Re: [gmx-users] REMD-error

Thank you for your email sir. On Wed, Sep 4, 2019 at 2:42 PM Mark Abraham wrote: > Hi, > > On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in > > > wrote: > > > Respected Mark Abraham, > > The command-line and the job > >

Re: [gmx-users] REMD-error

Hi, On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Respected Mark Abraham, > The command-line and the job > submission script is given below > > #!/bin/bash > #SBATCH -n 130 # Number of cores > Per the docs, this is

Re: [gmx-users] REMD-error

Respected Mark Abraham, The command-line and the job submission script is given below #!/bin/bash #SBATCH -n 130 # Number of cores #SBATCH -N 5 # no of nodes #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM #SBATCH -p cpu # Partition to submit to #SBATCH -o

Re: [gmx-users] REMD-error

Hi, We need to see your command line in order to have a chance of helping. Mark On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Dear all, > I am running one REMD simulation with 65 replicas. I am using > 130 cores for the simulation. I am

[gmx-users] REMD-error

Dear all, I am running one REMD simulation with 65 replicas. I am using 130 cores for the simulation. I am getting the following error. Fatal error: Your choice of number of MPI ranks and amount of resources results in using 16 OpenMP threads per rank, which is most likely

Re: [gmx-users] remd error

Thank you On Mon 29 Jul, 2019, 6:45 PM Justin Lemkul, wrote: > > > On 7/29/19 7:55 AM, Bratin Kumar Das wrote: > > Hi Szilard, > > Thank you for your reply. I rectified as you said. For > trial > > purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is > running > >

Re: [gmx-users] remd error

On 7/29/19 7:55 AM, Bratin Kumar Das wrote: Hi Szilard, Thank you for your reply. I rectified as you said. For trial purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is running or not. I gave the following command to run remd *mpirun -np 8 gmx_mpi_d mdrun -v

Re: [gmx-users] remd error

Hi Szilard, Thank you for your reply. I rectified as you said. For trial purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is running or not. I gave the following command to run remd *mpirun -np 8 gmx_mpi_d mdrun -v -multi 8 -replex 1000 -deffnm remd* After giving the

Re: [gmx-users] remd error

This is an MPI / job scheduler error: you are requesting 2 nodes with 20 processes per node (=40 total), but starting 80 ranks. -- Szilárd On Thu, Jul 18, 2019 at 8:33 AM Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > > Hi, >I am running remd simulation in gromacs-2016.5. After

[gmx-users] remd error

Hi, I am running remd simulation in gromacs-2016.5. After generating the multiple .tpr file in each directory by the following command *for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done* I run *mpirun -np 80 gmx_mpi mdrun -s

Re: [gmx-users] REMD error

Hi, If you've configured with GMX_MPI, then the resulting GROMACS binary is called gmx_mpi, so mpirun -np X gmx_mpi mdrun -multi ... Mark On Fri, May 13, 2016 at 10:09 AM YanhuaOuyang <15901283...@163.com> wrote: > Hi, > I have installed the openmpi 1.10, and I can run mpirun. When I installed

Re: [gmx-users] REMD error

Hi, I have installed the openmpi 1.10, and I can run mpirun. When I installed grimaces 5.1, I configured -DGMX_MPI=on. And the error still happens . > 在 2016年5月13日，下午3:59，Mark Abraham 写道： > > Hi, > > Yes. Exactly as the error message says, you need to compile GROMACS

Re: [gmx-users] REMD error

Hi, Yes. Exactly as the error message says, you need to compile GROMACS differently, with real MPI support. See http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations Mark On Fri, May 13, 2016 at 9:47 AM YanhuaOuyang <15901283...@163.com> wrote:

[gmx-users] REMD error

Hi, I am running a REMD of a protein, when I submit "gmx mdrun -s md_0_${i}.tpr -multi 46 -replex 1000 -reseed -1", it fails as the below Fatal error: mdrun -multi or -multidir are not supported with the thread-MPI library. Please compile GROMACS with a proper external MPI library. I have