Re: [gmx-users] grompp is using a very large amount of memory on a modestly-sized system
Hi, Mark, I'd be happy to, as soon as I get a chance. I know very little about how GROMACS works internally, but I had a few ideas I wanted to share in the hopes that they might help. One is that pairwise parameters for electrostatics could be implemented in the same way that LJ parameters are stored. That would provide a tremendous amount of flexibility for use cases far beyond my own. Or there could simply be an FEP flag for only scaling between molecule types, rather than also between molecules of a given type. Again, you guys are the experts and I know you have other priorities. Just my thoughts. Best, Sean On Fri, Mar 8, 2019 at 3:44 PM Mark Abraham wrote: > Hi, > > I don't have a solution for the question at hand, but it'd be great to have > your inputs attached to a new issue at https://redmine.gromacs.org, so > that > we can have such an input case to test with, so that we can improve the > simplistic implementation! Please upload it if you can. > > Mark > > On Fri., 8 Mar. 2019, 19:24 Sean Marks, wrote: > > > Scratch that comment about sparseness. I am short on sleep, and for a > > moment thought I was talking about constraints, not electrostatics. > > > > On Fri, Mar 8, 2019 at 1:12 PM Sean Marks > wrote: > > > > > I understand now, thank you for the prompt response. While the matrix > > > would actually be quite sparse (since the constraints are localized to > > each > > > ice molecule), I take it that memory is being allocated for a dense > > matrix. > > > > > > That aside, is it feasible to accomplish my stated goal of scaling > > > ice-water electrostatics while leaving other interactions unaffected? > One > > > alternative I considered was manually scaling down the charges > > themselves, > > > but doing this causes the lattice to lose its form. > > > > > > On Fri, Mar 8, 2019 at 12:28 PM Justin Lemkul wrote: > > > > > >> > > >> > > >> On 3/8/19 11:04 AM, Sean Marks wrote: > > >> > Hi, everyone, > > >> > > > >> > I am running into an issue where grompp is using a tremendous amount > > of > > >> > memory and crashing, even though my system is not especially large > > >> (63976 > > >> > atoms). > > >> > > > >> > I am using GROMACS 2016.3. > > >> > > > >> > My system consists of liquid water (7,930 molecules) next to a block > > of > > >> ice > > >> > (8,094 molecules). The ice oxygens are restrained to their lattice > > >> position > > >> > with a harmonic potential with strength k = 4,000 kJ/mol/nm^2. I am > > >> using > > >> > the TIP4P/Ice model, which is a rigid 4-site model with a negative > > >> partial > > >> > charge located on a virtual site rather than the oxygen. > > >> > > > >> > My goal is to systematically reduce the electrostatic interactions > > >> between > > >> > the water molecules and the position-restrained ice, while leaving > > >> > water-water and ice-ice interactions unaffected. > > >> > > > >> > To accomplish this, I am modeling all of the ice molecules using a > > >> single > > >> > moleculetype so that I can take advantages of GROMACS' FEP features > to > > >> > selectively scale interactions. I explicitly specify all constraints > > and > > >> > exclusions in the topology file. This moleculetype contains one > > virtual > > >> > site, 3 constraints, and 4 exclusions per "residue" (ice molecule). > > >> > > > >> > When I run grompp, I receive the following error, which I think > means > > >> that > > >> > a huge block of memory (~9 GB) was requested but could not be > > allocated: > > >> > > > >> > = > > >> > Command line: > > >> >gmx grompp -f npt.mdp -c md.gro -p topol.top -n index.ndx -r > > >> > initconf_packmol.gro -o input.tpr -maxwarn 2 -pp processed.top > > >> > > > >> > ... > > >> > > > >> > Generated 21 of the 21 non-bonded parameter combinations > > >> > Generating 1-4 interactions: fudge = 0.5 > > >> > Generated 21 of the 21 1-4 parameter combinations > > >> > Excluding 3 bonded neighbours molecule type 'ICE' > > >> > turning H bonds into constraints... > > >> > Excluding 3 bonded nei
Re: [gmx-users] grompp is using a very large amount of memory on a modestly-sized system
Scratch that comment about sparseness. I am short on sleep, and for a moment thought I was talking about constraints, not electrostatics. On Fri, Mar 8, 2019 at 1:12 PM Sean Marks wrote: > I understand now, thank you for the prompt response. While the matrix > would actually be quite sparse (since the constraints are localized to each > ice molecule), I take it that memory is being allocated for a dense matrix. > > That aside, is it feasible to accomplish my stated goal of scaling > ice-water electrostatics while leaving other interactions unaffected? One > alternative I considered was manually scaling down the charges themselves, > but doing this causes the lattice to lose its form. > > On Fri, Mar 8, 2019 at 12:28 PM Justin Lemkul wrote: > >> >> >> On 3/8/19 11:04 AM, Sean Marks wrote: >> > Hi, everyone, >> > >> > I am running into an issue where grompp is using a tremendous amount of >> > memory and crashing, even though my system is not especially large >> (63976 >> > atoms). >> > >> > I am using GROMACS 2016.3. >> > >> > My system consists of liquid water (7,930 molecules) next to a block of >> ice >> > (8,094 molecules). The ice oxygens are restrained to their lattice >> position >> > with a harmonic potential with strength k = 4,000 kJ/mol/nm^2. I am >> using >> > the TIP4P/Ice model, which is a rigid 4-site model with a negative >> partial >> > charge located on a virtual site rather than the oxygen. >> > >> > My goal is to systematically reduce the electrostatic interactions >> between >> > the water molecules and the position-restrained ice, while leaving >> > water-water and ice-ice interactions unaffected. >> > >> > To accomplish this, I am modeling all of the ice molecules using a >> single >> > moleculetype so that I can take advantages of GROMACS' FEP features to >> > selectively scale interactions. I explicitly specify all constraints and >> > exclusions in the topology file. This moleculetype contains one virtual >> > site, 3 constraints, and 4 exclusions per "residue" (ice molecule). >> > >> > When I run grompp, I receive the following error, which I think means >> that >> > a huge block of memory (~9 GB) was requested but could not be allocated: >> > >> > = >> > Command line: >> >gmx grompp -f npt.mdp -c md.gro -p topol.top -n index.ndx -r >> > initconf_packmol.gro -o input.tpr -maxwarn 2 -pp processed.top >> > >> > ... >> > >> > Generated 21 of the 21 non-bonded parameter combinations >> > Generating 1-4 interactions: fudge = 0.5 >> > Generated 21 of the 21 1-4 parameter combinations >> > Excluding 3 bonded neighbours molecule type 'ICE' >> > turning H bonds into constraints... >> > Excluding 3 bonded neighbours molecule type 'SOL' >> > turning H bonds into constraints... >> > Coupling 1 copies of molecule type 'ICE' >> > Setting gen_seed to 1021640799 >> > Velocities were taken from a Maxwell distribution at 273 K >> > Cleaning up constraints and constant bonded interactions with virtual >> sites >> > Removing all charge groups because cutoff-scheme=Verlet >> > >> > --- >> > Program: gmx grompp, version 2016.3 >> > Source file: src/gromacs/utility/smalloc.cpp (line 226) >> > >> > Fatal error: >> > Not enough memory. Failed to realloc -8589934588 bytes for il->iatoms, >> > il->iatoms=25e55010 >> > (called from file >> > >> /home/semarks/source/gromacs/2016.3/icc/serial/gromacs-2016.3/src/gromacs/ >> > gmxpreprocess/convparm.cpp, >> > line 565) >> > >> > For more information and tips for troubleshooting, please check the >> GROMACS >> > website at http://www.gromacs.org/Documentation/Errors >> > --- >> > === >> > >> > In the hope that it helps with diagnosing the problem, here is my mdp >> file: >> >> The problem is this: >> > couple-intramol = no; don't adjust ice-ice interactions >> > >> This setting causes the creation of a large exclusion matrix, which in >> your case is approximately 32,376 x 32,376 elements. For small >> molecules, this generally isn't an issue, but since you're trying to >> modulate a large number of molecules within a much larger >> [moleculetype], the memory requirem
Re: [gmx-users] grompp is using a very large amount of memory on a modestly-sized system
I understand now, thank you for the prompt response. While the matrix would actually be quite sparse (since the constraints are localized to each ice molecule), I take it that memory is being allocated for a dense matrix. That aside, is it feasible to accomplish my stated goal of scaling ice-water electrostatics while leaving other interactions unaffected? One alternative I considered was manually scaling down the charges themselves, but doing this causes the lattice to lose its form. On Fri, Mar 8, 2019 at 12:28 PM Justin Lemkul wrote: > > > On 3/8/19 11:04 AM, Sean Marks wrote: > > Hi, everyone, > > > > I am running into an issue where grompp is using a tremendous amount of > > memory and crashing, even though my system is not especially large (63976 > > atoms). > > > > I am using GROMACS 2016.3. > > > > My system consists of liquid water (7,930 molecules) next to a block of > ice > > (8,094 molecules). The ice oxygens are restrained to their lattice > position > > with a harmonic potential with strength k = 4,000 kJ/mol/nm^2. I am using > > the TIP4P/Ice model, which is a rigid 4-site model with a negative > partial > > charge located on a virtual site rather than the oxygen. > > > > My goal is to systematically reduce the electrostatic interactions > between > > the water molecules and the position-restrained ice, while leaving > > water-water and ice-ice interactions unaffected. > > > > To accomplish this, I am modeling all of the ice molecules using a single > > moleculetype so that I can take advantages of GROMACS' FEP features to > > selectively scale interactions. I explicitly specify all constraints and > > exclusions in the topology file. This moleculetype contains one virtual > > site, 3 constraints, and 4 exclusions per "residue" (ice molecule). > > > > When I run grompp, I receive the following error, which I think means > that > > a huge block of memory (~9 GB) was requested but could not be allocated: > > > > = > > Command line: > >gmx grompp -f npt.mdp -c md.gro -p topol.top -n index.ndx -r > > initconf_packmol.gro -o input.tpr -maxwarn 2 -pp processed.top > > > > ... > > > > Generated 21 of the 21 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 0.5 > > Generated 21 of the 21 1-4 parameter combinations > > Excluding 3 bonded neighbours molecule type 'ICE' > > turning H bonds into constraints... > > Excluding 3 bonded neighbours molecule type 'SOL' > > turning H bonds into constraints... > > Coupling 1 copies of molecule type 'ICE' > > Setting gen_seed to 1021640799 > > Velocities were taken from a Maxwell distribution at 273 K > > Cleaning up constraints and constant bonded interactions with virtual > sites > > Removing all charge groups because cutoff-scheme=Verlet > > > > --- > > Program: gmx grompp, version 2016.3 > > Source file: src/gromacs/utility/smalloc.cpp (line 226) > > > > Fatal error: > > Not enough memory. Failed to realloc -8589934588 bytes for il->iatoms, > > il->iatoms=25e55010 > > (called from file > > > /home/semarks/source/gromacs/2016.3/icc/serial/gromacs-2016.3/src/gromacs/ > > gmxpreprocess/convparm.cpp, > > line 565) > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > === > > > > In the hope that it helps with diagnosing the problem, here is my mdp > file: > > The problem is this: > > couple-intramol = no; don't adjust ice-ice interactions > > > This setting causes the creation of a large exclusion matrix, which in > your case is approximately 32,376 x 32,376 elements. For small > molecules, this generally isn't an issue, but since you're trying to > modulate a large number of molecules within a much larger > [moleculetype], the memory requirement goes up exponentially. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-User
[gmx-users] grompp is using a very large amount of memory on a modestly-sized system
Hi, everyone, I am running into an issue where grompp is using a tremendous amount of memory and crashing, even though my system is not especially large (63976 atoms). I am using GROMACS 2016.3. My system consists of liquid water (7,930 molecules) next to a block of ice (8,094 molecules). The ice oxygens are restrained to their lattice position with a harmonic potential with strength k = 4,000 kJ/mol/nm^2. I am using the TIP4P/Ice model, which is a rigid 4-site model with a negative partial charge located on a virtual site rather than the oxygen. My goal is to systematically reduce the electrostatic interactions between the water molecules and the position-restrained ice, while leaving water-water and ice-ice interactions unaffected. To accomplish this, I am modeling all of the ice molecules using a single moleculetype so that I can take advantages of GROMACS' FEP features to selectively scale interactions. I explicitly specify all constraints and exclusions in the topology file. This moleculetype contains one virtual site, 3 constraints, and 4 exclusions per "residue" (ice molecule). When I run grompp, I receive the following error, which I think means that a huge block of memory (~9 GB) was requested but could not be allocated: = Command line: gmx grompp -f npt.mdp -c md.gro -p topol.top -n index.ndx -r initconf_packmol.gro -o input.tpr -maxwarn 2 -pp processed.top ... Generated 21 of the 21 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 21 of the 21 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ICE' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Coupling 1 copies of molecule type 'ICE' Setting gen_seed to 1021640799 Velocities were taken from a Maxwell distribution at 273 K Cleaning up constraints and constant bonded interactions with virtual sites Removing all charge groups because cutoff-scheme=Verlet --- Program: gmx grompp, version 2016.3 Source file: src/gromacs/utility/smalloc.cpp (line 226) Fatal error: Not enough memory. Failed to realloc -8589934588 bytes for il->iatoms, il->iatoms=25e55010 (called from file /home/semarks/source/gromacs/2016.3/icc/serial/gromacs-2016.3/src/gromacs/ gmxpreprocess/convparm.cpp, line 565) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- === In the hope that it helps with diagnosing the problem, here is my mdp file: === ; Water and ice ; RUN CONTROL PARAMETERS ; Molecular dynamics integrator = md ; Leapfrog dt = 0.002; 2 fs - time step [ps] nsteps = 500 ; 10 ns - run time [steps] ; Center of mass motion (COMM) removal comm-mode= none ; Linear nstcomm = 10; Removal frequency (>= nstcalcenergy) [steps] comm-grps= System ; Groups for COMM removal (blank => whole system) ; Initial velocities gen_vel = yes; Generate velocities using Boltzmann distribution gen_temp = 273; Temperature for Boltzmann distribution [K] gen_seed = -1 ; Seed for RNG is the job ID ; OUTPUT CONTROL OPTIONS nstcalcenergy= 1 ; Frequency of energy calculation [steps] ; Output frequency for coords (x), velocities (v) and forces (f) ; trr nstxout = 0 ; never - print coordinates [steps] nstvout = 0 ; never - print velocities [steps] nstfout = 0 ; never - print forces [steps] ; Log end edr files nstlog = 2500; 5 ps - print energies to log file [steps] nstenergy= 2500; 5 ps - print energies to energy file [steps] ; xtc nstxout-compressed = 2500; 5 ps - print coordinates to xtc file [steps] compressed-x-precision = 1000; Number of zeros = number of places after decimal point compressed-x-grps= System ; Groups to write to xtc file ; BOUNDARY CONDITIONS pbc = xyz periodic_molecules = no ; Rigid graphene has no intramolecule interactions ; NEIGHBOR LIST cutoff-scheme= Verlet nstlist = 10 ; Neighbor list update frequency [steps] ns-type = grid; More efficient than simple search verlet-buffer-tolerance = 0.005 ; [kJ/mol/ps] (-1.0 --> use rlist) rlist= 1.0 ; Cutoff distance for short-range neighbor list [nm] ; VAN DER WAALS vdwtype = Cut-off vdw-modifier = Potential-shift-Verlet rvdw = 1.0; Radius for vdW cutoff [nm] DispCorr = no ; ELECTROSTATICS coulombtype = PME; Fast, smooth, particle mesh
