[Pw_forum] problems with running Quantum Espresso in parallel

[torstein.fjermestad at unito.it]

Yes, they are in the same directory.

The problem seems to be related to the installation of open MPI, and I 
think you are right that I should ask someone else.

Thanks.

On 22.04.2014 12:20, Lorenzo Paulatto wrote:
> Check that the output of:
> which mpirun
> which mpif90
> are in the same directory: if they are not, you are in troubles.
>
> I would recommend you ask whoever set up the cluster for help, it 
> will
> definitely save both of you time.
>
>
> cheers
>
>
> On 04/22/2014 12:02 PM, torstein.fjermestad at unito.it wrote:
>> Dear Axel Kohlmeyer,
>>
>> thank you for your fast reply.
>> Unfortunately, I am not really sure if I have understood all the
>> details of your suggestions.
>> The version of mpirun is 1.4.5. This information I got from the 
>> output
>> of "mpirun -V":
>> mpirun (Open MPI) 1.4.5
>>
>> I am configuring and compiling pw.x on the same (virtual) machine as
>> Open MPI is installed. I do this in the following way:
>> ./configure
>> make pw
>>
>> I doubt that there are several versions of Open MPI installed on the
>> same machine, but in case there are, is the version of Open MPI 
>> written
>> somewhere in the output of "make pw"?
>>
>> I understand that this problem is not a pure Quantum Espresso 
>> problem,
>> and I have therefore also described the problem to the mailing list 
>> of
>> StarCluster.
>>
>> Thanks in advance for your help.
>>
>> Yours sincerely,
>> Torstein Fjermestad
>>
>>
>> On 17.04.2014 13:03, Axel Kohlmeyer wrote:
>>> On Thu, Apr 17, 2014 at 6:41 AM,  <torstein.fjermestad at unito.it>
>>> wrote:
>>>> Dear all,
>>>>
>>>> I recently installed QE on a virtual cluster configured with
>>>> StarCluster.
>>>> QE configures and compiles without errors. However, when I submit 
>>>> a
>>>> parallel calculation on 16 processors, the following is written 
>>>> near
>>>> the
>>>> start of the output file:
>>>>
>>>> Parallel version (MPI), running on     1 processors
>>>> The line is repeated 16 times in the output. To me it seems like I
>>>> am
>>>> actually running 16 single processor calculations that all write 
>>>> to
>>>> the
>>>> same output file (stdout in this case).
>>> this indicates that you are using an mpirun command that "belongs" 
>>> to
>>> a different MPI library than the one the pw.x you are using was
>>> compiled with. please have a close look at the version output, to 
>>> see
>>> if it is really the pw.x you expect to be using. also re-check the
>>> cluster documentation that you include the correct mpirun matching
>>> your MPI.
>>>
>>>> The way I submit this calculation, is the following:
>>>>
>>>> I write the following submit script (submit.sh):
>>>> cp /path/to/executable/pw.x
>>>> mpirun -np 16 pw.x -in input.inp
>>>>
>>> here is a problem: unlike on windows, the current directory is not
>>> part of the search path, so you would have to use './pw.x' instead 
>>> of
>>> 'pw.x'
>>> to use the pw.x directory in your current working directory (unless
>>> you have changed your profile to have '.' included in your $PATH
>>> variable, which is a very, very bad idea).
>>>
>>>> Then I submit the job with the following command:
>>>>
>>>> qsub -cwd -pe orte 16 ./submit.sh
>>>>
>>>> The queuing system of StarCluster is Open Grid Scheduler.
>>>>
>>>> For the line in the submit script, I have also tried several
>>>> alternatives such as:
>>>>
>>>> mpirun pw.x -in input.inp
>>>> mpirun pw.x -inp input.inp
>>>> mpirun -np 16 pw.x -inp input.inp
>>>> mpirun -np 16 pw.x < input.inp
>>>>
>>>> In the archives of this mailing list I have seen some similar
>>>> problems,
>>>> but in spite of this I was still not able to solve my problem.
>>>>
>>>> I would appreciate very much if someone could give me suggestions 
>>>> on
>>>> how to solve the problem.
>>>>
>>>> Thanks in advance.
>>>>
>>>> Yours sincerely,
>>>> Torstein Fjermestad
>>>> University of Turin,
>>>> Italy
>>>>
>>>>
>>>>
>>>>
>>>>
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