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

[Berk Hess]

Hi,

This bug has been fixed in 4.0.3,
but I forgot about it when writing the release notes.

Berk

> From: ydubief at uvm.edu
> To: gmx-users at gromacs.org
> Date: Tue, 20 Jan 2009 08:53:15 -0500
> Subject: [gmx-users] deform option in parallel with Gromacs 4.0.2
> 
> 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/
> 
> 
> 
> 
> 
> 
> 
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