AMBER Archive (2008)

Subject: Re: AMBER: ld: cannot find -lgcc_s

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Dec 12 2008 - 08:26:00 CST

On Fri, Dec 12, 2008, moitrayee_at_mbu.iisc.ernet.in wrote:
>
> I am trying to install AMBER8 on a 32-bit laptop with ubuntu 8.04.
>
> I am getting the following error message on make serial:
>
> Starting installation of Amber8 (serial) at Fri Dec 12 19:07:31 IST 2008.
> mkdir ../exe
> mkdir: cannot create directory `../exe': File exists
> make: [serial] Error 1 (ignored)
> cd lib; make install
> make[1]: Entering directory `/soft/amber8/src/lib'
> /opt/intel/bin/Compiler/11.0/074/bin/ia32/ifort -o new2oldparm new2oldparm.o
> nxtsec.o
> ipo: warning #11010: file format not recognized for
> /usr/lib/gcc/x86_64-linux-gnu/4.2.3/crtbegin.o, possible linker script
> ipo: warning #11010: file format not recognized for
> /usr/lib/gcc/x86_64-linux-gnu/4.2.3//libgcc_s.so, possible linker script
> ipo: warning #11010: file format not recognized for
> /usr/lib/gcc/x86_64-linux-gnu/4.2.3/crtend.o, possible linker script
               ^^^^^^^^^^^^^^^^^

Looks like you have x86_64 libraries installed, but maybe not the 32-bit
versions(?) It's unclear why you would have directories like those above on a
32-bit laptop.

> ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.2.3//libgcc_s.so when
> searching for -lgcc_s
> ld: cannot find -lgcc_s

Certainly, you should google on "cannot find -lgcc_s". Which solution depends
on characteristics of your machine.

Failure to compile new2oldparm is almost always a compiler installation
failure: you probably can't compile any fortran programs.

Since you are (a) on a laptop; and (b) still using Amber8, I suspect that
absolute best performance is not your top priority. Hence, if you can't solve
the ifort problem easily, I'd suggest compiling with g95 or gfortran.

...dac

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