[Nek5000-users] Run time error
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Mon Jul 23 04:25:18 CDT 2018
Thank you very much. I found the problem and I hope it should work.
Thanks for the help.
----- Mail original -----
De: "nek5000-users" <nek5000-users at lists.mcs.anl.gov>
À: "nek5000-users" <nek5000-users at lists.mcs.anl.gov>
Envoyé: Lundi 23 Juillet 2018 11:19:00
Objet: Re: [Nek5000-users] Run time error
well, you get a segfault somewhere at the end of step 5016 or beginning
of 5017. I guess you need to debug your code, first identify where it
happens and then find a solution. But this is not something that the
mailing list can help.
On 2018-07-23 11:16, nek5000-users at lists.mcs.anl.gov wrote:
>
>
> Here is the last 15 time steps,
>
>
>
> Step 5002, t= 2.5060730E-01, DT= 2.6334630E-05, C= .499 2.9631E+03 6.4746E-01
> Solving for fluid
> 5002 Helmh3 fluid 4 3.2301E-09 2.8687E-03 1.0000E-07
> 5002 reorthogo: 0
> 5002 U-PRES gmres 1 9.7902E-07 1.0848E-06 1.0000E-06 1.0687E-02 2.0345E-02
> 5002 DNORM, DIVEX 0.979017414251552405E-06 0.979017414244615416E-06
> 5002 Fluid done 2.5061E-01 1.0325E-01
> 5002 2.50607295376E-01 6.91348098900E-01 2.43521097680E-01 4.47827001220E-01 1dragx
> 5002 2.50607295376E-01 7.39003317407E-07 9.98073784120E-07 -2.59070466713E-07 1dragy
> 5002 2.50607295376E-01 -2.89434103178E-07 -2.61006442373E-07 -2.84276608050E-08 1dragz
> 5002 2.50607295376E-01 1.26466785801E-07 1.23449081749E-07 3.01770405268E-09 1torqx
> 5002 2.50607295376E-01 4.66210074735E-09 -2.18142386531E-08 2.64763394004E-08 1torqy
> 5002 2.50607295376E-01 -1.39245119998E-06 -1.37178097352E-06 -2.06702264562E-08 1torqz
> Step 5003, t= 2.5063363E-01, DT= 2.6334630E-05, C= .499 2.9636E+03 5.0625E-01
> Solving for fluid
> 5003 Helmh3 fluid 4 3.2284E-09 2.8685E-03 1.0000E-07
> 5003 reorthogo: 0
> 5003 U-PRES gmres 2 9.9844E-07 1.2476E-06 1.0000E-06 2.1245E-02 4.0459E-02
> 5003 DNORM, DIVEX 0.998438496961438229E-06 0.998438496995218115E-06
> 5003 Fluid done 2.5063E-01 1.2349E-01
> 5003 2.50633630006E-01 6.91343372331E-01 2.43530821430E-01 4.47812550901E-01 1dragx
> 5003 2.50633630006E-01 1.33883527191E-06 1.59788610149E-06 -2.59050829576E-07 1dragy
> 5003 2.50633630006E-01 -2.89455853305E-07 -2.61026965361E-07 -2.84288879440E-08 1dragz
> 5003 2.50633630006E-01 1.26408336357E-07 1.23391016237E-07 3.01732012020E-09 1torqx
> 5003 2.50633630006E-01 3.68027948823E-09 -2.27921145675E-08 2.64723940558E-08 1torqy
> 5003 2.50633630006E-01 -1.00290395946E-06 -9.82230311773E-07 -2.06736476910E-08 1torqz
> Step 5004, t= 2.5065996E-01, DT= 2.6334630E-05, C= .499 2.9641E+03 5.2639E-01
> Solving for fluid
> 5004 Helmh3 fluid 4 3.2288E-09 2.8683E-03 1.0000E-07
> 5004 reorthogo: 0
> 5004 U-PRES gmres 6 9.6173E-07 1.2811E-06 1.0000E-06 6.3583E-02 1.2089E-01
> 5004 DNORM, DIVEX 0.961733547539616817E-06 0.961733547511125381E-06
> 5004 Fluid done 2.5066E-01 2.0408E-01
> 5004 2.50659964636E-01 6.91338822904E-01 2.43540719422E-01 4.47798103482E-01 1dragx
> 5004 2.50659964636E-01 1.24874530961E-06 1.50777140270E-06 -2.59026093090E-07 1dragy
> 5004 2.50659964636E-01 -2.89465334698E-07 -2.61035223976E-07 -2.84301107230E-08 1dragz
> 5004 2.50659964636E-01 1.26265232830E-07 1.23248343597E-07 3.01688923232E-09 1torqx
> 5004 2.50659964636E-01 3.78573331524E-09 -2.26826739824E-08 2.64684072976E-08 1torqy
> 5004 2.50659964636E-01 -1.06339152264E-06 -1.04271435718E-06 -2.06771654598E-08 1torqz
> Step 5005, time= 2.50686E-01, DT= 2.633E-05
> Solving for fluid
> 5005 Helmh3 fluid 4 3.2297E-09 2.8681E-03 1.0000E-07
> 5005 reorthogo: 0
> 5005 U-PRES gmres 1 9.9687E-07 1.3440E-06 1.0000E-06 1.0692E-02 2.0364E-02
> 5005 DNORM, DIVEX 0.996871725480759347E-06 0.996871725467780684E-06
> 5005 Fluid done 2.5069E-01 1.0281E-01
> 5005 2.50686299266E-01 6.91334194687E-01 2.43550535727E-01 4.47783658960E-01 1dragx
> 5005 2.50686299266E-01 1.09616851227E-06 1.35517473326E-06 -2.59006220992E-07 1dragy
> 5005 2.50686299266E-01 -2.89485215237E-07 -2.61053885728E-07 -2.84313295093E-08 1dragz
> 5005 2.50686299266E-01 1.26237500989E-07 1.23221079188E-07 3.01642180084E-09 1torqx
> 5005 2.50686299266E-01 3.39617827483E-09 -2.30681746374E-08 2.64643529123E-08 1torqy
> 5005 2.50686299266E-01 -1.14135276097E-06 -1.12067128456E-06 -2.06814764025E-08 1torqz
> Step 5006, time= 2.50713E-01, DT= 2.633E-05
> Solving for fluid
> 5006 Helmh3 fluid 4 3.2410E-09 2.8679E-03 1.0000E-07
> 5006 reorthogo: 0
> 5006 U-PRES gmres 5 8.8161E-07 2.1599E-06 1.0000E-06 5.2977E-02 1.0074E-01
> 5006 DNORM, DIVEX 0.881613814330421712E-06 0.881613814311075056E-06
> 5006 Fluid done 2.5071E-01 1.8287E-01
> 5006 2.50712633896E-01 6.91329604485E-01 2.43560387135E-01 4.47769217350E-01 1dragx
> 5006 2.50712633896E-01 1.43777322353E-06 1.69676731276E-06 -2.58994089237E-07 1dragy
> 5006 2.50712633896E-01 -2.89383022126E-07 -2.60950472113E-07 -2.84325500128E-08 1dragz
> 5006 2.50712633896E-01 1.27224824060E-07 1.24208987648E-07 3.01583641282E-09 1torqx
> 5006 2.50712633896E-01 4.44760336876E-09 -2.20126903424E-08 2.64602937112E-08 1torqy
> 5006 2.50712633896E-01 -9.84677597850E-07 -9.63990647078E-07 -2.06869507719E-08 1torqz
> Step 5007, time= 2.50739E-01, DT= 2.633E-05
> Solving for fluid
> 5007 Helmh3 fluid 4 3.2591E-09 2.8677E-03 1.0000E-07
> 5007 reorthogo: 0
> 5007 U-PRES gmres 18 9.5587E-07 2.2352E-06 1.0000E-06 1.9039E-01 3.6388E-01
> 5007 DNORM, DIVEX 0.955873119537653350E-06 0.955873119540012972E-06
> 5007 Fluid done 2.5074E-01 4.4597E-01
> 5007 2.50738968526E-01 6.91324862597E-01 2.43570083958E-01 4.47754778640E-01 1dragx
> 5007 2.50738968526E-01 1.20307297002E-06 1.46204641771E-06 -2.58973447692E-07 1dragy
> 5007 2.50738968526E-01 -2.89417069365E-07 -2.60983294754E-07 -2.84337746105E-08 1dragz
> 5007 2.50738968526E-01 1.26831695982E-07 1.23816089695E-07 3.01560628701E-09 1torqx
> 5007 2.50738968526E-01 5.02139157632E-09 -2.14350565571E-08 2.64564481335E-08 1torqy
> 5007 2.50738968526E-01 -7.82904411358E-07 -7.62214464704E-07 -2.06899466533E-08 1torqz
> Step 5008, time= 2.50765E-01, DT= 2.633E-05
> Solving for fluid
> 5008 Helmh3 fluid 4 3.2323E-09 2.8676E-03 1.0000E-07
> 5008 reorthogo: 0
> 5008 U-PRES gmres 20 9.0835E-07 2.3092E-06 1.0000E-06 2.1137E-01 4.0465E-01
> 5008 DNORM, DIVEX 0.908352025925184963E-06 0.908352025900079859E-06
> 5008 Fluid done 2.5077E-01 4.8687E-01
> 5008 2.50765303155E-01 6.91321406040E-01 2.43581063104E-01 4.47740342936E-01 1dragx
> 5008 2.50765303155E-01 2.74890528450E-06 3.00786518867E-06 -2.58959904170E-07 1dragy
> 5008 2.50765303155E-01 -2.89468785686E-07 -2.61033794512E-07 -2.84349911742E-08 1dragz
> 5008 2.50765303155E-01 1.26559461360E-07 1.23544367051E-07 3.01509430869E-09 1torqx
> 5008 2.50765303155E-01 3.49653887985E-09 -2.29559476187E-08 2.64524864985E-08 1torqy
> 5008 2.50765303155E-01 -7.50639979415E-07 -7.29944028055E-07 -2.06959513604E-08 1torqz
> Step 5009, time= 2.50792E-01, DT= 2.633E-05
> Solving for fluid
> 5009 Helmh3 fluid 4 3.2421E-09 2.8674E-03 1.0000E-07
> 5009 reorthogo: 0
> 5009 U-PRES gmres 11 9.8214E-07 1.8725E-06 1.0000E-06 1.1646E-01 2.2180E-01
> 5009 DNORM, DIVEX 0.982139696736965556E-06 0.982139696702795612E-06
> 5009 Fluid done 2.5079E-01 3.0396E-01
> 5009 2.50791637785E-01 6.91315353362E-01 2.43589443294E-01 4.47725910069E-01 1dragx
> 5009 2.50791637785E-01 2.33682354097E-07 4.92616702902E-07 -2.58934348805E-07 1dragy
> 5009 2.50791637785E-01 -2.89487372587E-07 -2.61051167514E-07 -2.84362050730E-08 1dragz
> 5009 2.50791637785E-01 1.26715143423E-07 1.23700456898E-07 3.01468652550E-09 1torqx
> 5009 2.50791637785E-01 4.22547531068E-09 -2.22232504981E-08 2.64487258088E-08 1torqy
> 5009 2.50791637785E-01 -1.15647147333E-06 -1.13577307601E-06 -2.06983973201E-08 1torqz
> Step 5010, time= 2.50818E-01, DT= 2.633E-05
> Solving for fluid
> 5010 Helmh3 fluid 4 3.2557E-09 2.8672E-03 1.0000E-07
> 5010 reorthogo: 0
> 5010 U-PRES gmres 11 9.7871E-07 1.4643E-06 1.0000E-06 1.1647E-01 2.2184E-01
> 5010 DNORM, DIVEX 0.978713374125623103E-06 0.978713374145168176E-06
> 5010 Fluid done 2.5082E-01 3.0435E-01
> 5010 2.50817972415E-01 6.91311580633E-01 2.43600100518E-01 4.47711480115E-01 1dragx
> 5010 2.50817972415E-01 1.59900014887E-07 4.18822790393E-07 -2.58922775507E-07 1dragy
> 5010 2.50817972415E-01 -2.89375448630E-07 -2.60938030333E-07 -2.84374182969E-08 1dragz
> 5010 2.50817972415E-01 1.27146994632E-07 1.24132866323E-07 3.01412830971E-09 1torqx
> 5010 2.50817972415E-01 3.86222016209E-09 -2.25823729936E-08 2.64445931557E-08 1torqy
> 5010 2.50817972415E-01 -1.75555627025E-06 -1.73485211374E-06 -2.07041565045E-08 1torqz
> Step 5011, time= 2.50844E-01, DT= 2.633E-05
> Solving for fluid
> 5011 Helmh3 fluid 4 3.2445E-09 2.8670E-03 1.0000E-07
> 5011 reorthogo: 0
> 5011 U-PRES gmres 3 9.8584E-07 1.4800E-06 1.0000E-06 3.1853E-02 6.0543E-02
> 5011 DNORM, DIVEX 0.985840182003174908E-06 0.985840181989730166E-06
> 5011 Fluid done 2.5084E-01 1.4313E-01
> 5011 2.50844307045E-01 6.91307006675E-01 2.43609953588E-01 4.47697053087E-01 1dragx
> 5011 2.50844307045E-01 1.19376086041E-06 1.45267214241E-06 -2.58911282002E-07 1dragy
> 5011 2.50844307045E-01 -2.89518324212E-07 -2.61079698806E-07 -2.84386254057E-08 1dragz
> 5011 2.50844307045E-01 1.26538004874E-07 1.23524339762E-07 3.01366511130E-09 1torqx
> 5011 2.50844307045E-01 3.50102159475E-09 -2.29395957657E-08 2.64406173605E-08 1torqy
> 5011 2.50844307045E-01 -1.15532190933E-06 -1.13461210583E-06 -2.07098035033E-08 1torqz
> Step 5012, time= 2.50871E-01, DT= 2.633E-05
> Solving for fluid
> 5012 Helmh3 fluid 4 3.2319E-09 2.8668E-03 1.0000E-07
> 5012 reorthogo: 0
> 5012 U-PRES gmres 5 9.5655E-07 1.5593E-06 1.0000E-06 5.3007E-02 1.0077E-01
> 5012 DNORM, DIVEX 0.956545576069178046E-06 0.956545576089094120E-06
> 5012 Fluid done 2.5087E-01 1.8317E-01
> 5012 2.50870641675E-01 6.91302353472E-01 2.43619724517E-01 4.47682628955E-01 1dragx
> 5012 2.50870641675E-01 9.11226385968E-07 1.17011932510E-06 -2.58892939132E-07 1dragy
> 5012 2.50870641675E-01 -2.89432479322E-07 -2.60992645110E-07 -2.84398342115E-08 1dragz
> 5012 2.50870641675E-01 1.27073588160E-07 1.24060305180E-07 3.01328297995E-09 1torqx
> 5012 2.50870641675E-01 4.82584823477E-09 -2.16110082294E-08 2.64368564641E-08 1torqy
> 5012 2.50870641675E-01 -1.17588004419E-06 -1.15516521543E-06 -2.07148287560E-08 1torqz
> Step 5013, time= 2.50897E-01, DT= 2.633E-05
> Solving for fluid
> 5013 Helmh3 fluid 4 3.2287E-09 2.8666E-03 1.0000E-07
> 5013 reorthogo: 0
> 5013 U-PRES gmres 2 9.5713E-07 1.2499E-06 1.0000E-06 2.1281E-02 4.0455E-02
> 5013 DNORM, DIVEX 0.957134034958327482E-06 0.957134034942669443E-06
> 5013 Fluid done 2.5090E-01 1.2291E-01
> 5013 2.50896976305E-01 6.91297902394E-01 2.43629694642E-01 4.47668207752E-01 1dragx
> 5013 2.50896976305E-01 6.14485394545E-07 8.73364124021E-07 -2.58878729476E-07 1dragy
> 5013 2.50896976305E-01 -2.89427209756E-07 -2.60986168111E-07 -2.84410416450E-08 1dragz
> 5013 2.50896976305E-01 1.27234413257E-07 1.24221620967E-07 3.01279228989E-09 1torqx
> 5013 2.50896976305E-01 4.31696301276E-09 -2.21160739899E-08 2.64330370026E-08 1torqy
> 5013 2.50896976305E-01 -1.42260629409E-06 -1.40188632877E-06 -2.07199653204E-08 1torqz
> Step 5014, time= 2.50923E-01, DT= 2.633E-05
> Solving for fluid
> 5014 Helmh3 fluid 4 3.2263E-09 2.8664E-03 1.0000E-07
> 5014 reorthogo: 0
> 5014 U-PRES gmres 8 9.8677E-07 1.7248E-06 1.0000E-06 8.4772E-02 1.6120E-01
> 5014 DNORM, DIVEX 0.986772488382639047E-06 0.986772488403645888E-06
> 5014 Fluid done 2.5092E-01 2.4381E-01
> 5014 2.50923310934E-01 6.91293384013E-01 2.43639594562E-01 4.47653789451E-01 1dragx
> 5014 2.50923310934E-01 1.72936300045E-06 1.98822152750E-06 -2.58858527045E-07 1dragy
> 5014 2.50923310934E-01 -2.89481745085E-07 -2.61039500236E-07 -2.84422448489E-08 1dragz
> 5014 2.50923310934E-01 1.27107116717E-07 1.24094741942E-07 3.01237477520E-09 1torqx
> 5014 2.50923310934E-01 3.69583275881E-09 -2.27333237863E-08 2.64291565451E-08 1torqy
> 5014 2.50923310934E-01 -8.03349762879E-07 -7.82624357654E-07 -2.07254052255E-08 1torqz
> Step 5015, time= 2.50950E-01, DT= 2.633E-05
> Solving for fluid
> 5015 Helmh3 fluid 4 3.2296E-09 2.8662E-03 1.0000E-07
> 5015 reorthogo: 0
> 5015 U-PRES gmres 6 9.0937E-07 1.6936E-06 1.0000E-06 6.3624E-02 1.2093E-01
> 5015 DNORM, DIVEX 0.909368958162372379E-06 0.909368958244082366E-06
> 5015 Fluid done 2.5095E-01 2.0366E-01
> 5015 2.50949645564E-01 6.91288889659E-01 2.43649515583E-01 4.47639374076E-01 1dragx
> 5015 2.50949645564E-01 2.90375481535E-06 3.16258818400E-06 -2.58833368651E-07 1dragy
> 5015 2.50949645564E-01 -2.89416582294E-07 -2.60973134708E-07 -2.84434475857E-08 1dragz
> 5015 2.50949645564E-01 1.27171125092E-07 1.24159210559E-07 3.01191453351E-09 1torqx
> 5015 2.50949645564E-01 3.80951637878E-09 -2.26155828231E-08 2.64250992019E-08 1torqy
> 5015 2.50949645564E-01 -7.71080501129E-08 -5.63790769972E-08 -2.07289731157E-08 1torqz
> Step 5016, time= 2.50976E-01, DT= 2.633E-05
> Solving for fluid
> 5016 Helmh3 fluid 4 3.2378E-09 2.8660E-03 1.0000E-07
> 5016 reorthogo: 0
> 5016 U-PRES gmres 2 8.5015E-07 1.3656E-06 1.0000E-06 2.1316E-02 4.0472E-02
> 5016 DNORM, DIVEX 0.850149772194823341E-06 0.850149772234970797E-06
> 5016 Fluid done 2.5098E-01 1.2322E-01
> 5016 2.50975980194E-01 6.91284214594E-01 2.43659253020E-01 4.47624961574E-01 1dragx
> 5016 2.50975980194E-01 1.87017133482E-06 2.12898116805E-06 -2.58809833233E-07 1dragy
> 5016 2.50975980194E-01 -2.89458661275E-07 -2.61014009813E-07 -2.84446514627E-08 1dragz
> 5016 2.50975980194E-01 1.27081549294E-07 1.24070042436E-07 3.01150685798E-09 1torqx
> 5016 2.50975980194E-01 2.90577561646E-09 -2.35150990040E-08 2.64208746205E-08 1torqy
> 5016 2.50975980194E-01 -7.33394593524E-07 -7.12661120859E-07 -2.07334726643E-08 1torqz
> 2018-07-22 09:30:52.570 (WARN ) [0xffef6aa91b0] :497945:ibm.runjob.client.Job: terminated by signal 11
> 2018-07-22 09:30:52.570 (WARN ) [0xffef6aa91b0] :497945:ibm.runjob.client.Job: abnormal termination by signal 11 from rank 1040
>
> ----- Mail original -----
> De: "nek5000-users" <nek5000-users at lists.mcs.anl.gov>
> À: "nek5000-users" <nek5000-users at lists.mcs.anl.gov>
> Envoyé: Lundi 23 Juillet 2018 10:58:37
> Objet: Re: [Nek5000-users] Run time error
>
> can you perhaps post the last 20 or so lines of your output?
>
> This appears more like a problem of your system. Did you check potential
> standard error output?
>
> On 2018-07-23 10:56, nek5000-users at lists.mcs.anl.gov wrote:
>> Hi Neks,
>>
>> I am facing an error while running the simulation which I never had before.
>>
>> after 5001 time step the CFL number disappears and it gives an error
>> stops running.
>>
>> (It is not CFL blowing. I mean if CFL blows it will show something like
>> CFL : ******* right? In my case it is not like this. The CFL dis appears
>> it is not even showing the CFL letters. ) Also it saves my output files
>> unto there.
>>
>>
>> Any one had the same problem before?
>>
>> Thank you
>>
>> Sijo
>>
>>
>> _______________________________________________
>> Nek5000-users mailing list
>> Nek5000-users at lists.mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>
> _______________________________________________
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