[gmx-users] Why does "system is not well equilibrated" error come out when using multiple GPUs but not one GPUs?
Dear everyone, I am trying to run a MD simulation with gromacs-2019.3 on a workstation with multiple GPUs. When I run the simulation with only one GPU by the command: mpirun_mpi -np 1 gmx_mpi mdrun -ntomp 6 -gpu_id 0 -v -deffnm md it can run normally. However, when I try to run the simulation with multiple GPUs by the command: gmx_mpi mdrun -v -deffnm md It gives out the follow error information: Fatal error: atal error: 120 particles communicated to PME rank 4 are more than 2/3 times the cut-off --- out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. I am very confused that why the simulation can run with one GPU but cannot run with multiple GPUs. The error information seem to tell that the system is not been well equilibrated， but if it is really related to equilibration, why it also related to the number of GPUs? Could you tell me what causes the problem and how to solve it? Best regard. Yeping Sun -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pressure is coming 1.39
For two examples that show this, see https://twitter.com/dr_dbw/status/968624615063937025 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 9 Sep 2019 at 04:53, David van der Spoel wrote: > Den 2019-09-08 kl. 06:36, skrev Bratin Kumar Das: > > Thanks sir for your reply. My target pressure was 1 atm.. > The fluctuations depend on the system size as 1/sqrt(natoms). To obtain > a std dev of 3 bar you need a really big system. > > > > On Sat 7 Sep, 2019, 8:15 PM Mark Abraham, > wrote: > > > >> Hi, > >> > >> Without a statistical error estimation and a target pressure, the > question > >> can't be answered. Pressure takes time to measure, and you need to do so > >> only after equilibration. 1.39 +/- 3 bar might be fine > >> > >> Mark > >> > >> On Sat., 7 Sep. 2019, 07:48 Bratin Kumar Das, < > 177cy500.bra...@nitk.edu.in > >>> > >> wrote: > >> > >>> Hi,, > >>> I am doing a simulation of peptide in water. After 10 ns npt > >>> equilibration the average pressure is coming 1.39 and density is coming > >>> 1005.71 kg/m3. Can I proceed for production run? And what is the upper > >> and > >>> lower limit for the pressure ...after which we can continue production > >> run? > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-requ...@gromacs.org. > >>> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pressure is coming 1.39
Den 2019-09-08 kl. 06:36, skrev Bratin Kumar Das: Thanks sir for your reply. My target pressure was 1 atm.. The fluctuations depend on the system size as 1/sqrt(natoms). To obtain a std dev of 3 bar you need a really big system. On Sat 7 Sep, 2019, 8:15 PM Mark Abraham, wrote: Hi, Without a statistical error estimation and a target pressure, the question can't be answered. Pressure takes time to measure, and you need to do so only after equilibration. 1.39 +/- 3 bar might be fine Mark On Sat., 7 Sep. 2019, 07:48 Bratin Kumar Das, <177cy500.bra...@nitk.edu.in wrote: Hi,, I am doing a simulation of peptide in water. After 10 ns npt equilibration the average pressure is coming 1.39 and density is coming 1005.71 kg/m3. Can I proceed for production run? And what is the upper and lower limit for the pressure ...after which we can continue production run? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD
Hello gmx users, I am getting an error "load imbalance " in remd nvt equilibrium step. Can anyone help me regarding this issue? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cannot run short-ranged nonbonded interactions on a GPU
Hi With the following config command cmake .. -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=`pwd`/../single -DGMX_BUILD_OWN_FFTW=ON I get the following error for "gmx mdrun -nb gpu -v -deffnm inp_nvp" Fatal error: Cannot run short-ranged nonbonded interactions on a GPU because there is none detected. deviceQuery command shows that GPU is detected. $ ./deviceQuery ./deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) Detected 1 CUDA Capable device(s) Device 0: "GeForce GTX 1080 Ti" ... With the same input, I haven't seen that error before. Did I miss something? Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Hi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Obtaining AMBER parameters for Mn2+ and zwitterion form Arginine
Hi, I have found a AMBER database with the Mn2+ ion and Arginine (zwitterion) from the following link: http://research.bmh.manchester.ac.uk/bryce/amber How can I convert these parameters so that I can use them in Gromacs. Any help would be much appreciated. Best wishes, Akash -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Add MSVC binary and build method on MSVC Re: gromacs binaries for windows (Cygwin 64)
- Original Message - > From: Tatsuro MATSUOKA > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Cc: > Date: 2019/9/6, Fri 12:33 > Subject: [gmx-users] gromacs binaries for windows (Cygwin 64) > > I have prepared gromacs binaries for windows (Cygwin 64) on my own web site. > (For testing purpose.) > > http://tmacchant3.starfree.jp/gromacs/win/ > > Tatsuro > I have upload Gromacs 2018.7 on Windows build VC++ 2019. I also described my method to build Gromacs using VC++ 2019. http://tmacchant3.starfree.jp/gromacs/win/ I think that VC+ build is not longer difficult and more effective than build on WSL. Tatsuro -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
