Re: [AMBER-Developers] 31 March release candidates for Amber

From: Volodymyr Babin <>
Date: Fri, 2 Apr 2010 17:08:53 -0400 (EDT)

>> 0. configure -noX11 gnu -- OK (but there was a minor annoyance: 4.4.2
>> binaries are named gcc44/gfortran44/g++44 contrary to what is
>> expected)
> Not sure what to do here--same things pops up on RedHat, etc. Personally,
> I set links (e.g. ln -s /usr/bin/gcc44 gcc) in ~/bin, and put that first
> in my path. Not sure what there is that is better.

I did the same and for now this is probably the way to go.

>> 1. 'make install' stops with
>> (cd leap && make install )
>> "Makefile", line 14: Missing dependency operator
> grrr....I was going to try to remove all dependencies on gmake, but I
> think
> they actually exist in netcdf (for which we need to track external code).
> So for now, I think we just have to say the Amber requires gmake. [sleap
> has always required gmake, as well, so we may be stuck. I have a feeling
> that BSD folks are used to this.

gmake seems to be everywhere and this is not an unreasonable requirement;
on the other hand, to actually switch to gmake I had to make another link
in ~/bin [not a big deal, but ideally toplevel Makefile should pass make
down, so that if user types 'gmake install', it just works]

>> #ifdef getchar
>> # undef getchar
>> #endif
>> before "virtual getchar()" in mortsrc/guilib/console.hpp to make it
>> through

Wei should take a look at this because it might alter semantics.

> Also fixed....not sure why things are so slow....suggests some other
> errors.

I tried unpatched RC and the slowness mainly seems to be somewhere in pbsa;
will look closer at another RC [since a number of changes already went in]



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Received on Fri Apr 02 2010 - 14:30:03 PDT
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