[gpaw-users] questions about GPAW installation on a supercomputer

[Vladislav Ivanistsev]

Thank you for the help, Marcin
Archie-West is indeed based on modules. As i understood, it is possible to
install separately different GPAW installations and test them one after an
other.


On Wed, Jul 11, 2012 at 2:46 PM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>wrote:

> Hi,
>
> measuring code performance is tricky.
> Some combinations of compiler/libraries are fast but result in an unstable
> program (see for example
> https://wiki.fysik.dtu.dk/**gpaw/devel/benchmarks.html#**
> dual-socket-quad-core-64-bit-**intel-nehalem-xeon-x5570-quad-**
> core-2-93-ghz-3-gb-ram-per-**core-el5<https://wiki.fysik.dtu.dk/gpaw/devel/benchmarks.html#dual-socket-quad-core-64-bit-intel-nehalem-xeon-x5570-quad-core-2-93-ghz-3-gb-ram-per-core-el5>
> ).
>
> The system (Archie-West) is probably managed using modules.
> Here are example instructions (https://wiki.fysik.dtu.dk/**
> gpaw/install/Linux/sun_chpc.**html<https://wiki.fysik.dtu.dk/gpaw/install/Linux/sun_chpc.html>)
> how to install ase/gpaw using modules.
> That with a small change in the modulefiles name for gpaw will allow you
> to easily switch between different gpaw versions
> in order to compare stability/performance.
>
> Specific software recommendations:
> I'm note sure about openmpi, just use the latest released one.
>
> Most likely you will have to build your own numpy, use 1.6.1 or later.
>
> For GPAW I would recommend first trying the following combination:
> the latest gcc available on the cluster + the corresponding acml.
> The customize.py will be similar to this: https://trac.fysik.dtu.dk/**
> projects/gpaw/browser/trunk/**doc/install/Linux/Niflheim/**
> el5-xeon-gcc43-acml-4.3.0.py<https://trac.fysik.dtu.dk/projects/gpaw/browser/trunk/doc/install/Linux/Niflheim/el5-xeon-gcc43-acml-4.3.0.py>
>
> Later you can try open64 4.2.4 + acml 4.4.0 (if you plan to run
> calculations with > 500 bands also scalapack 2.0.2).
> The customize will be similar to this one:
> https://trac.fysik.dtu.dk/**projects/gpaw/browser/trunk/**
> doc/install/Linux/Niflheim/**el5-xeon-open64-acml-4.4.0-**
> acml-4.4.0-hdf-SL-2.0.1.py<https://trac.fysik.dtu.dk/projects/gpaw/browser/trunk/doc/install/Linux/Niflheim/el5-xeon-open64-acml-4.4.0-acml-4.4.0-hdf-SL-2.0.1.py>
>
> I would recommend trying also the latest releases of open64/acml.
>
> Most likely there will be intel mkl installed on the cluster.
> Consider it with intel (https://wiki.fysik.dtu.dk/**
> gpaw/install/Linux/SUNCAT/**SUNCAT.html<https://wiki.fysik.dtu.dk/gpaw/install/Linux/SUNCAT/SUNCAT.html>)
> or gcc compilers
> (https://trac.fysik.dtu.dk/**projects/gpaw/browser/trunk/**
> doc/install/Linux/Niflheim/**el5-xeon-gcc43-mkl-10.3.1.107.**py<https://trac.fysik.dtu.dk/projects/gpaw/browser/trunk/doc/install/Linux/Niflheim/el5-xeon-gcc43-mkl-10.3.1.107.py>
> )
>
> The first thing to do for each version is to test the installation:
> https://wiki.fysik.dtu.dk/**gpaw/install/**installationguide.html#run-**
> the-tests<https://wiki.fysik.dtu.dk/gpaw/install/installationguide.html#run-the-tests>
> (first on one core, and then on the available number of cores per node,
> but not larger than 8),
> then you can use for example this scalability test
> https://wiki.fysik.dtu.dk/**gpaw/devel/benchmarks.html#**
> medium-size-system<https://wiki.fysik.dtu.dk/gpaw/devel/benchmarks.html#medium-size-system>
> Make sure to run each test few times (take average, or the fastest run) on
> the nodes exclusively reserved for you when collecting timing results.
>
> Marcin
>
>
> On 07/11/12 14:58, Ole Holm Nielsen wrote:
>
>> Dear Vladislav,
>>
>> I recommend you to ask the gpaw-users mailing list.  I cannot help you.
>>
>> Best regards,
>> Ole
>>
>> On 07/11/2012 02:56 PM, Vladislav Ivanistsev wrote:
>>
>>> Dear Ole,
>>> I rely on experience asking for a council about GPAW installation on
>>> Archie-West<http://www.archie-**west.ac.uk/<http://www.archie-west.ac.uk/>
>>> >.
>>>
>>> Would it be most efficient to install GPAW 0.9
>>> (lapack;blas/scalapack+**openmpi) at Intel Xeon (X5650,E7-430) under
>>> Scientific Linux? Might ACML be better than Lapack in this case? Is the
>>> difference between openmpi 1.4.5 and 1.6.0 important for GPAW
>>> performance? Are there any special options to optimize installation for
>>> Xeon?
>>>
>>> Sincerely yours,
>>> --
>>> M.Sc. Vladislav Ivaništšev
>>> Institute of Chemistry, University of Tartu
>>> Ravila 14a, 50411, Tartu, Estonia
>>> +372 55 685357
>>>
>>>
>
> --
> *************************************
>
> Marcin Dulak
> Technical University of Denmark
> Department of Physics
> Building 307, Room 229
> DK-2800 Kongens Lyngby
> Denmark
> Tel.: (+45) 4525 3157
> Fax.: (+45) 4593 2399
> email: Marcin.Dulak at fysik.dtu.dk
>
> *************************************
>
>


-- 
M.Sc. Vladislav Ivaništšev
Institute of Chemistry, University of Tartu
Ravila 14a, 50411, Tartu, Estonia
+372 55 685357
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