Re: Charm++ nodelist commands

From: Gengbin Zheng (
Date: Tue Dec 30 2003 - 13:14:52 CST

oops, I guess I forgot to check in some changes for Cygwin-i686.
I will fix them later today. However, please compile NAMD
with Win32-i686-MSVC and with net-win32 of Charm++ (using VC++ instead of
gcc) since I found some tricky things with Cygwin/gcc - one seems to have
to use -fpack-struct gcc compile option to pack structures in order to
generate same structure alignment as Linux gcc.

I have fully tested Win32-i686-MSVC with VC++ and checked in all the
changes for it already several days ago, so it should compile and work out
of cvs server without any change.

> Well, I was trying to compile NAMD under Cygwin, but encountered some
> problems compiling NAMD:
> - Apparently the Cygwin-i686.plugins file is missing.
> - (using config without plugins) gcc complains it cannot find
> strstream.h, wich seems to be missing in GCC 3.3.
> - (When downgrading to GCC 3.2) Linking crashes. The log of the crash
> command in an attached document.

I had same problem with Cygwin/GCC3.2. GCC 3.3 links fine with some fixes
in NAMD for compile errors.

> Charm++ compiles Ok.
> Would it be too much to ask for a copy of the binaries for Win32?

  I normally don't bother to compile NAMD with tcl and plugins. I only
worry about fftw for my benchmark testing purpose.
  I don't have precompiled library for tcl and plugins for cygwin/gcc,
and I don't know how to make them. So I guess I can only compile the VC++
version of NAMD for you (the precompiled tcl, plugins libs are available
online at namd website i think).

> > Here is a sample nodelist file when I start charmrun on Cygwin box.
> > (
> >
> > group main
> > host ++pathfix /home/work/ /home/gzheng/
> > host ++pathfix /home/work/ C:\cygwin\home\work\
> So, here you launch NAMD from a computer where your files are in
> "/home/work/..." on 2 nodes in the first the files are in
> "/home/gzheng/..." and the second (Win) "c:\cygwin\home\work\". Am I
> right?

  Actually I was launching NAMD from the second computer in the nodelist
under cygwin. The cygwin path is "/home/work/", however, as you can
see I still need to map it to the corresponding Win path of
"C:\cygwin\home\work\" even it is on the same machine.

 Also remember to deal with firewall if you have it enabled on Linux or

> Another question: is it possible to set process priority (nice level)
> for NAMD node programs?

 No. It can be implemented but not for windows I guess.


> Best regards
> --
> ================= Gadi ORON, PhD -o- Proteologics ======================
> ========== gadi/at/ ========== +972 8 9475666 ==========
> If you lose your temper at a newspaper columnist, he'll get rich,
> or famous or both.

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