[gmx-users] How do I examine the results didn't write issue

2011-09-12 Thread lina 
Hi,

I am confused, why the job is running,

but they did not write the .edr, .log .xtc ... files.

Everything showed so normal, just not writing,

when I used thread, all is fine, the writing is normal.

just use mpi, I tried different nodes, still not work, now two hours later,
still no writing, just running.

Thanks for providing any clue for me to examine.


-- 
Best Regards,

lina
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Re: [gmx-users] How do I examine the results didn't write issue

2011-09-12 Thread Justin A. Lemkul 



lina wrote:

Hi,

I am confused, why the job is running,

but they did not write the .edr, .log .xtc ... files.

Everything showed so normal, just not writing,

when I used thread, all is fine, the writing is normal.

just use mpi, I tried different nodes, still not work, now two hours 
later, still no writing, just running.


Thanks for providing any clue for me to examine.




Sounds like your MPI implementation is broken or you haven't issued the command 
right.  If you have a test command that you know should work, run that. 
Otherwise, it's impossible to know if the problem is with Gromacs or something 
external.  If you compiled with threading support, but not MPI (in a separate 
binary) then MPI will not work on the thread-enabled executable.


-Justin

--


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


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Re: [gmx-users] How do I examine the results didn't write issue

2011-09-12 Thread Mark Abraham 

On 12/09/2011 10:23 PM, lina wrote:

Hi,

I am confused, why the job is running,

but they did not write the .edr, .log .xtc ... files.

Everything showed so normal, just not writing,

when I used thread, all is fine, the writing is normal.

just use mpi, I tried different nodes, still not work, now two hours 
later, still no writing, just running.


If you can run mdrun_threads -np 4 and get output and your mpirun -np 4 
mdrun_mpi does not write output, then there must be something wrong with 
your MPI environment. Try another MPI program and see what it does.


Mark
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Re: [gmx-users] How do I examine the results didn't write issue

2011-09-12 Thread lina 
On Mon, Sep 12, 2011 at 8:33 PM, Justin A. Lemkul  wrote:

>
>
> lina wrote:
>
>> Hi,
>>
>> I am confused, why the job is running,
>>
>> but they did not write the .edr, .log .xtc ... files.
>>
>> Everything showed so normal, just not writing,
>>
>> when I used thread, all is fine, the writing is normal.
>>
>> just use mpi, I tried different nodes, still not work, now two hours
>> later, still no writing, just running.
>>
>> Thanks for providing any clue for me to examine.
>>
>>
>>
> Sounds like your MPI implementation is broken or you haven't issued the
> command right.  If you have a test command that you know should work, run
> that. Otherwise, it's impossible to know if the problem is with Gromacs or
> something external.  If you compiled with threading support, but not MPI (in
> a separate binary) then MPI will not work on the thread-enabled executable.
>

I suspected it's MPI issue, but couple of days ago it's fine, and the
results was able to write.

I installed both MPI and thread but with different prefix to distinguish.

Thanks,

>
> -Justin
>
> --
> ==**==
>
> 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
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> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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> or send it to gmx-users-requ...@gromacs.org.
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> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Best Regards,

lina
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Re: [gmx-users] How do I examine the results didn't write issue

2011-09-12 Thread lina 
On Mon, Sep 12, 2011 at 8:35 PM, Mark Abraham wrote:

> On 12/09/2011 10:23 PM, lina wrote:
>
>> Hi,
>>
>> I am confused, why the job is running,
>>
>> but they did not write the .edr, .log .xtc ... files.
>>
>> Everything showed so normal, just not writing,
>>
>> when I used thread, all is fine, the writing is normal.
>>
>> just use mpi, I tried different nodes, still not work, now two hours
>> later, still no writing, just running.
>>
>
> If you can run mdrun_threads -np 4 and get output and your mpirun -np 4
> mdrun_mpi does not write output, then there must be something wrong with
> your MPI environment. Try another MPI program and see what it does.
>

I guess I will drop an email to the administrator.

might be an MPI issue.

Thanks for your time,


> Mark
>
> --
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> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Best Regards,

lina
-- 
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