> Jason, can you give the details for your ubuntu installation-
> version and apt-gets again ?
> Of course, my advice is for a full OS installation.
Ubuntu 9.04 (amd64) (uname -a : Linux Batman 2.6.28-16-generic
#55-Ubuntu SMP Tue Oct 20 19:48:32 UTC 2009 x86_64 GNU/Linux ).
The apt-gets that are critical to amber are Mingjuei's list (csh,
flex, xorg-dev, gfortran). g++ is needed if it's not included, but as
I remember, Ubuntu 9.04 (and 8.10 and 8.04 LTS) had it by default. I
could not build a working ptraj.MPI with netcdf support until I
installed bison and/or byacc. However, pnetcdf needed it, not amber
itself (and for some reason, netcdf built fine without it as well...)
As I understand it, bison/byacc are parser generators. I see that
amber ships with byacc, but for some reason pnetcdf wouldn't use that
one and apt-get install bison was easier than trying to get pnetcdf to
use amber's byacc.
>
>> > before I start to work on src/configure
>> > 2) Ubuntu's sh hates src/configure, I HAVE TO CHANGE IT TO
>> > /bin/bash TO MAKE IT WORK.
>
> Jason, Mengjuei, what are your results for ll /bin/sh ?
> Dec 09 1:33:06pm ubuntu 24> / ll /bin/sh
> 0 lrwxrwxrwx 1 root root 4 2009-04-13 15:03 /bin/sh -> dash
>
> https://wiki.ubuntu.com/DashAsBinSh
> In Ubuntu 6.10, the default system shell, /bin/sh,
> was changed to dash from bash.
> The major reason to switch the default shell was efficiency.
>
> Sigh, they didnt learn anything from Bill Gates let alone Don Knuth.
>
I had seen that before, but the performance hit I got by switching
back to bash was unnoticeable to me, and having scripts work again
were well worth it. I actually found this problem with other software
I was building, so my motive for making this change was not actually
amber. ls -l /bin/sh doesn't "point" anywhere, but it is /bin/bash
(as I explicitly did sudo rm /bin/sh;sudo ln /bin/bash /bin/sh).
> This is a classic FAQ entry.
> I'll add a link to the platform pages in the amber faq.
> Our main page could use a table of contents; its 20 pagedowns
> from top to bottom with a 16 size font.
THat seems as good a place as any to put that :).
> Thanks for the note,
> Scott
>
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> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Dec 09 2009 - 15:30:02 PST
