[gmx-users] parallel simulation
I would like to run one simulation in parallel so that it utilises all the available nodes and cores. For that, I have compiled gromacs with mpi enabled and also installed openmpi on my machine. I am using the following command: mpirun -np 4 mdrun_mpi -v -s *.tpr When i use top command, I get: PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22449 root 20 0 107m 59m 3152 R25 2.9 0:05.42 mdrun_mpi 22450 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22451 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22452 root 20 0 107m 59m 3152 R25 2.9 0:05.40 mdrun_mpi Similarly when i use mpirun -np 2 mdrun_mpi -v -s *.tpr, I get PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22461 root 20 0 108m 59m 3248 R 50 3.0 5:58.64 mdrun_mpi 22462 root 20 0 108m 59m 3248 R 50 3.0 5:58.56 mdrun_mpi If I look at %CPU column, it is actually 100/(no. of processes) Why is all the cpu not 100% utilised? Also if I compare my performance, it is significantly hampered. Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. Thanks in advance. -- 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] parallel simulation
Hi, Is it a local work station or cluster with multiple CPUs? Which gromacs version did you install? On Mon, Oct 7, 2013 at 1:55 PM, pratibha kapoor kapoorpratib...@gmail.comwrote: I would like to run one simulation in parallel so that it utilises all the available nodes and cores. For that, I have compiled gromacs with mpi enabled and also installed openmpi on my machine. I am using the following command: mpirun -np 4 mdrun_mpi -v -s *.tpr When i use top command, I get: PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22449 root 20 0 107m 59m 3152 R25 2.9 0:05.42 mdrun_mpi 22450 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22451 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22452 root 20 0 107m 59m 3152 R25 2.9 0:05.40 mdrun_mpi Similarly when i use mpirun -np 2 mdrun_mpi -v -s *.tpr, I get PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22461 root 20 0 108m 59m 3248 R 50 3.0 5:58.64 mdrun_mpi 22462 root 20 0 108m 59m 3248 R 50 3.0 5:58.56 mdrun_mpi If I look at %CPU column, it is actually 100/(no. of processes) Why is all the cpu not 100% utilised? Also if I compare my performance, it is significantly hampered. Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. Thanks in advance. -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] parallel simulation in dual core PC
On 21/04/2010 11:29 PM, Hsin-Lin wrote: Hi, I compare the run times. The calculation of two processors is faster than one. And I saw the utility of the two cores large than 85% separately. I can sure it's exactly parallel simulation in my PC now. Another question is: someone told me the interconnect, 1G Ethernet, of the machine in our lab. is too slow to do parallel simulation. What the effect should be in this kind of slow Ethernet environment? GROMACS will run very slowly, because it needs low latency communication. Gigabit ethernet is too slow here. See papers by Carsten Kutzner, for example. Mark Is it why the utility of CPU are always less than 35% when I submit the same job to the machine in our lab.? Hsin-Lin Hi, I want to use my dual core PC to do the simulation. The version of GROMACS installed is version 4.0.5. According the message post by others on mailing list before. I type lamboot first, and type the commend: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro. When the simulation starts, I use the commend, top, to check the utility of CPU. I found there is only one core which is used by GROMACS. And the utility of this core is separated to 52% and 48% for two mdrun_mpi jobs. Depending what is being measured by what, this could be a correct result. We can't really tell because we don't know how you've set up LAM, or how your top works. Do a short test calculation with one and two processors and compare the run times. 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/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
Re: [gmx-users] parallel simulation in dual core PC
Did you preprocess the .tpr file for 2 cores with grompp? Also, I believe you have to have an additional -np 2 after the mdrun_mpi command: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro -np 2 -- at least this is what I understand from what my prof told me. We just started running parallel simulations for an undergraduate research project and I believe that is how we input commands. I'm sure the gromacs experts will correct me if I'm wrong. Good luck! Arden On Tue, Apr 20, 2010 at 7:55 AM, Hsin-Lin jian...@phys.sinica.edu.twwrote: Hi, I want to use my dual core PC to do the simulation. The version of GROMACS installed is version 4.0.5. According the message post by others on mailing list before. I type lamboot first, and type the commend: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro. When the simulation starts, I use the commend, top, to check the utility of CPU. I found there is only one core which is used by GROMACS. And the utility of this core is separated to 52% and 48% for two mdrun_mpi jobs. How can I do for that? Any and all assistance is greatly appreciated. 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/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 -- 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
Re: [gmx-users] parallel simulation in dual core PC
Arden Perkins wrote: Did you preprocess the .tpr file for 2 cores with grompp? Also, I believe you have to have an additional -np 2 after the mdrun_mpi command: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro -np 2 -- at least this is what I understand from what my prof told me. We just started running parallel simulations for an undergraduate research project and I believe that is how we input commands. I'm sure the gromacs experts will correct me if I'm wrong. Since this is Gromacs 4.0.5, there is no differentiation when running grompp regarding the number of processors, so there is no -np flag for grompp. There is also no need for mdrun_mpi -np; the number of nodes is taken from mpirun -np. In addition, if all the output files are named 200ns.*, then you can save yourself some typing: mpirun -np 2 mdrun_mpi -deffnm 200ns -Justin Good luck! Arden On Tue, Apr 20, 2010 at 7:55 AM, Hsin-Lin jian...@phys.sinica.edu.tw mailto:jian...@phys.sinica.edu.tw wrote: Hi, I want to use my dual core PC to do the simulation. The version of GROMACS installed is version 4.0.5. According the message post by others on mailing list before. I type lamboot first, and type the commend: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro. When the simulation starts, I use the commend, top, to check the utility of CPU. I found there is only one core which is used by GROMACS. And the utility of this core is separated to 52% and 48% for two mdrun_mpi jobs. How can I do for that? Any and all assistance is greatly appreciated. Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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/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
Re: [gmx-users] parallel simulation in dual core PC
On 22/04/2010 3:12 AM, Arden Perkins wrote: Did you preprocess the .tpr file for 2 cores with grompp? This was only necessary for GROMACS 3. Also, I believe you have to have an additional -np 2 after the mdrun_mpi This was only necessary with early versions of MPI libraries. command: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro -np 2 -- at least this is what I understand from what my prof told me. We just started running parallel simulations for an undergraduate research project and I believe that is how we input commands. I'm sure the gromacs experts will correct me if I'm wrong. :-) Mark Good luck! Arden On Tue, Apr 20, 2010 at 7:55 AM, Hsin-Lin jian...@phys.sinica.edu.tw mailto:jian...@phys.sinica.edu.tw wrote: Hi, I want to use my dual core PC to do the simulation. The version of GROMACS installed is version 4.0.5. According the message post by others on mailing list before. I type lamboot first, and type the commend: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro. When the simulation starts, I use the commend, top, to check the utility of CPU. I found there is only one core which is used by GROMACS. And the utility of this core is separated to 52% and 48% for two mdrun_mpi jobs. How can I do for that? Any and all assistance is greatly appreciated. Hsin-Lin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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
[gmx-users] parallel simulation in dual core PC
Hi, I want to use my dual core PC to do the simulation. The version of GROMACS installed is version 4.0.5. According the message post by others on mailing list before. I type lamboot first, and type the commend: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro. When the simulation starts, I use the commend, top, to check the utility of CPU. I found there is only one core which is used by GROMACS. And the utility of this core is separated to 52% and 48% for two mdrun_mpi jobs. How can I do for that? Any and all assistance is greatly appreciated. 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/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
Re: [gmx-users] parallel simulation in dual core PC
On 21/04/2010 12:55 AM, Hsin-Lin wrote: Hi, I want to use my dual core PC to do the simulation. The version of GROMACS installed is version 4.0.5. According the message post by others on mailing list before. I type lamboot first, and type the commend: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro. When the simulation starts, I use the commend, top, to check the utility of CPU. I found there is only one core which is used by GROMACS. And the utility of this core is separated to 52% and 48% for two mdrun_mpi jobs. Depending what is being measured by what, this could be a correct result. We can't really tell because we don't know how you've set up LAM, or how your top works. Do a short test calculation with one and two processors and compare the run times. 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/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
[gmx-users] parallel simulation crash on 6 processors
I tried to run a gromacs simulation (gromacs 3.3.1, MD, 18000 atoms) on 2 systems: Intel(R) Pentium(R) CPU 2.40GHz with 100Mbit network and AMD Opteron(tm) Processor 250 with 1Gbit network On both systems I had a crash when I tried to run with more then 5 processors. From 1-5 there was no problem. kind regards, servaas michielssens___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] parallel simulation crash on 6 processors
servaas michielssens wrote: I tried to run a gromacs simulation (gromacs 3.3.1, MD, 18000 atoms) on 2 systems: Intel(R) Pentium(R) CPU 2.40GHz with 100Mbit network and AMD Opteron(tm) Processor 250 with 1Gbit network On both systems I had a crash when I tried to run with more then 5 processors. From 1-5 there was no problem. more details please. kind regards, servaas michielssens ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
