AMBER Archive (2008)

Subject: Re: AMBER: Amber 9 installation problems

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Nov 10 2008 - 11:32:39 CST

On Mon, Nov 10, 2008, drugdesign wrote:

> cpp -traditional -P -xassembler-with-cpp new2oldparm.f > _new2oldparm.f
> g95 -c -O0 -fno-second-underscore -march=nocona -o new2oldparm.o _new2oldparm.f
> /tmp/cculsjxO.s: Assembler messages:
> /tmp/cculsjxO.s:138: Error: suffix or operands invalid for `push'
> /tmp/cculsjxO.s:140: Error: suffix or operands invalid for `push'
> /tmp/cculsjxO.s:7440: Error: suffix or operands invalid for `pop'
> /tmp/cculsjxO.s:7441: Error: suffix or operands invalid for `pop'
> make[1]: *** [new2oldparm.o] Error 1
> make[1]: Leaving directory `/usr/local/TESTAMBER/amber9/src/lib'
> make: *** [serial] Error 2

This suggests that your g95 cannot compile any real programs, since new2oldparm.f
is very simple. Check that you have the correct version (x86_64) installed.

> g++ -c -o elsize.o elsize.cc
> elsize.cc: In function ???int main(int, char**)???:
> elsize.cc:117: error: ???exit??? was not declared in this scope
> elsize.cc:124: error: ???strcmp??? was not declared in this scope
> elsize.cc:145: error: ???strcmp??? was not declared in this scope
> elsize.cc:160: error: ???calloc??? was not declared in this scope
> elsize.cc:171: error: ???exit??? was not declared in this scope
> elsize.cc:233: error: ???exit??? was not declared in this scope
> elsize.cc:295: error: ???exit??? was not declared in this scope
> elsize.cc:339: error: ???exit??? was not declared in this scope
> elsize.cc: In function ???atom_count GetNumberOfAtoms(const char*, int)???:
> elsize.cc:504: error: ???exit??? was not declared in this scope
> elsize.cc: In function ???atom_count ReadAtomicCoordinates(const char*, int, atom_count, double*, double*, double*, double*,
>
> double*)???:
> elsize.cc:565: error: ???exit??? was not declared in this scope
> make[1]: *** [elsize.o] Error 1
> make[1]: Leaving directory `/usr/local/amber9/src/etc'
> make: *** [serial] Error 2

see bugfix.2 for Amber10, which should also work for Amber 9. [Can some
developer post this to the Amber9 bugfix list?]

Or, just skip building elsize.cc: it is only needed for one very specific
task.

...dac

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