[gmx-users] LINCS and number of nodes

[Mark Abraham]

On 16/03/11, Moeed  <lecielll at googlemail.com> wrote:
> Dear experts,
> 
> I am trying to build up a polymer in hexane system by increasing the density.
> 

This seems to have been taking months. Why aren't you using genbox on your polymer starting configuration and an equilibrated box of hexane of the right density?

Mark

>  After PR step, my NVT and NPT trailes failed. Initially I used to get LINCS and 1-4 warnings (even for NVT) which were not because of flawed topology file. It turned out that simulations crashed just because of using -np > 4. But still even with this -np, NPT did not work which made me to swtich to berendsen from parrinelo rahman scheme. As I approched the desired density again simulation crashed, so I used 
> 
> 
> trjconv -s .tpr -f .trr -o frame2300.gro -dump 2300
> 
> to extract one of the frames before crash I did another NVT to equilibrate. 
> mpirun -np 4 mdrun_mpi -deffnm PE60-110Hex-NPT3-frame2300_md -s -o -c -g -e -x -v -pd 
> 
> 
> after around 1 ns I get the error below ( mdp file is also included). I described above since I encountered the situation where root cause of problem was not topology and just the computational issue ( I mean -np), I am just curious if the same thing applies here. Please help me with this. Thank you in advance.
> 
> 
> more details: There is only one polyethylene chain ( 60 units) in 110 hexane. The chain is not convoluted and has a little extended shape, which make it not easy fit in the box. 
> 
> Moeed
> ===========================================
> 
> 
> step 449800, will finish Tue Mar 15 11:23:55 2011
> step 449900, will finish Tue Mar 15 11:23:55 2011
> [node5:09563] *** Process received signal ***
> [node5:09563] Signal: Segmentation fault (11)
> [node5:09563] Signal code: Address not mapped (1)
> 
> [node5:09563] Failing at address: 0xffffffff80849dc0
> [node5:09563] [ 0] /lib64/libpthread.so.0 [0x3a2660eb10]
> [node5:09563] [ 1] mdrun_mpi [0x4f0155]
> [node5:09563] [ 2] mdrun_mpi(gmx_pme_do+0x216d) [0x4f9c1d]
> 
> [node5:09563] [ 3] mdrun_mpi(do_force_lowlevel+0x21c8) [0x49c658]
> [node5:09563] [ 4] mdrun_mpi(do_force+0xc59) [0x50db19]
> [node5:09563] [ 5] mdrun_mpi(do_md+0x5623) [0x43e353]
> [node5:09563] [ 6] mdrun_mpi(mdrunner+0xa07) [0x435e07]
> 
> [node5:09563] [ 7] mdrun_mpi(main+0x1269) [0x443319]
> [node5:09563] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3a25e1d994]
> [node5:09563] [ 9] mdrun_mpi [0x420449]
> [node5:09563] *** End of error message ***
> 
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 9563 on node node5.reyclus.loc exited on signal 11 (Segmentation fault).
> -----------------------------------------------------------------------
> 
> 
> 
> 
> pbc              =  xyz                   
> ;energygrps          =  PE HEX
>         
> ;        Run control                    
> integrator          =  md                 
> dt                  =  0.002                
> 
> nsteps              =  1000000 ;5000          
> nstcomm             =  100            
> 
> ;        Output control
> nstenergy           =  100                 
> nstxout             =  100                 
> nstvout             =  0
> 
> nstfout             =  0
> nstlog              =  1000            
> nstxtcout          =  1000                 
> 
> ;        Neighbor searching
> nstlist             =  10                
> ns_type             =  grid                
> 
> 
> ;        Electrostatics/VdW 
> coulombtype         =  PME                     
> vdw-type            =  Shift              
> rcoulomb-switch     =  0                   
> rvdw-switch         =  0.9 ;0                
> 
> 
> ;        Cut-offs
> rlist               =  1.25                 
> rcoulomb            =  1.25 ;1.1            
> rvdw                =  1.0                
> 
> ;        PME parameters
> fourierspacing      =  0.12                
> 
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order          =  4                  
> ewald_rtol          =  1e-5
> optimize_fft      =  yes
> 
> ;        Temperature coupling    
> 
> Tcoupl              =  v-rescale                 
> tc-grps             =  System  ;HEX                    
> tau_t               =  0.1     ;0.1            
> ref_t               =  300     ;300        
>     
> ;        Pressure coupling
> 
> Pcoupl              =  no;berendsen              
> Pcoupltype          =  isotropic                
> tau_p               =  0.5                ;0.5    
> compressibility     =  4.5e-5 4.5e-5         
> ref_p               =  30    30              
> 
> 
> ;        Velocity generation                
> gen_vel             =  yes                 
> gen_temp            =  300.0                
> gen_seed            =  173529                 
> 
> ;        Bonds
> constraints             = all-bonds               
> 
> constraint-algorithm = lincs
> 
> 
> 
> 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110316/b43151fc/attachment.html>