Re: [gmx-users] g_tune_pme for multiple nodes
On Tue, Dec 4, 2012 at 7:18 PM, Carsten Kutzner wrote: > > On Dec 4, 2012, at 2:45 PM, Chandan Choudhury wrote: > > > Hi Carsten, > > > > Thanks for the reply. > > > > If PME nodes for the g_tune is half of np, then if it exceeds the ppn of > of > > a node, how would g_tune perform. What I mean if $NPROCS=36, the its half > > is 18 ppn, but 18 ppns are not present in a single node (max. ppn = 12 > per > > node). How would g_tune function in such scenario? > Typically mdrun allocates the PME and PP nodes in an interleaved way, > meaning > you would end up with 9 PME nodes on each of your two nodes. > > Check the -ddorder of mdrun. > > Interleaving is normally fastest unless you could have all PME processes > exclusively > on a single node. > Thanks Carsten for the explanation. Chandan > > Carsten > > > > > Chandan > > > > > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > > > > > On Tue, Dec 4, 2012 at 6:39 PM, Carsten Kutzner wrote: > > > >> Hi Chandan, > >> > >> the number of separate PME nodes in Gromacs must be larger than two and > >> smaller or equal to half the number of MPI processes (=np). Thus, > >> g_tune_pme > >> checks only up to npme = np/2 PME nodes. > >> > >> Best, > >> Carsten > >> > >> > >> On Dec 4, 2012, at 1:54 PM, Chandan Choudhury > wrote: > >> > >>> Dear Carsten and Florian, > >>> > >>> Thanks for you useful suggestions. It did work. I still have a doubt > >>> regarding the execution : > >>> > >>> export MPIRUN=`which mpirun` > >>> export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" > >>> g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e > >>> tune.edr -g tune.log > >>> > >>> I am suppling $NPROCS as 24 [2 (nodes)*12(ppn)], so that g_tune_pme > tunes > >>> the no. of pme nodes. As I am executing it on a single node, mdrun > never > >>> checks pme for greater than 12 ppn. So, how do I understand that the > pme > >> is > >>> tuned for 24 ppn spanning across the two nodes. > >>> > >>> Chandan > >>> > >>> > >>> -- > >>> Chandan kumar Choudhury > >>> NCL, Pune > >>> INDIA > >>> > >>> > >>> On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner > >> wrote: > >>> > Hi Chandan, > > On Nov 29, 2012, at 3:30 PM, Chandan Choudhury > >> wrote: > > > Hi Carsten, > > > > Thanks for your suggestion. > > > > I did try to pass to total number of cores with the np flag to the > > g_tune_pme, but it didnot help. Hopefully I am doing something > silliy. > >> I > > have pasted the snippet of the PBS script. > > > > #!/bin/csh > > #PBS -l nodes=2:ppn=12:twelve > > #PBS -N bilayer_tune > > > > > > > > > > cd $PBS_O_WORKDIR > > export > MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" > from here on you job file should read: > > export MPIRUN=`which mpirun` > g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e > tune.edr -g tune.log > > > mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c > tune.pdb > >> -x > > tune.xtc -e tune.edr -g tune.log -nice 0 > this way you will get $NPROCS g_tune_pme instances, each trying to run > >> an > mdrun job on 24 cores, > which is not what you want. g_tune_pme itself is a serial program, it > >> just > spawns the mdrun's. > > Carsten > > > > > > Then I submit the script using qsub. > > When I login to the compute nodes there I donot find and mdrun > >> executable > > running. > > > > I also tried using nodes=1 and np 12. It didnot work through qsub. > > > > Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 > -np > 12 > > -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice > 0 > > > > It worked. > > > > Also, if I just use > > $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e > tune.edr > > -g tune.log -nice 0 > > g_tune_pme executes on the head node and writes various files. > > > > Kindly let me know what am I missing when I submit through qsub. > > > > Thanks > > > > Chandan > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > > > > > On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner > >> wrote: > > > >> Hi Chandan, > >> > >> g_tune_pme also finds the optimal number of PME cores if the cores > >> are distributed on multiple nodes. Simply pass the total number of > >> cores to the -np option. Depending on the MPI and queue environment > >> that you use, the distribution of the cores over the nodes may have > >> to be specified in a hostfile / machinefile. Check g_tune_pme -h > >> on how to set that. > >> > >> Best, > >> Carsten > >> > >> > >> On Aug 28, 2012, at 8:33 PM, Chandan Choudhury > wrote: > >> > >>> Dear gmx users, > >>> >
Re: [gmx-users] g_tune_pme for multiple nodes
On Dec 4, 2012, at 2:45 PM, Chandan Choudhury wrote: > Hi Carsten, > > Thanks for the reply. > > If PME nodes for the g_tune is half of np, then if it exceeds the ppn of of > a node, how would g_tune perform. What I mean if $NPROCS=36, the its half > is 18 ppn, but 18 ppns are not present in a single node (max. ppn = 12 per > node). How would g_tune function in such scenario? Typically mdrun allocates the PME and PP nodes in an interleaved way, meaning you would end up with 9 PME nodes on each of your two nodes. Check the -ddorder of mdrun. Interleaving is normally fastest unless you could have all PME processes exclusively on a single node. Carsten > > Chandan > > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Tue, Dec 4, 2012 at 6:39 PM, Carsten Kutzner wrote: > >> Hi Chandan, >> >> the number of separate PME nodes in Gromacs must be larger than two and >> smaller or equal to half the number of MPI processes (=np). Thus, >> g_tune_pme >> checks only up to npme = np/2 PME nodes. >> >> Best, >> Carsten >> >> >> On Dec 4, 2012, at 1:54 PM, Chandan Choudhury wrote: >> >>> Dear Carsten and Florian, >>> >>> Thanks for you useful suggestions. It did work. I still have a doubt >>> regarding the execution : >>> >>> export MPIRUN=`which mpirun` >>> export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" >>> g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e >>> tune.edr -g tune.log >>> >>> I am suppling $NPROCS as 24 [2 (nodes)*12(ppn)], so that g_tune_pme tunes >>> the no. of pme nodes. As I am executing it on a single node, mdrun never >>> checks pme for greater than 12 ppn. So, how do I understand that the pme >> is >>> tuned for 24 ppn spanning across the two nodes. >>> >>> Chandan >>> >>> >>> -- >>> Chandan kumar Choudhury >>> NCL, Pune >>> INDIA >>> >>> >>> On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner >> wrote: >>> Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury >> wrote: > Hi Carsten, > > Thanks for your suggestion. > > I did try to pass to total number of cores with the np flag to the > g_tune_pme, but it didnot help. Hopefully I am doing something silliy. >> I > have pasted the snippet of the PBS script. > > #!/bin/csh > #PBS -l nodes=2:ppn=12:twelve > #PBS -N bilayer_tune > > > > > cd $PBS_O_WORKDIR > export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" from here on you job file should read: export MPIRUN=`which mpirun` g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log > mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb >> -x > tune.xtc -e tune.edr -g tune.log -nice 0 this way you will get $NPROCS g_tune_pme instances, each trying to run >> an mdrun job on 24 cores, which is not what you want. g_tune_pme itself is a serial program, it >> just spawns the mdrun's. Carsten > > > Then I submit the script using qsub. > When I login to the compute nodes there I donot find and mdrun >> executable > running. > > I also tried using nodes=1 and np 12. It didnot work through qsub. > > Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 > -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 > > It worked. > > Also, if I just use > $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr > -g tune.log -nice 0 > g_tune_pme executes on the head node and writes various files. > > Kindly let me know what am I missing when I submit through qsub. > > Thanks > > Chandan > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner >> wrote: > >> Hi Chandan, >> >> g_tune_pme also finds the optimal number of PME cores if the cores >> are distributed on multiple nodes. Simply pass the total number of >> cores to the -np option. Depending on the MPI and queue environment >> that you use, the distribution of the cores over the nodes may have >> to be specified in a hostfile / machinefile. Check g_tune_pme -h >> on how to set that. >> >> Best, >> Carsten >> >> >> On Aug 28, 2012, at 8:33 PM, Chandan Choudhury wrote: >> >>> Dear gmx users, >>> >>> I am using 4.5.5 of gromacs. >>> >>> I was trying to use g_tune_pme for a simulation. I intend to execute >>> mdrun at multiple nodes with 12 cores each. Therefore, I would like >> to >>> optimize the number of pme nodes. I could execute g_tune_pme -np 12 >>> md.tpr. But this will only find the optimal PME nodes for single >> nodes >>> run. How do I find the optimal PME nodes for
Re: [gmx-users] g_tune_pme for multiple nodes
Hi Carsten, Thanks for the reply. If PME nodes for the g_tune is half of np, then if it exceeds the ppn of of a node, how would g_tune perform. What I mean if $NPROCS=36, the its half is 18 ppn, but 18 ppns are not present in a single node (max. ppn = 12 per node). How would g_tune function in such scenario? Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Dec 4, 2012 at 6:39 PM, Carsten Kutzner wrote: > Hi Chandan, > > the number of separate PME nodes in Gromacs must be larger than two and > smaller or equal to half the number of MPI processes (=np). Thus, > g_tune_pme > checks only up to npme = np/2 PME nodes. > > Best, > Carsten > > > On Dec 4, 2012, at 1:54 PM, Chandan Choudhury wrote: > > > Dear Carsten and Florian, > > > > Thanks for you useful suggestions. It did work. I still have a doubt > > regarding the execution : > > > > export MPIRUN=`which mpirun` > > export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" > > g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e > > tune.edr -g tune.log > > > > I am suppling $NPROCS as 24 [2 (nodes)*12(ppn)], so that g_tune_pme tunes > > the no. of pme nodes. As I am executing it on a single node, mdrun never > > checks pme for greater than 12 ppn. So, how do I understand that the pme > is > > tuned for 24 ppn spanning across the two nodes. > > > > Chandan > > > > > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > > > > > On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner > wrote: > > > >> Hi Chandan, > >> > >> On Nov 29, 2012, at 3:30 PM, Chandan Choudhury > wrote: > >> > >>> Hi Carsten, > >>> > >>> Thanks for your suggestion. > >>> > >>> I did try to pass to total number of cores with the np flag to the > >>> g_tune_pme, but it didnot help. Hopefully I am doing something silliy. > I > >>> have pasted the snippet of the PBS script. > >>> > >>> #!/bin/csh > >>> #PBS -l nodes=2:ppn=12:twelve > >>> #PBS -N bilayer_tune > >>> > >>> > >>> > >>> > >>> cd $PBS_O_WORKDIR > >>> export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" > >> from here on you job file should read: > >> > >> export MPIRUN=`which mpirun` > >> g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e > >> tune.edr -g tune.log > >> > >>> mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb > -x > >>> tune.xtc -e tune.edr -g tune.log -nice 0 > >> this way you will get $NPROCS g_tune_pme instances, each trying to run > an > >> mdrun job on 24 cores, > >> which is not what you want. g_tune_pme itself is a serial program, it > just > >> spawns the mdrun's. > >> > >> Carsten > >>> > >>> > >>> Then I submit the script using qsub. > >>> When I login to the compute nodes there I donot find and mdrun > executable > >>> running. > >>> > >>> I also tried using nodes=1 and np 12. It didnot work through qsub. > >>> > >>> Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np > >> 12 > >>> -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 > >>> > >>> It worked. > >>> > >>> Also, if I just use > >>> $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e > >> tune.edr > >>> -g tune.log -nice 0 > >>> g_tune_pme executes on the head node and writes various files. > >>> > >>> Kindly let me know what am I missing when I submit through qsub. > >>> > >>> Thanks > >>> > >>> Chandan > >>> -- > >>> Chandan kumar Choudhury > >>> NCL, Pune > >>> INDIA > >>> > >>> > >>> On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner > wrote: > >>> > Hi Chandan, > > g_tune_pme also finds the optimal number of PME cores if the cores > are distributed on multiple nodes. Simply pass the total number of > cores to the -np option. Depending on the MPI and queue environment > that you use, the distribution of the cores over the nodes may have > to be specified in a hostfile / machinefile. Check g_tune_pme -h > on how to set that. > > Best, > Carsten > > > On Aug 28, 2012, at 8:33 PM, Chandan Choudhury > >> wrote: > > > Dear gmx users, > > > > I am using 4.5.5 of gromacs. > > > > I was trying to use g_tune_pme for a simulation. I intend to execute > > mdrun at multiple nodes with 12 cores each. Therefore, I would like > to > > optimize the number of pme nodes. I could execute g_tune_pme -np 12 > > md.tpr. But this will only find the optimal PME nodes for single > nodes > > run. How do I find the optimal PME nodes for multiple nodes. > > > > Any suggestion would be helpful. > > > > Chandan > > > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)
Re: [gmx-users] g_tune_pme for multiple nodes
Hi Chandan, the number of separate PME nodes in Gromacs must be larger than two and smaller or equal to half the number of MPI processes (=np). Thus, g_tune_pme checks only up to npme = np/2 PME nodes. Best, Carsten On Dec 4, 2012, at 1:54 PM, Chandan Choudhury wrote: > Dear Carsten and Florian, > > Thanks for you useful suggestions. It did work. I still have a doubt > regarding the execution : > > export MPIRUN=`which mpirun` > export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" > g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e > tune.edr -g tune.log > > I am suppling $NPROCS as 24 [2 (nodes)*12(ppn)], so that g_tune_pme tunes > the no. of pme nodes. As I am executing it on a single node, mdrun never > checks pme for greater than 12 ppn. So, how do I understand that the pme is > tuned for 24 ppn spanning across the two nodes. > > Chandan > > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner wrote: > >> Hi Chandan, >> >> On Nov 29, 2012, at 3:30 PM, Chandan Choudhury wrote: >> >>> Hi Carsten, >>> >>> Thanks for your suggestion. >>> >>> I did try to pass to total number of cores with the np flag to the >>> g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I >>> have pasted the snippet of the PBS script. >>> >>> #!/bin/csh >>> #PBS -l nodes=2:ppn=12:twelve >>> #PBS -N bilayer_tune >>> >>> >>> >>> >>> cd $PBS_O_WORKDIR >>> export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" >> from here on you job file should read: >> >> export MPIRUN=`which mpirun` >> g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e >> tune.edr -g tune.log >> >>> mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x >>> tune.xtc -e tune.edr -g tune.log -nice 0 >> this way you will get $NPROCS g_tune_pme instances, each trying to run an >> mdrun job on 24 cores, >> which is not what you want. g_tune_pme itself is a serial program, it just >> spawns the mdrun's. >> >> Carsten >>> >>> >>> Then I submit the script using qsub. >>> When I login to the compute nodes there I donot find and mdrun executable >>> running. >>> >>> I also tried using nodes=1 and np 12. It didnot work through qsub. >>> >>> Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np >> 12 >>> -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 >>> >>> It worked. >>> >>> Also, if I just use >>> $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e >> tune.edr >>> -g tune.log -nice 0 >>> g_tune_pme executes on the head node and writes various files. >>> >>> Kindly let me know what am I missing when I submit through qsub. >>> >>> Thanks >>> >>> Chandan >>> -- >>> Chandan kumar Choudhury >>> NCL, Pune >>> INDIA >>> >>> >>> On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner wrote: >>> Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury >> wrote: > Dear gmx users, > > I am using 4.5.5 of gromacs. > > I was trying to use g_tune_pme for a simulation. I intend to execute > mdrun at multiple nodes with 12 cores each. Therefore, I would like to > optimize the number of pme nodes. I could execute g_tune_pme -np 12 > md.tpr. But this will only find the optimal PME nodes for single nodes > run. How do I find the optimal PME nodes for multiple nodes. > > Any suggestion would be helpful. > > Chandan > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
Re: [gmx-users] g_tune_pme for multiple nodes
Dear Carsten and Florian, Thanks for you useful suggestions. It did work. I still have a doubt regarding the execution : export MPIRUN=`which mpirun` export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log I am suppling $NPROCS as 24 [2 (nodes)*12(ppn)], so that g_tune_pme tunes the no. of pme nodes. As I am executing it on a single node, mdrun never checks pme for greater than 12 ppn. So, how do I understand that the pme is tuned for 24 ppn spanning across the two nodes. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner wrote: > Hi Chandan, > > On Nov 29, 2012, at 3:30 PM, Chandan Choudhury wrote: > > > Hi Carsten, > > > > Thanks for your suggestion. > > > > I did try to pass to total number of cores with the np flag to the > > g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I > > have pasted the snippet of the PBS script. > > > > #!/bin/csh > > #PBS -l nodes=2:ppn=12:twelve > > #PBS -N bilayer_tune > > > > > > > > > > cd $PBS_O_WORKDIR > > export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" > from here on you job file should read: > > export MPIRUN=`which mpirun` > g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e > tune.edr -g tune.log > > > mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x > > tune.xtc -e tune.edr -g tune.log -nice 0 > this way you will get $NPROCS g_tune_pme instances, each trying to run an > mdrun job on 24 cores, > which is not what you want. g_tune_pme itself is a serial program, it just > spawns the mdrun's. > > Carsten > > > > > > Then I submit the script using qsub. > > When I login to the compute nodes there I donot find and mdrun executable > > running. > > > > I also tried using nodes=1 and np 12. It didnot work through qsub. > > > > Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np > 12 > > -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 > > > > It worked. > > > > Also, if I just use > > $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e > tune.edr > > -g tune.log -nice 0 > > g_tune_pme executes on the head node and writes various files. > > > > Kindly let me know what am I missing when I submit through qsub. > > > > Thanks > > > > Chandan > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > > > > > On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner wrote: > > > >> Hi Chandan, > >> > >> g_tune_pme also finds the optimal number of PME cores if the cores > >> are distributed on multiple nodes. Simply pass the total number of > >> cores to the -np option. Depending on the MPI and queue environment > >> that you use, the distribution of the cores over the nodes may have > >> to be specified in a hostfile / machinefile. Check g_tune_pme -h > >> on how to set that. > >> > >> Best, > >> Carsten > >> > >> > >> On Aug 28, 2012, at 8:33 PM, Chandan Choudhury > wrote: > >> > >>> Dear gmx users, > >>> > >>> I am using 4.5.5 of gromacs. > >>> > >>> I was trying to use g_tune_pme for a simulation. I intend to execute > >>> mdrun at multiple nodes with 12 cores each. Therefore, I would like to > >>> optimize the number of pme nodes. I could execute g_tune_pme -np 12 > >>> md.tpr. But this will only find the optimal PME nodes for single nodes > >>> run. How do I find the optimal PME nodes for multiple nodes. > >>> > >>> Any suggestion would be helpful. > >>> > >>> Chandan > >>> > >>> -- > >>> Chandan kumar Choudhury > >>> NCL, Pune > >>> INDIA > >>> -- > >>> gmx-users mailing listgmx-users@gromacs.org > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > >> > >> > >> -- > >> Dr. Carsten Kutzner > >> Max Planck Institute for Biophysical Chemistry > >> Theoretical and Computational Biophysics > >> Am Fassberg 11, 37077 Goettingen, Germany > >> Tel. +49-551-2012313, Fax: +49-551-2012302 > >> http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne > >> > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > >> > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gr
Re: [gmx-users] g_tune_pme for multiple nodes
Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury wrote: > Hi Carsten, > > Thanks for your suggestion. > > I did try to pass to total number of cores with the np flag to the > g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I > have pasted the snippet of the PBS script. > > #!/bin/csh > #PBS -l nodes=2:ppn=12:twelve > #PBS -N bilayer_tune > > > > > cd $PBS_O_WORKDIR > export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" from here on you job file should read: export MPIRUN=`which mpirun` g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log > mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x > tune.xtc -e tune.edr -g tune.log -nice 0 this way you will get $NPROCS g_tune_pme instances, each trying to run an mdrun job on 24 cores, which is not what you want. g_tune_pme itself is a serial program, it just spawns the mdrun's. Carsten > > > Then I submit the script using qsub. > When I login to the compute nodes there I donot find and mdrun executable > running. > > I also tried using nodes=1 and np 12. It didnot work through qsub. > > Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 > -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 > > It worked. > > Also, if I just use > $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr > -g tune.log -nice 0 > g_tune_pme executes on the head node and writes various files. > > Kindly let me know what am I missing when I submit through qsub. > > Thanks > > Chandan > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner wrote: > >> Hi Chandan, >> >> g_tune_pme also finds the optimal number of PME cores if the cores >> are distributed on multiple nodes. Simply pass the total number of >> cores to the -np option. Depending on the MPI and queue environment >> that you use, the distribution of the cores over the nodes may have >> to be specified in a hostfile / machinefile. Check g_tune_pme -h >> on how to set that. >> >> Best, >> Carsten >> >> >> On Aug 28, 2012, at 8:33 PM, Chandan Choudhury wrote: >> >>> Dear gmx users, >>> >>> I am using 4.5.5 of gromacs. >>> >>> I was trying to use g_tune_pme for a simulation. I intend to execute >>> mdrun at multiple nodes with 12 cores each. Therefore, I would like to >>> optimize the number of pme nodes. I could execute g_tune_pme -np 12 >>> md.tpr. But this will only find the optimal PME nodes for single nodes >>> run. How do I find the optimal PME nodes for multiple nodes. >>> >>> Any suggestion would be helpful. >>> >>> Chandan >>> >>> -- >>> Chandan kumar Choudhury >>> NCL, Pune >>> INDIA >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> >> >> -- >> Dr. Carsten Kutzner >> Max Planck Institute for Biophysical Chemistry >> Theoretical and Computational Biophysics >> Am Fassberg 11, 37077 Goettingen, Germany >> Tel. +49-551-2012313, Fax: +49-551-2012302 >> http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
AW: [gmx-users] g_tune_pme for multiple nodes
> -Ursprüngliche Nachricht- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] Im Auftrag von Chandan Choudhury > Gesendet: Donnerstag, 29. November 2012 15:31 > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] g_tune_pme for multiple nodes > > Hi Carsten, > > Thanks for your suggestion. > > I did try to pass to total number of cores with the np flag to the g_tune_pme, > but it didnot help. Hopefully I am doing something silliy. I have pasted the > snippet of the PBS script. > > #!/bin/csh > #PBS -l nodes=2:ppn=12:twelve > #PBS -N bilayer_tune > > > > > cd $PBS_O_WORKDIR > export > MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" > mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x > tune.xtc -e tune.edr -g tune.log -nice 0 Hi, Don't start an MPI process. Run: g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x and everything should work fine. /Flo > > > Then I submit the script using qsub. > When I login to the compute nodes there I donot find and mdrun executable > running. > > I also tried using nodes=1 and np 12. It didnot work through qsub. > > Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 - > s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 > > It worked. > > Also, if I just use > $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g > tune.log -nice 0 g_tune_pme executes on the head node and writes various files. > > Kindly let me know what am I missing when I submit through qsub. > > Thanks > > Chandan > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner wrote: > > > Hi Chandan, > > > > g_tune_pme also finds the optimal number of PME cores if the cores are > > distributed on multiple nodes. Simply pass the total number of cores > > to the -np option. Depending on the MPI and queue environment that you > > use, the distribution of the cores over the nodes may have to be > > specified in a hostfile / machinefile. Check g_tune_pme -h on how to > > set that. > > > > Best, > > Carsten > > > > > > On Aug 28, 2012, at 8:33 PM, Chandan Choudhury > wrote: > > > > > Dear gmx users, > > > > > > I am using 4.5.5 of gromacs. > > > > > > I was trying to use g_tune_pme for a simulation. I intend to execute > > > mdrun at multiple nodes with 12 cores each. Therefore, I would like > > > to optimize the number of pme nodes. I could execute g_tune_pme -np > > > 12 md.tpr. But this will only find the optimal PME nodes for single > > > nodes run. How do I find the optimal PME nodes for multiple nodes. > > > > > > Any suggestion would be helpful. > > > > > > Chandan > > > > > > -- > > > Chandan kumar Choudhury > > > NCL, Pune > > > INDIA > > > -- > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > > > -- > > Dr. Carsten Kutzner > > Max Planck Institute for Biophysical Chemistry Theoretical and > > Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany > > Tel. +49-551-2012313, Fax: +49-551-2012302 > > http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_tune_pme for multiple nodes
Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune cd $PBS_O_WORKDIR export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 Then I submit the script using qsub. When I login to the compute nodes there I donot find and mdrun executable running. I also tried using nodes=1 and np 12. It didnot work through qsub. Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 It worked. Also, if I just use $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 g_tune_pme executes on the head node and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner wrote: > Hi Chandan, > > g_tune_pme also finds the optimal number of PME cores if the cores > are distributed on multiple nodes. Simply pass the total number of > cores to the -np option. Depending on the MPI and queue environment > that you use, the distribution of the cores over the nodes may have > to be specified in a hostfile / machinefile. Check g_tune_pme -h > on how to set that. > > Best, > Carsten > > > On Aug 28, 2012, at 8:33 PM, Chandan Choudhury wrote: > > > Dear gmx users, > > > > I am using 4.5.5 of gromacs. > > > > I was trying to use g_tune_pme for a simulation. I intend to execute > > mdrun at multiple nodes with 12 cores each. Therefore, I would like to > > optimize the number of pme nodes. I could execute g_tune_pme -np 12 > > md.tpr. But this will only find the optimal PME nodes for single nodes > > run. How do I find the optimal PME nodes for multiple nodes. > > > > Any suggestion would be helpful. > > > > Chandan > > > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry > Theoretical and Computational Biophysics > Am Fassberg 11, 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_tune_pme for multiple nodes
Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury wrote: > Dear gmx users, > > I am using 4.5.5 of gromacs. > > I was trying to use g_tune_pme for a simulation. I intend to execute > mdrun at multiple nodes with 12 cores each. Therefore, I would like to > optimize the number of pme nodes. I could execute g_tune_pme -np 12 > md.tpr. But this will only find the optimal PME nodes for single nodes > run. How do I find the optimal PME nodes for multiple nodes. > > Any suggestion would be helpful. > > Chandan > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_tune_pme for multiple nodes
Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
