Re: [AMBER-Developers] sander.MPI tests randomly stall in Ubuntu 9.10

From: Lachele Foley <lfoley.ccrc.uga.edu> Date: Wed, 12 May 2010 14:05:42 -0400

--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
----- Original Message -----
From: Lachele Foley
[mailto:lfoley.ccrc.uga.edu]
To: AMBER Developers Mailing List
[mailto:amber-developers.ambermd.org]
Sent: Wed, 12 May 2010 14:03:40
-0400
Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in
Ubuntu 9.10
> Actually... it's the other compiler.  But, not for lack of trying.  
> 
> I totally did not expect this...
> 
> Here, the user has gcc aliased at login:
> 
> [installer.aarya src]$ which gcc
> gcc:     aliased to /usr/bin/gcc44
> [installer.aarya src]$ gcc --version
> gcc44 (GCC) 4.4.0 20090514 (Red Hat 4.4.0-6)
> 
> ...but the config is finding something different...
> 
> ========================================================
> [installer.aarya src]$ ./configure gnu
> Your AMBERHOME environment variable should be set to
> /usr/local/programs64/amber11
>  
> 
> Obtaining the gnu suite version:
>       gcc -v
> The version is 4.1.2
> ========================================================
> 
> GAAAAUUUGHHHHH!!!!
> Is it because the script is in sh?
> 
> 
> It obviously pays attention to the .cshrc file, because when I made a
> directory $HOME/bin, set that first in the path, with sym links inside to
> the various places, it found the right compilers.
> 
> sh doesn't recognize the term "alias"...
> 
> :-) Lachele
> --
> B. Lachele Foley, PhD '92,'02
> Assistant Research Scientist
> Complex Carbohydrate Research Center, UGA
> 706-542-0263
> lfoley.ccrc.uga.edu
> 
> 
> ----- Original Message -----
> From: Volodymyr Babin
> [mailto:vbabin.ncsu.edu]
> To: AMBER Developers Mailing List
> [mailto:amber-developers.ambermd.org]
> Sent: Wed, 12 May 2010 13:15:12
> -0400
> Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in
> Ubuntu 9.10
> 
> 
> > Hi Lachele,
> > 
> > thank you. It might be indeed something else. If it fails again with
> > 4.4.0, please give me the outputs [or .diff(s)] to look at. I am not
> > sure to what extent this can be relevant, but 'man alias' says
> > 
> > ...
> > the alias definition shall not affect the parent process of the current
> > shell nor any utility environment invoked by the shell; see Shell
> Exe&#8208;
> > cution Environment
> > ...
> > 
> > and it thus may be worthwhile to try making 'gcc->gcc44' symlinks
> > somewhere and then add this somewhere to the front of the PATH.
> > 
> > Thank you & best regards,
> > 
> > Volodymyr
> > 
> > On Wed, May 12, 2010 12:03, Lachele Foley wrote:
> > > 4.4.0
> > >
> > > I'll have her re-do from a clean un-tar (even if she did this time),
> just
> > > to be sure.  I checked her paths.  She has gcc aliased to /usr/bin/gcc44
> > > and so forth, and gcc --version yields 4.4.0, etc.  The MPI execs all
> just
> > > point to "gcc", so they should go wherever her gcc points.
> > >
> > > It might not be RHEL.  Could be the machine.  Has an AMD processor...
> any
> > > chance that matters?
> > >
> > > :-) Lachele
> > > --
> > > B. Lachele Foley, PhD '92,'02
> > > Assistant Research Scientist
> > > Complex Carbohydrate Research Center, UGA
> > > 706-542-0263
> > > lfoley.ccrc.uga.edu
> > >
> > >
> > > ----- Original Message -----
> > > From: case
> > > [mailto:case.biomaps.rutgers.edu]
> > > To: AMBER Developers Mailing List
> > > [mailto:amber-developers.ambermd.org]
> > > Sent: Wed, 12 May 2010 11:49:33
> > > -0400
> > > Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in
> > > Ubuntu 9.10
> > >
> > >
> > >> On Wed, May 12, 2010, Lachele Foley wrote:
> > >>
> > >> >
> > >> > The failures are all from the ncsu set:
> > >>
> > >> Is this with gcc 4.1.2 or gcc 4.4.0?  The ncsu errors with 4.1.2 are
> > >> well
> > >> known (and will probably never be fixed); if you had errors with 4.4.0,
> > >> it would be of interest to know what they are.  I've used gcc44 on
> > >> Ubuntu
> > >> and on CentOS with no such failures, fwiw.
> > >>
> > >> ....thx...dave
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER-Developers mailing list
> > >> AMBER-Developers.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >>
> > >
> > > _______________________________________________
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> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >
> > 
> > 
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> > 
> 
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