[gmx-users] LINCS and number of nodes
Justin A. Lemkul
jalemkul at vt.edu
Sat Mar 19 02:41:38 CET 2011
Moeed wrote:
> Hello Justin,
>
> Thanks for you reply. My late response is because I have been trying to
> resolve the problem.
>
> 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?
>
> I am using openmpi.1.4.3. Once I try mdrun in serial I get many LINCS
> and 1-4 warnings ending with segmentation fault at the very beginning.
>
Whatever you're doing to the system is physically unreasonable.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Warning: 1-4 interaction between 1433 and 1441 at distance 2.472 which
> is larger than the 1-4 table size 2.250 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> Step 11, time 0.022 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.004346, max 0.036836 (between atoms 116 and 119)
>
> parallel run does not work for -np >4
>
>
> 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.
>
>
>
> I am not forcing it in to the box. I am just increasing the density but
> since it becomes to extended it crashes into itself as you predicted. I
> have no control on this..Then I had to take another frame before crash
> and try a new conformation hoping that a long simulation with this
> starting structure does not crash.
>
Can you please remind me (and everyone on the list) what exactly you're doing?
It seems as if I've been sending advice for many months and I'm losing track of
what you're doing. What do you mean you're increasing the density - are you
compressing the system? If so, that's your problem - the physics of compression
is breaking down. Whatever you're doing to the system can't be done.
> Also I tried FE, but I am getting no output file dhdl. even when I
> include -dhdl in the command line...
>
What does free energy have to do with anything? If you're making rapid changes
to the system (i.e. you're not at equilibrium), whatever free energy
calculations you carry out won't be worth much of anything.
-Justin
> free_energy = yes
> init_lambda = 0
> delta_lambda = 0
> sc_alpha = 0.5
> sc-power = 1
> sc_sigma = 0.3
> foreign_lambda = 0.1
> dhdl_derivatives = yes
> couple-moltype = Polymer
> couple-lambda0 = vdw-q ;vdw
> couple-lambda1 = none ;vdw;none
> couple-intramol = yes
> nstdhdl = 10
> separate_dhdl_file = yes
> dh_hist_size = 0
> dh_hist_spacing = 0.1
>
> Please give me some advice..
> Thanks
>
>
> -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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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--
========================================
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
========================================
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