[gmx-users] mdrun -nc
Hi, I tried gromacs 4.5.4 in these days and last version I used is 4.0.5. I found when I add --enable-threads in installation. I can use mdrun -nc 12 to run 12 CPUs together within one machine. It also amazing me when I type top to check the job, only one process in computer and the CPU utility is 1200%!! But I tried to execute it on two machines, then the second machines didn't work. I don't need mdrun_mpi any more because mdrun -nc is faster the mdrun_mpi. That make me confused. Am I right to use mdrun -nc to run parallel job in this way? Does the result is the same as which is employed by mdrun_mpi? (Exactly I never use mdrun_mpi more than one machine since the ethernet between machines is very slow here.) If mdrun -nc is available. Do we have another commend support CPUs more than one in the same machine. Sincerely yours, Hsin-Lin -- 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] mdrun -nc
Hsin-Lin Chiang wrote: Hi, I tried gromacs 4.5.4 in these days and last version I used is 4.0.5. I found when I add --enable-threads in installation. I can use mdrun -nc 12 to run 12 CPUs together within one machine. I assume you mean -nt? It also amazing me when I type top to check the job, only one process in computer and the CPU utility is 1200%!! Sounds about right. I see the same on my dual-core workstation. One process, 2 threads, and just less than 200% CPU usage. But I tried to execute it on two machines, then the second machines didn't work. You can't execute threads over multiple machines. For that you need MPI, not threading (they are mutually exclusive). You haven't provided much detail on what you actually did in this case and didn't work doesn't exactly provide any relevant diagnostic information. I don't need mdrun_mpi any more because mdrun -nc is faster the mdrun_mpi. That make me confused. Am I right to use mdrun -nc to run parallel job in this way? For a single, multi-core workstation, mdrun -nt is correct. Does the result is the same as which is employed by mdrun_mpi? A variety of factors influence whether or not the results are the same. http://www.gromacs.org/Documentation/Terminology/Reproducibility (Exactly I never use mdrun_mpi more than one machine since the ethernet between machines is very slow here.) If mdrun -nc is available. Do we have another commend support CPUs more than one in the same machine. That's what threading is doing, assuming you're invoking the command correctly. As stated above, the option is -nt, not -nc. mdrun doesn't check for whether or not command line arguments are actually valid, so if you're using -nc you're not actually doing threading, but the 1200% usage suggests you probably are. -Justin -- 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] mdrun -nc
On most of my multi-core machines, an attempt is made to detect the number of threads to start at run-time (there may be a check for the MAXIMUM number of threads at compile-time, but a developer would need to chime in to determine if this is the case). For instance, I have a dual quadcore machine (eight cores total). When I just run a command like so on 4.5.4: mdrun -v -deffnm trp-cage I get: Starting 8 threads Loaded with Money Making 2D domain decomposition 4 x 2 x 1 starting mdrun 'Good ROcking Metal Altar for Chronical Sinners in water' 10 steps,200.0 ps. step 200, will finish Tue Jun 14 12:01:01 2011imb F 8% ... So, by default the threaded version will start the maximum number of threads that it can (if it can find a good decomposition for all cores, otherwise fewer threads are used). So, -nt is used to explicitly control the number of threads used (not -nc). As Justin said, for running across multiple machines, MPI is necessary and precludes using threads. -- Josh On Tue, 2011-06-14 at 11:15 -0400, Justin A. Lemkul wrote: Hsin-Lin Chiang wrote: Hi, I tried gromacs 4.5.4 in these days and last version I used is 4.0.5. I found when I add --enable-threads in installation. I can use mdrun -nc 12 to run 12 CPUs together within one machine. I assume you mean -nt? It also amazing me when I type top to check the job, only one process in computer and the CPU utility is 1200%!! Sounds about right. I see the same on my dual-core workstation. One process, 2 threads, and just less than 200% CPU usage. But I tried to execute it on two machines, then the second machines didn't work. You can't execute threads over multiple machines. For that you need MPI, not threading (they are mutually exclusive). You haven't provided much detail on what you actually did in this case and didn't work doesn't exactly provide any relevant diagnostic information. I don't need mdrun_mpi any more because mdrun -nc is faster the mdrun_mpi. That make me confused. Am I right to use mdrun -nc to run parallel job in this way? For a single, multi-core workstation, mdrun -nt is correct. Does the result is the same as which is employed by mdrun_mpi? A variety of factors influence whether or not the results are the same. http://www.gromacs.org/Documentation/Terminology/Reproducibility (Exactly I never use mdrun_mpi more than one machine since the ethernet between machines is very slow here.) If mdrun -nc is available. Do we have another commend support CPUs more than one in the same machine. That's what threading is doing, assuming you're invoking the command correctly. As stated above, the option is -nt, not -nc. mdrun doesn't check for whether or not command line arguments are actually valid, so if you're using -nc you're not actually doing threading, but the 1200% usage suggests you probably are. -Justin -- 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 -- Joshua L. Phillips Ph.D. Candidate - School of Engineering University of California, Merced jphilli...@ucmerced.edu -- 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
