[gmx-users] LINCS and number of nodes

[Justin A. Lemkul]

Moeed wrote:
> Dear experts,
> 
> I am trying to build up a polymer in hexane system by increasing the 
> density. 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.
> 

What MPI library (and version) are you using?  Do your runs work in serial?

> 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.
> 

What do you mean it doesn't fit in the box?  If you've got a system that you're 
trying to force into some shape or size, your PE chain is probably just crashing 
into itself across periodic boundaries.  Watch the trajectory to see what's 
going on prior to the crash.

-Justin

> 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
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================