' changed from 3 to 15 in /storage/SCSI/st12/home/user/siocrxw/MD/amber7/src/Machines/standard/sys.a(erfcfun.o)
> /usr/bin/ld: /storage/SCSI/st12/home/user/siocrxw/MD/amber7/src/Machines/standard/sys.a(erfcfun.o): invalid string offset 1835425631 >= 374 for section `.strtab'
> /storage/SCSI/st12/home/user/siocrxw/MD/amber7/src/Machines/standard/sys.a(erfcfun.o)(*ABS*+0x707865645f): multiple definition of `no symbol'
> /usr/bin/ld: Warning: size of symbol `' changed from 26861573295531634 to 53 in /storage/SCSI/st12/home/user/siocrxw/MD/amber7/src/Machines/standard/sys.a(erfcfun.o)
> /usr/bin/ld: Warning: type of symbol `' changed from 15 to 4 in /storage/SCSI/st12/home/user/siocrxw/MD/amber7/src/Machines/standard/sys.a(erfcfun.o)
> /usr/bin/ld: BFD 2.13.90.0.16 20021126 assertion fail ../../bfd/elflink.h:2539
> /usr/bin/ld: BFD 2.13.90.0.16 20021126 assertion fail ../../bfd/elflink.h:2539
> /usr/bin/ld: BFD 2.13.90.0.16 20021126 internal error, aborting at ../../bfd/elfcode.h line 228 in bfd_elf64_swap_symbol_in
> /usr/bin/ld: Please report this bug.

This appears to be a compiler/linker bug.
Determine the versions of your tools and report the bug.

General advice for these types of situations is to
make -i clean
and
make -i install

If this doesn't produce the Amber executables of interest then try other
compilers, like gnu. BTW, amber 7 is dated; we just released amber 9.

Scott

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