[gmx-users] deform option in parallel with Gromacs 4.0.2

[Yves Dubief]

Hi,

I am running stress simulations of vesicles and lipid bilayer  
membranes, which work on one processor but fail when using multiple  
processors. The simulations run Marrink's CGMD model with Gromacs  
4.0.2 (sorry I am unable to upgrade until next week) on openmpi and  
mpich. The simulations run fine with the deform option set to zero for  
all six components but crashes for 2 processors or more. Here is an  
example of what I get on a mac with openmpi (fink package of gromacs):
[ip138195:37938] *** Process received signal ***
[ip138195:37938] Signal: Segmentation fault (11)
[ip138195:37938] Signal code: Address not mapped (1)
[ip138195:37938] Failing at address: 0x8fe830
[ip138195:37938] [ 0] 2   libSystem.B.dylib                    
0x925882bb _sigtramp + 43
[ip138195:37938] [ 1] 3   ???                                  
0xffffffff 0x0 + 4294967295
[ip138195:37938] [ 2] 4   libgmx_mpi.5.dylib                   
0x003d24f1 do_nonbonded + 1361
[ip138195:37938] *** End of error message ***
[ip138195:37939] *** Process received signal ***
[ip138195:37939] Signal: Segmentation fault (11)
[ip138195:37939] Signal code: Address not mapped (1)
[ip138195:37939] Failing at address: 0xfb890
[ip138195:37939] [ 0] 2   libSystem.B.dylib                    
0x925882bb _sigtramp + 43
[ip138195:37939] [ 1] 3   ???                                  
0xffffffff 0x0 + 4294967295
[ip138195:37939] [ 2] 4   libgmx_mpi.5.dylib                   
0x003d24f1 do_nonbonded + 1361
[ip138195:37939] *** End of error message ***
mpiexec noticed that job rank 0 with PID 37938 on node  
ip138195.uvm.edu exited on signal 11 (Segmentation fault).
1 additional process aborted (not shown)
I have checked the wiki, manuals and searched this list but I can't  
find any report of bugs nor an indication that I am doing something  
wrong. It seems that there might be a bug associated with the deform  
option in parallel.
Thanks for any insight, advice on this.

.
  --
Yves Dubief, Ph.D., Assistant Professor
Graduate program coordinator
University of Vermont, School of Engineering
Mechanical Engineering Program
201 D Votey Bldg, 33 Colchester Ave, Burlington, VT 05405
Tel: (1) 802 656 1930 Fax: (1) 802 656 3358
Also:
Vermont Advanced Computing Center
206 Farrell Hall, 210 Colchester Ave, Burlington, VT 05405
Tel: (1) 802 656 9830 Fax: (1) 802 656 9892
email: ydubief at uvm.edu
web: http://www.uvm.edu/~ydubief/