----- Forwarded message from Fabian Glaser <fglaser.technion.ac.il> -----
From: Fabian Glaser <fabian.glaser.gmail.com>
Date: 13 July 2023 at 15:10:04 GMT+3
To: AMBER Mailing List <amber.ambermd.org>
Cc: Fabian Glaser <fglaser.techunix.technion.ac.il>
Subject: MaxNumberTIAtom on PPI-GaMD - BUG?
Dear amber experts,
I am trying to run PPI-GaMD for a dimer of my interest, but I am repeatedly getting sigfault errors (see below). Normal GaMD Equilibration and Production runs perfectly OK, but when I try to run a PPI-GaMD Production, I get sigfault. Below I pasted the input file for EQ and PROD I used, the output error, and gti_controlVariable.i file.
As the a runtime error mentions the TI atom limits of 500 atoms, I changed the MaxNumberTIAtom = 2000 in gti_controlVariable.i file to 2000 and recompiled, but the result was exactly the same (I also tried to use very few atoms a 100, this does not seem to be the problem). Even the TI atom limits error persists. I did several additional tests both with amber20 and amber22, using several different configurations of the input file, with two different machines, and I keep getting the same type of segfault. I even asked from a colleague to run the same code in his machine, to be sure there is not a compilation problem on my system or a system problem in my machines. With the same result….
Do you think this maybe an amber code bug?
If not, could you please advise what could be done?
Thanks a lot in advance,
I am using GaMD for some time successfully, but I would be very happy to be able to sample complexes properly, as this is one of the main lines of my research.
Best regards,
Fabian
--------------------------
Fabian Glaser, PhD
Structural and Computational Biology Unit
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
terminate called after throwing an instance of 'std::runtime_error'
what(): Too many TI atoms--current limit: 500 atoms
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0x7f6095108d21 in ???
#1 0x7f6095107ef5 in ???
#2 0x7f6094f1e08f in ???
at /build/glibc-SzIz7B/glibc-2.31/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0
#3 0x7f6094f1e00b in __GI_raise
at ../sysdeps/unix/sysv/linux/raise.c:51
#4 0x7f6094efd858 in __GI_abort
at /build/glibc-SzIz7B/glibc-2.31/stdlib/abort.c:79
#5 0x7f6095473910 in ???
#6 0x7f609547f38b in ???
#7 0x7f609547f3f6 in ???
#8 0x7f609547f6a8 in ???
#9 0x557b53e8ddbf in ???
#10 0x557b540889b6 in ???
#11 0x557b53f602fa in ???
#12 0x557b53e8e81e in ???
#13 0x7f6094eff082 in __libc_start_main
at ../csu/libc-start.c:308
#14 0x557b53eaa4dd in ???
#15 0xffffffffffffffff in ???
./LAT12.PPI-GaMD.1.eq.prod: line 39: 2194499 Aborted (core dumped) pmemd.cuda -O -i 2-GaMD-PPI/PPI-GaMD.PROD -p 0-PAR/$prefix.prmtop -c 2-GaMD-PPI/$prefix.PPI-GaMD.EQ.1.rst7 -ref 2-GaMD-PPI/$prefix.PPI-GaMD.EQ.1.rst7 -o 2-GaMD-PPI/$prefix.PPI-GaMD.PROD.1.mdout -x 2-GaMD-PPI/$prefix.PPI-GaMD.PROD.1.nc -inf 2-GaMD-PPI/$prefix.PPI-GaMD.PROD.1.mdinfo -r 2-GaMD-PPI/$prefix.PPI-GaMD.PROD.1.rst7
Executing finished
#ifndef GTI_CONTROL
#define GTI_CONTROL
#ifdef C_COMPILER
#define STATIC_CONST_INT static const int
#else /* for FORTRAN */
#define STATIC_CONST_INT integer, parameter::
#endif
STATIC_CONST_INT MaxNumberTIAtom = 2000;
STATIC_CONST_INT MaxNumberTIPair = 300;
STATIC_CONST_INT MaxNumberNBPerAtom = 3072;
STATIC_CONST_INT MaxNumberREAFAtom = 500;
STATIC_CONST_INT GPUPotEnergyTerms = 54;
STATIC_CONST_INT NumberTIEnergyTerms = 17;
STATIC_CONST_INT GPUKinEnergyTerms = 10;
STATIC_CONST_INT TIEnergyBufferMultiplier = 9;
STATIC_CONST_INT TIEnergyDLShift = 3;
STATIC_CONST_INT TIEnergySCShift = 6;
STATIC_CONST_INT TIExtraShift = 44;
STATIC_CONST_INT TINumberExtraTerms = 6;
STATIC_CONST_INT TISpecialShift = 52;
STATIC_CONST_INT TINumberSpecialTerms = 2;
#ifdef C_COMPILER
#define TCV_BEG typedef struct {
#define TCV_END } TypeCtrlVar;
#define TCV_DOUBLE double
#define TCV_INT int
#define TCV_SP ;
EQUILIBRATION PPI-GaMD
&cntrl
imin = 0,
nstlim = 2500000,
dt = 0.002,
temp0 = 300,
ntc = 2, !Flag for SHAKE to perform bond length constraints NTC=NTF = 2 for TIP, OPC water, etc.
ntf = 2, !Force evaluation, calculations for H-atoms bonds are omitted (ntf=2) (use with NTC=2)
tol = 0.00001, !Relative geometrical tolerance for coordinate resetting in shake
ntwx = 5000, !save coordinates every ntwx steps
ntwe = 0, !Every ntwe steps, energies and T written to "mden" in a compact form
ntwr = 5000, !restart file written very ntwr stesp
ntpr = 5000, !Print the progress of the minimization (or MD) every ntpr steps. This goes to the "mdout"
cut = 10.0, !non bonded cutoff
nscm = 1000, !avoids flying cube effec by removing center of mass
iwrap = 1, !periodic image closest to the midle of box written rest are "wrapped",
ntt = 3, !Langevin thermostat control ntt=3 with low viscosity (gamma_ln=1.0) used in explicit solv MD
gamma_ln=1.0, !Collision frequency
ntb = 2, !constant volume (ntb=1, ntp=0) for production runs (step 10 and on), especially on GPUs
ntp = 1, !constant volume
barostat = 2,
taup = 1.0, !controls strength of the pressure coupling; smaller values give tighter coupling to the barostat
irest = 0, !irest=1 to restart
ntx = 1, !read velocities
ioutfm = 1, !ioutfm=1 to write NetCDF trajectories, used in initial calc
ntxo = 2, !ntxo=2 to write a NetCDF restart file, used in initial calc
ig = -1, !ig=-1 to use the wall clock for the pseudo-random number generator seed, used in initial calc
igamd = 3, !Flag to apply boost potential
iE = 1, !Flag to set the threshold energy E
irest_gamd = 0, !Flag to restart GaMD simulation
ntcmd = 1000000, !The number of initial conventional molecular dynamics simulation steps
nteb = 25000000, !The number of biasing molecular dynamics simulation steps
ntave = 200000, !The number of simulation steps used to calculate the average and standard deviation of potential energies
ntcmdprep = 200000, !The number of preparation conventional molecular dynamics steps
ntebprep = 800000, !The number of preparation biasing molecular dynamics simulation steps
sigma0P = 6.0, !The upper limit of the standard deviation of the first potential boost that allows for accurate reweighting. default is 6.0 (unit: kcal/mol).
sigma0D = 6.0, !The upper limit of the standard deviation of the second potential boost that allows for accurate reweighting
/
PRODUCTION GaMD
&cntrl
imin = 0, ! no minimization
nstlim = 250000000, !total steps
dt = 0.002, !time step
tempi=300.0, ! Initial temperature
temp0=300.0, ! Target temperature
irest = 0,
ntx = 1,
ntc = 2, !Flag for SHAKE to perform bond length constraints NTC=NTF = 2 for TIP, OPC water, etc.
ntf = 2, !Force evaluation, calculations for H-atoms bonds are omitted (ntf=2) (use with NTC=2)
tol = 0.00001, !Relative geometrical tolerance for coordinate resetting in shake
ntwx = 5000, !save coordinates every ntwx steps
ntwe = 0, !Every ntwe steps, energies and T written to "mden" in a compact form
ntwr = 5000, !restart file written very ntwr stesp
ntpr = 5000, !Print the progress of the minimization (or MD) every ntpr steps. This goes to the "mdout"
cut = 10.0, !non bonded cutoff
nscm = 1000, !avoids flying cube effec by removing center of mass
iwrap = 1, !periodic image closest to the midle of box written rest are "wrapped",
ntt = 3, !Langevin thermostat control ntt=3 with low viscosity (gamma_ln=1.0) used in explicit solv MD
gamma_ln=1.0, !Collision frequency
ntb = 2, !constant volume (ntb=1, ntp=0) for production runs (step 10 and on), especially on GPUs
ntp = 1, !constant volume
barostat = 2 ! MC Barostat
taup = 1.0, !controls strength of the pressure coupling; smaller values give tighter coupling to the barostat
ioutfm = 1, !ioutfm=1 to write NetCDF trajectories, used in initial calc
ntxo = 2, !ntxo=2 to write a NetCDF restart file, used in initial calc
ig = -1, !ig=-1 to use the wall clock for the pseudo-random number generator seed, used in initial calc
icfe = 1,
ifsc = 1,
gti_cpu_output = 0,
gti_add_sc = 1,
timask1 = ':1-97(!.H=)',
scmask1 = ':1-97(!.H=)',
timask2 = '',
scmask2 = '',
bgpro2atm=1604,
edpro2atm=3199,
igamd = 17,
iE = 1,
iEP = 1,
iED = 1,
irest_gamd = 0,
ntcmd = 1000000,
nteb = 1000000,
ntave = 50000,
ntcmdprep = 200000,
ntebprep = 200000,
sigma0P = 6.0,
sigma0D = 6.0,
/
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Received on Mon Jul 17 2023 - 05:00:02 PDT
