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 > > submission script is given below > > > > #!/bin/bash > > #SBATCH -n 130 # Number of cores > > > > Per the docs, this is a guide to sbatch about how many (MPI) tasks you want > to run. It's not a core request. > > #SBATCH -N 5 # no of nodes > > > > This requires a certain number of nodes. So to implement both your > instructions, MPI has to start 26 tasks per node. That would make sense if > you had nodes with a multiple 26 cores. My guess is that your nodes have a > multiple of 16 cores, based on the error message. MPI saw that you asked to > allocate more tasks on cores than available cores, and decided not to set a > number of OpenMP threads per MPI task, so that fell back on a default, > which produced 16, which GROMACS can see doesn't make sense. > > If you want to use -N and -n, then you need to make a choice that makes > sense for the number of cores per node. Easier might be to use -n 130 and > -c 2 to express what I assume is your intent to have 2 cores per MPI task. > Now slurm+MPI can pass that message along properly to OpenMP. > > Your other message about -ntomp can only have come from running gmx_mpi_d > -ntmpi, so just a typo we don't need to worry about further. > > Mark > > #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM > > #SBATCH -p cpu # Partition to submit to > > #SBATCH -o hostname_%j.out # File to which STDOUT will be written > > #SBATCH -e hostname_%j.err # File to which STDERR will be written > > #loading gromacs > > module load gromacs/2018.4 > > #specifying work_dir > > WORKDIR=/home/chm_bratin/GMX_Projects/REMD/4wbu-REMD-inst-clust_1/stage-1 > > > > > > mpirun -np 130 gmx_mpi_d mdrun -v -s remd_nvt_next2.tpr -multidir equil0 > > equil1 equil2 equil3 equil4 equil5 equil6 equil7 equil8 equil9 equil10 > > equil11 equil12 equil13 equil14 equil15 equil16 equil17 equil18 equil19 > > equil20 equil21 equil22 equil23 equil24 equil25 equil26 equil27 equil28 > > equil29 equil30 equil31 equil32 equil33 equil34 equil35 equil36 equil37 > > equil38 equil39 equil40 equil41 equil42 equil43 equil44 equil45 equil46 > > equil47 equil48 equil49 equil50 equil51 equil52 equil53 equil54 equil55 > > equil56 equil57 equil58 equil59 equil60 equil61 equil62 equil63 equil64 > > -deffnm remd_nvt -cpi remd_nvt.cpt -append > > > > On Wed, Sep 4, 2019 at 2:13 PM Mark Abraham > > wrote: > > > > > 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 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 inefficient. The > optimum > > is > > > > usually between 1 and 6 threads per rank. If you want to run with > this > > > > setup, > > > > specify the -ntomp option. But we suggest to change the number of MPI > > > > ranks. > > > > > > > > when I am using -ntomp option ...it is throwing another error > > > > > > > > Fatal error: > > > > Setting the number of thread-MPI ranks is only supported with > > thread-MPI > > > > and > > > > GROMACS was compiled without thread-MPI > > > > > > > > > > > > while GROMACS is compiled with threated-MPI... > > > > > > > > plerase help me in this regard. > > > > -- > > > > 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. > > > > > -- > > 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 > >
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 a guide to sbatch about how many (MPI) tasks you want to run. It's not a core request. #SBATCH -N 5 # no of nodes > This requires a certain number of nodes. So to implement both your instructions, MPI has to start 26 tasks per node. That would make sense if you had nodes with a multiple 26 cores. My guess is that your nodes have a multiple of 16 cores, based on the error message. MPI saw that you asked to allocate more tasks on cores than available cores, and decided not to set a number of OpenMP threads per MPI task, so that fell back on a default, which produced 16, which GROMACS can see doesn't make sense. If you want to use -N and -n, then you need to make a choice that makes sense for the number of cores per node. Easier might be to use -n 130 and -c 2 to express what I assume is your intent to have 2 cores per MPI task. Now slurm+MPI can pass that message along properly to OpenMP. Your other message about -ntomp can only have come from running gmx_mpi_d -ntmpi, so just a typo we don't need to worry about further. Mark #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM > #SBATCH -p cpu # Partition to submit to > #SBATCH -o hostname_%j.out # File to which STDOUT will be written > #SBATCH -e hostname_%j.err # File to which STDERR will be written > #loading gromacs > module load gromacs/2018.4 > #specifying work_dir > WORKDIR=/home/chm_bratin/GMX_Projects/REMD/4wbu-REMD-inst-clust_1/stage-1 > > > mpirun -np 130 gmx_mpi_d mdrun -v -s remd_nvt_next2.tpr -multidir equil0 > equil1 equil2 equil3 equil4 equil5 equil6 equil7 equil8 equil9 equil10 > equil11 equil12 equil13 equil14 equil15 equil16 equil17 equil18 equil19 > equil20 equil21 equil22 equil23 equil24 equil25 equil26 equil27 equil28 > equil29 equil30 equil31 equil32 equil33 equil34 equil35 equil36 equil37 > equil38 equil39 equil40 equil41 equil42 equil43 equil44 equil45 equil46 > equil47 equil48 equil49 equil50 equil51 equil52 equil53 equil54 equil55 > equil56 equil57 equil58 equil59 equil60 equil61 equil62 equil63 equil64 > -deffnm remd_nvt -cpi remd_nvt.cpt -append > > On Wed, Sep 4, 2019 at 2:13 PM Mark Abraham > wrote: > > > 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 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 inefficient. The optimum > is > > > usually between 1 and 6 threads per rank. If you want to run with this > > > setup, > > > specify the -ntomp option. But we suggest to change the number of MPI > > > ranks. > > > > > > when I am using -ntomp option ...it is throwing another error > > > > > > Fatal error: > > > Setting the number of thread-MPI ranks is only supported with > thread-MPI > > > and > > > GROMACS was compiled without thread-MPI > > > > > > > > > while GROMACS is compiled with threated-MPI... > > > > > > plerase help me in this regard. > > > -- > > > 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. > > > -- > 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
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 hostname_%j.out # File to which STDOUT will be written #SBATCH -e hostname_%j.err # File to which STDERR will be written #loading gromacs module load gromacs/2018.4 #specifying work_dir WORKDIR=/home/chm_bratin/GMX_Projects/REMD/4wbu-REMD-inst-clust_1/stage-1 mpirun -np 130 gmx_mpi_d mdrun -v -s remd_nvt_next2.tpr -multidir equil0 equil1 equil2 equil3 equil4 equil5 equil6 equil7 equil8 equil9 equil10 equil11 equil12 equil13 equil14 equil15 equil16 equil17 equil18 equil19 equil20 equil21 equil22 equil23 equil24 equil25 equil26 equil27 equil28 equil29 equil30 equil31 equil32 equil33 equil34 equil35 equil36 equil37 equil38 equil39 equil40 equil41 equil42 equil43 equil44 equil45 equil46 equil47 equil48 equil49 equil50 equil51 equil52 equil53 equil54 equil55 equil56 equil57 equil58 equil59 equil60 equil61 equil62 equil63 equil64 -deffnm remd_nvt -cpi remd_nvt.cpt -append On Wed, Sep 4, 2019 at 2:13 PM Mark Abraham wrote: > 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 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 inefficient. The optimum is > > usually between 1 and 6 threads per rank. If you want to run with this > > setup, > > specify the -ntomp option. But we suggest to change the number of MPI > > ranks. > > > > when I am using -ntomp option ...it is throwing another error > > > > Fatal error: > > Setting the number of thread-MPI ranks is only supported with thread-MPI > > and > > GROMACS was compiled without thread-MPI > > > > > > while GROMACS is compiled with threated-MPI... > > > > plerase help me in this regard. > > -- > > 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. > -- 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] 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 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 inefficient. The optimum is > usually between 1 and 6 threads per rank. If you want to run with this > setup, > specify the -ntomp option. But we suggest to change the number of MPI > ranks. > > when I am using -ntomp option ...it is throwing another error > > Fatal error: > Setting the number of thread-MPI ranks is only supported with thread-MPI > and > GROMACS was compiled without thread-MPI > > > while GROMACS is compiled with threated-MPI... > > plerase help me in this regard. > -- > 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.
[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 inefficient. The optimum is usually between 1 and 6 threads per rank. If you want to run with this setup, specify the -ntomp option. But we suggest to change the number of MPI ranks. when I am using -ntomp option ...it is throwing another error Fatal error: Setting the number of thread-MPI ranks is only supported with thread-MPI and GROMACS was compiled without thread-MPI while GROMACS is compiled with threated-MPI... plerase help me in this regard. -- 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] 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 > > 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 command it is giving following error > > Program: gmx mdrun, version 2018.4 > > Source file: src/gromacs/utility/futil.cpp (line 514) > > MPI rank:0 (out of 32) > > > > File input/output error: > > remd0.tpr > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > I am not able to understand why it is coming > > The error means the input file (remd0.tpr) does not exist in the working > directory. > > -Justin > > > > > On Thu 25 Jul, 2019, 2:31 PM Szilárd Páll, > wrote: > > > >> 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 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 remd.tpr -multi 8 -replex 1000 > >>> -reseed 175320 -deffnm remd_equil* > >>> It is giving the following error > >>> There are not enough slots available in the system to satisfy the 40 > >> slots > >>> that were requested by the application: > >>>gmx_mpi > >>> > >>> Either request fewer slots for your application, or make more slots > >>> available > >>> for use. > >>> > >> > -- > >> > -- > >>> There are not enough slots available in the system to satisfy the 40 > >> slots > >>> that were requested by the application: > >>>gmx_mpi > >>> > >>> Either request fewer slots for your application, or make more slots > >>> available > >>> for use. > >>> > >> > -- > >>> I am not understanding the error. Any suggestion will be highly > >>> appriciated. The mdp file and the qsub.sh file is attached below > >>> > >>> qsub.sh... > >>> #! /bin/bash > >>> #PBS -V > >>> #PBS -l nodes=2:ppn=20 > >>> #PBS -l walltime=48:00:00 > >>> #PBS -N mdrun-serial > >>> #PBS -j oe > >>> #PBS -o output.log > >>> #PBS -e error.log > >>> #cd /home/bratin/Downloads/GROMACS/Gromacs_fibril > >>> cd $PBS_O_WORKDIR > >>> module load openmpi3.0.0 > >>> module load gromacs-2016.5 > >>> NP='cat $PBS_NODEFILE | wc -1' > >>> # mpirun --machinefile $PBS_PBS_NODEFILE -np $NP 'which gmx_mpi' mdrun > -v > >>> -s nvt.tpr -deffnm nvt > >>> #/apps/gromacs-2016.5/bin/mpirun -np 8 gmx_mpi mdrun -v -s remd.tpr > >> -multi > >>> 8 -replex 1000 -deffnm remd_out > >>> for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro > -r > >>> em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done > >>> > >>> for i in {0..7}; do cd equil${i}; mpirun -np 40 gmx_mpi mdrun -v -s > >>> remd.tpr -multi 8 -replex 1000 -deffnm remd$i_out ; cd ..; done > >>> -- > >>> 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. > > -- > == > > 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-Users_List before > posting! > > * Can't post? Read
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 -multi 8 -replex 1000 -deffnm remd* After giving the command it is giving following error Program: gmx mdrun, version 2018.4 Source file: src/gromacs/utility/futil.cpp (line 514) MPI rank:0 (out of 32) File input/output error: remd0.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am not able to understand why it is coming The error means the input file (remd0.tpr) does not exist in the working directory. -Justin On Thu 25 Jul, 2019, 2:31 PM Szilárd Páll, wrote: 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 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 remd.tpr -multi 8 -replex 1000 -reseed 175320 -deffnm remd_equil* It is giving the following error There are not enough slots available in the system to satisfy the 40 slots that were requested by the application: gmx_mpi Either request fewer slots for your application, or make more slots available for use. -- -- There are not enough slots available in the system to satisfy the 40 slots that were requested by the application: gmx_mpi Either request fewer slots for your application, or make more slots available for use. -- I am not understanding the error. Any suggestion will be highly appriciated. The mdp file and the qsub.sh file is attached below qsub.sh... #! /bin/bash #PBS -V #PBS -l nodes=2:ppn=20 #PBS -l walltime=48:00:00 #PBS -N mdrun-serial #PBS -j oe #PBS -o output.log #PBS -e error.log #cd /home/bratin/Downloads/GROMACS/Gromacs_fibril cd $PBS_O_WORKDIR module load openmpi3.0.0 module load gromacs-2016.5 NP='cat $PBS_NODEFILE | wc -1' # mpirun --machinefile $PBS_PBS_NODEFILE -np $NP 'which gmx_mpi' mdrun -v -s nvt.tpr -deffnm nvt #/apps/gromacs-2016.5/bin/mpirun -np 8 gmx_mpi mdrun -v -s remd.tpr -multi 8 -replex 1000 -deffnm remd_out for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -r em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done for i in {0..7}; do cd equil${i}; mpirun -np 40 gmx_mpi mdrun -v -s remd.tpr -multi 8 -replex 1000 -deffnm remd$i_out ; cd ..; done -- 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. -- == 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-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] 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 command it is giving following error Program: gmx mdrun, version 2018.4 Source file: src/gromacs/utility/futil.cpp (line 514) MPI rank:0 (out of 32) File input/output error: remd0.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am not able to understand why it is coming On Thu 25 Jul, 2019, 2:31 PM Szilárd Páll, wrote: > 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 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 remd.tpr -multi 8 -replex 1000 > > -reseed 175320 -deffnm remd_equil* > > It is giving the following error > > There are not enough slots available in the system to satisfy the 40 > slots > > that were requested by the application: > > gmx_mpi > > > > Either request fewer slots for your application, or make more slots > > available > > for use. > > > -- > > > -- > > There are not enough slots available in the system to satisfy the 40 > slots > > that were requested by the application: > > gmx_mpi > > > > Either request fewer slots for your application, or make more slots > > available > > for use. > > > -- > > I am not understanding the error. Any suggestion will be highly > > appriciated. The mdp file and the qsub.sh file is attached below > > > > qsub.sh... > > #! /bin/bash > > #PBS -V > > #PBS -l nodes=2:ppn=20 > > #PBS -l walltime=48:00:00 > > #PBS -N mdrun-serial > > #PBS -j oe > > #PBS -o output.log > > #PBS -e error.log > > #cd /home/bratin/Downloads/GROMACS/Gromacs_fibril > > cd $PBS_O_WORKDIR > > module load openmpi3.0.0 > > module load gromacs-2016.5 > > NP='cat $PBS_NODEFILE | wc -1' > > # mpirun --machinefile $PBS_PBS_NODEFILE -np $NP 'which gmx_mpi' mdrun -v > > -s nvt.tpr -deffnm nvt > > #/apps/gromacs-2016.5/bin/mpirun -np 8 gmx_mpi mdrun -v -s remd.tpr > -multi > > 8 -replex 1000 -deffnm remd_out > > for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -r > > em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done > > > > for i in {0..7}; do cd equil${i}; mpirun -np 40 gmx_mpi mdrun -v -s > > remd.tpr -multi 8 -replex 1000 -deffnm remd$i_out ; cd ..; done > > -- > > 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. -- 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] 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 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 remd.tpr -multi 8 -replex 1000 > -reseed 175320 -deffnm remd_equil* > It is giving the following error > There are not enough slots available in the system to satisfy the 40 slots > that were requested by the application: > gmx_mpi > > Either request fewer slots for your application, or make more slots > available > for use. > -- > -- > There are not enough slots available in the system to satisfy the 40 slots > that were requested by the application: > gmx_mpi > > Either request fewer slots for your application, or make more slots > available > for use. > -- > I am not understanding the error. Any suggestion will be highly > appriciated. The mdp file and the qsub.sh file is attached below > > qsub.sh... > #! /bin/bash > #PBS -V > #PBS -l nodes=2:ppn=20 > #PBS -l walltime=48:00:00 > #PBS -N mdrun-serial > #PBS -j oe > #PBS -o output.log > #PBS -e error.log > #cd /home/bratin/Downloads/GROMACS/Gromacs_fibril > cd $PBS_O_WORKDIR > module load openmpi3.0.0 > module load gromacs-2016.5 > NP='cat $PBS_NODEFILE | wc -1' > # mpirun --machinefile $PBS_PBS_NODEFILE -np $NP 'which gmx_mpi' mdrun -v > -s nvt.tpr -deffnm nvt > #/apps/gromacs-2016.5/bin/mpirun -np 8 gmx_mpi mdrun -v -s remd.tpr -multi > 8 -replex 1000 -deffnm remd_out > for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -r > em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done > > for i in {0..7}; do cd equil${i}; mpirun -np 40 gmx_mpi mdrun -v -s > remd.tpr -multi 8 -replex 1000 -deffnm remd$i_out ; cd ..; done > -- > 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.
[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 remd.tpr -multi 8 -replex 1000 -reseed 175320 -deffnm remd_equil* It is giving the following error There are not enough slots available in the system to satisfy the 40 slots that were requested by the application: gmx_mpi Either request fewer slots for your application, or make more slots available for use. -- -- There are not enough slots available in the system to satisfy the 40 slots that were requested by the application: gmx_mpi Either request fewer slots for your application, or make more slots available for use. -- I am not understanding the error. Any suggestion will be highly appriciated. The mdp file and the qsub.sh file is attached below qsub.sh... #! /bin/bash #PBS -V #PBS -l nodes=2:ppn=20 #PBS -l walltime=48:00:00 #PBS -N mdrun-serial #PBS -j oe #PBS -o output.log #PBS -e error.log #cd /home/bratin/Downloads/GROMACS/Gromacs_fibril cd $PBS_O_WORKDIR module load openmpi3.0.0 module load gromacs-2016.5 NP='cat $PBS_NODEFILE | wc -1' # mpirun --machinefile $PBS_PBS_NODEFILE -np $NP 'which gmx_mpi' mdrun -v -s nvt.tpr -deffnm nvt #/apps/gromacs-2016.5/bin/mpirun -np 8 gmx_mpi mdrun -v -s remd.tpr -multi 8 -replex 1000 -deffnm remd_out for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -r em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done for i in {0..7}; do cd equil${i}; mpirun -np 40 gmx_mpi mdrun -v -s remd.tpr -multi 8 -replex 1000 -deffnm remd$i_out ; cd ..; done -- 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] 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 > 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 > > 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: > > > >> 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 installed the openmpi and gromacs 5.1. > >> Do anyone know the problem. > >> > >> yours sincerelly, > >> Ouyang > >> -- > >> 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. > > -- > 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] 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 > 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: > >> 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 installed the openmpi and gromacs 5.1. >> Do anyone know the problem. >> >> yours sincerelly, >> Ouyang >> -- >> 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. -- 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] 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: > Hi, > I am running a REMD of a protein, when I submit "gmx mdrun -s > md_0_${i}.tpr -multi 46 -replex 1000 -reseed -1", it fails as the below > Fatal error: > mdrun -multi or -multidir are not supported with the thread-MPI library. > Please compile GROMACS with a proper external MPI library. > I have installed the openmpi and gromacs 5.1. > Do anyone know the problem. > > yours sincerelly, > Ouyang > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD error
Hi, I am running a REMD of a protein, when I submit "gmx mdrun -s md_0_${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 installed the openmpi and gromacs 5.1. Do anyone know the problem. yours sincerelly, Ouyang -- 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.