[gmx-users] g_tune_pme can't be executed
Hi everyone~ When I run g_tune_pme_mpi, it prompts: Fatal error: Need an MPI-enabled version of mdrun. This one (mdrun_mpi) seems to have been compiled without MPI support. I'm sure my gromacs is compiled WITH MPI support and mpiexec -n xx mdrun_mpi -s yy.tpr works normally. How to fix it? I'm using gromacs4.6 and Intel MPI 4.1.0. Thanks. -- Daniel Wang / npbool Computer Science Technology, Tsinghua University -- 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 can't be executed
Hi Daniel, are you using the newest version of 4.6? There was an issue with g_tune_pme, which I already fixed. I guess it could be responsible for the error that you see. Best, Carsten On Mar 21, 2013, at 2:26 PM, Daniel Wang iwnk...@gmail.com wrote: Hi everyone~ When I run g_tune_pme_mpi, it prompts: Fatal error: Need an MPI-enabled version of mdrun. This one (mdrun_mpi) seems to have been compiled without MPI support. I'm sure my gromacs is compiled WITH MPI support and mpiexec -n xx mdrun_mpi -s yy.tpr works normally. How to fix it? I'm using gromacs4.6 and Intel MPI 4.1.0. Thanks. -- Daniel Wang / npbool Computer Science Technology, Tsinghua University -- 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 http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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 can't be executed
Hi Carsten, Actually I tried 4.6.1 weeks ago. Howerev, it seems slighty slower than old version. It's lucky that I haven't deleted the 4.6.1 build from my disk. I'm now testing the newest g_tune_pme. It starts up normally but I have to wait to see the result. Thanks a lot! 2013/3/21 Carsten Kutzner ckut...@gwdg.de Hi Daniel, are you using the newest version of 4.6? There was an issue with g_tune_pme, which I already fixed. I guess it could be responsible for the error that you see. Best, Carsten On Mar 21, 2013, at 2:26 PM, Daniel Wang iwnk...@gmail.com wrote: Hi everyone~ When I run g_tune_pme_mpi, it prompts: Fatal error: Need an MPI-enabled version of mdrun. This one (mdrun_mpi) seems to have been compiled without MPI support. I'm sure my gromacs is compiled WITH MPI support and mpiexec -n xx mdrun_mpi -s yy.tpr works normally. How to fix it? I'm using gromacs4.6 and Intel MPI 4.1.0. Thanks. -- Daniel Wang / npbool Computer Science Technology, Tsinghua University -- 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 http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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 -- 王凝枰 Daniel Wang / npbool Computer Science Technology, Tsinghua University -- 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
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 ckut...@gwdg.de wrote: Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com 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 ckut...@gwdg.de 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 iitd...@gmail.com 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
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 iitd...@gmail.com 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 ckut...@gwdg.de wrote: Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com 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 ckut...@gwdg.de 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 iitd...@gmail.com 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
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 ckut...@gwdg.de 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 iitd...@gmail.com 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 ckut...@gwdg.de wrote: Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com 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 ckut...@gwdg.de 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 iitd...@gmail.com 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
Re: [gmx-users] g_tune_pme for multiple nodes
On Dec 4, 2012, at 2:45 PM, Chandan Choudhury iitd...@gmail.com 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 ckut...@gwdg.de 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 iitd...@gmail.com 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 ckut...@gwdg.de wrote: Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com 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 ckut...@gwdg.de 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 iitd...@gmail.com 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
Re: [gmx-users] g_tune_pme for multiple nodes
On Tue, Dec 4, 2012 at 7:18 PM, Carsten Kutzner ckut...@gwdg.de wrote: On Dec 4, 2012, at 2:45 PM, Chandan Choudhury iitd...@gmail.com 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 ckut...@gwdg.de 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 iitd...@gmail.com 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 ckut...@gwdg.de wrote: Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com 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 ckut...@gwdg.de 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 iitd...@gmail.com 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
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 ckut...@gwdg.de 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 iitd...@gmail.com 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
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 ckut...@gwdg.de 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 iitd...@gmail.com 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 Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com 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 ckut...@gwdg.de 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 iitd...@gmail.com 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
Re: [gmx-users] g_tune_pme cannot be executed
Hi Zifeng, have you tried to use g_tune_pme -npstring none … Carsten On Aug 20, 2012, at 5:07 PM, zifeng li lizife...@gmail.com wrote: Dear Gromacs users, Morning! I am using Gromacs 4.5.4 version and tries to use the magic power of g_tune_pme. However, it cannot be executed with the error in benchtest.log file: mpirun error: do not specify a -np argument. it is set for you. The cluster I use needs to submit mpirun job though PBS script, which looks like following: #PBS -l nodes=8 #PBS -l walltime=2:00:00 #PBS -l pmem=2gb cd $PBS_O_WORKDIR # echo echo echo Job started on `hostname` at `date` g_tune_pme -s npt echo echo Job Ended at `date` echo ~ I can run the command mpirun mdrun_mpi -deffnm npt using this PBS script before and as you notice, -np for g_tune_mpe is not used. Any suggestions about this issue? What I have tried for your reference: 1. to delete the first line. well...it won't help. 2. to set the environmental variable as Manual suggests curiously: export MPIRUN=/usr/local/mpirun -machinefile hostsuse my account name as the hosts here. Thanks in advance! Good day :) -Zifeng -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
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 iitd...@gmail.com 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
[gmx-users] g_tune_pme optimal PME nodes 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 * Only plain text messages are allowed! * 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 restart
Dear: I use g_tune_pme for MD production but it clashed before the job finished since it is over cluster walltime limitation. I get the following information from perf.out: mpirun -np 144 mdrun -npme -1 -s tuned.tpr -v -o md.trr -c md.gro -e md.edr -g md.log I am just wondering, is it correct using the following command to append the jobs? mpirun -np 144 mdrun -npme -1 -s tuned.tpr -v -f md.trr -e md.edr -g md.log -o md.trr -cpi -append thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 restart
On Fri, Aug 24, 2012 at 12:23 PM, Albert mailmd2...@gmail.com wrote: Dear: I use g_tune_pme for MD production but it clashed before the job finished since it is over cluster walltime limitation. I get the following information from perf.out: mpirun -np 144 mdrun -npme -1 -s tuned.tpr -v -o md.trr -c md.gro -e md.edr -g md.log I am just wondering, is it correct using the following command to append the jobs? mpirun -np 144 mdrun -npme -1 -s tuned.tpr -v -f md.trr -e md.edr -g md.log -o md.trr -cpi -append mdrun doesn't have -f as option. It has to be -o. Otherwise it seems OK. Roland thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 cannot be executed
Dear Gromacs users, Morning! I am using Gromacs 4.5.4 version and tries to use the magic power of g_tune_pme. However, it cannot be executed with the error in benchtest.log file: mpirun error: do not specify a -np argument. it is set for you. The cluster I use needs to submit mpirun job though PBS script, which looks like following: #PBS -l nodes=8 #PBS -l walltime=2:00:00 #PBS -l pmem=2gb cd $PBS_O_WORKDIR # echo echo echo Job started on `hostname` at `date` g_tune_pme -s npt echo echo Job Ended at `date` echo ~ I can run the command mpirun mdrun_mpi -deffnm npt using this PBS script before and as you notice, -np for g_tune_mpe is not used. Any suggestions about this issue? What I have tried for your reference: 1. to delete the first line. well...it won't help. 2. to set the environmental variable as Manual suggests curiously: export MPIRUN=/usr/local/mpirun -machinefile hostsuse my account name as the hosts here. Thanks in advance! Good day :) -Zifeng -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 error in blue gene
Hello:
I am trying to run g_tune_pme in blue gene with following script:
# @ job_name = bm
# @ class = kdm-large
# @ account_no = G07-13
# @ error = gromacs.info
# @ output = gromacs.out
# @ environment = COPY_ALL
# @ wall_clock_limit = 160:00:00
# @ notification = error
# @ job_type = bluegene
# @ bg_size = 64
# @ queue
mpirun -exe /opt/gromacs/4.5.5/bin/g_tune_pme -args -v -s md.tpr -o
bm.trr -cpo bm.cpt -g bm.log -launch -mode VN -np 256
but I've got the following messages as soon as I submit jobs and it
terminate soon:
---gromacs.info--
Mar 31 20:45:57.677742 BE_MPI (ERROR): Job execution failed
Mar 31 20:45:57.677803 BE_MPI (ERROR): Job 10969 is in state ERROR ('E')
Mar 31 20:44:58.476985 FE_MPI (ERROR): Job execution failed (error
code - 50)
Mar 31 20:44:58.477065 FE_MPI (ERROR): - Job execution failed - job
switched to an error state
Mar 31 20:45:57.714358 BE_MPI (ERROR): The error message in the job
record is as follows:
Mar 31 20:45:57.714376 BE_MPI (ERROR): Load failed on
192.168.101.49: Executable file is not a 32-bit ELF file
Mar 31 20:44:58.691897 FE_MPI (ERROR): Failure list:
Mar 31 20:44:58.691923 FE_MPI (ERROR): - 1. Job execution failed -
job switched to an error state (failure #50)
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Re: [gmx-users] g_tune_pme error in blue gene
On 1/04/2012 4:50 AM, Albert wrote:
Hello:
I am trying to run g_tune_pme in blue gene with following script:
# @ job_name = bm
# @ class = kdm-large
# @ account_no = G07-13
# @ error = gromacs.info
# @ output = gromacs.out
# @ environment = COPY_ALL
# @ wall_clock_limit = 160:00:00
# @ notification = error
# @ job_type = bluegene
# @ bg_size = 64
# @ queue
mpirun -exe /opt/gromacs/4.5.5/bin/g_tune_pme -args -v -s md.tpr -o
bm.trr -cpo bm.cpt -g bm.log -launch -mode VN -np 256
but I've got the following messages as soon as I submit jobs and it
terminate soon:
---gromacs.info--
Mar 31 20:45:57.677742 BE_MPI (ERROR): Job execution failed
Mar 31 20:45:57.677803 BE_MPI (ERROR): Job 10969 is in state ERROR ('E')
Mar 31 20:44:58.476985 FE_MPI (ERROR): Job execution failed (error
code - 50)
Mar 31 20:44:58.477065 FE_MPI (ERROR): - Job execution failed - job
switched to an error state
Mar 31 20:45:57.714358 BE_MPI (ERROR): The error message in the job
record is as follows:
Mar 31 20:45:57.714376 BE_MPI (ERROR): Load failed on
192.168.101.49: Executable file is not a 32-bit ELF file
This means the executable is unsuitable for the hardware to run. Front
and back ends of BlueGene are different hardware, of course.
Mar 31 20:44:58.691897 FE_MPI (ERROR): Failure list:
Mar 31 20:44:58.691923 FE_MPI (ERROR): - 1. Job execution failed -
job switched to an error state (failure #50)
g_tune_pme relies on being able to spawn mpirun processes and measure
their performance. Back-end BlueGene/L jobs cannot spawn new processes,
and I'm skeptical that BlueGene/P would be able to do this either (but P
is less restrictive). So you will need to run g_tune_pme compiled for
the front end in your job script, and consult g_tune_pme -h for clues on
how to set up your job script so that g_tune_pme can correctly call
mpirun to invoke mdrun_mpi on the back end.
Mark
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Re: [gmx-users] g_tune_pme error in blue gene
On 1/04/2012 9:13 AM, Mark Abraham wrote:
On 1/04/2012 4:50 AM, Albert wrote:
Hello:
I am trying to run g_tune_pme in blue gene with following script:
# @ job_name = bm
# @ class = kdm-large
# @ account_no = G07-13
# @ error = gromacs.info
# @ output = gromacs.out
# @ environment = COPY_ALL
# @ wall_clock_limit = 160:00:00
# @ notification = error
# @ job_type = bluegene
# @ bg_size = 64
# @ queue
mpirun -exe /opt/gromacs/4.5.5/bin/g_tune_pme -args -v -s md.tpr -o
bm.trr -cpo bm.cpt -g bm.log -launch -mode VN -np 256
but I've got the following messages as soon as I submit jobs and it
terminate soon:
---gromacs.info--
Mar 31 20:45:57.677742 BE_MPI (ERROR): Job execution failed
Mar 31 20:45:57.677803 BE_MPI (ERROR): Job 10969 is in state ERROR
('E')
Mar 31 20:44:58.476985 FE_MPI (ERROR): Job execution failed (error
code - 50)
Mar 31 20:44:58.477065 FE_MPI (ERROR): - Job execution failed -
job switched to an error state
Mar 31 20:45:57.714358 BE_MPI (ERROR): The error message in the job
record is as follows:
Mar 31 20:45:57.714376 BE_MPI (ERROR): Load failed on
192.168.101.49: Executable file is not a 32-bit ELF file
This means the executable is unsuitable for the hardware to run. Front
and back ends of BlueGene are different hardware, of course.
Mar 31 20:44:58.691897 FE_MPI (ERROR): Failure list:
Mar 31 20:44:58.691923 FE_MPI (ERROR): - 1. Job execution failed
- job switched to an error state (failure #50)
g_tune_pme relies on being able to spawn mpirun processes and measure
their performance. Back-end BlueGene/L jobs cannot spawn new
processes, and I'm skeptical that BlueGene/P would be able to do this
either (but P is less restrictive). So you will need to run g_tune_pme
compiled for the front end in your job script, and consult g_tune_pme
-h for clues on how to set up your job script so that g_tune_pme can
correctly call mpirun to invoke mdrun_mpi on the back end.
Posting your successful job script would be a welcome contribution for
those in the community who will face this problem in the future.
Mark
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[gmx-users] g_tune_pme
Hi everyone, please I was running simulations with gromacs version 4.0.3
,but I got the following error:
Average load imbalance: 12.1 %
Part of the total run time spent waiting due to load imbalance: 6.9 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0
% Y 9 %
Average PME mesh/force load: 0.807
Part of the total run time spent waiting due to PP/PME imbalance: 5.3 %
NOTE: 6.9 % performance was lost due to load imbalance
in the domain decomposition.
NOTE: 5.3 % performance was lost because the PME nodes
had less work to do than the PP nodes.
You might want to decrease the number of PME nodes
or decrease the cut-off and the grid spacing.
After searching the archive mailing list and reading the manual , I decided
to use g_tune_pme so I switched to gromacs 4.5.4. Here's my script:
#PBS -S /bin/bash
#PBS -N job_md6ns
#PBS -e job_md6ns.err
#PBS -o job_md6ns.log
#PBS -m ae -M carlajam...@gmail.com
#PBS -l select=2:ncpus=8:mpiprocs=8
#PBS -l walltime=024:00:00
cd $PBS_O_WORKDIR
export GMXLIB=$GMXLIB:/scratch/carla/top:.
module load gromacs
chem=/opt/software/SGI/gromacs/4.5.4/bin/
mdrunmpi=mpiexec /opt/software/SGI/gromacs/4.5.4/bin/
${chem}grompp -v -f md6ns.mdp -c 1rlu_apo_mdeq.gro -o 1rlu_apo_md6ns.tpr -p
1rlu_apo.top
${mdrunmpi}g_tune_pme -v -s 1rlu_apo_md6ns.tpr -o 1rlu_apo_md6ns.trr -cpo
state_6ns.cpt -c 1rlu_apo_md6ns.gro -x 1rlu_apo_md6ns.xtc -e md6ns.edr -g
md6ns.log -np 4 -ntpr 1 -launch
But now, I have the following error message:
Fatal error:
Library file residuetypes.dat not found in current dir nor in your GMXLIB
path.
Except that I'm using amber94 force-field and that my topology files are in
a special directory called top where I modified certain things. With gromacs
4.0.3, it always worked so I don't know what is happening here.
Please does anyone have an idea of what it might be?
Do I have to run pdb2gmx, editconf, etc... with the gromacs 4.5.4 for it to
work?
Thank you,
Carla
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Re: [gmx-users] g_tune_pme
Hi Carla,
On Jul 28, 2011, at 9:38 AM, Carla Jamous wrote:
Hi everyone, please I was running simulations with gromacs version 4.0.3 ,but
I got the following error:
Average load imbalance: 12.1 %
Part of the total run time spent waiting due to load imbalance: 6.9 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 %
Y 9 %
Average PME mesh/force load: 0.807
Part of the total run time spent waiting due to PP/PME imbalance: 5.3 %
This is not an error but just a hint how you could optimize your performance.
NOTE: 6.9 % performance was lost due to load imbalance
in the domain decomposition.
NOTE: 5.3 % performance was lost because the PME nodes
had less work to do than the PP nodes.
You might want to decrease the number of PME nodes
or decrease the cut-off and the grid spacing.
After searching the archive mailing list and reading the manual , I decided
to use g_tune_pme so I switched to gromacs 4.5.4. Here's my script:
Note that there is also a g_tune_pme version for 4.0.7:
http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/index.html
As another possibility, you can use the tpr file you created with 4.0.x as
input for
Gromcas 4.5.x, also for g_tune_pme, this is probably the easiest solution.
#PBS -S /bin/bash
#PBS -N job_md6ns
#PBS -e job_md6ns.err
#PBS -o job_md6ns.log
#PBS -m ae -M carlajam...@gmail.com
#PBS -l select=2:ncpus=8:mpiprocs=8
#PBS -l walltime=024:00:00
cd $PBS_O_WORKDIR
export GMXLIB=$GMXLIB:/scratch/carla/top:.
module load gromacs
chem=/opt/software/SGI/gromacs/4.5.4/bin/
mdrunmpi=mpiexec /opt/software/SGI/gromacs/4.5.4/bin/
${chem}grompp -v -f md6ns.mdp -c 1rlu_apo_mdeq.gro -o 1rlu_apo_md6ns.tpr -p
1rlu_apo.top
${mdrunmpi}g_tune_pme -v -s 1rlu_apo_md6ns.tpr -o 1rlu_apo_md6ns.trr -cpo
state_6ns.cpt -c 1rlu_apo_md6ns.gro -x 1rlu_apo_md6ns.xtc -e md6ns.edr -g
md6ns.log -np 4 -ntpr 1 -launch
But now, I have the following error message:
Fatal error:
Library file residuetypes.dat not found in current dir nor in your GMXLIB
path.
Why don't you build your tpr file on your workstation and then switch over
to the cluster? I guess this will make life easier for you.
Also note that you must not call g_tune_pme in parallel (which you do by
${mdrunmpi}g_tune_pme. g_tune_pme will spawn its own MPI processes with the
help of the MPIRUN and MDRUN environment variables. See g_tune_pme -h,
probably you need do set
export MDRUN=/opt/software/SGI/gromacs/4.5.4/bin/mdrun
export MPIRUN=`which mpiexec`
Hope that helps,
Carsten
Except that I'm using amber94 force-field and that my topology files are in a
special directory called top where I modified certain things. With gromacs
4.0.3, it always worked so I don't know what is happening here.
Please does anyone have an idea of what it might be?
Do I have to run pdb2gmx, editconf, etc... with the gromacs 4.5.4 for it to
work?
Thank you,
Carla
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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/home/grubmueller/ihp/ckutzne
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Re: [gmx-users] g_tune_pme big standard deviation in perf.out output
Dear Yanbin, On Dec 30, 2010, at 9:20 PM, WU Yanbin wrote: I'm simulating a SPC/E water box with the size of 4nm by 4nm by 4nm. The command g_tune_pme was used to find the optimal PME node numbers, Coulomb cutoff radius and grid spacing size. The following command is used: g_tune_pme -np 24 -steps 5000 -resetstep 500 ... rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 The simulation is done with no error. Below is the output: --- Line tpr PME nodes Gcycles Av. Std.dev. ns/dayPME/fDD grid 0 0 12 2813.762 187.1159.6040.3614 3 1 1 0 11 2969.826 251.2109.1120.510 13 1 1 2 0 10 2373.469 154.005 11.3850.4452 7 1 3 09 2129.519 58.132 12.6650.6015 3 1 4 08 2411.653 265.233 11.2480.5704 4 1 5 07 2062.770 514.023 13.4900.616 17 1 1 6 06 1539.237 89.189 17.5470.7486 3 1 7 00 1633.318 113.037 16.548 - 6 4 1 8 0 -1( 4) 1330.146 32.362 20.2761.0504 5 1 --- The optimal -npme is 4. It seems to me that the Std. dev is too huge. This is the standard deviation resulting from multiple runs with the same settings. If you do not specify -r for the number of repeats explicitly to g_tune_pme, it will do two tests for each setting. For the optimum of 4 PME nodes the standard deviation is 2.4 percent of the mean, thus not large at all. Can anyone tell me the meaning of Gcycles Av. and Std. dev and their relations to the accuracy of ns/day? Both the number of CPU cycles as the ns/day values are determined from the md.log output file of the respective runs. g_tune_pme does the averaging for you, but you can also look at the individual results, these log files are still there after the tuning run. The standard deviation is printed only for the Gcycles - maybe it is a good idea to also print the standard deviation for the ns/day values. If the standard dev is X percent of the mean for the cycles, then it is also X percent of the mean ns/day. Another question: I tried g_tune_pme -np 24 -steps 1000 -resetstep 100 ... (the default value of g_tune_pme) rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 The optimal -npme is 6, different from -npme=4 as obtained with big -nsteps. Should I increase -nsteps even more to get better estimate, or what else parameters should I try? In principle the results will become more exact, the longer the test runs are. For your system it seems that the load between the processes is not yet optimally balanced after the default 100 steps so that -resetstep 500 gives you a more accurate value. I think the -steps 5000 value is large enough, but another test with a higher resetstep value would answer your question. Since you already know that 7-12 PME nodes will not perform well, I would try g_tune_pme -np 24 -steps 5000 -resetstep 5000 -min 0.16 -max 0.25 ... Regards, Carsten Do let me know if the questions are not made clear. Thank you. Best, Yanbin -- 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/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 big standard deviation in perf.out output
Dear GMXers, I'm simulating a SPC/E water box with the size of 4nm by 4nm by 4nm. The command g_tune_pme was used to find the optimal PME node numbers, Coulomb cutoff radius and grid spacing size. The following command is used: g_tune_pme -np 24 -steps 5000 -resetstep 500 ... rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 The simulation is done with no error. Below is the output: --- Line tpr PME nodes Gcycles Av. Std.dev. ns/dayPME/fDD grid 0 0 12 2813.762 187.1159.6040.361 4 3 1 1 0 11 2969.826 251.2109.1120.510 13 1 1 2 0 10 2373.469 154.005 11.3850.445 2 7 1 3 09 2129.519 58.132 12.6650.601 5 3 1 4 08 2411.653 265.233 11.2480.570 4 4 1 5 07 2062.770 514.023 13.4900.616 17 1 1 6 06 1539.237 89.189 17.5470.748 6 3 1 7 00 1633.318 113.037 16.548 - 6 4 1 8 0 -1( 4) 1330.146 32.362 20.2761.050 4 5 1 --- The optimal -npme is 4. It seems to me that the Std. dev is too huge. Can anyone tell me the meaning of Gcycles Av. and Std. dev and their relations to the accuracy of ns/day? Another question: I tried g_tune_pme -np 24 -steps 1000 -resetstep 100 ... (the default value of g_tune_pme) rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 The optimal -npme is 6, different from -npme=4 as obtained with big -nsteps. Should I increase -nsteps even more to get better estimate, or what else parameters should I try? Do let me know if the questions are not made clear. Thank you. Best, Yanbin -- 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 in Ranger
Hi, I wonder whether somebody has been able to install g_tune_pme in Ranger (one of the tacc clusters). If so, please contact me off list as I have a couple of questions to ask. Patricia. -- Dr. Patricia Soto patricia.sot...@gmail.com ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
