Re: [gmx-users] mpi run in Gromacs
On 2/03/2011 11:37 PM, Erik Marklund wrote: Selina Nawaz skrev 2011-03-02 11.54: Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble using a semi-isotropic pressure coupling. The simulation seems to run perfect in serial however I am having problems to run the simulation in parallel. You're going to have to be much more specific if you want useful help. I understand that this version of Gromacs uses threading to parallelise the system. I wanted to know whether it is possible to run this using openmpi and if not how do i use this thread base parallelisation. Many Thanks Selina Hi, It's slightly different than you think. Gromacs uses a thread based MPI implementation for communications between cores on the same machine. If you compile without threads it would use e.g. OpenMPI instead of threads as far as I know. Note that it will still use OpenMPI (or equivalent) for inter-node communication. Not in 4.5.x. You can configure with MPI or threads (the default) or neither. The two cannot co-exist. Threading is only useful if a network is not involved. OpenMPI will do approximately the same via shared-memory as you can get from threading in the cases where it is useful. The OP should consult the GROMACS webpage for MPI installation instructions. 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
Selina Nawaz skrev 2011-03-02 11.54: Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble using a semi-isotropic pressure coupling. The simulation seems to run perfect in serial however I am having problems to run the simulation in parallel. I understand that this version of Gromacs uses threading to parallelise the system. I wanted to know whether it is possible to run this using openmpi and if not how do i use this thread base parallelisation. Many Thanks Selina Hi, It's slightly different than you think. Gromacs uses a thread based MPI implementation for communications between cores on the same machine. If you compile without threads it would use e.g. OpenMPI instead of threads as far as I know. Note that it will still use OpenMPI (or equivalent) for inter-node communication. Cheers, -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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] mpi run in Gromacs
Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble using a semi-isotropic pressure coupling. The simulation seems to run perfect in serial however I am having problems to run the simulation in parallel. I understand that this version of Gromacs uses threading to parallelise the system. I wanted to know whether it is possible to run this using openmpi and if not how do i use this thread base parallelisation. Many Thanks Selina -- 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
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
[gmx-users] mpi run in Gromacs 4.5.3
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. 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) or mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes depending on availability) 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? I could provide more details if needed Thanks, JT -- 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: RE: [gmx-users] mpi run
- Original Message -
From: #ZHAO LINA#
Date: Thursday, July 8, 2010 18:53
Subject: RE: [gmx-users] mpi run
To: Discussion list for GROMACS users
P {margin-top:0;margin-bottom:0;}
---
|
> During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi
> will work.
--program-suffix merely appends that suffix. --enable-mpi is necessary to
actually create MPI-enable mdrun. It is normal to use both of them together.
Mark
> I suggest you to check the nodes of the cluster, probably try pbsnodes, on a
> master node no job may be run.
> Note that I do not know much about your information, so the (guessing)
> suggestion maybe not fit for your problems, just cause I once confused about
> why mine 4cpus barely used before too.
>
> Best,
>
> lina
---
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Carsten Kutzner [ckut...@gwdg.de]
> Sent: Thursday, July 08, 2010 4:04 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] mpi run
>
> Hi Mahmoud,
> for anyone to be able to help you, you need to provide > a lot more
information, at least: > - which mpi library are you using? > - how did you
compile and/or install Gromacs? > - what commands do you use to run mdrun and
what was > the output of it? >
> Best, > Carsten >
>
> On Jul 8, 2010, at 9:41 AM, nanogroup wrote: >
---
| > Dear GMX Users,
>
> I have a PC with 4 CPU, but the Gromacs only use one CPU.
>
> the command of mpiru works on linux; however, the command of mdrun_mpi does
> not work.
>
> Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4
>
> Many thanks,
> Mahmoud
>
|
---
>
> --
> 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 >
> > -- > 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
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> before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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--
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RE: [gmx-users] mpi run
During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi will work. I suggest you to check the nodes of the cluster, probably try pbsnodes, on a master node no job may be run. Note that I do not know much about your information, so the (guessing) suggestion maybe not fit for your problems, just cause I once confused about why mine 4cpus barely used before too. Best, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Carsten Kutzner [ckut...@gwdg.de] Sent: Thursday, July 08, 2010 4:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run Hi Mahmoud, for anyone to be able to help you, you need to provide a lot more information, at least: - which mpi library are you using? - how did you compile and/or install Gromacs? - what commands do you use to run mdrun and what was the output of it? Best, Carsten On Jul 8, 2010, at 9:41 AM, nanogroup wrote: Dear GMX Users, I have a PC with 4 CPU, but the Gromacs only use one CPU. the command of mpiru works on linux; however, the command of mdrun_mpi does not work. Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4 Many thanks, Mahmoud -- 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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/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] mpi run
Hi Mahmoud, for anyone to be able to help you, you need to provide a lot more information, at least: - which mpi library are you using? - how did you compile and/or install Gromacs? - what commands do you use to run mdrun and what was the output of it? Best, Carsten On Jul 8, 2010, at 9:41 AM, nanogroup wrote: > Dear GMX Users, > > I have a PC with 4 CPU, but the Gromacs only use one CPU. > > the command of mpiru works on linux; however, the command of mdrun_mpi does > not work. > > Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4 > > Many thanks, > Mahmoud > > > -- > 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 -- 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/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] mpi run
Dear GMX Users, I have a PC with 4 CPU, but the Gromacs only use one CPU. the command of mpiru works on linux; however, the command of mdrun_mpi does not work. Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4 Many thanks, Mahmoud -- 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] mpi-run
nanogroup wrote: Dear GMX Users, I want to run Gromacs on a multiprocessor PC. The MPI files are correctly installed and the gromacs is also configured. However, at the end of configuration section, an Error appears that the FFTW can not be found! Indeed, the FFTW is already installed but the configuration can not locate it! Would you please help me to locate the fftw! Please follow the installation instructions, most notably the information in the "Configuration" section: http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions#Configuration If you're still having difficulty, please provide more detail, like the actual commands you're issuing, where FFTW is installed, and what the actual error messages are. -Justin Many thanks Mahmoud -- 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
[gmx-users] mpi-run
Dear GMX Users, I want to run Gromacs on a multiprocessor PC. The MPI files are correctly installed and the gromacs is also configured. However, at the end of configuration section, an Error appears that the FFTW can not be found! Indeed, the FFTW is already installed but the configuration can not locate it! Would you please help me to locate the fftw! Many thanks Mahmoud -- 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
