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From: David A Case via AMBER <amber.ambermd.org>

Date: Mon, 17 Jul 2023 07:41:30 -0400

----- 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,

/

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Jul 17 2023 - 05:00:02 PDT

Date: Mon, 17 Jul 2023 07:41:30 -0400

----- 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,

/

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Jul 17 2023 - 05:00:02 PDT

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