AMBER Archive (2009)

Subject: Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala

From: case (case_at_biomaps.rutgers.edu)
Date: Mon Nov 09 2009 - 14:02:42 CST

On Mon, Nov 09, 2009, Wallace Kunin wrote:

> Hello all, I am trying to install AmberTools 1.2 on Ubuntu 9.10 (Karmic
> Koala). I have read through many posts about installing ambertools on
> ubuntu but none of the methods described have been totally successful. It
> appears that I am having issues with compiling some of the fortran code. I
> have every x11 package available and every fortran package available. I
> also downloaded g77 3.4 and its associated packages from the Ubuntu Hardy
> 8.04 (Hardy Herron) archive so that I have both gfortran and g77. I also
> have f2c, fort77, csh, g95 and the other current gcc compilers.

First, g77 just complicates things; gfortran should be fine.
>
> 1. Ubuntu uses /usr/lib as the location of its x11 libraries not
> user/X11R6/lib. Does this affect my installation?

It should not affect anything: configure looks in both /usr/lib and
/usr/X11R6/lib.

If xLeap compiles fine, you are in good shape. (Note that xleap has no
fortran code, so setting gfortran should not be relevant.)

>
> 2. It seems that with gfortran, my compilation errors out in installing
> gleap

Again, gleap has no fortran code, so the explicit setting of which fortran
compiler should have no effect. There may be something else going on.

> Below are two makefile outputs. The first is with g77. The second is with
> gfortran.

> g77 aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o
> bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o
....
> readmo.o: In function `readmo_':
> readmo.f:(.text+0x54): undefined reference to `_gfortran_string_index'

You clearly are mixing up g77 and gfortran compilation here. Be sure to do
a "make clean" when changing compilers.

>
> GFORTRAN
>
> make[2]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc'
> cd common;make
> make[3]: Entering directory `/home/kunin/amber10/src/gleap/mortsrc/common'
> g++ -c -O2 -Wall -W -D_REENTRANT -I../../freelib -I../../freelib -o
> fortran.o fortran.cpp
> fortran.cpp: In function ‘void mort::write_ivalue(std::ostream&, const
> std::string&, const boost::any&)’:
> fortran.cpp:19: error: ‘sprintf’ was not declared in this scope
> fortran.cpp: In function ‘void mort::write_dvalue(std::ostream&, const
> std::string&, const boost::any&)’:
> fortran.cpp:36: error: ‘sprintf’ was not declared in this scope
> fortran.cpp: In function ‘void mort::write_svalue(std::ostream&, const
> std::string&, const boost::any&)’:
> fortran.cpp:52: error: ‘sprintf’ was not declared in this scope
> fortran.cpp: In member function ‘void mort::format::write(std::ostream&)
> const’:
> fortran.cpp:133: warning: comparison between signed and unsigned integer
> expressions
> fortran.cpp:138: warning: comparison between signed and unsigned integer
> expressions
> fortran.cpp:145: warning: comparison between signed and unsigned integer
> expressions
> fortran.cpp:153: warning: comparison between signed and unsigned integer
> expressions
> make[3]: *** [fortran.o] Error 1

This is a bit weird. What result do you get on typing "g++ --version"?

....dac

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