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' 100000 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 [email protected] -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
