Re: [gmx-users] slurm and gromacs
This link should help: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts - John > Dear gromacs users > > I am doing md simulation of protein in a cluster system with > Slurm Workload Manager using following job file: > --- > #! /bin/bash > #SBATCH --job-name Pr_lig > #SBATCH -n 28 > #SBATCH --time 300:30:00 > #SBATCH --mem 5 > #SBATCH --partition gpu > > module load gnu8 > module load openmpi3 > module load gromacs > > #gmx grompp -f nvt.mdp -c em2.gro -p topol.top -o nvt.tpr -n index.ndx > #gmx mdrun -v -nb gpu -deffnm nvt >& nvt.job & > gmx energy -f nvt.edr -o temperature.xvg > --- > After runing job file, How to select temperature to compute using gmx > energy? > > In clusters without Slurm Workload Manager, for gmx energy analysis, > there was a list of parameters to select by user. > > Please guide me. > > Best, > Atila > -- > 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] slurm and gromacs
Dear gromacs users I am doing md simulation of protein in a cluster system with Slurm Workload Manager using following job file: --- #! /bin/bash #SBATCH --job-name Pr_lig #SBATCH -n 28 #SBATCH --time 300:30:00 #SBATCH --mem 5 #SBATCH --partition gpu module load gnu8 module load openmpi3 module load gromacs #gmx grompp -f nvt.mdp -c em2.gro -p topol.top -o nvt.tpr -n index.ndx #gmx mdrun -v -nb gpu -deffnm nvt >& nvt.job & gmx energy -f nvt.edr -o temperature.xvg --- After runing job file, How to select temperature to compute using gmx energy? In clusters without Slurm Workload Manager, for gmx energy analysis, there was a list of parameters to select by user. Please guide me. Best, Atila -- 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] Slurm for GROMACS
Thanks sir for your response. I have two questions. 1. What should be the minimum number of computers to be in my personal cluster (i7 - 4 physical and 8 logical cores) 2. How should I build GROMACS on them statically or dynamically? Thank you On Wed, 6 Nov, 2019, 9:35 PM Alexander Tzanov, < alexander.tza...@csi.cuny.edu> wrote: > No you do not. If you are the only user. > > On Nov 6, 2019 9:04 AM, "Shradheya R.R. Gupta" > wrote: > Thank you sir for your response. > For personal cluster of 6 computers where I will be using all the nodes to > its fullest everytime still needed slurm? > > Thank you > > On Tue, 5 Nov, 2019, 7:32 PM Mark Abraham, > wrote: > > > Hi, > > > > SLURM and OpenMPI do different things. SLURM is a resource manager, from > > which you might request multiple compute nodes. OpenMPI is a parallelism > > library that allows a program to run on those nodes. GROMACS is the > > program, and it doesn't care which MPI library is in use, or which > resource > > manager sits above that. So SLURM + OpenMPI + GROMACS is fine. > > > > Mark > > > > On Tue, 5 Nov 2019 at 14:51, Shradheya R.R. Gupta < > > shradheyagu...@gmail.com> > > wrote: > > > > > Researchers, > > > Is slrum required to run GROMACS on multiple computers or OpenMPI is > > fine? > > > > > > Thank you > > > Shradheya > > > DBT-BIF University of Rajasthan > > > -- > > > 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. > -- 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] Slurm for GROMACS
Unless you have multiple users and want to use SLURM as your scheduler/Manager for who gets to run when, you could just make a machines file and feed that to mpirun to use all of the computers (nodes) all of the time. === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Alexander Tzanov Sent: Wednesday, November 6, 2019 10:46 AM To: gmx-us...@gromacs.org Subject: [EXTERNAL] Re: [gmx-users] Slurm for GROMACS No you do not. If you are the only user. On Nov 6, 2019 9:04 AM, "Shradheya R.R. Gupta" wrote: Thank you sir for your response. For personal cluster of 6 computers where I will be using all the nodes to its fullest everytime still needed slurm? Thank you On Tue, 5 Nov, 2019, 7:32 PM Mark Abraham, wrote: > Hi, > > SLURM and OpenMPI do different things. SLURM is a resource manager, from > which you might request multiple compute nodes. OpenMPI is a parallelism > library that allows a program to run on those nodes. GROMACS is the > program, and it doesn't care which MPI library is in use, or which resource > manager sits above that. So SLURM + OpenMPI + GROMACS is fine. > > Mark > > On Tue, 5 Nov 2019 at 14:51, Shradheya R.R. Gupta < > shradheyagu...@gmail.com> > wrote: > > > Researchers, > > Is slrum required to run GROMACS on multiple computers or OpenMPI is > fine? > > > > Thank you > > Shradheya > > DBT-BIF University of Rajasthan > > -- > > 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. -- 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] Slurm for GROMACS
No you do not. If you are the only user. On Nov 6, 2019 9:04 AM, "Shradheya R.R. Gupta" wrote: Thank you sir for your response. For personal cluster of 6 computers where I will be using all the nodes to its fullest everytime still needed slurm? Thank you On Tue, 5 Nov, 2019, 7:32 PM Mark Abraham, wrote: > Hi, > > SLURM and OpenMPI do different things. SLURM is a resource manager, from > which you might request multiple compute nodes. OpenMPI is a parallelism > library that allows a program to run on those nodes. GROMACS is the > program, and it doesn't care which MPI library is in use, or which resource > manager sits above that. So SLURM + OpenMPI + GROMACS is fine. > > Mark > > On Tue, 5 Nov 2019 at 14:51, Shradheya R.R. Gupta < > shradheyagu...@gmail.com> > wrote: > > > Researchers, > > Is slrum required to run GROMACS on multiple computers or OpenMPI is > fine? > > > > Thank you > > Shradheya > > DBT-BIF University of Rajasthan > > -- > > 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] Slurm for GROMACS
Thank you sir for your response. For personal cluster of 6 computers where I will be using all the nodes to its fullest everytime still needed slurm? Thank you On Tue, 5 Nov, 2019, 7:32 PM Mark Abraham, wrote: > Hi, > > SLURM and OpenMPI do different things. SLURM is a resource manager, from > which you might request multiple compute nodes. OpenMPI is a parallelism > library that allows a program to run on those nodes. GROMACS is the > program, and it doesn't care which MPI library is in use, or which resource > manager sits above that. So SLURM + OpenMPI + GROMACS is fine. > > Mark > > On Tue, 5 Nov 2019 at 14:51, Shradheya R.R. Gupta < > shradheyagu...@gmail.com> > wrote: > > > Researchers, > > Is slrum required to run GROMACS on multiple computers or OpenMPI is > fine? > > > > Thank you > > Shradheya > > DBT-BIF University of Rajasthan > > -- > > 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] Slurm for GROMACS
Hi, SLURM and OpenMPI do different things. SLURM is a resource manager, from which you might request multiple compute nodes. OpenMPI is a parallelism library that allows a program to run on those nodes. GROMACS is the program, and it doesn't care which MPI library is in use, or which resource manager sits above that. So SLURM + OpenMPI + GROMACS is fine. Mark On Tue, 5 Nov 2019 at 14:51, Shradheya R.R. Gupta wrote: > Researchers, > Is slrum required to run GROMACS on multiple computers or OpenMPI is fine? > > Thank you > Shradheya > DBT-BIF University of Rajasthan > -- > 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] Slurm for GROMACS
Researchers, Is slrum required to run GROMACS on multiple computers or OpenMPI is fine? Thank you Shradheya DBT-BIF University of Rajasthan -- 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.
