On Thu, Apr 7, 2011 at 8:54 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> Re: "my bad" $AMBERHOME not set appropriately...
>
> (bad news: experienced user == trusting idiot / not so experienced)
> (good news: we now know what happens if you do not set $AMBERHOME)
>
> I apologize for the hassle and frustration especially as release is
> pending. What I did was simply extract the tarball, configure intel and
> make install. Nothing else. I uncovered the python issue and then
> started to blindly dig on multiple machines (like kraken, exposing other
> issues that we still should resolve).
>
But if I recall on kraken it still appeared that there were weird
intel-specific symbols (svml) that shouldn't be there (I don't think kraken
even has the intel compilers, does it?). I'll have a hack at it.
> I think, however, that Jason nailed it. I wasn't setting $AMBERHOME and
> had assumed that it was automagically set. As this had been set
> automatically previously, I assumed it was set in the current install
> scripts and I was incorrect in this assumption. [It may be beneficial
> behavior however to reset AMBERHOME automatically however!].
>
It's unclear to me how to accomplish this. If you look at configure, around
lines 288, you see
workdir=`pwd`
AMBERTOOLSHOME=`dirname $workdir`
AMBERHOME=`dirname $AMBERTOOLSHOME`
echo "Your AMBERHOME environment variable should be set to $AMBERHOME"
echo " "
So the configure script *does* reset AMBERHOME, from which everything is
configured. The problem is this is not inheritable by the shell you launch
it from. From my recollection, this is the only way it's ever been done.
The only way to apply an environment variable in your current shell is to
source some file (or set it by hand, of course). Unless you can launch a
shell with a funky flag/option. Thus, AMBERHOME is reset to where it should
be in configure, but that evaporates when configure ends.
> The only upside is that perhaps we now know what errors people will see if
> they do not set AMBERHOME correctly; perhaps this has not been a total
> waste of all of our time...
>
More of an indication of what will happen if AMBERHOME is set incorrectly.
There are places that check to make sure that AMBERHOME is set
(mmpbsa_py/setup.sh for one), just not set to the *correct* directory.
I'll try with Kraken and check back.
Thanks!
Jason
> I went back and did it all over again, this time with $AMBERHOME set
> appropriately and after the wait for recompile, it all worked fine.
>
> --tom
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Thu Apr 07 2011 - 21:30:04 PDT
