Hi Paolo,
I sent this email a few days ago, along with the input file and
pseudopotentials. It was rejected because of size. I am resending with
only the input file:
The system I am simulating is a bit big, so I didn't share it.
Unfortunately I was not able to reproduce the error with a smaller
system. Neither the problem is about the system itself -I can run the
dynamics using the usual sd/damp/verlet way.
I am attached the relevant files anyway, in case someone would be
interested in help me spotting the problem.
Best,
Sencer
On Fri, Jul 8, 2016 at 3:44 AM, Paolo Giannozzi <[email protected]>
wrote:
Please provide an example that can be run
Paolo
On Thu, Jul 7, 2016 at 11:33 PM, Sencer Selcuk
<[email protected]> wrote:
Dear all,
I am trying to use 'cg' for electronic minimization in cp.x
(version 5.4.0).
I have these in the &electrons section of my input file:
electron_dynamics = 'cg'
tcg = .TRUE.
orthogonalization = 'Gram-Schmidt'
passop = 0.1
However, the program dies after saying "PERFORMING CONJUGATE
GRADIENT
MINIMIZATION OF EL. STATES" with the following error message:
Error in routine cft_1z (5):
stopped in DftiComputeBackward
I am using QE compiled with the FFT module of Intel MKL. However, I
tried
with FFTW3 and my calculation died, similarly with the following
error:
*** Error in
`/global/homes/s/sselcuk/software/cori/espresso-fftw/bin/cp.x':
corrupted double-linked list: 0x00000000077c77d0 ***
*** Error in
`/global/homes/s/sselcuk/software/cori/espresso-fftw/bin/cp.x':
malloc(): smallbin double linked list corrupted: 0x00000000047c8b80
***
and with the internal FFT engine, which died complaining:
Rank 65 [Thu Jul 7 14:31:39 2016] [c0-0c2s15n2] Fatal error in
PMPI_Isend:
Other MPI error, error stack:
PMPI_Isend(161).....................: MPI_Isend(buf=0x7811e00,
count=48,
MPI_DOUBLE_COMPLEX, dest=26, tag=66, comm=0xc4000007,
request=0x7ffffffe64e8) failed
MPIDI_EagerContigIsend(607).........: failure occurred while
attempting to
send an eager message
I couldn't find any relevant information in the group, and would
appreciate
any help.
Best,
Sencer
Postdoc @ Princeton University.
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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&control
restart_mode = 'from_scratch'
nstep = 10
dt = 5
ndr = 50
ndw = 50
iprint = 50
isave = 50
max_seconds = 1000
tprnfor = .TRUE.
etot_conv_thr = 1.0d-3
forc_conv_thr = 1.0d-2
/
&system
ibrav = 8
celldm(1) = 18.205620
celldm(2) = 1.181130
celldm(3) = 3.465852
nat = 342
ntyp = 4
ecutwfc = 25.D0
ecutrho = 200.D0
nr1b = 28
nr2b = 28
nr3b = 28
nspin = 2
lda_plus_u = .TRUE.
hubbard_u(1) = 3.9
/
&electrons
electron_dynamics = 'cg'
tcg = .TRUE.
orthogonalization = 'Gram-Schmidt'
passop = 0.2
emass = 450.0
emass_cutoff = 3.0d0
! electron_temperature = 'nose'
! ekincw = 0.15
/
&ions
ion_dynamics = 'none'
! ion_temperature = 'nose'
! fnosep = 20
! tempw = 400.0
/
ATOMIC_SPECIES
Ti 47.867 ti_pbe_2_new.van
Nb 92.906 Nb.pbe-nsp-van.UPF
O 15.999 O_pbe_1.van
H 2.008 H_pbe_1.van
ATOMIC_POSITIONS (angstrom)
Ti 6.0047187805 2.8363864422 7.4035577774
Ti 5.7710666656 6.5921082497 7.0374159813
Ti 5.7915334702 10.3456239700 6.9766011238
Ti 8.4073390961 0.8781314492 7.1043677330
Ti 8.4106798172 4.6780524254 7.0927591324
Ti 8.2475099564 8.4905633926 7.0466384888
Ti 1.0046229362 0.8324082494 8.9605484009
Ti 1.1190879345 4.7623662949 8.8594532013
Ti 1.0228396654 8.4160995483 8.9439296722
Ti 3.3818171024 2.7606568336 8.9460783005
Ti 3.5788896084 6.5538187027 8.9644327164
Ti 3.5466310978 10.3758068085 8.9689216614
Ti 5.8597006798 2.7029190063 11.0843667984
Ti 5.8286776543 6.6447911263 10.9493618011
Ti 5.8721165657 10.4256896973 10.9890069962
Ti 8.3757343292 0.9895883203 10.9480981827
Ti 8.1943273544 4.8022098541 11.0044355392
Ti 8.3194561005 8.5656242371 10.9786691666
Ti 1.1066696644 0.9575926661 12.8981752396
Ti 0.9956045747 4.7956142426 12.8192358017
Ti 0.9486083984 8.5004777908 12.8849916458
Ti 3.3587205410 2.7632944584 12.8284730911
Ti 3.4723207951 6.6343684196 12.7541055679
Ti 3.3818497658 10.2836751938 12.8403358459
Ti 5.8114147186 2.8808498383 14.7319726944
Ti 5.7990188599 6.6411046982 14.7939929962
Ti 5.8414812088 10.5130844116 14.7451324463
Ti 8.3622236252 0.8483409882 14.9118032455
Ti 8.2940149307 4.6577348709 14.8867168427
Ti 8.3135070801 8.5104179382 14.9022960663
Ti 0.8952274323 0.8014447689 16.8753204346
Ti 1.0534119606 4.7388329506 16.7559318542
Ti 0.9399223924 8.5816183090 16.8495121002
Ti 3.5505475998 6.6151356697 16.6565666199
Ti 3.4157667160 10.4396896362 16.8108291626
Ti 5.8811001778 2.8403148651 18.7176990509
Ti 5.7876286507 6.5925598145 18.6334629059
Ti 5.8146405220 10.3675079346 18.5556163788
Ti 8.3130655289 0.9242547154 18.7024154663
Ti 8.3579092026 4.7824091911 18.7020359039
Ti 8.2315483093 8.5098590851 18.6867694855
Ti 1.0490885973 0.9398613572 20.7453460693
Ti 1.0823875666 4.7138333321 20.6813926697
Ti 1.0490990877 8.4764366150 20.7805366516
Ti 3.5849025249 2.9167037010 20.7457122803
Ti 3.4200828075 6.6538906097 20.5985698700
Ti 3.4454569817 10.3969030380 20.5889015198
Ti 5.9628076553 2.8058919907 22.5896720886
Ti 5.8798818588 6.6969556808 22.4052677155
Ti 5.9102745056 10.3687286377 22.3661384583
Ti 8.4358720779 0.9516621232 22.6555061340
Ti 8.3475332260 4.6804027557 22.5934371948
Ti 8.3644323349 8.5406293869 22.6677665710
Ti 1.0267306566 0.9208921194 24.6115570068
Ti 0.9643879533 4.8382730484 24.5187072754
Ti 1.0414741039 8.5582771301 24.5970001221
Ti 3.5721156597 2.7811007500 24.5577526093
Ti 3.5046546459 6.6438550949 24.6571331024
Ti 3.5905108452 10.4305467606 24.6081142426
Ti 5.8993248940 2.7817399502 26.3538208008
Ti 5.8572936058 6.7621011734 26.3457717896
Ti 6.0070376396 10.4729366302 26.2018966675
Ti 8.3552722931 1.0178283453 26.5393848419
Ti 8.4060134888 4.6832170486 26.5257854462
Ti 8.5092086792 8.5976219177 26.5534667969
Nb 3.5708909035 2.7562835217 16.8475246429
O 6.2907881737 0.9441530704 7.0406451225
O 6.2564640045 4.7330842018 7.1160426140
O 6.2577514648 8.4164075851 6.7906942368
O 7.9796757698 2.7376520634 6.8784275055
O 7.9206137657 6.6604537964 6.9895524979
O 7.9720206261 10.3966360092 6.8122262955
O 0.6272789836 0.9836711884 7.1321139336
O 0.5371421576 4.6399135590 6.9801344872
O 0.6219480038 8.4676246643 7.1114110947
O 4.0722808838 2.6744668484 7.0514488220
O 3.9698116779 6.6855812073 7.1085124016
O 3.9493536949 10.4746313095 6.9624300003
O 1.5582976341 2.7598733902 8.9089622498
O 1.3759073019 6.5700469017 8.9417133331
O 1.5400496721 10.4039154053 9.0122194290
O 2.9978168011 0.8826014996 8.9230508804
O 2.9866456985 4.7629666328 8.8699932098
O 2.9859521389 8.4426708221 9.0849981308
O 5.6266493797 2.6896467209 9.1073789597
O 5.4887194633 6.5934023857 8.9840373993
O 5.4372611046 10.4162559509 8.9393987656
O 8.5279912949 0.8261886239 8.9494676590
O 8.6502847672 4.6051125526 9.0573053360
O 8.6413059235 8.5743198395 9.0919027328
O 0.5881263018 0.9448666573 10.9306974411
O 0.5376515388 4.6175236702 10.9866104126
O 0.5876380801 8.5575733185 10.9781169891
O 3.8951079845 2.8238308430 10.9650058746
O 3.9631772041 6.6081991196 10.9211053848
O 3.8739218712 10.3672685623 10.9274616241
O 6.3327269554 0.9038704634 10.9339694977
O 6.3129014969 4.6893472672 10.8865032196
O 6.2301011086 8.5560474396 10.9968185425
O 7.9584813118 2.7772655487 10.9251165390
O 7.9116663933 6.6863827705 10.8816804886
O 7.7850794792 10.3876609802 10.9750127792
O 1.4637682438 2.7999856472 12.9641456604
O 1.4225919247 6.5827369690 12.8212070465
O 1.4112119675 10.4122819901 12.9877386093
O 3.0236961842 0.8273084164 12.8900690079
O 3.0899229050 4.7122058868 12.9903793335
O 2.9638755322 8.4728212357 12.8248987198
O 5.4324884415 2.7796227932 12.8635177612
O 5.5193371773 6.6843647957 12.9133138657
O 5.4172873497 10.3738946915 12.9724874496
O 8.7656040192 0.9121109247 12.9844198227
O 8.6028432846 4.8167405128 12.8949146271
O 8.6643877029 8.4348058701 12.9710750580
O 0.6039720178 0.9225218892 14.9441070557
O 0.5946173072 4.6177310944 14.7788085938
O 0.6134423018 8.6223068237 14.9137382507
O 3.8403439522 2.9215707779 14.8490276337
O 3.7906968594 6.5926651955 14.8581809998
O 3.7827808857 10.4700098038 14.8627443314
O 6.1917743683 0.9925674200 14.9048728943
O 6.2196145058 4.7658801079 14.9382638931
O 6.2540612221 8.4775133133 14.9452323914
O 7.9272832870 2.8152735233 14.9446144104
O 7.9142093658 6.6198768616 14.8325834274
O 7.8011717796 10.4687061310 14.7456645966
O 1.5105719566 2.8876354694 16.7271862030
O 1.4462553263 6.5753445625 16.8757629395
O 1.4451986551 10.4187660217 16.8970527649
O 3.0903697014 0.9613655806 16.7888126373
O 3.1252350807 4.7033095360 16.8448963165
O 3.1352720261 8.5733261108 16.8418273926
O 5.4904165268 2.8126747608 16.7586402893
O 5.4322514534 6.7271385193 16.7975292206
O 5.4727144241 10.5330305099 16.8260478973
O 8.6608285904 1.0198062658 16.8212184906
O 8.6588554382 4.8432807922 16.8005905151
O 8.6634988785 8.5582351685 16.7642974854
O 6.3353214264 0.9972871542 18.7906360626
O 6.2054738998 4.7776112556 18.6787967682
O 6.1710724831 8.4851665497 18.7833271027
O 7.8460507393 2.8810570240 18.6557884216
O 7.9809904099 6.6198191643 18.6803970337
O 7.8670315742 10.3779506683 18.6455078125
O 0.7323767543 0.9308658242 18.6840076447
O 0.6165319085 4.6364903450 18.6778488159
O 0.5586888790 8.5574150085 18.7161483765
O 3.8062951565 2.8953614235 18.7624340057
O 3.9340016842 6.7183675766 18.8065910339
O 3.8903222084 10.3345165253 18.6880321503
O 1.5015468597 2.9003224373 20.7652511597
O 1.3849930763 6.5985980034 20.7206325531
O 1.4238479137 10.4235019684 20.5947971344
O 3.0233461857 0.8641042113 20.6264171600
O 3.1699509621 4.7444334030 20.6818790436
O 3.1541433334 8.4852952957 20.7246665955
O 5.4182476997 2.8169174194 20.5835781097
O 5.5756721497 6.5507779121 20.6053676605
O 5.3956260681 10.4406280518 20.6633815765
O 8.7533817291 0.9904468656 20.6955337524
O 8.7088985443 4.7266426086 20.6324539185
O 8.7751550674 8.5589208603 20.5956230164
O 0.7342182398 0.9377330542 22.5714149475
O 0.6478199363 4.8064074516 22.5920543671
O 0.5938414931 8.4705200195 22.5863857269
O 4.0246548653 2.9294662476 22.5925426483
O 4.0204482079 6.6045556068 22.5579128265
O 3.8879570961 10.4458608627 22.6155395508
O 6.3668112755 0.9442028999 22.6254596710
O 6.2192635536 4.6644468307 22.4937076569
O 6.3204727173 8.5914134979 22.4448909760
O 7.8739776611 2.8607738018 22.6232280731
O 7.9554176331 6.6648941040 22.5137672424
O 8.0250072479 10.3625354767 22.5802688599
O 3.0689995289 4.8172621727 24.5974464417
O 3.0947084427 8.6065053940 24.6250839233
O 5.6034097672 2.9705855846 24.5476436615
O 5.6528167725 6.5928325653 24.5707912445
O 8.6316595078 0.9588361979 24.5564594269
O 8.6736030579 4.7537536621 24.5395278931
O 8.7840633392 8.4045648575 24.6147327423
O 1.4648523331 2.8880305290 24.4540157318
O 1.5324671268 6.6573739052 24.5009174347
O 1.5126104355 10.5179634094 24.6203536987
O 3.1881659031 0.9706695676 24.6232395172
O 5.5318989754 10.4790143967 24.4912185669
O 6.2513918877 0.9902352691 26.6100406647
O 6.3372850418 4.6570510864 26.7505397797
O 6.1784915924 8.5641613007 26.6124897003
O 7.9261426926 2.8331270218 26.6056594849
O 7.9721851349 6.7417993546 26.5659255981
O 7.9066305161 10.5088682175 26.3354778290
O 0.6391347647 1.2029274702 26.4784965515
O 0.5789585710 4.8691158295 26.5183906555
O 0.7129961848 8.5770635605 26.5484867096
O 4.0948138237 2.8804278374 26.5218544006
O 3.9976553917 6.6637091637 26.4656772614
O 4.1464242935 10.4534072876 26.5842666626
O 1.0093985796 3.0477101803 28.6940917969
O 9.3925800323 6.2637057304 2.5816082954
O 8.5262565613 0.3586571813 28.5506172180
O 6.1707000732 10.6971559525 0.6661216617
O 3.7507879734 9.0217428207 28.8869667053
O 8.4487962723 10.3725147247 3.4518458843
O -0.6043909788 6.0722107887 31.1110515594
O 7.3053879738 8.9024820328 32.4070281982
O 8.1611452103 8.8950586319 28.7136955261
O 7.6424756050 8.0290231705 1.6557189226
O 4.7849483490 1.7150987387 30.3604660034
O 1.9282760620 6.9959926605 28.4580745697
O 2.6294131279 3.3349127769 31.3433551788
O 5.6371231079 10.5875129700 4.7996072769
O 3.3457250595 0.9605839849 28.1725463867
O 0.8508359194 11.6436920166 1.9984282255
O 6.6750621796 4.9744300842 31.7036838531
O 5.7738118172 6.0567741394 4.9880218506
O 1.1863349676 0.3729360700 29.6839771271
O 4.6727290154 9.6693649292 2.6382312775
O 2.0464980602 9.4845848083 5.2117500305
O 5.5103263855 5.5575771332 29.2641334534
O 4.6566319466 1.7864596844 4.5289349556
O 2.3666493893 2.2270631790 3.1255435944
O 3.7798793316 5.5021471977 1.3203859329
O 7.1003904343 1.6655584574 1.3824754953
O 7.2584924698 2.9123570919 30.2662162781
O 1.0464403629 4.4872055054 34.2762489319
O 9.4739322662 2.1066367626 0.5084875226
O 4.3141689301 6.8369541168 32.4447174072
O 8.6238002777 8.2898941040 4.8774085045
O 5.9985718727 8.2219219208 29.7824821472
O 8.2011594772 4.9307727814 4.7346329689
O 4.0783963203 11.4705009460 32.3216667175
O 5.5849676132 3.6234917641 0.5727923512
O 2.1378993988 5.9906406403 31.0980224609
O 1.8828403950 4.3562502861 4.6547589302
O 3.0930101871 4.5803008080 28.3013191223
O 3.1879239082 2.2376184464 0.3236570060
O 0.0961315110 2.0624577999 31.3552417755
O 4.3231458664 7.1206178665 3.2061567307
O 2.5572991371 9.8728885651 1.3101968765
O 7.1081247330 2.5864708424 3.7788314819
O 1.9545638561 7.1355376244 3.9621658325
O 9.4664611816 8.6421670914 30.8620109558
O 2.2582736015 9.7759342194 30.9416427612
O 8.7376451492 4.5234022141 28.7126522064
O 8.7350902557 1.0470365286 4.9082522392
H 1.8143769503 3.6154301167 28.6612434387
H 1.0223855972 2.4738688469 27.8837203979
H 1.1006532907 7.0538969040 3.2109944820
H 8.4841041565 7.0544061661 2.1196820736
H 8.2430572510 -0.6046138406 28.6275444031
H 9.4894962311 0.4078672826 28.9593372345
H 5.6091613770 10.1274280548 1.4684135914
H 7.5096945763 8.2596197128 0.6741050482
H 3.8242011070 9.4516620636 27.9869880676
H 3.1983644962 8.2631893158 28.7784652710
H 6.7320661545 0.5724650621 1.0067641735
H 8.5986452103 11.3427610397 4.3811588287
H -0.6960777044 5.6298336983 30.2320632935
H 0.3422279656 5.8838300705 31.3681850433
H 6.7324166298 8.6354722977 31.6820316315
H 8.2477064133 9.0278263092 31.9421081543
H 7.0623393059 8.5744400024 29.1726169586
H 8.7792634964 8.7728776932 29.4827842712
H 7.7371497154 9.0207920074 2.2074878216
H 1.7852598429 10.5841598511 1.5531283617
H 4.5918216705 0.8794555664 31.2972278595
H 4.3343124390 1.2440305948 29.4319210052
H 8.0694360733 3.8982245922 29.1062335968
H 1.2891339064 7.6671333313 27.4808731079
H 2.7896244526 3.0339462757 32.1994781494
H 3.7143902779 2.6510798931 30.6644916534
H 6.4705672264 10.6305379868 4.4371323586
H 5.0450830460 10.1750650406 3.9922130108
H 3.5273036957 1.7119278908 27.4903774261
H 3.5903048515 -0.0852299631 27.4432163239
H 0.4511004984 12.3898296356 1.2845993042
H 1.3564940691 12.2086410522 2.6405255795
H 6.9019751549 4.0568223000 31.3017730713
H 7.6838984489 5.4383783340 31.7145214081
H 5.2096338272 5.1202325821 5.1477169991
H 9.8000946045 1.4689009190 4.9759297371
H 1.5239506960 -0.3691375852 30.1879177094
H 1.9300158024 0.7130268812 29.0885906219
H 4.6681199074 8.7584266663 2.7510612011
H 2.9388790131 9.9327306747 5.8096861839
H 1.3807685375 9.2233943939 6.0020203590
H 6.5556597710 10.0661554337 0.0069896779
H 5.9358587265 5.2644796371 30.0673255920
H 2.0501444340 6.3293924332 30.0789966583
H 4.3120222092 2.0548582077 5.3606643677
H 4.9640402794 0.7537359595 4.7278342247
H 3.2750082016 1.9385952950 3.6664905548
H 5.1719188690 6.5801215172 4.2169203758
H 3.8896071911 6.0172510147 0.4927578270
H 4.4527835846 4.7971467972 1.2837880850
H 8.0562124252 1.8446966410 1.0176364183
H 6.6280508041 2.4010634422 0.9176257849
H 6.4858098030 2.4053320885 30.2920818329
H 8.0471439362 2.3856189251 30.5995121002
H 2.1405732632 4.7232770920 34.5064010620
H 0.5595403910 5.1065783501 34.8674468994
H 9.9032497406 2.9104695320 0.7520483136
H 9.5873355865 1.9796500206 -0.4697060287
H 5.0766043663 6.2761907578 32.0286788940
H 3.5360722542 6.6257658005 31.9501056671
H 9.3916196823 7.5998320580 4.6998286247
H 8.7176342010 9.1931972504 4.1696796417
H 5.8779768944 7.2715325356 29.6395378113
H 5.0337529182 8.6384496689 29.4211006165
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H 7.3599863052 5.5132174492 4.7358269691
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