[gmx-developers] grompp and vsites

Michel Cuendet michel.cuendet at isb-sib.ch
Thu Jun 25 15:00:57 CEST 2009

Hi David,
> This doesn't look good. Are you certain compilation went fine? Did you 
> run the test set?
> Did you compile double and single from exactly the same source? And did 
> you run make distclean in between?
> The only other thing I can think of is that there were strange 
> characters in the mdp file.
After recompiling, all grompp versions suddenly give the same output 
with vsites (without the -e option).  No idea what happened there.  :0S

After that, the other problem kept happening consistently: using the -e 
option to read an edr file would create a Segmentation fault (as 
mentioned in previous email). Gdb output:
Program received signal SIGSEGV, Segmentation fault.
0xb78d64ac in free () from /lib/tls/i686/cmov/libc.so.6
(gdb) bt
#0  0xb78d64ac in free () from /lib/tls/i686/cmov/libc.so.6
#1  0xb7a8fccd in save_free ()
#2  0xb7a8fcb4 in save_free ()
#3  0xb7a40e4f in do_enxnms ()
#4  0x0000003d in ?? ()
Cannot access memory at address 0xfff5a8ed

I figured out that compiling without the --enable-shared option solves 
the problem!! The grompp on the 64bit machines (which was working, see 
previous email) was compiled without shared libraries, and that was the 
only significant difference. So there is a problem in the way shared 
libraries are called.

Now I think I have all the CVS grompps working properly. Note that 
disabling the shared libraries did NOT improve the SegFault with pdb2gmx 
mentioned in a separate thread.

However, I still see some errors in the gmxtests, depending on which CVS 
version I look at. Could you confirm if the latest CVS should actually 
pass all the gmxtests ?



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