AMBER Archive (2008)

Subject: Re: AMBER: Amber 9 installation problems

From: drugdesign (drugdesign_at_yandex.ru)
Date: Tue Nov 11 2008 - 08:13:32 CST

Thank you very much. This works.
But now I have xleap installation problem, which is described here:
http://structbio.vanderbilt.edu/archives/amber-archive/2006/0656.php
Is there now a bugfix for it now?

Best regards,
Andrew

10.11.08, 19:37, "Shozeb Haider" <shozeb.haider_at_pharmacy.ac.uk>:

> The way I got rid of this error was to edit
> /usr/local/amber9/src/etc/elsize.cc and included the lines #include
> <string.h> and #include<cstdlib>
> Hope it helps.
> Best wishes
> Shozeb
> drugdesign wrote:
> > Dear Amber community,
> > I have problems in installation of Amber 9 on OpenSuse 11, 64 bit system.
> >
> > I have unpacked amber9 -> I've applied all bugfixes for amber9 -> set up an environment (bashrc is in the attachment).
> > Then I've tried to configure Amber 9 with g95 and ifort (each time removing amber 9 folder before new installation).
> > g95 was installed according to instruction with link ln -s $PWD/g95-install/bin/i686-pc-linux-gnu-g95 /usr/bin/g95 and also making source in bashrc file. For ifort I've also have written source in bashrc.
> > User evironment was used for amber9 installation under /su user.
> >
> > 1) in case of g95 i get an error after "./configure g95" and "make serial":
> > linux-yalu:/usr/local/TESTAMBER/amber9/src # make serial
> > Starting installation of Amber9 (serial) at Thu Aug 28 18:32:14 EEST 2008.
> > cd lib; make install
> > make[1]: Entering directory `/usr/local/TESTAMBER/amber9/src/lib'
> > 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
> >
> >
> > 2)in case of ifort afeter ./configure -p4 -static ifort_x86_64 and "make serial" I get an error:
> >
> > ifort -static -o nucgen nucgen.o ngfil.o ../lib/amopen.o ../lib/mexit.o ../lib/nxtsec.o
> > 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
> >
> >
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