Re: Charm++ nodelist commands

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Wed Dec 31 2003 - 11:59:00 CST

Oops, forgot to mention, you need to recompile Linux version of NAMD from
scratch also. The pre-compiled version is not compatiable with the latest
CVS version due to my recent changes in structure layout. Also, the
pre-compiled version is built with Intel C++ compiler which I have not
tested the compatibility with Win32 VC++ yet. So I would suggest going
with gcc on Linux before I tested it with Intel C++.

Since I don't know which verison of Linux you are running, I don't know
how to make pre-compiled binary for you. But compiling for Linux is
fairely easy, check out:
http://www.ks.uiuc.edu/Research/namd/development.html
Please download both Charm++ and NAMD source from the two different CVS
servers.

I myself rarely use tcl and plugins features (being a mostly Charm++
developer). Based on my limited knowledge, tcl is used to enable
scripting features (so you can write tcl scripts in config file), and
plugins tools are from VMD's Plugins to enable trajectory analysis. The
NAMD user manual should have more detailed information.

Gengbin

On Wed, 31 Dec 2003, Gadi Oron wrote:

> On Wed, 2003-12-31 at 02:05, Gengbin Zheng wrote:
> > Hi,
> >
> > Please find the NAMD binary compiled with Windows VC++ 6.0 at:
> > http://www.ks.uiuc.edu/~gzheng/NAMD_Win32-i686.zip
>
> Thank you, but still no luck...
> I manage to start NAMD alone on a Win2K node and on Linux node,
> so probably my nodelist is Ok. But together I get either:
>
> Info: SUMMARY OF PARAMETERS:
> Info: 180 BONDS
> Info: 442 ANGLES
> Info: 534 DIHEDRAL
> Info: 50 IMPROPER
> Info: 91 VDW
> Info: 0 VDW_PAIRS
> Charmrun: error on request socket--
> Error on socket recv!
>
> when the Linux box is first in the nodelist and:
>
> Charmrun> node programs all connected
> ------------- Processor 1 Exiting: Caught Signal ------------
> Signal: segmentation violation
> Suggestion: Try running with '++debug', or linking with '-memory
> paranoid'.
> Fatal error on PE 1> segmentation violation
>
> when the order is inverted.
>
> I am using charmd compiled from the last source and NAMD 2.5 from
> the pre-compiled binaries for linux and your Windows executables.
>
> Any idea?
>
> Best regards.
>
> P.S. It is not really explained what "plugins" and "tcl" libraries are
> needed for... Could you give me a hint on that?
> --
> ================= Gadi ORON, PhD -o- Proteologics ======================
> ========== gadi/at/proteologics.com ========== +972 8 9475666 ==========
> The questions remain the same. The answers are eternally variable.
>

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