AMBER Archive (2007)

Subject: Fwd: RE: Re: AMBER: on PATH

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Jun 29 2007 - 00:58:19 CDT

Dear Ross:
here again, just to say that I have learned that VMD is no substitute for
xleap. However, my initial problems for amber9 will be dealt with through
antechamber (no polymeric molecules, just very complex organic molecules of MW
up to 3000 Da) and therefore may be leap/xleap are not directly called. I can
provide pdb files (with hydrogens at right places) from a MM package, though I
have to set explicit solvent, which is a problem for amber.

As to why xleap resisted compilation, I remark that the X system - though
perfectly functioning at 2D acceleration - lacks OpenGL, just because I was
trying not to pollute too much with 32-bit libraries (or, that is my
idiosyncrasy against 32 when the stuff is 64).

I have to investigate whether OpenGL is now available pure 64-bit on debian. If
so, probably my system can be adapted to the compilation of xleap.

Thanks

francesco

--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> Date: Thu, 28 Jun 2007 13:55:53 -0700 (PDT)
> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: RE: Re: AMBER: $AMBERHOME on PATH
> To: amber_at_scripps.edu
> CC: zweig_at_scripps.edu
>
> Dear Ross;
> For the X expert, I provide here some info about X on my system were amber9
> is
> being installed. If redundant please disregard.
>
> francesco_at_deb64:~$ lspci |egrep -i '(video|vga|display)'
> 81:00.0 VGA compatible controller: nVidia Corporation NV43 [GeForce 6600]
> (rev
> a 2)
> francesco_at_deb64:~$
>
>
> francesco_at_deb64:~$ awk '/Section
> "(Module|Device|ServerFlags|extensions)"/,/EndSection/' /etc/X11/xorg.conf
> Section "Module"
> Load "bitmap"
> Load "dbe"
> Load "ddc"
> Load "dri"
> Load "extmod"
> Load "freetype"
> Load "glx"
> Load "int10"
> Load "record"
> Load "v4l"
> Load "vbe"
> EndSection
> Section "Device"
> Identifier "nVidia Corporation NV43 [GeForce 6600] (rev a2)"
> Driver "nv"
> # BusID "PCI:129:0:0"
>
> EndSection
> francesco_at_deb64:~$
>
>
> The following was run from console on gnome, that is when both X and gnome
> had
> been started
>
>
>
> francesco_at_deb64:~$ egrep '^\((EE|WW)\)' /var/log/Xorg.0.log (WW) The
> directory
> "/usr/X11R6/lib/X11/fonts/misc" does not exist.
> (WW) The directory "/usr/share/fonts/X11/cyrillic" does not exist.
> (WW) The directory "/usr/X11R6/lib/X11/fonts/cyrillic" does not exist.
> (WW) The directory "/usr/X11R6/lib/X11/fonts/100dpi/" does not exist.
> (WW) The directory "/usr/X11R6/lib/X11/fonts/75dpi/" does not exist.
> (WW) The directory "/usr/X11R6/lib/X11/fonts/Type1" does not exist.
> (WW) The directory "/usr/X11R6/lib/X11/fonts/100dpi" does not exist.
> (WW) The directory "/usr/X11R6/lib/X11/fonts/75dpi" does not exist.
> (WW) The directory "/var/lib/defoma/x-ttcidfont-conf.d/dirs/TrueType" does
> not
> exist.
> (WW) (1024x768,Generic Monitor) mode clock 94.5MHz exceeds DDC maximum 80MHz
> (WW) (1152x864,Generic Monitor) mode clock 108MHz exceeds DDC maximum 80MHz
> (WW) (1280x960,Generic Monitor) mode clock 108MHz exceeds DDC maximum 80MHz
> (WW) (1280x960,Generic Monitor) mode clock 148.5MHz exceeds DDC maximum 80MHz
> (WW) (1280x1024,Generic Monitor) mode clock 108MHz exceeds DDC maximum 80MHz
> (WW) (1280x1024,Generic Monitor) mode clock 135MHz exceeds DDC maximum 80MHz
> (WW) (1280x1024,Generic Monitor) mode clock 157.5MHz exceeds DDC maximum
> 80MHz
> (WW) (1600x1200,Generic Monitor) mode clock 162MHz exceeds DDC maximum 80MHz
> (WW) (800x600,Generic Monitor) mode clock 81MHz exceeds DDC maximum 80MHz
> (WW) (1600x1200,Generic Monitor) mode clock 175.5MHz exceeds DDC maximum
> 80MHz
> (WW) (800x600,Generic Monitor) mode clock 87.75MHz exceeds DDC maximum 80MHz
> (WW) (1600x1200,Generic Monitor) mode clock 189MHz exceeds DDC maximum 80MHz
> (WW) (800x600,Generic Monitor) mode clock 94.5MHz exceeds DDC maximum 80MHz
> (WW) (1600x1200,Generic Monitor) mode clock 202.5MHz exceeds DDC maximum
> 80MHz
> (WW) (800x600,Generic Monitor) mode clock 101.25MHz exceeds DDC maximum 80MHz
> (WW) (1600x1200,Generic Monitor) mode clock 229.5MHz exceeds DDC maximum
> 80MHz
> (WW) (800x600,Generic Monitor) mode clock 114.75MHz exceeds DDC maximum 80MHz
> (WW) (1792x1344,Generic Monitor) mode clock 204.8MHz exceeds DDC maximum
> 80MHz
> (WW) (896x672,Generic Monitor) mode clock 102.4MHz exceeds DDC maximum 80MHz
> (WW) (1792x1344,Generic Monitor) mode clock 261MHz exceeds DDC maximum 80MHz
> (WW) (896x672,Generic Monitor) mode clock 130.5MHz exceeds DDC maximum 80MHz
> (WW) (1856x1392,Generic Monitor) mode clock 218.3MHz exceeds DDC maximum
> 80MHz
> (WW) (928x696,Generic Monitor) mode clock 109.15MHz exceeds DDC maximum 80MHz
> (WW) (1856x1392,Generic Monitor) mode clock 288MHz exceeds DDC maximum 80MHz
> (WW) (928x696,Generic Monitor) mode clock 144MHz exceeds DDC maximum 80MHz
> (WW) (1920x1440,Generic Monitor) mode clock 234MHz exceeds DDC maximum 80MHz
> (WW) (960x720,Generic Monitor) mode clock 117MHz exceeds DDC maximum 80MHz
> (WW) (1920x1440,Generic Monitor) mode clock 297MHz exceeds DDC maximum 80MHz
> (WW) (960x720,Generic Monitor) mode clock 148.5MHz exceeds DDC maximum 80MHz
> (WW) (1280x768,Generic Monitor) mode clock 80.14MHz exceeds DDC maximum 80MHz
> (WW) (1280x800,Generic Monitor) mode clock 83.46MHz exceeds DDC maximum 80MHz
> (WW) (1152x864,Generic Monitor) mode clock 121.5MHz exceeds DDC maximum 80MHz
> (WW) (1400x1050,Generic Monitor) mode clock 122MHz exceeds DDC maximum 80MHz
> (WW) (1400x1050,Generic Monitor) mode clock 151MHz exceeds DDC maximum 80MHz
> (WW) (1400x1050,Generic Monitor) mode clock 155.8MHz exceeds DDC maximum
> 80MHz
> (WW) (1400x1050,Generic Monitor) mode clock 184MHz exceeds DDC maximum 80MHz
> (WW) (700x525,Generic Monitor) mode clock 92MHz exceeds DDC maximum 80MHz
> (WW) (1440x900,Generic Monitor) mode clock 108.84MHz exceeds DDC maximum
> 80MHz
> (WW) (1600x1024,Generic Monitor) mode clock 106.91MHz exceeds DDC maximum
> 80MHz
> (WW) (1680x1050,Generic Monitor) mode clock 147.14MHz exceeds DDC maximum
> 80MHz
> (WW) (1920x1200,Generic Monitor) mode clock 193.16MHz exceeds DDC maximum
> 80MHz
> (WW) (960x600,Generic Monitor) mode clock 96.58MHz exceeds DDC maximum 80MHz
> (WW) (1920x1200,Generic Monitor) mode clock 230MHz exceeds DDC maximum 80MHz
> (WW) (960x600,Generic Monitor) mode clock 115MHz exceeds DDC maximum 80MHz
> (WW) (1920x1440,Generic Monitor) mode clock 341.35MHz exceeds DDC maximum
> 80MHz
> (WW) (960x720,Generic Monitor) mode clock 170.675MHz exceeds DDC maximum
> 80MHz
> (WW) (2048x1536,Generic Monitor) mode clock 266.95MHz exceeds DDC maximum
> 80MHz
> (WW) (1024x768,Generic Monitor) mode clock 133.475MHz exceeds DDC maximum
> 80MHz
> (WW) (2048x1536,Generic Monitor) mode clock 340.48MHz exceeds DDC maximum
> 80MHz
> (WW) (1024x768,Generic Monitor) mode clock 170.24MHz exceeds DDC maximum
> 80MHz
> (WW) (2048x1536,Generic Monitor) mode clock 388.04MHz exceeds DDC maximum
> 80MHz
> (WW) (1024x768,Generic Monitor) mode clock 194.02MHz exceeds DDC maximum
> 80MHz
> (WW) NV(0): Failed to set up write-combining range (0xd0000000,0x10000000)
> (EE) AIGLX: Screen 0 is not DRI capable
> francesco_at_deb64:~$
>
> Thanks again
>
> francesco
>
>
>
>
>
> --- Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> > Hi Francesco,
> >
> > > After a long session it exited with Error 2
> > >
> > > Those errors that I can see on the screen comprise:
> > >
> > > WcActCB.c:1448: error: expected declaration specifiers before XEvent.
> > > WcActCB.c:1448: error: expected declaration specifiers before
> > > Cardinal.
> > >
> > >
> > > WcActCB.c: In function WcDynamicActionACT:
> > >
> > > WcActCB.c:1450: error: expected declaration specifiers before Widget.
> > >
> > > WcActCB.c:1450: error: expected declaration specifiers before XEvent.
> > >
> > > WcActCB.c:1450: error: expected declaration specifiers before
> > > Cardinal.
> >
> > At this point everything should have been built with the exception of xleap
> > so you are good to run everything but can only use the non-graphical
> version
> > of leap (tleap) to build the molecules. Normally problems with xleap come
> > from not having the X11 development libraries installed but this would give
> > a file not found error. I am not sure what the errors you are seeing are
> > coming from and I'm not overly familiar with the way xleap works so I
> copied
> > this email to Wei Zhang who is the xleap expert and will hopefully be able
> > to help here.
> >
> > In the meantime you can run all the tests, everything should be good except
> > the tests of xleap which should report that the executable is missing.
> >
> > > If relevant, I have seen during the process calling "gcc" and
> > > "g++" (for
> > > openmpi I have used intel for both fortran, C and C++).
> >
> > You don't need to worry here. Only sander and pmemd are 'parallel' using
> MPI
> > and these are all fortran so the c/c++ compiler is irrelevant for compiling
> > in parallel.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> > be read every day, and should not be used for urgent or sensitive issues.
> >
> >
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>
>
>
>
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