Re: [OMPI users] running external program on same processor (Fortran)
On Mar 5, 2010, at 8:52 AM, abc def wrote:
> Hello,
> From within the MPI fortran program I run the following command:
>
> CALL SYSTEM("cd " // TRIM(dir) // " ; mpirun -machinefile ./machinefile -np 1
> /home01/group/Execute/DLPOLY.X > job.out 2> job.err ; cd - > /dev/null")
That is guaranteed not to work. The problem is that mpirun sets environmental
variables for the original launch. Your system call carries over those envars,
causing mpirun to become confused.
>
> where "dir" is a process-number-dependent directory, to ensure the processes
> don't over-write each other, and machinefile is written earlier by using
> hostname to obtain the node of the current process, so this new program
> launches using the same node as the one that launches it.
>
> In fortran, the program automatically waits until the system call is complete.
>
> Since you mentioned MPI_COMM_SPAWN, I looked into this. I read that it's
> non-blocking, so somehow I'd have to prevent the program from moving forwards
> until it was complete, and secondly, I need to "cd" into the directory I
> mentioned above, before running the external command, and I don't know how
> one would achieve this with this command.
>
> Do you think MPI_COMM_SPAWN can help?
It's the only method supported by the MPI standard. If you need it to block
until this new executable completes, you could use a barrier or other MPI
method to determine it.
> I appreciate your time.
>
> From: r...@open-mpi.org
> Date: Fri, 5 Mar 2010 07:55:59 -0700
> To: us...@open-mpi.org
> Subject: Re: [OMPI users] running external programon same
> processor (Fortran)
>
> How are you trying to start this external program? With an MPI_Comm_spawn? Or
> are you just fork/exec'ing it?
>
> How are you waiting for this external program to finish?
>
> On Mar 5, 2010, at 7:52 AM, abc def wrote:
>
> Hello,
>
> Thanks for the comments. Indeed, until yesterday, I didn't realise the
> difference between MVAPICH, MVAPICH2 and Open-MPI.
>
> This problem has moved from mvapich2 to open-mpi now however, because I now
> realise that the production environment uses Open-MPI, which means my
> solution for mvapich2 doesn't work now. So if I may ask your kind assistance:
>
> Just to re-cap, I have an MPI fortran program, which runs on N nodes, and
> each node needs to run an external program. This is external program was
> written for MPI, although I want to run it in serial as part of the process
> on each node.
>
> Is there any way at all to launch this external MPI program so it's treated
> simply as a (serial) extension of the current node's processes? As I say, the
> MPI originating program simply waits for the external program to finish
> before continuing, so it it's essentially a bit like a "subroutine", in that
> sense.
>
> I'm having problems launching this external program from within my MPI
> program, under the open-mpi system, even without worrying about node
> assignment, and I think this might be because the system detects that I'm
> trying to launch another process from one of the nodes, and stops it. I'm
> guessing here, but it simply stops with an error saying the MPI process was
> stopped.
>
> Any help is very much appreciated; I have been going at this for more than a
> day now and don't seem to be getting anywhere.
>
> Thank you!
>
> From: r...@open-mpi.org
> Date: Wed, 3 Mar 2010 07:24:32 -0700
> To: us...@open-mpi.org
> Subject: Re: [OMPI users] running external program on sameprocessor
> (Fortran)
>
> It also would have been really helpful to know that you were using MVAPICH
> and -not- Open MPI as this mailing list is for the latter. We could have
> directed you to the appropriate place if we had known.
>
>
> On Mar 3, 2010, at 5:17 AM, abc def wrote:
>
> I don't know (I'm a little new to this area), but I figured out how to get
> around the problem:
>
> Using SGE and MVAPICH2, the "-env MV2_CPU_MAPPING 0:1." option in mpiexec
> seems to do the trick.
>
> So when calling the external program with mpiexec, I map the called process
> to the current core rank, and it seems to stay distributed and separated as I
> want.
>
> Hope someone else finds this useful in the future.
>
> > Date: Wed, 3 Mar 2010 13:13:01 +1100
> > Subject: Re: [OMPI users] running external program on same processor
> > (Fortran)
> >
> > Surely this is the problem of the scheduler that your system uses,
> > rather than MPI?
> >
> >
> > On Wed, 2010-03-03 at 00:48 +, abc def wrote:
> > > Hello,
>
Re: [OMPI users] running external program on same processor (Fortran)
Hello,
>From within the MPI fortran program I run the following command:
CALL SYSTEM("cd " // TRIM(dir) // " ; mpirun -machinefile ./machinefile -np 1
/home01/group/Execute/DLPOLY.X > job.out 2> job.err ; cd - > /dev/null")
where "dir" is a process-number-dependent directory, to ensure the processes
don't over-write each other, and machinefile is written earlier by using
hostname to obtain the node of the current process, so this new program
launches using the same node as the one that launches it.
In fortran, the program automatically waits until the system call is complete.
Since you mentioned MPI_COMM_SPAWN, I looked into this. I read that it's
non-blocking, so somehow I'd have to prevent the program from moving forwards
until it was complete, and secondly, I need to "cd" into the directory I
mentioned above, before running the external command, and I don't know how one
would achieve this with this command.
Do you think MPI_COMM_SPAWN can help?
I appreciate your time.
From: r...@open-mpi.org
List-Post: users@lists.open-mpi.org
Date: Fri, 5 Mar 2010 07:55:59 -0700
To: us...@open-mpi.org
Subject: Re: [OMPI users] running external program on same
processor (Fortran)
How are you trying to start this external program? With an MPI_Comm_spawn? Or
are you just fork/exec'ing it?
How are you waiting for this external program to finish?
On Mar 5, 2010, at 7:52 AM, abc def wrote:Hello,
Thanks for the comments. Indeed, until yesterday, I didn't realise the
difference between MVAPICH, MVAPICH2 and Open-MPI.
This problem has moved from mvapich2 to open-mpi now however, because I now
realise that the production environment uses Open-MPI, which means my solution
for mvapich2 doesn't work now. So if I may ask your kind assistance:
Just to re-cap, I have an MPI fortran program, which runs on N nodes, and each
node needs to run an external program. This is external program was written for
MPI, although I want to run it in serial as part of the process on each node.
Is there any way at all to launch this external MPI program so it's treated
simply as a (serial) extension of the current node's processes? As I say, the
MPI originating program simply waits for the external program to finish before
continuing, so it it's essentially a bit like a "subroutine", in that sense.
I'm having problems launching this external program from within my MPI program,
under the open-mpi system, even without worrying about node assignment, and I
think this might be because the system detects that I'm trying to launch
another process from one of the nodes, and stops it. I'm guessing here, but it
simply stops with an error saying the MPI process was stopped.
Any help is very much appreciated; I have been going at this for more than a
day now and don't seem to be getting anywhere.
Thank you!
From: r...@open-mpi.org
List-Post: users@lists.open-mpi.org
Date: Wed, 3 Mar 2010 07:24:32 -0700
To: us...@open-mpi.org
Subject: Re: [OMPI users] running external program on sameprocessor
(Fortran)
It also would have been really helpful to know that you were using MVAPICH and
-not- Open MPI as this mailing list is for the latter. We could have directed
you to the appropriate place if we had known.
On Mar 3, 2010, at 5:17 AM, abc def wrote:I don't know (I'm a little new to
this area), but I figured out how to get around the problem:
Using SGE and MVAPICH2, the "-env MV2_CPU_MAPPING 0:1." option in mpiexec
seems to do the trick.
So when calling the external program with mpiexec, I map the called process to
the current core rank, and it seems to stay distributed and separated as I want.
Hope someone else finds this useful in the future.
> Date: Wed, 3 Mar 2010 13:13:01 +1100
> Subject: Re: [OMPI users] running external program on sameprocessor
> (Fortran)
>
> Surely this is the problem of the scheduler that your system uses,
> rather than MPI?
>
>
> On Wed, 2010-03-03 at 00:48 +, abc def wrote:
> > Hello,
> >
> > I wonder if someone can help.
> >
> > The situation is that I have an MPI-parallel fortran program. I run it
> > and it's distributed on N cores, and each of these processes must call
> > an external program.
> >
> > This external program is also an MPI program, however I want to run it
> > in serial, on the core that is calling it, as if it were part of the
> > fortran program. The fortran program waits until the external program
> > has completed, and then continues.
> >
> > The problem is that this external program seems to run on any core,
> > and not necessarily the (now idle) core that called it. This slows
> > things down a lot as you get one core doing multiple tasks.
> >
> > Can anyone tell me how I can call the program and e
Re: [OMPI users] running external program on same processor (Fortran)
How are you trying to start this external program? With an MPI_Comm_spawn? Or
are you just fork/exec'ing it?
How are you waiting for this external program to finish?
On Mar 5, 2010, at 7:52 AM, abc def wrote:
> Hello,
>
> Thanks for the comments. Indeed, until yesterday, I didn't realise the
> difference between MVAPICH, MVAPICH2 and Open-MPI.
>
> This problem has moved from mvapich2 to open-mpi now however, because I now
> realise that the production environment uses Open-MPI, which means my
> solution for mvapich2 doesn't work now. So if I may ask your kind assistance:
>
> Just to re-cap, I have an MPI fortran program, which runs on N nodes, and
> each node needs to run an external program. This is external program was
> written for MPI, although I want to run it in serial as part of the process
> on each node.
>
> Is there any way at all to launch this external MPI program so it's treated
> simply as a (serial) extension of the current node's processes? As I say, the
> MPI originating program simply waits for the external program to finish
> before continuing, so it it's essentially a bit like a "subroutine", in that
> sense.
>
> I'm having problems launching this external program from within my MPI
> program, under the open-mpi system, even without worrying about node
> assignment, and I think this might be because the system detects that I'm
> trying to launch another process from one of the nodes, and stops it. I'm
> guessing here, but it simply stops with an error saying the MPI process was
> stopped.
>
> Any help is very much appreciated; I have been going at this for more than a
> day now and don't seem to be getting anywhere.
>
> Thank you!
>
> From: r...@open-mpi.org
> Date: Wed, 3 Mar 2010 07:24:32 -0700
> To: us...@open-mpi.org
> Subject: Re: [OMPI users] running external program on sameprocessor
> (Fortran)
>
> It also would have been really helpful to know that you were using MVAPICH
> and -not- Open MPI as this mailing list is for the latter. We could have
> directed you to the appropriate place if we had known.
>
>
> On Mar 3, 2010, at 5:17 AM, abc def wrote:
>
> I don't know (I'm a little new to this area), but I figured out how to get
> around the problem:
>
> Using SGE and MVAPICH2, the "-env MV2_CPU_MAPPING 0:1." option in mpiexec
> seems to do the trick.
>
> So when calling the external program with mpiexec, I map the called process
> to the current core rank, and it seems to stay distributed and separated as I
> want.
>
> Hope someone else finds this useful in the future.
>
> > Date: Wed, 3 Mar 2010 13:13:01 +1100
> > Subject: Re: [OMPI users] running external program on same processor
> > (Fortran)
> >
> > Surely this is the problem of the scheduler that your system uses,
> > rather than MPI?
> >
> >
> > On Wed, 2010-03-03 at 00:48 +, abc def wrote:
> > > Hello,
> > >
> > > I wonder if someone can help.
> > >
> > > The situation is that I have an MPI-parallel fortran program. I run it
> > > and it's distributed on N cores, and each of these processes must call
> > > an external program.
> > >
> > > This external program is also an MPI program, however I want to run it
> > > in serial, on the core that is calling it, as if it were part of the
> > > fortran program. The fortran program waits until the external program
> > > has completed, and then continues.
> > >
> > > The problem is that this external program seems to run on any core,
> > > and not necessarily the (now idle) core that called it. This slows
> > > things down a lot as you get one core doing multiple tasks.
> > >
> > > Can anyone tell me how I can call the program and ensure it runs only
> > > on the core that's calling it? Note that there are several cores per
> > > node. I can ID the node by running the hostname command (I don't know
> > > a way to do this for individual cores).
> > >
> > > Thanks!
> > >
> > >
> > >
> > > Extra information that might be helpful:
> > >
> > > If I simply run the external program from the command line (ie, type
> > > "/path/myprogram.ex "), it runs fine. If I run it within the
> > > fortran program by calling it via
> > >
> > > CALL SYSTEM("/path/myprogram.ex")
> > >
> > > it doesn't run at all (doesn't even start) and everything crashes. I
> > > don't know why this is.
> > >
> > > If I call it usi
Re: [OMPI users] running external program on same processor (Fortran)
Hello,
Thanks for the comments. Indeed, until yesterday, I didn't realise the
difference between MVAPICH, MVAPICH2 and Open-MPI.
This problem has moved from mvapich2 to open-mpi now however, because I now
realise that the production environment uses Open-MPI, which means my solution
for mvapich2 doesn't work now. So if I may ask your kind assistance:
Just to re-cap, I have an MPI fortran program, which runs on N nodes, and each
node needs to run an external program. This is external program was written for
MPI, although I want to run it in serial as part of the process on each node.
Is there any way at all to launch this external MPI program so it's treated
simply as a (serial) extension of the current node's processes? As I say, the
MPI originating program simply waits for the external program to finish before
continuing, so it it's essentially a bit like a "subroutine", in that sense.
I'm having problems launching this external program from within my MPI program,
under the open-mpi system, even without worrying about node assignment, and I
think this might be because the system detects that I'm trying to launch
another process from one of the nodes, and stops it. I'm guessing here, but it
simply stops with an error saying the MPI process was stopped.
Any help is very much appreciated; I have been going at this for more than a
day now and don't seem to be getting anywhere.
Thank you!
From: r...@open-mpi.org
List-Post: users@lists.open-mpi.org
Date: Wed, 3 Mar 2010 07:24:32 -0700
To: us...@open-mpi.org
Subject: Re: [OMPI users] running external program on same processor
(Fortran)
It also would have been really helpful to know that you were using MVAPICH and
-not- Open MPI as this mailing list is for the latter. We could have directed
you to the appropriate place if we had known.
On Mar 3, 2010, at 5:17 AM, abc def wrote:I don't know (I'm a little new to
this area), but I figured out how to get around the problem:
Using SGE and MVAPICH2, the "-env MV2_CPU_MAPPING 0:1." option in mpiexec
seems to do the trick.
So when calling the external program with mpiexec, I map the called process to
the current core rank, and it seems to stay distributed and separated as I want.
Hope someone else finds this useful in the future.
> Date: Wed, 3 Mar 2010 13:13:01 +1100
> Subject: Re: [OMPI users] running external program on sameprocessor
> (Fortran)
>
> Surely this is the problem of the scheduler that your system uses,
> rather than MPI?
>
>
> On Wed, 2010-03-03 at 00:48 +, abc def wrote:
> > Hello,
> >
> > I wonder if someone can help.
> >
> > The situation is that I have an MPI-parallel fortran program. I run it
> > and it's distributed on N cores, and each of these processes must call
> > an external program.
> >
> > This external program is also an MPI program, however I want to run it
> > in serial, on the core that is calling it, as if it were part of the
> > fortran program. The fortran program waits until the external program
> > has completed, and then continues.
> >
> > The problem is that this external program seems to run on any core,
> > and not necessarily the (now idle) core that called it. This slows
> > things down a lot as you get one core doing multiple tasks.
> >
> > Can anyone tell me how I can call the program and ensure it runs only
> > on the core that's calling it? Note that there are several cores per
> > node. I can ID the node by running the hostname command (I don't know
> > a way to do this for individual cores).
> >
> > Thanks!
> >
> >
> >
> > Extra information that might be helpful:
> >
> > If I simply run the external program from the command line (ie, type
> > "/path/myprogram.ex "), it runs fine. If I run it within the
> > fortran program by calling it via
> >
> > CALL SYSTEM("/path/myprogram.ex")
> >
> > it doesn't run at all (doesn't even start) and everything crashes. I
> > don't know why this is.
> >
> > If I call it using mpiexec:
> >
> > CALL SYSTEM("mpiexec -n 1 /path/myprogram.ex")
> >
> > then it does work, but I get the problem that it can go on any core.
> >
> > __
> > Do you want a Hotmail account? Sign-up now - Free
> > ___
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
Not got a Hotmail accoun
Re: [OMPI users] running external program on same processor (Fortran)
On Wed, 2010-03-03 at 12:57 -0500, Prentice Bisbal wrote:
> Reuti wrote:
> > Are you speaking of the same?
>
> Good point, Reuti. I was thinking of a cluster scheduler like SGE or
> Torque.
Yeah, I meant the scheduler in the CPU time slice sense.
http://en.wikipedia.org/wiki/Scheduling_(computing)
vs.
http://en.wikipedia.org/wiki/Job_scheduler
> > Am 03.03.2010 um 17:32 schrieb Prentice Bisbal:
> >
> >> Terry Frankcombe wrote:
> >>> Surely this is the problem of the scheduler that your system uses,
> >
> > This I would also state.
> >
> >
> >>> rather than MPI?
> >
> > Scheduler in the Linux kernel?
> >
> >
> >> That's not true. The scheduler only assigns the initial processes to
> >> nodes
> >
> > Scheduler in MPI?
> >
> >
> >> and starts them. It can kill the processes it starts if they use
> >> too much memory or run too long, but doesn't prevent them from spawning
> >> more processes, and once spawned,
> >
> > When the processes are bound to one and the same core, these addititonal
> > processes won't intefere with other jobs' processes on the same node
> > which run on the other cores.
> >
> > -- Reuti
> >
> >
> >> unless they are spawned through the
> >> scheduler, it has no control over them.
> >>>
> >>>
> >>> On Wed, 2010-03-03 at 00:48 +, abc def wrote:
> Hello,
>
> I wonder if someone can help.
>
> The situation is that I have an MPI-parallel fortran program. I run it
> and it's distributed on N cores, and each of these processes must call
> an external program.
>
> This external program is also an MPI program, however I want to run it
> in serial, on the core that is calling it, as if it were part of the
> fortran program. The fortran program waits until the external program
> has completed, and then continues.
>
> The problem is that this external program seems to run on any core,
> and not necessarily the (now idle) core that called it. This slows
> things down a lot as you get one core doing multiple tasks.
>
> Can anyone tell me how I can call the program and ensure it runs only
> on the core that's calling it? Note that there are several cores per
> node. I can ID the node by running the hostname command (I don't know
> a way to do this for individual cores).
>
> Thanks!
>
>
>
> Extra information that might be helpful:
>
> If I simply run the external program from the command line (ie, type
> "/path/myprogram.ex "), it runs fine. If I run it within the
> fortran program by calling it via
>
> CALL SYSTEM("/path/myprogram.ex")
>
> it doesn't run at all (doesn't even start) and everything crashes. I
> don't know why this is.
>
> If I call it using mpiexec:
>
> CALL SYSTEM("mpiexec -n 1 /path/myprogram.ex")
>
> then it does work, but I get the problem that it can go on any core.
>
> __
> Do you want a Hotmail account? Sign-up now - Free
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
> >>>
> >>> ___
> >>> users mailing list
> >>> us...@open-mpi.org
> >>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> >>>
> >>
> >> --
> >> Prentice Bisbal
> >> Linux Software Support Specialist/System Administrator
> >> School of Natural Sciences
> >> Institute for Advanced Study
> >> Princeton, NJ
> >> ___
> >> users mailing list
> >> us...@open-mpi.org
> >> http://www.open-mpi.org/mailman/listinfo.cgi/users
> >
> > ___
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
> >
>
Re: [OMPI users] running external program on same processor (Fortran)
Reuti wrote:
> Are you speaking of the same?
Good point, Reuti. I was thinking of a cluster scheduler like SGE or
Torque.
>
> Am 03.03.2010 um 17:32 schrieb Prentice Bisbal:
>
>> Terry Frankcombe wrote:
>>> Surely this is the problem of the scheduler that your system uses,
>
> This I would also state.
>
>
>>> rather than MPI?
>
> Scheduler in the Linux kernel?
>
>
>> That's not true. The scheduler only assigns the initial processes to
>> nodes
>
> Scheduler in MPI?
>
>
>> and starts them. It can kill the processes it starts if they use
>> too much memory or run too long, but doesn't prevent them from spawning
>> more processes, and once spawned,
>
> When the processes are bound to one and the same core, these addititonal
> processes won't intefere with other jobs' processes on the same node
> which run on the other cores.
>
> -- Reuti
>
>
>> unless they are spawned through the
>> scheduler, it has no control over them.
>>>
>>>
>>> On Wed, 2010-03-03 at 00:48 +, abc def wrote:
Hello,
I wonder if someone can help.
The situation is that I have an MPI-parallel fortran program. I run it
and it's distributed on N cores, and each of these processes must call
an external program.
This external program is also an MPI program, however I want to run it
in serial, on the core that is calling it, as if it were part of the
fortran program. The fortran program waits until the external program
has completed, and then continues.
The problem is that this external program seems to run on any core,
and not necessarily the (now idle) core that called it. This slows
things down a lot as you get one core doing multiple tasks.
Can anyone tell me how I can call the program and ensure it runs only
on the core that's calling it? Note that there are several cores per
node. I can ID the node by running the hostname command (I don't know
a way to do this for individual cores).
Thanks!
Extra information that might be helpful:
If I simply run the external program from the command line (ie, type
"/path/myprogram.ex "), it runs fine. If I run it within the
fortran program by calling it via
CALL SYSTEM("/path/myprogram.ex")
it doesn't run at all (doesn't even start) and everything crashes. I
don't know why this is.
If I call it using mpiexec:
CALL SYSTEM("mpiexec -n 1 /path/myprogram.ex")
then it does work, but I get the problem that it can go on any core.
__
Do you want a Hotmail account? Sign-up now - Free
___
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>>> ___
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>>
>> --
>> Prentice Bisbal
>> Linux Software Support Specialist/System Administrator
>> School of Natural Sciences
>> Institute for Advanced Study
>> Princeton, NJ
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
--
Prentice Bisbal
Linux Software Support Specialist/System Administrator
School of Natural Sciences
Institute for Advanced Study
Princeton, NJ
Re: [OMPI users] running external program on same processor (Fortran)
Are you speaking of the same?
Am 03.03.2010 um 17:32 schrieb Prentice Bisbal:
Terry Frankcombe wrote:
Surely this is the problem of the scheduler that your system uses,
This I would also state.
rather than MPI?
Scheduler in the Linux kernel?
That's not true. The scheduler only assigns the initial processes to
nodes
Scheduler in MPI?
and starts them. It can kill the processes it starts if they use
too much memory or run too long, but doesn't prevent them from
spawning
more processes, and once spawned,
When the processes are bound to one and the same core, these
addititonal processes won't intefere with other jobs' processes on
the same node which run on the other cores.
-- Reuti
unless they are spawned through the
scheduler, it has no control over them.
On Wed, 2010-03-03 at 00:48 +, abc def wrote:
Hello,
I wonder if someone can help.
The situation is that I have an MPI-parallel fortran program. I
run it
and it's distributed on N cores, and each of these processes must
call
an external program.
This external program is also an MPI program, however I want to
run it
in serial, on the core that is calling it, as if it were part of the
fortran program. The fortran program waits until the external
program
has completed, and then continues.
The problem is that this external program seems to run on any core,
and not necessarily the (now idle) core that called it. This slows
things down a lot as you get one core doing multiple tasks.
Can anyone tell me how I can call the program and ensure it runs
only
on the core that's calling it? Note that there are several cores per
node. I can ID the node by running the hostname command (I don't
know
a way to do this for individual cores).
Thanks!
Extra information that might be helpful:
If I simply run the external program from the command line (ie, type
"/path/myprogram.ex "), it runs fine. If I run it within the
fortran program by calling it via
CALL SYSTEM("/path/myprogram.ex")
it doesn't run at all (doesn't even start) and everything crashes. I
don't know why this is.
If I call it using mpiexec:
CALL SYSTEM("mpiexec -n 1 /path/myprogram.ex")
then it does work, but I get the problem that it can go on any core.
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School of Natural Sciences
Institute for Advanced Study
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Re: [OMPI users] running external program on same processor (Fortran)
Terry Frankcombe wrote:
> Surely this is the problem of the scheduler that your system uses,
> rather than MPI?
That's not true. The scheduler only assigns the initial processes to
nodes and starts them. It can kill the processes it starts if they use
too much memory or run too long, but doesn't prevent them from spawning
more processes, and once spawned, unless they are spawned through the
scheduler, it has no control over them.
>
>
> On Wed, 2010-03-03 at 00:48 +, abc def wrote:
>> Hello,
>>
>> I wonder if someone can help.
>>
>> The situation is that I have an MPI-parallel fortran program. I run it
>> and it's distributed on N cores, and each of these processes must call
>> an external program.
>>
>> This external program is also an MPI program, however I want to run it
>> in serial, on the core that is calling it, as if it were part of the
>> fortran program. The fortran program waits until the external program
>> has completed, and then continues.
>>
>> The problem is that this external program seems to run on any core,
>> and not necessarily the (now idle) core that called it. This slows
>> things down a lot as you get one core doing multiple tasks.
>>
>> Can anyone tell me how I can call the program and ensure it runs only
>> on the core that's calling it? Note that there are several cores per
>> node. I can ID the node by running the hostname command (I don't know
>> a way to do this for individual cores).
>>
>> Thanks!
>>
>>
>>
>> Extra information that might be helpful:
>>
>> If I simply run the external program from the command line (ie, type
>> "/path/myprogram.ex "), it runs fine. If I run it within the
>> fortran program by calling it via
>>
>> CALL SYSTEM("/path/myprogram.ex")
>>
>> it doesn't run at all (doesn't even start) and everything crashes. I
>> don't know why this is.
>>
>> If I call it using mpiexec:
>>
>> CALL SYSTEM("mpiexec -n 1 /path/myprogram.ex")
>>
>> then it does work, but I get the problem that it can go on any core.
>>
>> __
>> Do you want a Hotmail account? Sign-up now - Free
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
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> us...@open-mpi.org
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--
Prentice Bisbal
Linux Software Support Specialist/System Administrator
School of Natural Sciences
Institute for Advanced Study
Princeton, NJ
Re: [OMPI users] running external program on same processor (Fortran)
I don't know (I'm a little new to this area), but I figured out how to get
around the problem:
Using SGE and MVAPICH2, the "-env MV2_CPU_MAPPING 0:1." option in mpiexec
seems to do the trick.
So when calling the external program with mpiexec, I map the called
process to the current core rank, and it seems to stay distributed and
separated as I want.
Hope someone else finds this useful in the future.
> Date: Wed, 3 Mar 2010 13:13:01 +1100
> Subject: Re: [OMPI users] running external program on sameprocessor
> (Fortran)
>
> Surely this is the problem of the scheduler that your system uses,
> rather than MPI?
>
>
> On Wed, 2010-03-03 at 00:48 +, abc def wrote:
> > Hello,
> >
> > I wonder if someone can help.
> >
> > The situation is that I have an MPI-parallel fortran program. I run it
> > and it's distributed on N cores, and each of these processes must call
> > an external program.
> >
> > This external program is also an MPI program, however I want to run it
> > in serial, on the core that is calling it, as if it were part of the
> > fortran program. The fortran program waits until the external program
> > has completed, and then continues.
> >
> > The problem is that this external program seems to run on any core,
> > and not necessarily the (now idle) core that called it. This slows
> > things down a lot as you get one core doing multiple tasks.
> >
> > Can anyone tell me how I can call the program and ensure it runs only
> > on the core that's calling it? Note that there are several cores per
> > node. I can ID the node by running the hostname command (I don't know
> > a way to do this for individual cores).
> >
> > Thanks!
> >
> >
> >
> > Extra information that might be helpful:
> >
> > If I simply run the external program from the command line (ie, type
> > "/path/myprogram.ex "), it runs fine. If I run it within the
> > fortran program by calling it via
> >
> > CALL SYSTEM("/path/myprogram.ex")
> >
> > it doesn't run at all (doesn't even start) and everything crashes. I
> > don't know why this is.
> >
> > If I call it using mpiexec:
> >
> > CALL SYSTEM("mpiexec -n 1 /path/myprogram.ex")
> >
> > then it does work, but I get the problem that it can go on any core.
> >
> > __
> > Do you want a Hotmail account? Sign-up now - Free
> > ___
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> > us...@open-mpi.org
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>
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Re: [OMPI users] running external program on same processor (Fortran)
Surely this is the problem of the scheduler that your system uses,
rather than MPI?
On Wed, 2010-03-03 at 00:48 +, abc def wrote:
> Hello,
>
> I wonder if someone can help.
>
> The situation is that I have an MPI-parallel fortran program. I run it
> and it's distributed on N cores, and each of these processes must call
> an external program.
>
> This external program is also an MPI program, however I want to run it
> in serial, on the core that is calling it, as if it were part of the
> fortran program. The fortran program waits until the external program
> has completed, and then continues.
>
> The problem is that this external program seems to run on any core,
> and not necessarily the (now idle) core that called it. This slows
> things down a lot as you get one core doing multiple tasks.
>
> Can anyone tell me how I can call the program and ensure it runs only
> on the core that's calling it? Note that there are several cores per
> node. I can ID the node by running the hostname command (I don't know
> a way to do this for individual cores).
>
> Thanks!
>
>
>
> Extra information that might be helpful:
>
> If I simply run the external program from the command line (ie, type
> "/path/myprogram.ex "), it runs fine. If I run it within the
> fortran program by calling it via
>
> CALL SYSTEM("/path/myprogram.ex")
>
> it doesn't run at all (doesn't even start) and everything crashes. I
> don't know why this is.
>
> If I call it using mpiexec:
>
> CALL SYSTEM("mpiexec -n 1 /path/myprogram.ex")
>
> then it does work, but I get the problem that it can go on any core.
>
> __
> Do you want a Hotmail account? Sign-up now - Free
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
[OMPI users] running external program on same processor (Fortran)
Hello,
I wonder if someone can help.
The situation is that I have an MPI-parallel fortran program. I run it
and it's distributed on N cores, and each of these processes must
call an external program.
This external program is also an MPI program, however I want to run it
in serial, on the core that is calling it, as if it were part of
the fortran program. The fortran program waits until the external
program has completed, and then continues.
The problem is that this external program seems to run on any core, and not
necessarily the (now idle) core that called it. This slows things down a lot as
you get one core doing multiple tasks.
Can anyone tell me how I can call the program and ensure it runs only on the
core that's calling it? Note that there are several cores per node. I can ID
the node by running the hostname command (I don't know a way to do this for
individual cores).
Thanks!
Extra information that might be helpful:
If I simply run the external program from the command line (ie, type
"/path/myprogram.ex "), it runs fine. If I run it within
the fortran program by calling it via
CALL SYSTEM("/path/myprogram.ex")
it doesn't run at all (doesn't even start) and everything crashes. I don't know
why this is.
If I call it using mpiexec:
CALL SYSTEM("mpiexec -n 1 /path/myprogram.ex")
then it does work, but I get the problem that it can go on any core.
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