[gmx-users] can not pass gmxtest

[Mark Abraham]

Li Qiang wrote:
> hi,
> 
> I just try to remove and rebuild and install GROMACS.
> 
> This time the self-built one also can not pass the test. The same errors
> are reported:
> 
> +++++++++++++++++++++++++++++++++++++++++
> liqiang at liqiang-desktop:~/gromacs-3.3.2$ sudo make tests

As a general rule, do not do installations and tests of installations as 
root. This makes it very easy to break your system. One symptom of a 
broken system is things not working any more. Sound familiar?

If you have a need to install as root, then do the unpack, configure & 
make (& make test) in your user space as yourself, and then sudo make 
install. This is just sensible... if someone messes up (the distributor, 
or more likely you) you'd much rather not be root.

> (if test -d "gmxtest"; then cd "gmxtest"; ./gmxtest.pl all; cd ..; \
>         else echo "No gmxtest directory found. Please download and
> unpack it here.";\
>         fi)
> *** glibc detected *** mdrun: realloc(): invalid next size: 0x08296ec8

Perhaps the authors can suggest whether gmxtest.pl uses the GROMACS 
binary from the same source tree, or whichever is pointed to by GMXLIB. 
If the latter, then you probably still have something broken somewhere.

On the above sudo evidence, I'd actually be tempted to scorched-earth 
your machine and re-install your OS rather than mess around any more.

Mark