[Wien] -machinefile _HOSTS_

[Luis Ogando]

Dear all,

   Dr. Gavin Abo pointed me out that I should have mentioned that I am
using mpiexec_mpt instead of mpiexec, so, in my case, the mpi execution is
controlled by the PBS_NODEFILE variable and not by a machines file (thanks
Dr. Abo for this).
   Anyway, I would like to know if it is safe to run MPI Wien2k with
mpiexec_mpt.
   All the best,
                   Luis

PS: I have no problem on generating the .machines file "on the fly"
(queuing system). Despite the fact that it will not be used by mpiexec_mpt,
I know that it is required by Wien2k.




---------- Forwarded message ----------
From: Gavin Abo <gsabo at crimson.ua.edu>
Date: 2013/4/8
Subject: Re: [Wien] -machinefile _HOSTS_
To: Luis Ogando <lcodacal at gmail.com>


 Dear Luis,

You probably should have mentioned that you are using 'mpiexec_mpt' not
'mpiexec'.

-machinefile is an option for mpiexec [http://linux.die.net/man/1/mpiexec],
but it doesn't seem to be a option for mpiexec_mpt [
http://techpubs.sgi.com/library/tpl/cgi-bin/getdoc.cgi?coll=linux&db=man&fname=/usr/share/catman/man1/mpiexec_mpt.1.html
].

mpiexec_mpt seems to use the PBS_NODEFILE variable instead of -machinefile [
http://www.arl.hpc.mil/docs/pbsUserGuide.html].  So your parallel_options
are probably fine as long as the PBS_NODEFILE variable is set automatically
by your system or you.

Kind Regards,

Gavin


On 4/8/2013 10:18 AM, Luis Ogando wrote:

Hi Gavin,

    Thank you for your answer.
   Actually, I generated the .machines files for the queuing system without
problems. The issue is that the " setenv WIEN_MPIRUN " in the
"parallel_options" file has to be " setenv WIEN_MPIRUN "mpiexec_mpt -np
_NP_  _EXEC_" ", without the "-machinefile" option because it is not
defined in the system.
   All the best,
                   Luis




2013/4/8 Gavin Abo <gsabo at crimson.ua.edu>

> Dear Luis,
>
> I'm sending this email off the mailing list as Prof. Marks or Blaha might
> respond with a better answer.
>
> I think the answer is yes, it can impact the Wien2k performance. This is
> because the machinefile variable contains the list of hostnames for
> 'multiple' nodes.  Without it, the calculation will likely run on only
> 'one' node.
>
> Even if you don't have admin privileges, you can likely still define the
> machinefile variable as a user by creating a .machines file in your case
> directory.  However, the creation of the .machines file may depend on
> whether or not you are required to use a queuing system.  If you are not
> required to use a queuing system, you should be able to copy the .machines
> file in SRC_templates to your case directory and then edit it a text editor
> (note: you might not see the .machines file unless you do a directory
> listing that includes hidden files).  The .machines file is should be
> described in the Wien2k userguide or you can search the internet for some
> examples [
> https://www.xsede.org/documents/10157/305826/ecss_hliu_051012.pdf]. If
> you are required to use a queuing system, you likely need to setup a script
> that will create the .machines file as described at the link:
>
> http://www.wien2k.at/reg_user/faq/pbs.html
>
> If you have problems creating the script, your administrator(s) or support
> person(s) should know the most about your computer system, so they can
> likely help you create a script that will work on your system.
>
> Kind Regards,
>
> Gavin
>
>
> On 4/8/2013 6:19 AM, Luis Ogando wrote:
>
>> Dear Prof. Marks, Blaha and Wien2k community,
>>
>>    I want to do calculations in a computer where the machinefile variable
>> is not defined for the mpiexec (I am not the administrator). I would like
>> to know if this will have some impact on the MPI Wien2k performance.
>>    Thanks in advance,
>>                                 Luis
>>
>>
>
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