Re: AMBER: question about the testing of AMBER9

From: Mark Williamson <Mark.Williamson.imperial.ac.uk>
Date: Mon, 08 Jan 2007 21:10:53 +0000

Ok,

First off, the error messages that you report in your latest email are
not the ones that you initially reported on 06/01/07:

>-L/usr/X11R6/lib -lXt -lXext -lSM -lICE -lX11 -lm -lpthread
>IPO link: can not find -lXt
>icc: error: problem during multi-file optimization compilation (code 1)

compared with 08/01/07:

>ScrolledTable.c:1167: error: conflicting types for
>‘XawScrolledTableSetLocation’
>ScrolledTable.h:99: error: previous declaration of
>‘XawScrolledTableSetLocation’ was here
>make[1]: *** [ScrolledTable.o] Error 1
>make[1]: Leaving directory `/home/amber9/amber9/src/leap/src/Xraw'
>make: *** [install] Error 2

Changing the problem halfway through a work-through to the old one
generally increases the amount of time taken to solve both problems.


Anyway, your processor is essentially a x86_64. It can run both 32 and
64 bit code. The reason that "rpm -qi libXt" returns twice is because
you have both the 32 bit and 64 bit libs for that package (libXt)
installed. I'm not sure why, but Fedora sometimes installs both i386 and
x86_64 RPMS for the same package. This can be confusing.

>Intel-icc91045 - 9.1.045-1.i386 - Intel(R) C++ Compiler for 32-bit
>applications, version 9.1 (9.1.045)
>Intel-ifort91040 - 9.1.040-1.i386 - Intel(R) C++ Compiler for 32-bit
>applications, version 9.1 (9.1.040)

It looks like you have the 32 bit ifort compiler already installed,
hence we'll compile in 32 bit. The reason for this decision is that more
problems may be generated by removing the 32 bit version of ifort and
installing the 64 bit version at this point in time. We can come back to
this later.

You will want to change to the $AMBERHOME/src dir and run:

./configure -static ifort_ia32

The error message:

>ScrolledTable.c:1167: error: conflicting types for ‘XawScrolledTableSetLocation’
>ScrolledTable.h:99: error: previous declaration of XawScrolledTableSetLocation’ was here

is the *real* problem here. It's been reported before:
  http://amber.ch.ic.ac.uk/archive/200605/0157.html

I could not get this suggestion to work, and my approach was to comment
out line 99 in $AMBERHOME/src/leap/src/Xraw/ScrolledTable.h :

OLD:
  extern void XawScrolledTableSetLocation( Widget w, double xoff, double
yoff );

==>
NEW:
/* extern void XawScrolledTableSetLocation( Widget w, double xoff,
double yoff ); */

I am not sure if this is the best solution, but it has worked for me
when using FC5.

Finally, in $AMBERHOME/src , do a

  make clean
  make


Please let us know if this method works for you.

Regards,

Mark



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Received on Wed Jan 10 2007 - 06:07:31 PST
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