Re: [gmx-users] Multithread run issues

[Mark Abraham]

Hi,

That user's input can't use OpenMP, like the message says. So try the other
options. (And again, don't run mpirun on a thread-MPI mdrun!)

Mark

On Mon, Oct 10, 2016 at 1:02 PM Mahmood Naderan 
wrote:

> Sorry for the previous incomplete email.
>
> Program mdrun, VERSION 5.1
> Source code file:
> /share/apps/chemistry/gromacs-5.1/src/programs/mdrun/resource-division.cpp,
> line: 746
>
> Fatal error:
> OpenMP threads have been requested with cut-off scheme Group, but these are
> only supported with cut-off scheme Verlet
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> I read that document from that web site but didn't understand what is the
> issue!
> Thanks
>
> Regards,
> Mahmood
>
>
>
> On Mon, Oct 10, 2016 at 2:29 PM, Mahmood Naderan 
> wrote:
>
> > >mpirun -np 1 mdrun_mpi -v -ntomp 2
> >
> > Agree with that.
> >
> > >This is not a problem to solve by running applications differently. You
> > >will have users running jobs with single ranks/processes that use
> > threading
> > >of various kinds to fill the cores. That's a feature, not a bug. Either
> > >configure PBS to cope with decades-old technology, or don't worry about
> > it.
> >
> > I found this document
> > ​(
> > https://wiki.anl.gov/cnm/HPC/Submitting_and_Managing_Jobs/
> > Advanced_node_selection#Multithreading_using_OpenMP)
> > ​That is what I want to be sure that number of threads and cores used for
> > gromacs fits to the PBS stats.
> >
> > Instead of the variable, I wrote
> >
> >
> >
> > #PBS -l nodes=1:ppn=2​
> > export OMP_NUM_THREADS=2
> > mpirun  mdrun -v
> >
> > So that will use two cores with 4 threads totally and PBS should report 4
> > processors are occupied.
> > However, gromacs failed with the following error
> >
> >
> >
> >
> > Regards,
> > Mahmood
> >
> >
> >
> > On Mon, Oct 10, 2016 at 1:41 PM, Mark Abraham 
> > wrote:
> >
> >> Hi,
> >>
> >> Yeah, but that run is very likely
> >>
> >> a) useless because you're just running two copies of the same simulation
> >> because you're not running MPI-enabled mdrun
> >> b) and even if not, less efficient than the thread-MPI version
> >>
> >> mdrun -v -nt 2
> >>
> >> c) and even if not, likely slightly less efficient than the real-MPI
> >> version
> >>
> >> mpirun -np 1 mdrun_mpi -v -ntomp 2
> >>
> >> top isn't necessarily reporting anything relevant. A CPU can be
> nominally
> >> idle while waiting for communication, but what does top think about
> that?
> >>
> >> Mark
> >>
> >> On Mon, Oct 10, 2016 at 11:47 AM Mahmood Naderan 
> >> wrote:
> >>
> >> > OK. I understood the  documents.
> >> > Thing that I want is to see two processes (for example) each consumes
> >> 100%
> >> > cpu. The command for that is
> >> >
> >> > mpirun -np 2 mdrun -v -nt 1
> >> >
> >> > ​Thanks Mark.​
> >> >
> >> > Regards,
> >> > Mahmood
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> > * For (un)subscribe requests visit
> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
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> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
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Re: [gmx-users] Multithread run issues

[Mahmood Naderan]

Sorry for the previous incomplete email.

Program mdrun, VERSION 5.1
Source code file:
/share/apps/chemistry/gromacs-5.1/src/programs/mdrun/resource-division.cpp,
line: 746

Fatal error:
OpenMP threads have been requested with cut-off scheme Group, but these are
only supported with cut-off scheme Verlet
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



I read that document from that web site but didn't understand what is the
issue!
Thanks

Regards,
Mahmood



On Mon, Oct 10, 2016 at 2:29 PM, Mahmood Naderan 
wrote:

> >mpirun -np 1 mdrun_mpi -v -ntomp 2
>
> Agree with that.
>
> >This is not a problem to solve by running applications differently. You
> >will have users running jobs with single ranks/processes that use
> threading
> >of various kinds to fill the cores. That's a feature, not a bug. Either
> >configure PBS to cope with decades-old technology, or don't worry about
> it.
>
> I found this document
> ​(
> https://wiki.anl.gov/cnm/HPC/Submitting_and_Managing_Jobs/
> Advanced_node_selection#Multithreading_using_OpenMP)
> ​That is what I want to be sure that number of threads and cores used for
> gromacs fits to the PBS stats.
>
> Instead of the variable, I wrote
>
>
>
> #PBS -l nodes=1:ppn=2​
> export OMP_NUM_THREADS=2
> mpirun  mdrun -v
>
> So that will use two cores with 4 threads totally and PBS should report 4
> processors are occupied.
> However, gromacs failed with the following error
>
>
>
>
> Regards,
> Mahmood
>
>
>
> On Mon, Oct 10, 2016 at 1:41 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Yeah, but that run is very likely
>>
>> a) useless because you're just running two copies of the same simulation
>> because you're not running MPI-enabled mdrun
>> b) and even if not, less efficient than the thread-MPI version
>>
>> mdrun -v -nt 2
>>
>> c) and even if not, likely slightly less efficient than the real-MPI
>> version
>>
>> mpirun -np 1 mdrun_mpi -v -ntomp 2
>>
>> top isn't necessarily reporting anything relevant. A CPU can be nominally
>> idle while waiting for communication, but what does top think about that?
>>
>> Mark
>>
>> On Mon, Oct 10, 2016 at 11:47 AM Mahmood Naderan 
>> wrote:
>>
>> > OK. I understood the  documents.
>> > Thing that I want is to see two processes (for example) each consumes
>> 100%
>> > cpu. The command for that is
>> >
>> > mpirun -np 2 mdrun -v -nt 1
>> >
>> > ​Thanks Mark.​
>> >
>> > Regards,
>> > Mahmood
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] Multithread run issues

[Mahmood Naderan]

>mpirun -np 1 mdrun_mpi -v -ntomp 2

Agree with that.

>This is not a problem to solve by running applications differently. You
>will have users running jobs with single ranks/processes that use threading
>of various kinds to fill the cores. That's a feature, not a bug. Either
>configure PBS to cope with decades-old technology, or don't worry about it.

I found this document
​(
https://wiki.anl.gov/cnm/HPC/Submitting_and_Managing_Jobs/Advanced_node_selection#Multithreading_using_OpenMP
)
​That is what I want to be sure that number of threads and cores used for
gromacs fits to the PBS stats.

Instead of the variable, I wrote



#PBS -l nodes=1:ppn=2​
export OMP_NUM_THREADS=2
mpirun  mdrun -v

So that will use two cores with 4 threads totally and PBS should report 4
processors are occupied.
However, gromacs failed with the following error




Regards,
Mahmood



On Mon, Oct 10, 2016 at 1:41 PM, Mark Abraham 
wrote:

> Hi,
>
> Yeah, but that run is very likely
>
> a) useless because you're just running two copies of the same simulation
> because you're not running MPI-enabled mdrun
> b) and even if not, less efficient than the thread-MPI version
>
> mdrun -v -nt 2
>
> c) and even if not, likely slightly less efficient than the real-MPI
> version
>
> mpirun -np 1 mdrun_mpi -v -ntomp 2
>
> top isn't necessarily reporting anything relevant. A CPU can be nominally
> idle while waiting for communication, but what does top think about that?
>
> Mark
>
> On Mon, Oct 10, 2016 at 11:47 AM Mahmood Naderan 
> wrote:
>
> > OK. I understood the  documents.
> > Thing that I want is to see two processes (for example) each consumes
> 100%
> > cpu. The command for that is
> >
> > mpirun -np 2 mdrun -v -nt 1
> >
> > ​Thanks Mark.​
> >
> > Regards,
> > Mahmood
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Multithread run issues

[Mark Abraham]

Hi,

Yeah, but that run is very likely

a) useless because you're just running two copies of the same simulation
because you're not running MPI-enabled mdrun
b) and even if not, less efficient than the thread-MPI version

mdrun -v -nt 2

c) and even if not, likely slightly less efficient than the real-MPI version

mpirun -np 1 mdrun_mpi -v -ntomp 2

top isn't necessarily reporting anything relevant. A CPU can be nominally
idle while waiting for communication, but what does top think about that?

Mark

On Mon, Oct 10, 2016 at 11:47 AM Mahmood Naderan 
wrote:

> OK. I understood the  documents.
> Thing that I want is to see two processes (for example) each consumes 100%
> cpu. The command for that is
>
> mpirun -np 2 mdrun -v -nt 1
>
> ​Thanks Mark.​
>
> Regards,
> Mahmood
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Multithread run issues

[Mahmood Naderan]

OK. I understood the  documents.
Thing that I want is to see two processes (for example) each consumes 100%
cpu. The command for that is

mpirun -np 2 mdrun -v -nt 1

​Thanks Mark.​

Regards,
Mahmood
-- 
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Re: [gmx-users] Multithread run issues

[Mark Abraham]

Hi,

On Sun, Oct 9, 2016 at 2:06 PM Mahmood Naderan  wrote:

> Hi,
>
> Users issue the command "mdrun -v" and that will automatically read input
>
> files in the working directory. There are two issue with that which I am
>
> not aware of the solution.
>
>
>
> 1- How the number of cores can be changed?
>

http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html


>
> 2- Viewing the output of "top" command, it is saying that mdrun uses 400%
>
> cpu. That mean 4 cores are occupied. Problem is that we prefer to see four
>
> processes each consumes 100% cpu. Why? Because in the first situation, PBS
>
> wrongly sees that one cores is used (while 4 cores are used), but in the
>
> later, it will correctly sees 4 cores.
>

This is not a problem to solve by running applications differently. You
will have users running jobs with single ranks/processes that use threading
of various kinds to fill the cores. That's a feature, not a bug. Either
configure PBS to cope with decades-old technology, or don't worry about it.
:-)

As I read the documentation, I think the replacement of "mdrun -v" should be
>
>
>
> mpirun -np N mdrun -v
>
>
>
> Am I correct?
>

No, because that mdrun isn't configured with MPI support (else it would be
called mdrun_mpi). If it was, then mpirun -np N mdrun_mpi is plausible, but
less efficient than the alternatives. Your mdrun is using the built in
thread-MPI that you can read about at that link.

Mark


>
>
>
> Regards,
>
> Mahmood
>
> --
>
> Gromacs Users mailing list
>
>
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
>
>
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>
>
>
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>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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>
>
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[gmx-users] Multithread run issues

[Mahmood Naderan]

Hi,
Users issue the command "mdrun -v" and that will automatically read input
files in the working directory. There are two issue with that which I am
not aware of the solution.

1- How the number of cores can be changed?
2- Viewing the output of "top" command, it is saying that mdrun uses 400%
cpu. That mean 4 cores are occupied. Problem is that we prefer to see four
processes each consumes 100% cpu. Why? Because in the first situation, PBS
wrongly sees that one cores is used (while 4 cores are used), but in the
later, it will correctly sees 4 cores.

As I read the documentation, I think the replacement of "mdrun -v" should be

mpirun -np N mdrun -v

Am I correct?

Regards,
Mahmood
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