[gmx-users] LINCS and number of nodes
Moeed
lecielll at googlemail.com
Tue Mar 15 18:16:09 CET 2011
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.
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
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