LAM: LAM doesn't work

Hi community!
I've a great problem:
two months ago I installed LAM on my centrino duo, debian
-kernel 2.6.
Later I compiled gromacs enabling mpi, and everything was
working well 
until four days ago.
Now the simulation time is increased like if there is only
one processor 
(it takes twice time than before).
I don't understand why.
I disinstalled and then reinstalled LAM and gromacs (LAM
7.1.2 (I 
compiled it on my own) + gromacs 3.3.1).
Nothing has changed.
I disinstalled linux and then reinstalled (debian kernel
2.6), and again 
LAM and gromacs: I've the same problem, like if one of the
two cores 
doesn't work.
I tried also to install gromacs NON mpi-enabled, and I've
the same 
simulation time (respect to the enabled-mpi gromacs).
In all these cases LAM seems to work (when I type lamboot
LAM starts 
without problem).

What's happened?
How can I understand if it's a software problem or an
hardware one?
thank you very much for the reply!

Bye
Beniamino
_______________________________________________
This list is archived at http://www.l
am-mpi.org/MailArchives/lam/

Beniamino Sciacca wrote:
> Hi community!
> I've a great problem:
> two months ago I installed LAM on my centrino duo,
debian -kernel 2.6.
> Later I compiled gromacs enabling mpi, and everything
was working well 
> until four days ago.
> Now the simulation time is increased like if there is
only one processor 
> (it takes twice time than before).
> I don't understand why.
> I disinstalled and then reinstalled LAM and gromacs
(LAM 7.1.2 (I 
> compiled it on my own) + gromacs 3.3.1).
> Nothing has changed.
> I disinstalled linux and then reinstalled (debian
kernel 2.6), and again 
> LAM and gromacs: I've the same problem, like if one of
the two cores 
> doesn't work.
> I tried also to install gromacs NON mpi-enabled, and
I've the same 
> simulation time (respect to the enabled-mpi gromacs).
> In all these cases LAM seems to work (when I type
lamboot LAM starts 
> without problem).
> 
> What's happened?
> How can I understand if it's a software problem or an
hardware one?
> thank you very much for the reply!

The first question I always ask is - what changed?  You say
it was 
working properly up to some point, something must have
happened at or 
before that point.

It's hard to tell based on the information you've given,
but the first 
thing I would do is make sure linux has both CPU's enabled,
and that any 
power management stuff isn't affecting your performance.

Can you test any other applications, to see if this problem
is specific 
to LAM/gromacs?

You might consider other support channels as well - I can't
recommend a 
good place for you off the top of my head, but LAM is not
likely the 
problem here.

Andrew
_______________________________________________
This list is archived at http://www.l
am-mpi.org/MailArchives/lam/

I don't know what is changed.. but I partially resolved the
problem:
is not an hardware problem (installing smp kernel it works).
Now I've to use mpirun (before I didn't use it), and I
don't succeed to 
tell the system to use both processors for only one process.
In fact using "mpirun -c 2" it makes two
processes, each for one cpu.
I need to work with only one process, and before I succeeded
in this. 
(with another computer dual core I'm able to do this.
Thanks

Andrew Friedley ha scritto:
> Beniamino Sciacca wrote:
>   
>> Hi community!
>> I've a great problem:
>> two months ago I installed LAM on my centrino duo,
debian -kernel 2.6.
>> Later I compiled gromacs enabling mpi, and
everything was working well 
>> until four days ago.
>> Now the simulation time is increased like if there
is only one processor 
>> (it takes twice time than before).
>> I don't understand why.
>> I disinstalled and then reinstalled LAM and gromacs
(LAM 7.1.2 (I 
>> compiled it on my own) + gromacs 3.3.1).
>> Nothing has changed.
>> I disinstalled linux and then reinstalled (debian
kernel 2.6), and again 
>> LAM and gromacs: I've the same problem, like if
one of the two cores 
>> doesn't work.
>> I tried also to install gromacs NON mpi-enabled,
and I've the same 
>> simulation time (respect to the enabled-mpi
gromacs).
>> In all these cases LAM seems to work (when I type
lamboot LAM starts 
>> without problem).
>>
>> What's happened?
>> How can I understand if it's a software problem or
an hardware one?
>> thank you very much for the reply!
>>     
>
> The first question I always ask is - what changed?  You
say it was 
> working properly up to some point, something must have
happened at or 
> before that point.
>
> It's hard to tell based on the information you've
given, but the first 
> thing I would do is make sure linux has both CPU's
enabled, and that any 
> power management stuff isn't affecting your
performance.
>
> Can you test any other applications, to see if this
problem is specific 
> to LAM/gromacs?
>
> You might consider other support channels as well - I
can't recommend a 
> good place for you off the top of my head, but LAM is
not likely the 
> problem here.
>
> Andrew
> _______________________________________________
> This list is archived at http://www.l
am-mpi.org/MailArchives/lam/
>
>   
_______________________________________________
This list is archived at http://www.l
am-mpi.org/MailArchives/lam/

Beniamino Sciacca wrote:
> I don't know what is changed.. but I partially
resolved the problem:
> is not an hardware problem (installing smp kernel it
works).
> Now I've to use mpirun (before I didn't use it), and
I don't succeed to 
> tell the system to use both processors for only one
process.
> In fact using "mpirun -c 2" it makes two
processes, each for one cpu.
> I need to work with only one process, and before I
succeeded in this. 
> (with another computer dual core I'm able to do this.
> Thanks

Apologies, I'm not sure I understand what you're saying
here.

You weren't using mpirun before?  What were you using?

I don't see why two processes is bad - this to me is
expected behavior, 
as LAM/MPI will start one process per processor.  Why do you
need only 
one process?

Another note.. does gromacs support some sort of native
multithreaded 
mode?  This might perform better for you than using MPI
would if you're 
only using the one system.

Andrew

> Andrew Friedley ha scritto:
> 
>>Beniamino Sciacca wrote:
>>  
>>
>>>Hi community!
>>>I've a great problem:
>>>two months ago I installed LAM on my centrino
duo, debian -kernel 2.6.
>>>Later I compiled gromacs enabling mpi, and
everything was working well 
>>>until four days ago.
>>>Now the simulation time is increased like if
there is only one processor 
>>>(it takes twice time than before).
>>>I don't understand why.
>>>I disinstalled and then reinstalled LAM and
gromacs (LAM 7.1.2 (I 
>>>compiled it on my own) + gromacs 3.3.1).
>>>Nothing has changed.
>>>I disinstalled linux and then reinstalled
(debian kernel 2.6), and again 
>>>LAM and gromacs: I've the same problem, like if
one of the two cores 
>>>doesn't work.
>>>I tried also to install gromacs NON mpi-enabled,
and I've the same 
>>>simulation time (respect to the enabled-mpi
gromacs).
>>>In all these cases LAM seems to work (when I
type lamboot LAM starts 
>>>without problem).
>>>
>>>What's happened?
>>>How can I understand if it's a software problem
or an hardware one?
>>>thank you very much for the reply!
>>>    
>>
>>The first question I always ask is - what changed? 
You say it was 
>>working properly up to some point, something must
have happened at or 
>>before that point.
>>
>>It's hard to tell based on the information you've
given, but the first 
>>thing I would do is make sure linux has both CPU's
enabled, and that any 
>>power management stuff isn't affecting your
performance.
>>
>>Can you test any other applications, to see if this
problem is specific 
>>to LAM/gromacs?
>>
>>You might consider other support channels as well -
I can't recommend a 
>>good place for you off the top of my head, but LAM
is not likely the 
>>problem here.
>>
>>Andrew
>>_______________________________________________
>>This list is archived at http://www.l
am-mpi.org/MailArchives/lam/
>>
>>  
> 
> _______________________________________________
> This list is archived at http://www.l
am-mpi.org/MailArchives/lam/

_______________________________________________
This list is archived at http://www.l
am-mpi.org/MailArchives/lam/

Before I compiled gromacs enabling mpi, and mdrun used both
the cpu 
starting only one process.
I need one process because in my case if I use two processes
mdrun 
return an error (I use constraint forces).
I'm not sure, but maybe this version doesn't support
native multithreaded...
Beniamino Sciacca

Andrew Friedley ha scritto:
> Beniamino Sciacca wrote:
>   
>> I don't know what is changed.. but I partially
resolved the problem:
>> is not an hardware problem (installing smp kernel
it works).
>> Now I've to use mpirun (before I didn't use it),
and I don't succeed to 
>> tell the system to use both processors for only one
process.
>> In fact using "mpirun -c 2" it makes
two processes, each for one cpu.
>> I need to work with only one process, and before I
succeeded in this. 
>> (with another computer dual core I'm able to do
this.
>> Thanks
>>     
>
> Apologies, I'm not sure I understand what you're
saying here.
>
> You weren't using mpirun before?  What were you using?
>
> I don't see why two processes is bad - this to me is
expected behavior, 
> as LAM/MPI will start one process per processor.  Why
do you need only 
> one process?
>
> Another note.. does gromacs support some sort of native
multithreaded 
> mode?  This might perform better for you than using MPI
would if you're 
> only using the one system.
>
> Andrew
>
>   
>> Andrew Friedley ha scritto:
>>
>>     
>>> Beniamino Sciacca wrote:
>>>  
>>>
>>>       
>>>> Hi community!
>>>> I've a great problem:
>>>> two months ago I installed LAM on my
centrino duo, debian -kernel 2.6.
>>>> Later I compiled gromacs enabling mpi, and
everything was working well 
>>>> until four days ago.
>>>> Now the simulation time is increased like
if there is only one processor 
>>>> (it takes twice time than before).
>>>> I don't understand why.
>>>> I disinstalled and then reinstalled LAM and
gromacs (LAM 7.1.2 (I 
>>>> compiled it on my own) + gromacs 3.3.1).
>>>> Nothing has changed.
>>>> I disinstalled linux and then reinstalled
(debian kernel 2.6), and again 
>>>> LAM and gromacs: I've the same problem,
like if one of the two cores 
>>>> doesn't work.
>>>> I tried also to install gromacs NON
mpi-enabled, and I've the same 
>>>> simulation time (respect to the enabled-mpi
gromacs).
>>>> In all these cases LAM seems to work (when
I type lamboot LAM starts 
>>>> without problem).
>>>>
>>>> What's happened?
>>>> How can I understand if it's a software
problem or an hardware one?
>>>> thank you very much for the reply!
>>>>    
>>>>         
>>> The first question I always ask is - what
changed?  You say it was 
>>> working properly up to some point, something
must have happened at or 
>>> before that point.
>>>
>>> It's hard to tell based on the information
you've given, but the first 
>>> thing I would do is make sure linux has both
CPU's enabled, and that any 
>>> power management stuff isn't affecting your
performance.
>>>
>>> Can you test any other applications, to see if
this problem is specific 
>>> to LAM/gromacs?
>>>
>>> You might consider other support channels as
well - I can't recommend a 
>>> good place for you off the top of my head, but
LAM is not likely the 
>>> problem here.
>>>
>>> Andrew
>>> _______________________________________________
>>> This list is archived at http://www.l
am-mpi.org/MailArchives/lam/
>>>
>>>  
>>>       
>> _______________________________________________
>> This list is archived at http://www.l
am-mpi.org/MailArchives/lam/
>>     
>
> _______________________________________________
> This list is archived at http://www.l
am-mpi.org/MailArchives/lam/
>
>   
_______________________________________________
This list is archived at http://www.l
am-mpi.org/MailArchives/lam/

Beniamino Sciacca wrote:
> Before I compiled gromacs enabling mpi, and mdrun used
both the cpu 
> starting only one process.

Okay, I'm not sure how you ever saw speedup via MPI running
only one 
process - LAM is not multithreaded at all.  This implies
that if you 
really were seeing speedups with one process, some sort of 
multithreading was used without MPI for communication.

> I need one process because in my case if I use two
processes mdrun 
> return an error (I use constraint forces).

I take it this means gromacs doesn't let you run in
parallel with 
constraint forces?  Are you sure you are setting up parallel
runs with 
gromacs correctly?

> I'm not sure, but maybe this version doesn't support
native multithreaded...

I would recommend looking into that, as it might give you
what you want.

Andrew

> Beniamino Sciacca
> 
> Andrew Friedley ha scritto:
> 
>>Beniamino Sciacca wrote:
>>  
>>
>>>I don't know what is changed.. but I partially
resolved the problem:
>>>is not an hardware problem (installing smp
kernel it works).
>>>Now I've to use mpirun (before I didn't use
it), and I don't succeed to 
>>>tell the system to use both processors for only
one process.
>>>In fact using "mpirun -c 2" it makes
two processes, each for one cpu.
>>>I need to work with only one process, and before
I succeeded in this. 
>>>(with another computer dual core I'm able to do
this.
>>>Thanks
>>>    
>>
>>Apologies, I'm not sure I understand what you're
saying here.
>>
>>You weren't using mpirun before?  What were you
using?
>>
>>I don't see why two processes is bad - this to me
is expected behavior, 
>>as LAM/MPI will start one process per processor. 
Why do you need only 
>>one process?
>>
>>Another note.. does gromacs support some sort of
native multithreaded 
>>mode?  This might perform better for you than using
MPI would if you're 
>>only using the one system.
>>
>>Andrew
>>
>>  
>>
>>>Andrew Friedley ha scritto:
>>>
>>>    
>>>
>>>>Beniamino Sciacca wrote:
>>>> 
>>>>
>>>>      
>>>>
>>>>>Hi community!
>>>>>I've a great problem:
>>>>>two months ago I installed LAM on my
centrino duo, debian -kernel 2.6.
>>>>>Later I compiled gromacs enabling mpi,
and everything was working well 
>>>>>until four days ago.
>>>>>Now the simulation time is increased
like if there is only one processor 
>>>>>(it takes twice time than before).
>>>>>I don't understand why.
>>>>>I disinstalled and then reinstalled LAM
and gromacs (LAM 7.1.2 (I 
>>>>>compiled it on my own) + gromacs 3.3.1).
>>>>>Nothing has changed.
>>>>>I disinstalled linux and then
reinstalled (debian kernel 2.6), and again 
>>>>>LAM and gromacs: I've the same problem,
like if one of the two cores 
>>>>>doesn't work.
>>>>>I tried also to install gromacs NON
mpi-enabled, and I've the same 
>>>>>simulation time (respect to the
enabled-mpi gromacs).
>>>>>In all these cases LAM seems to work
(when I type lamboot LAM starts 
>>>>>without problem).
>>>>>
>>>>>What's happened?
>>>>>How can I understand if it's a software
problem or an hardware one?
>>>>>thank you very much for the reply!
>>>>>   
>>>>>        
>>>>
>>>>The first question I always ask is - what
changed?  You say it was 
>>>>working properly up to some point, something
must have happened at or 
>>>>before that point.
>>>>
>>>>It's hard to tell based on the information
you've given, but the first 
>>>>thing I would do is make sure linux has both
CPU's enabled, and that any 
>>>>power management stuff isn't affecting your
performance.
>>>>
>>>>Can you test any other applications, to see
if this problem is specific 
>>>>to LAM/gromacs?
>>>>
>>>>You might consider other support channels as
well - I can't recommend a 
>>>>good place for you off the top of my head,
but LAM is not likely the 
>>>>problem here.
>>>>
>>>>Andrew
>>>>____________________________________________
___
>>>>This list is archived at http://www.l
am-mpi.org/MailArchives/lam/
>>>>
>>>> 
>>>>      
>>>
>>>_______________________________________________
>>>This list is archived at http://www.l
am-mpi.org/MailArchives/lam/
>>>    
>>
>>_______________________________________________
>>This list is archived at http://www.l
am-mpi.org/MailArchives/lam/
>>
>>  
> 
> _______________________________________________
> This list is archived at http://www.l
am-mpi.org/MailArchives/lam/

_______________________________________________
This list is archived at http://www.l
am-mpi.org/MailArchives/lam/