[Wien] Errori in mini
shamik chakrabarti
shamikphy at gmail.com
Fri Apr 4 11:23:23 CEST 2014
Dear Prof. Blaha Sir,
Thank you for your response. We have started the calculation by
following your suggestions. But as we are using MSR1a instead of
min_lapw...it may now take more time than earlier.
We have actually 16 cpus in our system & I have set OMP_NUM_THREADS=8 & for
a single calculation we are getting up to 800% usage. However, if we start
another calculation it then takes rest of the cpus and we can get all the
cpus running with two simultaneous calculation divided in 16 cpus with 800%
for each calculation. I have changed OMP_NUM_THREADS value starting from 8
to 16 with gradual increase, but the cpu usage remain same for all the
cases.
Yes, we should look for k-parallel run for optimum use of our
resources....but at the moment I don't have any expertise over that kind of
installation. We will try to installed k-parallelization with the help of
your suggestions and surely will try to improve calculation speed.
Thank you Sir....thank your for all your suggestions.
with regards,
On Fri, Apr 4, 2014 at 12:48 PM, Peter Blaha
<pblaha at theochem.tuwien.ac.at>wrote:
> The message does not say anything about the reason. You have to search for
> other messages with more information.
>
> My suggestion: MSR1a is MUCH more stable for an inexperienced user then
> min_lapw, which has problems when its "history" contains a "bad point".
>
> I suggest:
>
> cp case.inm case.inm_msr1a
> edit case.inm_msr1a and put MSR1a (instead of MSR1)
>
> in your optimize.job script:
>
> comment out the line min_lapw .....
> instead, activate again runsp -orb -fc 1 -cc 0.001
> and insert the following line just BEFORE the runsp line:
> cp case.inm_msr1a case.inm
>
>
> PS: from your dayfile I can see:
>
> > lapw1 -dn -orb -c (20:18:44)
> > 1603.746u 24.052s 4:26.95 609.7%0+0k 0+382600io 0pf+0w
>
> the 600% tells me that you are using OMP_NUM_THREADS=6
> which is completely useless. Set it to 2 and do a
> k-parallel run (study the UG about parallelization) and test it on a small
> testcase.
> I suppose you installed wien2k using "shared memory" machine ?
> Then you basically need to create .machines file with 3 lines:
> 1:localhost
> 1:localhost
> 1:localhost
>
> (and together with OMP_NUM_THREADS=2 you will use all 6 cores and your
> time will go down from 4:30 to 1:30 for an lapw1 step.
>
>
>
>
> On 04/04/2014 05:55 AM, shamik chakrabarti wrote:
>
>> Dear Prof. Blaha Sir,
>>
>> Sorry to bother you again. But our calculation again
>> get stopped after 4th iteration with the following message.
>>
>> stop error
>>
>> error: command /usr/local/WIEN2k/mini mini.def failed
>> > mini(20:24:31) 0.004u 0.003s 0:00.03 0.0%0+0k 2472+48io 11pf+0w
>>
>> > stop
>>
>> :CHARGE convergence: 0 0.0000 .0002465
>> :ENERGY convergence: 0 0 .0000073950000000
>> > mixer -orb(20:24:29) 7.820u 0.390s 0:01.65 497.5%0+0k 168+40568io
>> 1pf+0w
>> > lcore -dn(20:24:29) 0.046u 0.003s 0:00.05 80.0%0+0k 0+656io 0pf+0w
>> > lcore -up(20:24:29) 0.045u 0.006s 0:00.05 80.0%0+0k 0+656io 0pf+0w
>> > lapwdm -dn -c (20:24:27) 8.644u 0.378s 0:01.64 549.3%0+0k 0+48io
>> 0pf+0w
>> > lapwdm -up -c (20:24:25) 9.470u 0.403s 0:01.64 601.8%0+0k 0+48io
>>
>> 0pf+0w
>> > lapw2 -dn -c -orb (20:23:35) 282.734u 8.097s 0:49.73 584.7%0+0k
>> 0+9816io 0pf+0w
>> > lapw2 -up -c -orb (20:22:53) 226.301u 6.095s 0:42.32 549.1%0+0k
>> 0+9824io 0pf+0w
>> 1524.395u 21.656s 4:09.36 620.0%0+0k 0+385000io 0pf+0w
>>
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> > lapw1 -dn -orb -c (20:18:44) _nb in zhcgst.F 640
>> 128
>> 1603.746u 24.052s 4:26.95 609.7%0+0k 0+382600io 0pf+0w
>>
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> _nb in zhcgst.F 640 128
>> > lapw1 -up -orb -c (20:14:17) _nb in zhcgst.F 640
>> 128
>> > orb -dn (20:14:17) 0.002u 0.002s 0:00.00 0.0%0+0k 0+32io 0pf+0w
>> > orb -up (20:14:17) 0.002u 0.000s 0:00.00 0.0%0+0k 0+32io 0pf+0w
>>
>> :FORCE convergence: 1 1.0 .010 XCO .009 XCO .037 XCO .013 XCO .031 XCO
>> .014 XCO
>> > lapw0 (20:14:08) 8.316u 0.047s 0:08.36 99.8%0+0k 0+16424io 0pf+0w
>>
>>
>> cycle 4 (Thu Apr 3 20:14:08 IST 2014) (37/96 to go)
>>
>> *We have checked case.scf_mini and the forces in the structure are as
>> given below:*
>>
>>
>> TOTAL FORCE IN mRy/a.u. = |F| Fx Fy Fz
>> with/without FOR in
>> :FOR001: 1.ATOM 16.382428 -2.026946 -1.179494
>> 16.213705 total forces
>> :FOR002: 2.ATOM 13.581345 13.580984 0.098977
>> 0.000000 total forces
>> :FOR003: 3.ATOM 9.631644 6.298244 7.287022
>> 0.000000 total forces
>> :FOR004: 4.ATOM 9.227031 -1.691938 -2.752735
>> -8.642795 total forces
>> :FOR005: 5.ATOM 3.096054 -1.485397 2.716458
>> 0.000000 total forces
>> :FOR006: 6.ATOM 27.808540 -10.866967 -25.597343
>> 0.000000 total forces
>>
>> Sir now what could be the reason for this failure. Looking forward to
>> your reply eagerly
>>
>> Thanks in advance,
>>
>> with regards.
>>
>>
>> On Thu, Apr 3, 2014 at 8:19 PM, shamik chakrabarti <shamikphy at gmail.com
>> <mailto:shamikphy at gmail.com>> wrote:
>>
>> Dear Prof. Peter Blaha & Gavin Abo Sir,
>>
>> Thanks for your responses. Yes Prof. Blaha is right. It
>> was indeed the problem. We have removed case.scf and rerun the
>> calculation & now it is running smoothly. Thank you Sir.
>>
>> with regards,
>>
>>
>> On Thu, Apr 3, 2014 at 7:34 PM, Peter Blaha
>> <pblaha at theochem.tuwien.ac.at <mailto:pblaha at theochem.tuwien.ac.at>>
>>
>> wrote:
>>
>> You are using min_lapw ?
>>
>> I suggest:
>>
>> When the scf cycle crashes after a few steps and you restart,
>> you have to remove case.scf before resubmission. Otherwise it
>> attempts to start immediately the min program and generates a
>> new structure (with non-converged forces).
>>
>>
>>
>>
>> On 04/03/2014 02:34 PM, shamik chakrabarti wrote:
>>
>> Dear wien2k users,
>>
>> We are working on a Li based silicate materials. We
>> are trying to
>> do simultaneous optimization of lattice parameters and atomic
>> coordinates. For that we are using "Option 6" in volume
>> optimize program
>> while edited optimized.job to perform simultaneous force
>> minimization.
>> The calculation was run smoothly up to 2 structures i.e,
>> case_abc_1.0
>> and case_abc_2.0. Then due to power failure the calculation
>> was remain
>> stopped for several hours.. We restarted the calculation by
>> putting # to
>> the two lines corresponding to 1st and 2nd structure in
>> optimize.job...such that the calculation starts from the
>> structure
>> case_abc_3.0....However, while running for 3rd structure the
>> following
>> display came in "show dayfile" option.
>>
>> ERROR status in case_abc___3.0
>> mini 00000000004035D9 Unknown
>> Unknown Unknown
>> libc.so.6 000000349521ECDD Unknown
>> Unknown Unknown
>> mini 00000000004036E6 Unknown
>> Unknown Unknown
>> mini 0000000000412AA6 MAIN__
>> 25 mini.f
>> mini 000000000040C6AB haupt_
>> 593 haupt.f
>> mini 000000000041A39F wrtscf_
>> 23 wrtscf.f
>> mini 0000000000451F5A Unknown
>> Unknown Unknown
>> mini 0000000000453C1E Unknown
>> Unknown Unknown
>> Image PC Routine Line
>> Source
>> forrtl: severe (64): input conversion error, unit -5, file
>> Internal
>> Formatted Read
>> 3.887u 0.013s 0:03.90 99.7%0+0k 0+11912io 0pf+0w
>> DSTART ENDS
>> 3.879u 0.008s 0:03.88 99.7%0+0k 0+11904io 0pf+0w
>> DSTART ENDS
>> 3.879u 0.011s 0:03.89 99.7%0+0k 0+11904io 0pf+0w
>>
>> DSTART ENDS
>> clmextrapol_lapw has generated a new case.clmdn
>> 0.196u 0.007s 0:00.20 95.0%0+0k 0+8032io 0pf+0w
>> 3.888u 0.015s 0:03.90 99.7%0+0k 0+13528io 0pf+0w
>>
>> DSTART ENDS
>> running dstart in single mode
>> clmextrapol_lapw has generated a new case.clmup
>> 0.196u 0.010s 0:00.20 100.0%0+0k 0+8032io 0pf+0w
>> 3.929u 0.020s 0:03.94 100.0%0+0k 0+13528io 0pf+0w
>>
>> DSTART ENDS
>> running dstart in single mode
>> clmextrapol_lapw has generated a new case.clmsum
>> 0.195u 0.004s 0:00.20 95.0%0+0k 0+8032io 0pf+0w
>> 3.923u 0.017s 0:03.94 99.7%0+0k 0+13528io 0pf+0w
>>
>> DSTART ENDS
>> running dstart in single mode
>> 3.888u 0.003s 0:03.89 99.7%0+0k 0+11904io 0pf+0w
>> DSTART ENDS
>> 3.895u 0.010s 0:03.91 99.7%0+0k 0+11904io 0pf+0w
>> DSTART ENDS
>> 3.934u 0.010s 0:03.94 100.0%0+0k 0+11912io 0pf+0w
>>
>> DSTART ENDS
>>
>>
>> we are using wien2k 13.1
>>
>> What could be the possible reasons for this error?.any
>> response in this
>> regard will be fruitful for us. Thanks in advance.
>>
>> with regards,
>> --
>> Shamik Chakrabarti
>> Senior Research Fellow
>> Dept. of Physics & Meteorology
>> Material Processing & Solid State Ionics Lab
>> IIT Kharagpur
>> Kharagpur 721302
>> INDIA
>>
>>
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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
>> <mailto:blaha at theochem.tuwien.ac.at> WWW:
>> http://info.tuwien.ac.at/__theochem/
>> <http://info.tuwien.ac.at/theochem/>
>> ------------------------------__----------------------------
>> --__--------------
>>
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>>
>>
>>
>>
>> --
>> Shamik Chakrabarti
>> Senior Research Fellow
>> Dept. of Physics & Meteorology
>> Material Processing & Solid State Ionics Lab
>> IIT Kharagpur
>> Kharagpur 721302
>> INDIA
>>
>>
>>
>>
>> --
>> Shamik Chakrabarti
>> Senior Research Fellow
>> Dept. of Physics & Meteorology
>> Material Processing & Solid State Ionics Lab
>> IIT Kharagpur
>> Kharagpur 721302
>> INDIA
>>
>>
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
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>> SEARCH the MAILING-LIST at: http://www.mail-archive.com/
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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/
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--
Shamik Chakrabarti
Senior Research Fellow
Dept. of Physics & Meteorology
Material Processing & Solid State Ionics Lab
IIT Kharagpur
Kharagpur 721302
INDIA
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