subject:"\\\[gmx\\\-users\\\] parallel processing"

Re: [gmx-users] parallel processing

2016-12-08 Thread Mark Abraham

Hi,

On Sat, Dec 3, 2016 at 6:34 PM abhisek Mondal 
wrote:

> Hello Mark,
>
> I had gone through the page. Not finding any solution there.
>
> My architecture is:
> Architecture:  x86_64
> CPU op-mode(s):32-bit, 64-bit
> Byte Order:Little Endian
> CPU(s):16
> On-line CPU(s) list:   0-15
> Thread(s) per core:1
> Core(s) per socket:8
> Socket(s): 2
> NUMA node(s):  2
> Vendor ID: GenuineIntel
> CPU family:6
> Model: 45
> Stepping:  7
> CPU MHz:   2593.616
> BogoMIPS:  5186.82
> Virtualization:VT-x
> L1d cache: 32K
> L1i cache: 32K
> L2 cache:  256K
> L3 cache:  20480K
> NUMA node0 CPU(s): 0-7
> NUMA node1 CPU(s): 8-15
>
>
> When i put "mpirun -np 64 gmx_mpi mdrun  -v -deffnm npt" it just runs on a
> single node using 64 threads (16 availavle for a single node normally).
>
> How am I supposed to do node distribution efficiently ? I'm trying to run
> the job using 4 nodes and 16 threads.
> A little suggestion would be highly appreciated.
>

You read the documentation for your MPI library and e.g. set up a suitable
hostfile so that mpirun knows which nodes to use. mdrun doesn't know or
care how mpirun works, but mpirun has to be set up to work properly :-)

Mark


>
>
> On Fri, Dec 2, 2016 at 4:55 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Please check out
> > http://manual.gromacs.org/documentation/2016.1/user-
> > guide/mdrun-performance.html.
> > Your first sample command is woefully inefficient, but for em this likely
> > doesn't matter.
> >
> > Mark
> >
> > On Fri, 2 Dec 2016 09:01 abhisek Mondal  wrote:
> >
> > > But if I want to run the same job in 4 nodes (available cores= 4*16)
> then
> > > how would this work ?
> > >
> > > On Fri, Dec 2, 2016 at 2:20 PM,  wrote:
> > >
> > > > Hi Abhisek,
> > > >
> > > > You would need to use another version of gromacs with mpi rather than
> > > > thread-mpi (installed by adding DGMX_MPI=ON to the cmake command).
> You
> > > > could then use the following command
> > > >
> > > > mpirun -np 4 gmx_mpi mdrun -ntomp 16 -npme 0 -v -deffnm em
> > > >
> > > > I'm not sure why you are specifying -npme 0 but would suggest you
> don't
> > > do
> > > > this and instead let the number of separate pme ranks be set
> > > > automatically.
> > > >
> > > > Best wishes
> > > > James
> > > >
> > > > > Hi,
> > > > >
> > > > > I'm running gromacs on a cluster configuration as follows:
> > > > > 1 node = 16 cores
> > > > >
> > > > > I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16
> -npme
> > 0
> > > -v
> > > > > -deffnm em" command.
> > > > >
> > > > > How can I be able to run on multiple node (I have 20 nodes
> > available) ?
> > > > > "-nt" is not doing good here.
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Abhisek Mondal
> > > > >
> > > > > *Research Fellow*
> > > > >
> > > > > *Structural Biology and Bioinformatics Division*
> > > > > *CSIR-Indian Institute of Chemical Biology*
> > > > >
> > > > > *Kolkata 700032*
> > > > >
> > > > > *INDIA*
> > > > > --
> > > > > 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.
> > > >
> > >
> > >
> > >
> > > --
> > > Abhisek Mondal
> > >
> > > *Research Fellow*
> > >
> > > *Structural Biology and Bioinformatics Division*
> > > *CSIR-Indian Institute of Chemical Biology*
> > >
> > > *Kolkata 700032*
> > >
> > > *INDIA*
> > > --
> > > 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/
> >

Re: [gmx-users] parallel processing

2016-12-02 Thread abhisek Mondal

Hello Mark,

I had gone through the page. Not finding any solution there.

My architecture is:
Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):16
On-line CPU(s) list:   0-15
Thread(s) per core:1
Core(s) per socket:8
Socket(s): 2
NUMA node(s):  2
Vendor ID: GenuineIntel
CPU family:6
Model: 45
Stepping:  7
CPU MHz:   2593.616
BogoMIPS:  5186.82
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  256K
L3 cache:  20480K
NUMA node0 CPU(s): 0-7
NUMA node1 CPU(s): 8-15


When i put "mpirun -np 64 gmx_mpi mdrun  -v -deffnm npt" it just runs on a
single node using 64 threads (16 availavle for a single node normally).

How am I supposed to do node distribution efficiently ? I'm trying to run
the job using 4 nodes and 16 threads.
A little suggestion would be highly appreciated.



On Fri, Dec 2, 2016 at 4:55 PM, Mark Abraham 
wrote:

> Hi,
>
> Please check out
> http://manual.gromacs.org/documentation/2016.1/user-
> guide/mdrun-performance.html.
> Your first sample command is woefully inefficient, but for em this likely
> doesn't matter.
>
> Mark
>
> On Fri, 2 Dec 2016 09:01 abhisek Mondal  wrote:
>
> > But if I want to run the same job in 4 nodes (available cores= 4*16) then
> > how would this work ?
> >
> > On Fri, Dec 2, 2016 at 2:20 PM,  wrote:
> >
> > > Hi Abhisek,
> > >
> > > You would need to use another version of gromacs with mpi rather than
> > > thread-mpi (installed by adding DGMX_MPI=ON to the cmake command). You
> > > could then use the following command
> > >
> > > mpirun -np 4 gmx_mpi mdrun -ntomp 16 -npme 0 -v -deffnm em
> > >
> > > I'm not sure why you are specifying -npme 0 but would suggest you don't
> > do
> > > this and instead let the number of separate pme ranks be set
> > > automatically.
> > >
> > > Best wishes
> > > James
> > >
> > > > Hi,
> > > >
> > > > I'm running gromacs on a cluster configuration as follows:
> > > > 1 node = 16 cores
> > > >
> > > > I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16 -npme
> 0
> > -v
> > > > -deffnm em" command.
> > > >
> > > > How can I be able to run on multiple node (I have 20 nodes
> available) ?
> > > > "-nt" is not doing good here.
> > > >
> > > >
> > > >
> > > > --
> > > > Abhisek Mondal
> > > >
> > > > *Research Fellow*
> > > >
> > > > *Structural Biology and Bioinformatics Division*
> > > > *CSIR-Indian Institute of Chemical Biology*
> > > >
> > > > *Kolkata 700032*
> > > >
> > > > *INDIA*
> > > > --
> > > > 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.
> > >
> >
> >
> >
> > --
> > Abhisek Mondal
> >
> > *Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> > --
> > 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.
>



-- 
Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
-- 
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

Re: [gmx-users] parallel processing

2016-12-02 Thread Mark Abraham

Hi,

Please check out
http://manual.gromacs.org/documentation/2016.1/user-guide/mdrun-performance.html.
Your first sample command is woefully inefficient, but for em this likely
doesn't matter.

Mark

On Fri, 2 Dec 2016 09:01 abhisek Mondal  wrote:

> But if I want to run the same job in 4 nodes (available cores= 4*16) then
> how would this work ?
>
> On Fri, Dec 2, 2016 at 2:20 PM,  wrote:
>
> > Hi Abhisek,
> >
> > You would need to use another version of gromacs with mpi rather than
> > thread-mpi (installed by adding DGMX_MPI=ON to the cmake command). You
> > could then use the following command
> >
> > mpirun -np 4 gmx_mpi mdrun -ntomp 16 -npme 0 -v -deffnm em
> >
> > I'm not sure why you are specifying -npme 0 but would suggest you don't
> do
> > this and instead let the number of separate pme ranks be set
> > automatically.
> >
> > Best wishes
> > James
> >
> > > Hi,
> > >
> > > I'm running gromacs on a cluster configuration as follows:
> > > 1 node = 16 cores
> > >
> > > I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16 -npme 0
> -v
> > > -deffnm em" command.
> > >
> > > How can I be able to run on multiple node (I have 20 nodes available) ?
> > > "-nt" is not doing good here.
> > >
> > >
> > >
> > > --
> > > Abhisek Mondal
> > >
> > > *Research Fellow*
> > >
> > > *Structural Biology and Bioinformatics Division*
> > > *CSIR-Indian Institute of Chemical Biology*
> > >
> > > *Kolkata 700032*
> > >
> > > *INDIA*
> > > --
> > > 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.
> >
>
>
>
> --
> Abhisek Mondal
>
> *Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
> 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.

Re: [gmx-users] parallel processing

2016-12-02 Thread abhisek Mondal

But if I want to run the same job in 4 nodes (available cores= 4*16) then
how would this work ?

On Fri, Dec 2, 2016 at 2:20 PM,  wrote:

> Hi Abhisek,
>
> You would need to use another version of gromacs with mpi rather than
> thread-mpi (installed by adding DGMX_MPI=ON to the cmake command). You
> could then use the following command
>
> mpirun -np 4 gmx_mpi mdrun -ntomp 16 -npme 0 -v -deffnm em
>
> I'm not sure why you are specifying -npme 0 but would suggest you don't do
> this and instead let the number of separate pme ranks be set
> automatically.
>
> Best wishes
> James
>
> > Hi,
> >
> > I'm running gromacs on a cluster configuration as follows:
> > 1 node = 16 cores
> >
> > I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16 -npme 0 -v
> > -deffnm em" command.
> >
> > How can I be able to run on multiple node (I have 20 nodes available) ?
> > "-nt" is not doing good here.
> >
> >
> >
> > --
> > Abhisek Mondal
> >
> > *Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> > --
> > 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.
>



-- 
Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
-- 
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.

Re: [gmx-users] parallel processing

2016-12-02 Thread jkrieger

Hi Abhisek,

You would need to use another version of gromacs with mpi rather than
thread-mpi (installed by adding DGMX_MPI=ON to the cmake command). You
could then use the following command

mpirun -np 4 gmx_mpi mdrun -ntomp 16 -npme 0 -v -deffnm em

I'm not sure why you are specifying -npme 0 but would suggest you don't do
this and instead let the number of separate pme ranks be set
automatically.

Best wishes
James

> Hi,
>
> I'm running gromacs on a cluster configuration as follows:
> 1 node = 16 cores
>
> I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16 -npme 0 -v
> -deffnm em" command.
>
> How can I be able to run on multiple node (I have 20 nodes available) ?
> "-nt" is not doing good here.
>
>
>
> --
> Abhisek Mondal
>
> *Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
> 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.

[gmx-users] parallel processing

2016-12-01 Thread abhisek Mondal

Hi,

I'm running gromacs on a cluster configuration as follows:
1 node = 16 cores

I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16 -npme 0 -v
-deffnm em" command.

How can I be able to run on multiple node (I have 20 nodes available) ?
"-nt" is not doing good here.



-- 
Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
-- 
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.

Re: [gmx-users] parallel processing

Re: [gmx-users] parallel processing

Re: [gmx-users] parallel processing

Re: [gmx-users] parallel processing

Re: [gmx-users] parallel processing

[gmx-users] parallel processing

6 matches

Site Navigation

Mail list logo

Footer information