[gmx-users] Turn-off water optimisation
Thomas Schlesier
schlesi at uni-mainz.de
Fri Mar 5 16:05:30 CET 2010
Hi,
compiler could be a problem:
on local machine it was gcc version 4.3.3 (Ubuntu 4.3.3-5ubuntu4)
on the cluster it was some icc compiler (sorry don't know which version,
but we used also the intel mkl 10.0.011 libraris). (But the parallel and
serial version were compiled with the same settings:
./configure CC="icc" CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
-lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
-lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
--prefix="/share/apps/gromacs/4.0.5"
make
make install
make clean
./configure CC="icc" CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
-lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
-lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
--prefix="/share/apps/gromacs/4.0.5" --enable-mpi --disable-nice
--program-suffix=_mpi
make mdrun
make install-mdrun
I will try now the compile the GROMACS 4.0.5 version, on the cluster
with a gcc compiler. Think best will also to try 4.0.7 with the icc
compiler.
below are the mdp and the log (input; 2 steps of actual output, and the
averages) file from one run (spc water, with normal spc.itp and ffG53a5):
MDP-file:
> title = OPLS Lysozyme NVT equilibration
; Run parameters
integrator = md
nsteps = 250000
dt = 0.002
; Output control
nstxout = 2500
nstvout = 0
nstenergy = 2500
nstlog = 2500
; Bond parameters
continuation = no
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
; Temperature coupling is on
tcoupl = V-rescale
ld-seed = -1
tc-grps = system
tau_t = 0.1
ref_t = 300
; Pressure coupling is off
pcoupl = no
; Periodic boundary conditions
pbc = xyz
; Dispersion correction
DispCorr = EnerPres
; Velocity generation
gen_vel = yes
gen_temp = 300
gen_seed = -1
LOG-file
Input Parameters:
integrator = md
nsteps = 250000
init_step = 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 2500
nstxout = 2500
nstvout = 0
nstfout = 0
nstenergy = 2500
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 25
nky = 20
nkz = 20
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = V-rescale
epc = No
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
refcoord_scaling = No
compress (3x3):
posres_com[0]= 0.00000e+00
posres_com[1]= 0.00000e+00
posres_com[2]= 0.00000e+00
posres_comB (3):
posres_comB[0]= 0.00000e+00
posres_comB[1]= 0.00000e+00
posres_comB[2]= 0.00000e+00
andersen_seed = 815131
rlist = 1.4
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.4
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.4
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = EnerPres
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 703303
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 7101
ref_t: 300
tau_t: 0.1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.
*snip*
Using a Gaussian width (1/beta) of 0.448228 nm for Ewald
Cut-off's: NS: 1.4 Coulomb: 1.4 LJ: 1.4
System total charge: 0.000
Generated table with 1200 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 1184 molecules.
Configuring nonbonded kernels...
Testing x86_64 SSE support... present.
Removing pbc first time
*snip*
There are: 3552 Atoms
Max number of connections per atom is 2
Total number of connections is 4736
Max number of graph edges per atom is 2
Total number of graph edges is 4736
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 0.00e+00
Initial temperature: 303.041 K
Started mdrun on node 0 Thu Mar 4 11:20:10 2010
Step Time Lambda
0 0.00000 0.00000
Grid: 6 x 4 x 4 cells
Long Range LJ corr.: <C6> 2.9082e-04
Long Range LJ corr.: Epot -77.7923, Pres: -71.7651, Vir: 77.7923
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
1.13442e+04 -7.77923e+01 -7.05664e+04 -1.53951e+03 -6.08396e+04
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
8.93685e+03 -5.19027e+04 -5.18779e+04 3.02732e+02 -2.59307e+03
Step Time Lambda
2500 5.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
6.18686e+03 -7.77923e+01 -4.50870e+04 -1.36173e+03 -4.03397e+04
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
1.25168e+04 -2.78229e+04 1.22037e+05 4.24002e+02 2.25670e+03
*snip*
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
6.15659e+03 -7.77923e+01 -4.59217e+04 -1.32129e+03 -4.11642e+04
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
1.26205e+04 -2.85438e+04 9.37069e+06 4.27512e+02 1.82506e+03
Greetings
Thomas
> Hi,
>
> Can you also post your .mdp?
>
> Ran
>
> Berk Hess wrote:
>> Hi,
>>
>> I have never heard about problems like this before.
>> It seems highly unlikely to me that the innerloops are causing this.
>>
>> Are your running exacly the same tpr file on your local machine
>> and the cluster?
>>
>> You probably want to update to version 4.0.7 to be sure you have
>> all the latest bugfixes.
>>
>> Please keep us updated on this issue, since things like this should
>> never happen (unless there is a compiler bug).
>>
>> Berk
>>
>>> Date: Fri, 5 Mar 2010 14:41:02 +0100
>>> From: schlesi at uni-mainz.de
>>> To: gmx-users at gromacs.org
>>> Subject: Re: [gmx-users] Turn-off water optimisation
>>>
>>> Hi,
>>> i have the following problem: (GROMACS 4.0.5)
>>>
>>> when i simulated water in serial on our cluster with the brendsen or
>>> v-rescale thermostat i get to high temperatures (300 K goes in very
>>> short time up to around 425 K). If i simulate in parallel or at my
>> local
>>> machine i get no problems. Also if i change water to another molecule
>>> there are no such problems. (I use the same mdp file for all the
>>> simulations).
>>>
>>> Because the problem appears with water (spc and tip4p) but not with
>>> mesitylene i thought probably the special things for water (settle, and
>>> so on) could be the problem. So i wanted to simulate water without that
>>> fancy stuff.
>>> Thanks for the info with the enviroment variable, but where can i
>> set it?
>>> For the other problems (why it works on the cluster in parallel, but
>> not
>>> in serial, but works on the local-pc in serial) i have so far no idea,
>>> where to look. But first i'm happy to know if the problem comes from
>> the
>>> special water-loops.
>>>
>>> Thomas
>>>
>>>
>>>
>>>> Hi,
>>>>
>>>> You don't want to mess with the topology, you will be simulating a
>>> quit >different
>>>> system when you turn off constraints. Also Gromacs does not optimize
>>>> based
>>>> on names, since the name might not say anything about the molecule.
>>>> I don't know what effect of what optimizations you want to test,
>>>> but setting the environment variable GMX_NO_SOLV_OPT will turn off
>>>> the special inner-loops for water.
>>>>
>>>> Berk
>>>> Date: Fri, 5 Mar 2010 11:31:50 +0100
>>>> From: schlesi at uni-mainz.de
>>>> To: gmx-users at gromacs.org
>>>> Subject: [gmx-users] Turn-off water optimisation
>>>>
>>>> Dear all,
>>>> I simulated water (spc) with the ffG53a5 force field. For testing
>>>> propose i want to turn of the water optimisation. How do i do this?
>>>> So far i have tried:
>>>> * contraints = none
>>>> * define = -DFLEXIBLE
>>>> * took the spc.itp file and deleted all the stuff for settle and the
>>>> other force fields, changed resname from SOL to WAT (also spc.itp ->
>>>> wat.itp)
>>>>
>>>> But all the time i the log file there is this line:
>>>> Enabling SPC water optimization for 1184 molecules.
>>>>
>>>> Espically with the last option (change of the spc.itp) i don't how
>>>> GROMACS recorgnises that i simulate SPC water, because i has a
>> different
>>>> name and so.
>>>>
>>>> Thanks for your help in advance.
>>>> Greetings
>>>> Thomas
>>>> --
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