[gmx-users] Re: topology does not match
Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private help service. Your question has been asked and answered dozens, if not hundreds, of times and you should be able to find a solution in the list archive or on the Errors page: http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -Justin lena farnandis wrote: Dear sir, suffer from same one problem . when i was run drug enzyme MD. so how i can solve this problem. gromacs error as follows Fatal error: number of coordinates in coordinate file (trp.pdb, 169092) does not match topology (topology.top, 169071) -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] parallel
Hi gmx-users I have been using gromacs now for a few months and have ran several simulations in serial, which has been quit good. I now am trying to run the simulations in parallel but seem to be having one or two little problems. It seems that the computation does not run on more than two CPUs. It runs using one and two CPUs. Does anyone have any idea why this might be? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] parallel
On 2/03/2010 11:27 PM, Gavin Melaugh wrote: Hi gmx-users I have been using gromacs now for a few months and have ran several simulations in serial, which has been quit good. I now am trying to run the simulations in parallel but seem to be having one or two little problems. It seems that the computation does not run on more than two CPUs. It runs using one and two CPUs. Does anyone have any idea why this might be? No. does not run doesn't have any useful diagnostic value for us, I'm afraid. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_nmeig_d error: can't allocate region
Hi, I am trying to do normal mode analysis on a protein having 6398 atoms in vaccum. I tried to energy minimize the structure using steepest descent, followed by l-bfgs minimization. the .mdp file I used is define = -DFLEXIBLE constraints = none integrator = l-bfgs tinit= 0 nsteps = 15000 nbfgscorr= 50 emtol= .001 emstep = 0.1 gen_vel = yes gen-temp = 300 nstcomm = 1 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 0 ; ns algorithm (simple or grid) ns-type = simple ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = no ; nblist cut-off rlist= 0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-Off rcoulomb-switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0 after running the 15000 steps the Fmax was: Low-Memory BFGS Minimizer converged to Fmax 0.001 in 10197 steps Potential Energy = -8.26391832320506e+04 Maximum force = 9.37558560558845e-04 on atom 4562 Norm of force = 2.24887722104890e-04 Again the l-bfgs minimization was run using the same .mdp file( with emtol = 0.01) the output was' Low-Memory BFGS Minimizer converged to Fmax 1e-06 in 4143 steps Potential Energy = -8.26391832324998e+04 Maximum force = 9.67927896882578e-07 on atom 3271 Norm of force = 1.70637151528245e-07 After this I prepared the nm.mdp file for NMA, where I used exactly the same parameters as the ones used in lbfgs energy minimization( with integrator = nm) the commands that were used were: grompp_d -f new_nm.mdp -t new_lbfgs_2.trr -c new_lbfgs_2.gro -o new_nm.tpr -zero -p ../topol.top nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx nohup.out had the following message: Non-cutoff electrostatics used, forcing full Hessian format.Allocating Hessian memory...starting normal mode calculation 'Protein'6398 steps.Maximum force: 9.67928e- 07 The run ended successfully: Then i used the command g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr I get the following error: Reading file new_nm.tpr, VERSION 4.0.7 (double precision) Reading file new_nm.tpr, VERSION 4.0.7 (double precision) Reading double precision matrix generated by Gromacs VERSION 4.0.7 Full matrix storage format, nrow=19194, ncols=19194 Diagonalizing to find vectors 1 through 50... g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug I am not being able to understand the problem. the computer has a 16gb memory If I use different parameters in the nm.mdp file as rlist= 1.5 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = switch rcoulomb-switch = 1 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 1 rvdw = 1.2 then i get the message :Maximum force: 3.14171e+03 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. I am sorry to post such a lengthy query, but I have no clue about the root of the problem. Any suggestion will be of great help. Thanks in advance, Sarbani. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_nmeig_d error: can't allocate region
Hi, The allocation that causes the error should allocate about 3 GB. My guess is that you compiled Gromacs in 32bit mode, whereas 64bit mode is required for allocation of more than 2 GB. Berk Date: Tue, 2 Mar 2010 13:35:58 + To: gmx-users@gromacs.org From: sarbani_...@rediffmail.com Subject: [gmx-users] g_nmeig_d error: can't allocate region Hi, I am trying to do normal mode analysis on a protein having 6398 atoms in vaccum. I tried to energy minimize the structure using steepest descent, followed by l-bfgs minimization. the .mdp file I used is define = -DFLEXIBLE constraints = none integrator = l-bfgs tinit= 0 nsteps = 15000 nbfgscorr= 50 emtol= .001 emstep = 0.1 gen_vel = yes gen-temp = 300 nstcomm = 1 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 0 ; ns algorithm (simple or grid) ns-type = simple ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = no ; nblist cut-off rlist= 0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-Off rcoulomb-switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0 after running the 15000 steps the Fmax was: Low-Memory BFGS Minimizer converged to Fmax 0.001 in 10197 steps Potential Energy = -8.26391832320506e+04 Maximum force = 9.37558560558845e-04 on atom 4562 Norm of force = 2.24887722104890e-04 Again the l-bfgs minimization was run using the same .mdp file( with emtol = 0.01) the output was' Low-Memory BFGS Minimizer converged to Fmax 1e-06 in 4143 steps Potential Energy = -8.26391832324998e+04 Maximum force = 9.67927896882578e-07 on atom 3271 Norm of force = 1.70637151528245e-07 After this I prepared the nm.mdp file for NMA, where I used exactly the same parameters as the ones used in lbfgs energy minimization( with integrator = nm) the commands that were used were: grompp_d -f new_nm.mdp -t new_lbfgs_2.trr -c new_lbfgs_2.gro -o new_nm.tpr -zero -p ../topol.top nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx nohup.out had the following message: Non-cutoff electrostatics used, forcing full Hessian format.Allocating Hessian memory...starting normal mode calculation 'Protein'6398 steps.Maximum force: 9.67928e- 07 The run ended successfully: Then i used the command g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr I get the following error: Reading file new_nm.tpr, VERSION 4.0.7 (double precision) Reading file new_nm.tpr, VERSION 4.0.7 (double precision) Reading double precision matrix generated by Gromacs VERSION 4.0.7 Full matrix storage format, nrow=19194, ncols=19194 Diagonalizing to find vectors 1 through 50... g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug I am not being able to understand the problem. the computer has a 16gb memory If I use different parameters in the nm.mdp file as rlist= 1.5 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = switch rcoulomb-switch = 1 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 1 rvdw = 1.2 then i get the message :Maximum force: 3.14171e+03 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. I am sorry to post such a lengthy query, but I have no clue about the root of the problem. Any suggestion will be of great help. Thanks in advance, Sarbani. _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
[gmx-users] Re: Minimizing a structure having a heteroatom
Hi all I have modeled a structure with the active site residue as a heteroatom (formyl glycine) and when I am minimizing the structure gromacs is giving error that it cannot minimize it .. can anybody tell me how can i minimize it ... thanks -- Bharat M.Sc. Bioinformatics (Final year) Centre for Bioinformatics Pondicherry University Puducherry India Mob. +919962670525 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Minimizing a structure having a heteroatom
On 3/03/2010 10:13 AM, bharat gupta wrote: Hi all I have modeled a structure with the active site residue as a heteroatom (formyl glycine) and when I am minimizing the structure gromacs is giving error that it cannot minimize it .. can anybody tell me how can i minimize it ... No, because you haven't told us any useful diagnostics. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs memory usage
Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Thank you, Amit On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're using. Quoting such without attributing the source or describing the context is next to useless. You also dropped a parenthesis. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with the size of freeze groups
Dear Berk, Thanks for your previous responses, Can you please let me know if you have any solution for the size of freezing groups? I am still not able to do if i have larger freezing groups. Thanks again for your kind help. srinivas. On Fri, Feb 26, 2010 at 5:37 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I have checked my inputs and tcl scripts that i have used for the selection, i could see that my selection doesn't have any problem. I submitted it again still i am getting the same log file with nrdf 0 for non-freezing group. Please let me know if you want see any of my input files, and help me if you have solution for this problem. Thanks and Regards Srinivas. On Fri, Feb 26, 2010 at 12:39 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I am using VERSION 4.0.5. As you said if there is no problem i should get it correctly, i don't know where it is going wrong. I have written a small script in tcl to use in vmd to get my selections. i will check the script and the selection again. I will let you know my results again. Thanks for your valuable time and kind help. Srinivas. On Fri, Feb 26, 2010 at 12:29 PM, Berk Hess g...@hotmail.com wrote: Hi, Which version of Gromacs are you using? I can't see any issues in the 4.0 code, but some older version might have problems. Berk -- Date: Fri, 26 Feb 2010 12:05:56 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, They are same, freeze and Tmp2 are exactly the same groups. I just put them like that for my convenience, just to avoid confusion in my second email i made it uniform. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote: That is what I suspected, by I don't know why this is. Are you really sure you made a temperature coupling group that is exactly the freeze group? This first mdp file you mailed had a different group names for the freeze group and the tcoupl groups. Berk -- Date: Fri, 26 Feb 2010 11:53:49 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 + grpopts: (system with 25A) nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk -- Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk -- Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen
Re: [gmx-users] gromacs memory usage
On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're using. Quoting such without attributing the source or describing the context is next to useless. You also dropped a parenthesis. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs memory usage
Hi Mark, Yes thats one way to go about it. But it would have been great if i could get a rough estimation. Thank you. amit On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're using. Quoting such without attributing the source or describing the context is next to useless. You also dropped a parenthesis. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs memory usage
Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requirements of a (very) long simulation are equal to that of a very short one, so it doesn't need to cost much time. Cheers, Tsjerk On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Mark, Yes thats one way to go about it. But it would have been great if i could get a rough estimation. Thank you. amit On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're using. Quoting such without attributing the source or describing the context is next to useless. You also dropped a parenthesis. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs memory usage
Hi, last time I checked (summer) I got 40bytes per atom and 294byes per atom/core (RF with 12Å cut-off) 100M atoms works with that cut-off on 128 16GB nodes with 8 cores. I haven't tried on less than 128 nodes. (See http://cmb.ornl.gov/research/petascale-md ) We could relatively easy fix the 40bytes per atom (no one had time so far to work on it) but I don't think there is much which can be done about the 294bytes per atom/core. On how many nodes do you want to simulate? Thus are you limited by the 40bytes per atom or the 294bytes per atom/core? Roland On Tue, Mar 2, 2010 at 11:31 PM, Amit Choubey kgp.a...@gmail.com wrote: Hi Mark, Yes thats one way to go about it. But it would have been great if i could get a rough estimation. Thank you. amit On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're using. Quoting such without attributing the source or describing the context is next to useless. You also dropped a parenthesis. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs memory usage
Hi Tsjerk, I tried to do a test run based on the presentation. But there was a memory related error (I had given a leverage of more than 2 GB). I did not understand the 64 bit issue, could you let me know wheres the documentation? I need to look into that. Thank you, amit On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requirements of a (very) long simulation are equal to that of a very short one, so it doesn't need to cost much time. Cheers, Tsjerk On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Mark, Yes thats one way to go about it. But it would have been great if i could get a rough estimation. Thank you. amit On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're using. Quoting such without attributing the source or describing the context is next to useless. You also dropped a parenthesis. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] gromacs memory usage
Hi, do: file `which mdrun` and it should give: /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped If it is not 64 you need to compile with 64 and have a 64bit kernel. Since you asked before about 2GB large files this might indeed be your problem. Roland On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Tsjerk, I tried to do a test run based on the presentation. But there was a memory related error (I had given a leverage of more than 2 GB). I did not understand the 64 bit issue, could you let me know wheres the documentation? I need to look into that. Thank you, amit On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requirements of a (very) long simulation are equal to that of a very short one, so it doesn't need to cost much time. Cheers, Tsjerk On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Mark, Yes thats one way to go about it. But it would have been great if i could get a rough estimation. Thank you. amit On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're using. Quoting such without attributing the source or describing the context is next to useless. You also dropped a parenthesis. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] gromacs memory usage
Hi Roland I tried 'which mdrun' but it only gives the path name of installation. Is there any other way to know if the installation is 64 bit ot not? Thank you, Amit On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz rol...@utk.edu wrote: Hi, do: file `which mdrun` and it should give: /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped If it is not 64 you need to compile with 64 and have a 64bit kernel. Since you asked before about 2GB large files this might indeed be your problem. Roland On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Tsjerk, I tried to do a test run based on the presentation. But there was a memory related error (I had given a leverage of more than 2 GB). I did not understand the 64 bit issue, could you let me know wheres the documentation? I need to look into that. Thank you, amit On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requirements of a (very) long simulation are equal to that of a very short one, so it doesn't need to cost much time. Cheers, Tsjerk On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Mark, Yes thats one way to go about it. But it would have been great if i could get a rough estimation. Thank you. amit On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're using. Quoting such without attributing the source or describing the context is next to useless. You also dropped a parenthesis. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] gromacs memory usage
Amit, try the full line (with the file) Roland On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Roland I tried 'which mdrun' but it only gives the path name of installation. Is there any other way to know if the installation is 64 bit ot not? Thank you, Amit On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz rol...@utk.edu wrote: Hi, do: file `which mdrun` and it should give: /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped If it is not 64 you need to compile with 64 and have a 64bit kernel. Since you asked before about 2GB large files this might indeed be your problem. Roland On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Tsjerk, I tried to do a test run based on the presentation. But there was a memory related error (I had given a leverage of more than 2 GB). I did not understand the 64 bit issue, could you let me know wheres the documentation? I need to look into that. Thank you, amit On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requirements of a (very) long simulation are equal to that of a very short one, so it doesn't need to cost much time. Cheers, Tsjerk On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi Mark, Yes thats one way to go about it. But it would have been great if i could get a rough estimation. Thank you. amit On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 3/03/2010 12:53 PM, Amit Choubey wrote: Hi Mark, I quoted the memory usage requirements from a presentation by Berk Hess, Following is the link to it http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf l. In that presentation on pg 27,28 Berk does talk about memory usage but then I am not sure if he referred to any other specific thing. My system only contains SPC water. I want Berendsen T coupling and Coulomb interaction with Reaction Field. I just want a rough estimate of how big of a system of water can be simulated on our super computers. Try increasingly large systems until it runs out of memory. There's your answer. Mark On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com mailto: kgp.a...@gmail.com Date: Saturday, February 27, 2010 10:17 Subject: Re: [gmx-users] gromacs memory usage To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms. Well, try some smaller systems and work upwards to see if you have a limit in practice. 50K atoms can be run in less than 32GB over 64 processors. You didn't say whether your simulation system can run on 1 processor... if it does, then you can be sure the problem really is related to parallelism. I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? In general, no. It will vary with the simulation algorithm you're using. Quoting such without attributing the source or describing the context is next to useless. You also dropped a parenthesis. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
