I use a molecular visualization program (molekel-4.3) downloaded in binary form (only). It is compiled under SUSE 7.0 (g++ 2.9). Works fine under Gentoo 2.4.x kernel series (also on Mandrake, Fedora and others, but only under 2.4.x kernel). Switching to 2.6.x series (Gentoo dev and ck-sources, Mandrake, pclinux) makes unusable the program (an error : Segmentation fault at line ...). Is there any possibility to run such a program under 2.6.x kernel?
Thanks!

you sure it's the kernel and not the libstdc++.so.*?

Not quite sure, but in installation instructions there is a symbolic link which has to be done:
ln -s libstdc++-3-libc6-2.2.2-10.0.so libstdc++-libc6-1.2.so.3 ! For this I had to install libcompat. Is it possible to try another symbolic link, to another library?

I saw your post, in my (long) quest for the solution to my molekel issues, and now that got it right I returned to try to help you out. I used to get this error:

/home/agapito/opt/molekel/bin/molekel4.3.linux: relocation error: /home/agapito/opt/molekel/bin/molekel4.3.linux: undefined symbol: __builtin_new

This was due to libstdc++ issues, as I found out latter. All I did was install all the libstdc++ available for my distro (Ubuntu Hoary) and then tried to make the link that molekel needs to each one of them, one at a time. I found out that the package I had to install was called libstdc++2.10-glibc2.2. That installed libstdc++-3-libc6.2-2-2.10.0.so wich enabled me to run molekel.

Hope that works for you.

By the way, I think you'll be happy to know that the molekel project is back, and that it's going to be Open Source.

The alpha version is still very primitive and lacks a lot of features, but it looks nice.
Check it out here:

http://www.cscs.ch/a-display.php?id=138