RE: [gmx-users] mpi run in Gromacs 4.5.3
Thank you, Justin and Mark. I'll recompile gromacs. In my current version -nt is not available (using mdrun -h). Thanks again, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Mon 12/13/2010 5:49 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 Te, Jerez A., Ph.D. wrote: > Hi Mark, > > Thank you for your reply. Just to confirm, mdrun_mpi is still being used in > Gromacs 4.5.3? The gromacs manual (Appendix A.5- Running Gromacs in parallel) > suggested using "mdrun -np 8 -s topol -v -N 8" in running a single machine > with multiple (8) processors and "mpirun -p goofus,doofus,fred 10 mdrun -s > topol -v -N 30" to run three machines with ten processors each. You probably > already know this but I am confused as to whether these commands are correct Those commands are outdated. I am updating the manual to fix this. > in running parallel simulations (thus the assumption that mdrun_mpi is no > longer applicable in gromacs 4.5.3). So far I have not been successful in > running parallel simulations (as I mentioned before the two options above > would only start X identical serial processes). My bottom line is I want to > run Gromacs simulation in parallel (regardless of whether it is running on > one silicon with a number of processors or on different machines or nodes > with a specified number of processors). > The exact implementation depends on the nature of your cluster setup. For instance, our aging supercomputer does not support threading, so we have to compile with --enable-mpi to produce an mdrun_mpi binary that is called via mpirun. My laptop, however, supports threading, so I can initiate a process over both cores with mdrun -nt, no external MPI support necessary. > I assume that in order to get mdrun_mpi, Gromacs has to be recompiled using > the --enable-mpi option because currently our gromacs executable bin does not > have mdrun_mpi. Our system administrator said that all mpi-related options > have been enabled in compiling gromacs and still the mdrun_mpi is not found > as one of the exe files. Please help. > Just because your /bin subdirectory does not have mdrun_mpi does not necessarily mean the binary was not compiled with MPI support. Based on what you have reported, it sounds like you indeed only have a serial mdrun, but it is possible to suppress the default suffix. If you have threading support, the -nt option will be printed if you issue mdrun -h. -Justin > Thanks, JT > > > -Original Message- From: gmx-users-boun...@gromacs.org on behalf of > Mark Abraham Sent: Mon 12/13/2010 4:38 PM To: Discussion list for GROMACS > users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 > > On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: >> Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using >> openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version >> of Gromacs. >> > > I don't understand what (you think) you mean. You can use thread-based > parallelism for processors that share common silicon, or MPI-based > parallelism if a network connection is involved, but not both. The latter is > named mdrun_mpi by default. > >> Our system administrator told me that all mpi related options have been >> turned on while installing Gromacs. With either commands: mdrun -np X >> -deffnm topol -N X (run in an 8-cpu node) >> > > This won't run in parallel at all. mdrun ignores -np and -N > >> or mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes >> depending on availability) >> > > This will get you the symptoms below, but -N is still ignored. > >> I get X identical simulations instead of a parallel run. If X=4, I get 4 >> identical simulations (the same simulation ran 4 times) instead of 1 >> parallel simulation in 4 processors. The performance difference between a >> single-processor run and the X=4 run are also similar (no marked difference >> in the time it takes to finish the simulation). Has anyone encountered this >> problem? >> > > You're using a serial mdrun. Use a parallel mdrun. > > Mark > > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] mpi run in Gromacs 4.5.3
On 14/12/2010 11:14 AM, Te, Jerez A., Ph.D. wrote: Hi Mark, Thank you for your reply. Just to confirm, mdrun_mpi is still being used in Gromacs 4.5.3? The gromacs manual (Appendix A.5- Running Gromacs in parallel) suggested using "mdrun -np 8 -s topol -v -N 8" in running a single machine with multiple (8) processors and "mpirun -p goofus,doofus,fred 10 mdrun -s topol -v -N 30" to run three machines with ten processors each. You probably already know this but I am confused as to whether these commands are correct in running parallel simulations (thus the assumption that mdrun_mpi is no longer applicable in gromacs 4.5.3). So far I have not been successful in running parallel simulations (as I mentioned before the two options above would only start X identical serial processes). My bottom line is I want to run Gromacs simulation in parallel (regardless of whether it is running on one silicon with a number of processors or on different machines or nodes with a specified number of processors). I assume that in order to get mdrun_mpi, Gromacs has to be recompiled using the --enable-mpi option because currently our gromacs executable bin does not have mdrun_mpi. Our system administrator said that all mpi-related options have been enabled in compiling gromacs and still the mdrun_mpi is not found as one of the exe files. Please help. I echo Justin's comments. "all mpi-related options" seems suspicious. There's only one, --enable-mpi. Obviously you need a correctly-configured MPI compiler and environment for it to work Mark Thanks, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Mon 12/13/2010 4:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. I don't understand what (you think) you mean. You can use thread-based parallelism for processors that share common silicon, or MPI-based parallelism if a network connection is involved, but not both. The latter is named mdrun_mpi by default. Our system administrator told me that all mpi related options have been turned on while installing Gromacs. With either commands: mdrun -np X -deffnm topol -N X (run in an 8-cpu node) This won't run in parallel at all. mdrun ignores -np and -N or mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes depending on availability) This will get you the symptoms below, but -N is still ignored. I get X identical simulations instead of a parallel run. If X=4, I get 4 identical simulations (the same simulation ran 4 times) instead of 1 parallel simulation in 4 processors. The performance difference between a single-processor run and the X=4 run are also similar (no marked difference in the time it takes to finish the simulation). Has anyone encountered this problem? You're using a serial mdrun. Use a parallel mdrun. Mark -- 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] mpi run in Gromacs 4.5.3
Te, Jerez A., Ph.D. wrote: Hi Mark, Thank you for your reply. Just to confirm, mdrun_mpi is still being used in Gromacs 4.5.3? The gromacs manual (Appendix A.5- Running Gromacs in parallel) suggested using "mdrun -np 8 -s topol -v -N 8" in running a single machine with multiple (8) processors and "mpirun -p goofus,doofus,fred 10 mdrun -s topol -v -N 30" to run three machines with ten processors each. You probably already know this but I am confused as to whether these commands are correct Those commands are outdated. I am updating the manual to fix this. in running parallel simulations (thus the assumption that mdrun_mpi is no longer applicable in gromacs 4.5.3). So far I have not been successful in running parallel simulations (as I mentioned before the two options above would only start X identical serial processes). My bottom line is I want to run Gromacs simulation in parallel (regardless of whether it is running on one silicon with a number of processors or on different machines or nodes with a specified number of processors). The exact implementation depends on the nature of your cluster setup. For instance, our aging supercomputer does not support threading, so we have to compile with --enable-mpi to produce an mdrun_mpi binary that is called via mpirun. My laptop, however, supports threading, so I can initiate a process over both cores with mdrun -nt, no external MPI support necessary. I assume that in order to get mdrun_mpi, Gromacs has to be recompiled using the --enable-mpi option because currently our gromacs executable bin does not have mdrun_mpi. Our system administrator said that all mpi-related options have been enabled in compiling gromacs and still the mdrun_mpi is not found as one of the exe files. Please help. Just because your /bin subdirectory does not have mdrun_mpi does not necessarily mean the binary was not compiled with MPI support. Based on what you have reported, it sounds like you indeed only have a serial mdrun, but it is possible to suppress the default suffix. If you have threading support, the -nt option will be printed if you issue mdrun -h. -Justin Thanks, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Mon 12/13/2010 4:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. I don't understand what (you think) you mean. You can use thread-based parallelism for processors that share common silicon, or MPI-based parallelism if a network connection is involved, but not both. The latter is named mdrun_mpi by default. Our system administrator told me that all mpi related options have been turned on while installing Gromacs. With either commands: mdrun -np X -deffnm topol -N X (run in an 8-cpu node) This won't run in parallel at all. mdrun ignores -np and -N or mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes depending on availability) This will get you the symptoms below, but -N is still ignored. I get X identical simulations instead of a parallel run. If X=4, I get 4 identical simulations (the same simulation ran 4 times) instead of 1 parallel simulation in 4 processors. The performance difference between a single-processor run and the X=4 run are also similar (no marked difference in the time it takes to finish the simulation). Has anyone encountered this problem? You're using a serial mdrun. Use a parallel mdrun. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] mpi run in Gromacs 4.5.3
Hi Mark, Thank you for your reply. Just to confirm, mdrun_mpi is still being used in Gromacs 4.5.3? The gromacs manual (Appendix A.5- Running Gromacs in parallel) suggested using "mdrun -np 8 -s topol -v -N 8" in running a single machine with multiple (8) processors and "mpirun -p goofus,doofus,fred 10 mdrun -s topol -v -N 30" to run three machines with ten processors each. You probably already know this but I am confused as to whether these commands are correct in running parallel simulations (thus the assumption that mdrun_mpi is no longer applicable in gromacs 4.5.3). So far I have not been successful in running parallel simulations (as I mentioned before the two options above would only start X identical serial processes). My bottom line is I want to run Gromacs simulation in parallel (regardless of whether it is running on one silicon with a number of processors or on different machines or nodes with a specified number of processors). I assume that in order to get mdrun_mpi, Gromacs has to be recompiled using the --enable-mpi option because currently our gromacs executable bin does not have mdrun_mpi. Our system administrator said that all mpi-related options have been enabled in compiling gromacs and still the mdrun_mpi is not found as one of the exe files. Please help. Thanks, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Mon 12/13/2010 4:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: > > Hi, > I have been trying to run Gromacs 4.5.3 parallel simulations using > openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this > version of Gromacs. > I don't understand what (you think) you mean. You can use thread-based parallelism for processors that share common silicon, or MPI-based parallelism if a network connection is involved, but not both. The latter is named mdrun_mpi by default. > Our system administrator told me that all mpi related options have > been turned on while installing Gromacs. With either commands: > mdrun -np X -deffnm topol -N X (run in an 8-cpu node) > This won't run in parallel at all. mdrun ignores -np and -N > or > mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes > depending on availability) > This will get you the symptoms below, but -N is still ignored. > I get X identical simulations instead of a parallel run. If X=4, I get > 4 identical simulations (the same simulation ran 4 times) instead of 1 > parallel simulation in 4 processors. The performance difference > between a single-processor run and the X=4 run are also similar (no > marked difference in the time it takes to finish the simulation). > Has anyone encountered this problem? > You're using a serial mdrun. Use a parallel mdrun. Mark <>-- 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] mpi run in Gromacs 4.5.3
On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. I don't understand what (you think) you mean. You can use thread-based parallelism for processors that share common silicon, or MPI-based parallelism if a network connection is involved, but not both. The latter is named mdrun_mpi by default. Our system administrator told me that all mpi related options have been turned on while installing Gromacs. With either commands: mdrun -np X -deffnm topol -N X (run in an 8-cpu node) This won't run in parallel at all. mdrun ignores -np and -N or mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes depending on availability) This will get you the symptoms below, but -N is still ignored. I get X identical simulations instead of a parallel run. If X=4, I get 4 identical simulations (the same simulation ran 4 times) instead of 1 parallel simulation in 4 processors. The performance difference between a single-processor run and the X=4 run are also similar (no marked difference in the time it takes to finish the simulation). Has anyone encountered this problem? You're using a serial mdrun. Use a parallel mdrun. Mark -- 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
