[Wien] Multicore on i7 iMac
pluto at physics.ucdavis.edu
pluto at physics.ucdavis.edu
Fri Jul 19 11:31:47 CEST 2013
Dear WIEN2k experts,
My GdTiO3 bulk calculation (space group 62) works well on the iMac with
GGA+U. However, when I try to add SOC there is an error after the first
iteration:
lplucin at iff1276:GTO_GGAU_SOC % more STDOUT
LAPW0 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPWSO END
LAPWSO END
LAPW2 - FERMI; weighs written
LAPW2 END
LAPW2 END
SUMPARA END
LAPW2 - FERMI; weighs written
LAPW2 END
LAPW2 END
SUMPARA END
> stop error: the required input file GTO_GGAU_SOC.indmc for the next
step could not be found
Could you advise?
Regards,
Lukasz
> Dear Prof. Blaha,
>
> Thank you for your comment, it helps.
>
> My slab was indeed wrong not having the inversion symmetry. I have now
> constructed the slab with the inversions symmetry (was found automatic by
> nn and sgroup), and the calculation is running. Actually you have
> explained that to me already in 2008 (see below)... so I'm a bit
> embarrassed :-)
>
> The calculation is for Fe slab. UG says, that it is sufficient to do SCF
> without spin-orbit, and then initialize spin-orbit and do one single SCF
> iteration with spin-orbit. Or should I converge SCF again after including
> spin-orbit? In any case, once I get the slab running properly, I am
> planning to test and compare the results.
>
> Regards,
> Lukasz
>
>
>
>
> -------- Original Message --------
> Subject: Re: [Wien] Fe slab
> Date: Fri, 04 Jul 2008 14:56:26 +0200
> From: Peter Blaha <pblaha at theochem.tuwien.ac.at>
> Reply-To: A Mailing list for WIEN2k users
> <wien at zeus.theochem.tuwien.ac.at>
> To: A Mailing list for WIEN2k users <wien at zeus.theochem.tuwien.ac.at>
>
>
> Why would you use such a struct file ?
>
> a) With limited experience, start with small models, 5 or 7 layers only.
> b) I don't know how this struct file was created, but for sure a 15
> layer Fe(001) slab can have inversion symmetry and I'm pretty sure that
> WIEN should be able to find the proper symmetry (sgroup) when you allow
> for it. Remove ALL numbering for atomes (Fe1,2,3,...) and run the
> initialization. sgroup (or nn in most cases) should always group 2 atoms
> together (make them equivalent, except the center). sgroup should also
> shift the atoms along z.
> Your calculations will be 4 times faster when you have inversion symmetry!
> c) When going for thicker slabs, you should also improve your vacuum. It
> does not make sense to go to a thick slab, but have surface-surface
> interactions through the vacuum.
> d) k-mesh: why would one use a "2" fold k-mesh in z-direction. With
> recent WIEN2k versions you can also specify a 21x21x1 mesh for kgen.
> e) Some cases may need more than 40 iterations. As long as it does not
> diverge, just continue.
> f) Eventually TEMP with some broadening (0.005) may help convergence.
> However, in particular with magnetic systems, make sure that the
> broadening does not influence your magnetism and recheck with smaller
> broadening.
>
>
>
>
>
>
>
>
>
>
>
> From this message alone, we one cannot say anything, maybe except that the
> calculations seem to have diverged (large CTEST).
>
> But when starting from a converged calculation, this is very unusual.
>
> PS: In a "slab" calculation it is almost always possible to setup the slab
> such that it has inversion symmetry and thus you would have case.in1
> instead of case.in1c.
> Inversion for slabs is a) much faster, b) avoids spurious dipoles from two
> different surfaces.
>
> On 04/17/2013 11:03 PM, pluto at physics.ucdavis.edu wrote:
>> Dear Prof. Blaha and WIEN2k experts,
>>
>> I have 4 physical cores (Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz). It
>> seems that on my compilation using HT and filling up all 8 threads makes
>> some particular calculation just a bit faster compared to the settings
>> you
>> have suggested, but with HT CPU gets more hot (fan is on more often), so
>> it makes no sense. I will use the settings you have recommended.
>>
>> I have now an error for the slab with spin-polarized but without spin
>> orbit (see below part of STDOUT file). I tried to look at old emails
>> from
>> this group, but could not quickly find a solution. Same slab has
>> converged
>> before in a non-parallel mode with spin-polarized and with spin-orbit. I
>> use cutoff 8 Ry and:
>>
>> K-VECTORS FROM UNIT:4 -11.0 5.5 933 emin/emax/nband
>>
>> in case.in1c.
>>
>> Regards,
>> Lukasz
>>
>>
>> ...
>> CORE END
>> CORE END
>> MIXER END
>> in cycle 22 ETEST: .3816818050000000 CTEST: 1.9705727
>> LAPW0 END
>> LAPW1 END
>> LAPW1 END
>> LAPW1 END
>> LAPW1 END
>> LAPW2 - FERMI; weighs written
>> LAPW2 END
>> LAPW2 END
>> SUMPARA END
>> LAPW2 - FERMI; weighs written
>> LAPW2 END
>> LAPW2 END
>> SUMPARA END
>> CORE END
>> CORE END
>> MIXER END
>> in cycle 23 ETEST: .2942263650000000 CTEST: 2.3441252
>> LAPW0 END
>> LAPW1 END
>> LAPW1 END
>> LAPW1 END
>> LAPW1 END
>> FERMI - Error
>> cp: .in.tmp: No such file or directory
>>
>>> stop error
>>
>>
>>
>>
>> How many "real" cores do you have ? Most likely only 4 (the 8 comes from
>> hyperthreading, but for numerical intensive application one should
>> probably not use hyperthreading).
>>
>> So the "best" performance can probably be reached either by:
>>
>> OMP_NUM_THREADS=2 and 2 lines in .machines or
>> OMP_NUM_THREADS=1 and 4 lines in .machines
>>
>> (it may even depend on the number of k-points in the specific case ..)
>>
>>
>>
>> On 04/16/2013 02:49 PM, pluto at physics.ucdavis.edu wrote:
>>> Dear Prof. Blaha,
>>>
>>> Thank you for the answer. In the meantime I have realized this mistake.
>>>
>>> I have now all 8 threads practically fully utilized (HT Intel i7 in
>>> iMac)
>>> for lapw1 and lapw2. It reduced the iteration from approx. 7.2min to
>>> 5.5min (compared to utilizing 4 threads only with OMP_NUM_THREADS).
>>>
>>> I think it solves my problems for now. Again thank you for your support
>>> and rapid answers.
>>>
>>> Regards,
>>> Lukasz
>>>
>>>
>>>
>>>> Your .machines file is wrong. It contains more than one hostname per
>>>> line (or has a localhost:2)
>>>>
>>>> With the proper .machines file, mpirun is not needed:
>>>> > bash: mpirun: command not found
>>>>
>>>> -------------------- .machines --------------
>>>> 1:localhost
>>>> 1:localhost
>>>>
>>>> This file with split the klist into two parts and run two lapw1-jobs
>>>> simultaneously.
>>>>
>>>> On 04/16/2013 11:48 AM, pluto at physics.ucdavis.edu wrote:
>>>>> Hello Prof. Blaha, Prof. Marks,
>>>>>
>>>>> ssh localhost works now without login!!
>>>>>
>>>>> I have more errors now when trying to run parallel mode, see below.
>>>>>
>>>>> In UG there are sections 5.5.1 (k-point parallelization) and 5.5.2
>>>>> (MPI
>>>>> parallelization). I understand these two modes are separate, and I
>>>>> would
>>>>> like to focus on k-point parallelization for now. I am not sure why
>>>>> there
>>>>> is an error regarding the mpirun. My parallel_options file is now:
>>>>>
>>>>> setenv USE_REMOTE 0
>>>>> setenv MPI_REMOTE "1"
>>>>> setenv WIEN_GRANULARITY 1
>>>>>
>>>>> But with other options I have the same error.
>>>>>
>>>>> I would appreciate if there is something obvious which I do wrong. In
>>>>> any
>>>>> case I will continue to work on the issue with my IT department here.
>>>>>
>>>>> Regards,
>>>>> Lukasz
>>>>>
>>>>>
>>>>>
>>>>> LAPW0 END
>>>>> bash: mpirun: command not found
>>>>>
>>>>> real 0m0.001s
>>>>> user 0m0.000s
>>>>> sys 0m0.000s
>>>>> Mo-bulk-so.scf1_1: No such file or directory.
>>>>> ERROR IN OPENING UNIT: 9
>>>>> FILENAME:
>>>>> ./Mo-bulk-so.vector_1
>>>>> STATUS: old FORM:unformatted
>>>>> OPEN FAILED
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------- Original Message --------
>>>>> Subject: Re: [Wien] Multicore on i7 iMac
>>>>> Date: Mon, 15 Apr 2013 08:49:39 -0500
>>>>> From: Laurence Marks <L-marks at northwestern.edu>
>>>>> Reply-To: A Mailing list for WIEN2k users
>>>>> <wien at zeus.theochem.tuwien.ac.at>
>>>>> To: A Mailing list for WIEN2k users
> <wien at zeus.theochem.tuwien.ac.at>
>>>>>
>>>>> You may also be able to turn off USE_REMOTE and MPI_REMOTE (set both
>>>>> to 0) and/or use something other than ssh to launch processes.
>>>>>
>>>>> On Mon, Apr 15, 2013 at 8:33 AM, Peter Blaha
>>>>> <pblaha at theochem.tuwien.ac.at> wrote:
>>>>>> Try it again. I think it ask this disturbing question only once !
>>>>>>
>>>>>> otherwise: you must be able to do:
>>>>>>
>>>>>> ssh localhost
>>>>>>
>>>>>> and login without any other response.
>>>>>>
>>>>>>> The authenticity of host 'localhost (::1)' can't be established.
>>>>>>> RSA key fingerprint is
>>>>>>> 50:c3:da:fa:0c:35:c5:aa:d1:b4:c1:52:a1:18:08:c2.
>>>>>>> Are you sure you want to continue connecting (yes/no)? yes
>>>>>>>
>>>>>>> ^C
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -------- Original Message --------
>>>>>>> Subject: Re: [Wien] Multicore on i7 iMac
>>>>>>> Date: Mon, 15 Apr 2013 08:16:11 +0200
>>>>>>> From: Peter Blaha <pblaha at theochem.tuwien.ac.at>
>>>>>>> Reply-To: A Mailing list for WIEN2k users
>>>>> <wien at zeus.theochem.tuwien.ac.at>
>>>>>>> To: A Mailing list for WIEN2k users
>>>>>>> <wien at zeus.theochem.tuwien.ac.at>
>>>>>>>
>>>>>>> As you could see from your "top" command, only 1 core is used.
>>>>>>>
>>>>>>> The "simplest" thing is to set:
>>>>>>>
>>>>>>> export OMP_NUM_THREADS=2 (or 4) (a commented line is already in
>>>>>>> your
>>>>>>> .bashrc after "userconfig_lapw")
>>>>>>>
>>>>>>> This will use 2 (4) cores for parts of WIEN2k which uses the
>>>>>>> mkl-library.
>>>>>>> ---------------------------
>>>>>>> Next is k-parallel mode (see UG for description), where you can
>>>>>>> use
>>>>>>> all
>>>>>>> your cores.
>>>>>>>
>>>>>>> We also have mpi-parallel, but I would not recommend it for a
>>>>>>> single
>>>>>>> mac,
>>>>>>> unless you have a problem with just one k-point.
>>>>>>>
>>>>>>> Please also notice the recent posting on the mailing-list about a
>>>>>>> recommended compiler option for a Mac (-heap-arrays), otherwise you
>>>>>>> cannot
>>>>>>> run wien2k on larger systems
>>>>>>>
>>>>>>> Peter Blaha
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> From:pluto at physics.ucdavis.edu
>>>>>>> Date:04/14/2013 07:48 PM
>>>>>>> To:"A Mailing list for WIEN2k users"
>>>>>>> <wien at zeus.theochem.tuwien.ac.at>
>>>>>>>
>>>>>>> Hello WIEN2k experts,
>>>>>>>
>>>>>>> I have a very simple question.
>>>>>>>
>>>>>>> Do I need to edit the .machines file for the multicore operation of
>>>>>>> the
>>>>>>> Intel i7 Quad Core CPU?
>>>>>>>
>>>>>>> My IT department (in FZ Juelich, Germany) has helped to compile
>>>>>>> Wien2k
>>>>>>> on
>>>>>>> an iMac with i7 CPU. It works very nice, no problem to calculate 15
>>>>>>> layer
>>>>>>> slab. However, I have a feeling, that all is done on a single core,
>>>>>>> and
>>>>>>> this is a real waste to time. I attach the screenshot of "top"
>>>>>>> program
>>>>>>> under the terminal, with lapw1c doing 100 k-points for band
>>>>>>> structure.
>>>>>>>
>>>>>>> Regards,
>>>>>>> Lukasz
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Wien mailing list
>>>>>>> Wien at zeus.theochem.tuwien.ac.at
>>>>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>>>>> SEARCH the MAILING-LIST at:
>>>>>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Wien mailing list
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>>>>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>>>>> SEARCH the MAILING-LIST at:
>>>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>>> P.Blaha
>>>>>> --------------------------------------------------------------------------
>>>>>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>>>>>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
>>>>>> Email: blaha at theochem.tuwien.ac.at WWW:
>>>>>> http://info.tuwien.ac.at/theochem/
>>>>>> --------------------------------------------------------------------------
>>>>>> _______________________________________________
>>>>>> Wien mailing list
>>>>>> Wien at zeus.theochem.tuwien.ac.at
>>>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>>>> SEARCH the MAILING-LIST at:
>>>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>>>>
>>>>>
>>>>>
>>>>> -- Professor Laurence Marks Department of Materials Science and
>>>>> Engineering Northwestern University www.numis.northwestern.edu
>>>>> 1-847-491-3996 "Research is to see what everybody else has seen, and
>>>>> to
>>>>> think what nobody else has thought" Albert Szent-Gyorgi
>>>>> _______________________________________________ Wien mailing list
>>>>> Wien at zeus.theochem.tuwien.ac.at
>>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the
>>>>> MAILING-LIST at:
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>>>>>
>>>>> _______________________________________________
>>>>> Wien mailing list
>>>>> Wien at zeus.theochem.tuwien.ac.at
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>>>>> SEARCH the MAILING-LIST at:
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>>>>>
>>>>
>>>> --
>>>>
>>>> P.Blaha
>>>> --------------------------------------------------------------------------
>>>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>>>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
>>>> Email: blaha at theochem.tuwien.ac.at WWW:
>>>> http://info.tuwien.ac.at/theochem/
>>>> --------------------------------------------------------------------------
>>>> _______________________________________________
>>>> Wien mailing list
>>>> Wien at zeus.theochem.tuwien.ac.at
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>>>> SEARCH the MAILING-LIST at:
>>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>>>
>>>
>>>
>>> _______________________________________________
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>>> SEARCH the MAILING-LIST at:
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>>>
>>
>
> --
>
> P.Blaha
> --------------------------------------------------------------------------
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: blaha at theochem.tuwien.ac.at WWW:
> http://info.tuwien.ac.at/theochem/
> --------------------------------------------------------------------------
> _______________________________________________
> Wien mailing list
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