[gmx-users] MPI and PME

[Dmitry Kovalsky]

Dear All
I'm trying at first to start at cluster
that was built using rpm's from www.gromacs.org
The problem is that after 60 step of position restrains it crashes with 
message
MPI process rank 1 (n0, p8238) caught a SIGSEGV

I have looked at md0.log and there is the last lines
Testing x86 SSE capabilities...
CPU and OS support SSE.
Using Gromacs SSE single precision assembly innerloops.

           Step           Time         Lambda      Annealing
              0        0.00000        0.00000        1.00000

There are 23793 atoms in your xtc output selection
Large VCM(group rest):     -0.00218,     -0.00004,     -0.00843, ekin-cm:     
 5.84026
   Energies (kJ/mol)
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
    1.84683e+02    1.00152e+03    1.26552e+03    3.14014e+02    5.33486e+02
     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)
    2.26732e+04    5.35157e+04   -1.79857e+03   -3.60921e+05   -7.13160e+04
 Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
    3.76926e+06    3.41471e+06    3.10514e+04    3.44577e+06    1.50847e+02
 Pressure (bar)
   -5.07975e+04

Large VCM(group rest):     -0.00218,     -0.00004,     -0.00842, ekin-cm:     
 5.82455
Large VCM(group rest):     -0.00217,     -0.00004,     -0.00836, ekin-cm:     
 5.73443
Large VCM(group rest):     -0.00214,     -0.00004,     -0.00824, ekin-cm:     
 5.58445
(and again lines like above)...

As I understand the case is in mpd options 
here is my mdp file
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  none
integrator          =  md
dt                  =  0.002
nsteps              =  500000
nstxout             =  0
nstxtcout           =  250
nstvout             =  0
nstfout             =  0
nstcomm             =  1
coulombtype         =  PME
rcoulomb            =  0.9
rcoulomb_switch     =  0
pme_order           =  4
optimize_fft        =  no
fourierspacing      =  0.12
ns_type             =  grid
vdwtype             =  Cut-off
rlist               =  0.9
rvdw                =  1.5
nstlist             =  10
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  2651736
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tau_t               =  0.1	0.1   0.1   0.1
tc_grps		    =  protein	sol   CL-   NA+
ref_t               =  300	300   300   300
; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0

if I change optimize fftw = yes it doesn't help

When I use GenReactionField all is ok
Where is a fault?

Thanks in advance
-- 
Sincerely yours,

Dima

Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143
UKRAINE

E-mail: dikov at imbg.org.ua
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589