From NWChem
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Just Got Here
Threads 2
Posts 3
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| 1:15:47 PM PST - Mon, Nov 4th 2013 |
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Dear NWChem developers,
I've tried to calculate hessian for a quite large molecule, such as bacteriochlorophyll without aliphatic tail (85 atoms including Mg). I can perform this task in 6-31 basis but when I'm trying to do this in larger basis (cc-pvdz) I receive following error:
NWChem CPHF Module
------------------
scftype = RHF
nclosed = 171
nopen = 0
variables = 124488
# of vectors = 255
tolerance = 0.10D-03
level shift = 0.00D+00
max iterations = 50
max subspace = 2550
Grid integrated density: 342.000049006129
Requested integration accuracy: 0.10E-06
SCF residual: 8.5297123820759612E-004
Iterative solution of linear equations
No. of variables 124488
No. of equations 255
Maximum subspace 2550
Iterations 50
Convergence 1.0D-04
Start time 25707.3
iter nsub residual time
---- ------ -------- ---------
rohf_h2e: could not allocate g_fock 555
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current input line :
rohf_h2e: could not allocate g_fock 555
rohf_h2e: could not allocate g_fock 555
------------------------------------------------------------------------
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current input line :
0:
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rohf_h2e: could not allocate g_fock 555
------------------------------------------------------------------------
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current input line :
113: TASK dft hessian
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Google tells me that it problem in memory size, but memory directive was set 600 mw and RAM size is 24 Gb for 1 4-core processor.
Could you please help me with this? Is this task a really big for my machine or I'm doing something wrong?
Also, some system settings
------ Shared Memory Limits --------
max number of segments = 4096
max seg size (kbytes) = 4194304
max total shared memory (kbytes) = 20971520
min seg size (bytes) = 1
and input file:
TITLE "BChl a DFT/B3LYP cc-pvdz hessian"
START BCl_hess
MEMORY 600 mw
CHARGE 0
GEOMETRY units an
Mg 68.6498225237 1.0682417826 33.4119394445
C 70.0423879873 0.2317804898 30.3702690349
C 66.3209039567 2.9350568075 31.7901148353
H 65.5824515564 3.5511815949 31.2756874385
C 67.2969614933 1.8314373440 36.4222323241
H 66.8460641461 2.1076315320 37.3743826529
C 71.0628979431 -0.8724802993 35.0048294908
H 71.8096892061 -1.4959959813 35.5007010752
N 68.2527212807 1.5040652122 31.3502058912
N 67.0604723552 2.1788158187 34.0074709894
N 69.1186615815 0.5561049991 35.4084813430
N 70.2412768827 -0.0346650255 32.8713656000
C 68.9200408612 1.0363638991 30.2553501406
C 68.2474075425 1.4684210820 28.9712893451
H 68.9908326217 1.8571245146 28.2582902904
C 67.3028308986 2.5810313929 29.4626149572
H 66.2963601022 2.4696251345 29.0270320092
C 67.2539251567 2.3322304209 30.9594402690
C 67.8238040647 3.9846102302 29.1547875035
H 67.8848313620 4.1468348267 28.0673070127
H 67.1695556328 4.7597766526 29.5813827678
H 68.8316270094 4.1266555114 29.5764570475
C 67.5140989177 0.2960715831 28.3074341793
H 66.6609602820 -0.0143497900 28.9330961263
H 68.1748316037 -0.5814656698 28.2516918609
C 67.0393900936 0.6315380698 26.9043702842
H 67.8959428084 0.8707453431 26.2513279691
H 66.3939038894 1.5254944473 26.8823029664
C 66.2750957268 -0.4983512746 26.2669651773
O 66.0809306502 -1.5818022641 26.7609942560
O 65.8242130047 -0.1483119156 25.0494970049
C 66.2019770051 2.8634387943 33.1910489126
C 65.1800874402 3.5049539495 33.9757895676
C 65.4546743207 3.1910118873 35.3067868918
C 66.6463705693 2.3628578338 35.2946038253
C 64.0792369444 4.3310672532 33.3969820999
H 64.0619126899 5.3468289237 33.8185504889
H 64.1828544243 4.4341321257 32.3100921586
H 63.0895779537 3.8881234430 33.5872623806
C 64.7194763824 3.5835488271 36.5285289638
O 65.1227142574 3.2986933322 37.6466010561
C 63.4239690635 4.3512409137 36.4036128904
H 63.0172338824 4.4923875913 37.4115401818
H 63.5871356792 5.3340449141 35.9373604126
H 62.6951304713 3.8103331059 35.7823022840
C 68.4258201119 1.0247181936 36.4717799245
C 69.0610955640 0.5944364151 37.7795220134
H 68.2914909824 0.1612357971 38.4385693565
C 70.0709039663 -0.4760988514 37.3254606220
H 71.0646435972 -0.2905535765 37.7686035591
C 70.1249518221 -0.2620659790 35.8242263112
C 69.7091279264 1.7780797729 38.4964184826
H 68.9650381352 2.5508570260 38.7396137216
H 70.1843710468 1.4512809218 39.4346017152
H 70.4835541850 2.2411868596 37.8642612744
C 69.6509750043 -1.9096099106 37.6775628234
H 68.6315000738 -2.0851980930 37.2909754138
H 70.3045266048 -2.6130990564 37.1354879405
C 69.7099623536 -2.2089580676 39.1681709136
H 69.4031276401 -3.2447626085 39.3767135717
H 70.7319898213 -2.0774392194 39.5590630995
H 69.0474407566 -1.5480697878 39.7491398820
C 71.1390461159 -0.7853895442 33.6025792130
C 72.0813682732 -1.4478699544 32.7313634201
C 71.7046105992 -1.0646383239 31.4493196515
C 70.5851781310 -0.2108836417 31.5869015423
C 73.1980217317 -2.3467652252 33.1336018160
H 72.8349936459 -3.2131186541 33.7095404844
H 73.7213895282 -2.7213598226 32.2447544901
H 73.9308498432 -1.8223205574 33.7680319384
C 71.9814102377 -1.2334585909 30.0262530629
O 72.8222725816 -1.8978318234 29.4634364658
C 70.9106871126 -0.3718958198 29.2713481536
H 70.3436072988 -1.0296514565 28.5954940299
C 71.5435183080 0.6874125341 28.3925909631
O 71.1209090478 1.0358245198 27.3149639037
O 72.6190492421 1.2269322324 28.9768656048
C 73.2728604649 2.2460447105 28.2248745801
H 74.1412885433 2.5447617317 28.8218369638
H 73.5914783519 1.8606897425 27.2462562107
H 72.6020400442 3.1026999689 28.0655036368
C 65.0942782307 -1.1642404742 24.3663913535
H 64.8176385485 -0.7344282217 23.3971409650
H 64.1944584933 -1.4457149271 24.9324892927
H 65.7122721546 -2.0626743161 24.2267749465
END
BASIS
H library cc-pvdz
O library cc-pvdz
C library cc-pvdz
N library cc-pvdz
Mg library cc-pvdz
END
DFT
iterations 50
XC b3lyp
direct
END
TASK dft hessian
Or maybe I should run this task on 1 core with extended memory limit?
Thank in advance,
Daniil Khokhlov.
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Huub Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Regular
Threads 1
Posts 185
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| 4:48:54 PM PST - Mon, Nov 4th 2013 |
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Hi Daniil,
This memory issue is definitely related to problems trying to allocate a global array. So running it on 1 core with an extended memory limit is not going to help. The global array that the program tries to allocate has a size of 3*nat*nbf*nbf double precision numbers where nat is the number of atoms and nbf is the number of basis functions. To accommodate such an array you'll need to make sure that the global portion of you memory setting is as large as possible. Your memory specification equates to 150 mw stack, 150 mw heap and 300 mw global memory. Heap memory is actually used very little so you should be able to reduce that considerably (say reduce that to 50 mw), and the stack memory can also be reduced a bit. Otherwise you should increase the global section as much as possible. Note that all these memory settings are per process. With 14 cores and 24 GB you should be able to get 1.5 GB per process. Putting most of that into the global memory section might get you there.
Huub
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Just Got Here
Threads 2
Posts 3
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| 12:34:32 AM PST - Tue, Nov 5th 2013 |
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Thank you, Huub.
I will try it - 500 mw for global and 100 mw spread between heap and stack.
Also, maybe I didn't clearly described my system - it isn't 14-core processor (unfortunately), but only one 4-core processor, so I allow NWChem to use 6 Gb per process.
And another one question, can this problem be connected with MPI? I propose it due to some ARMCI offset warnings which appear only for 3 processes from 4, such as "WARNING: armci_set_mem_offset: offset changed". Or they are also connected with global memory problems?
Upd. It really works, iterative process began. Many thanks!
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Edited On 5:14:29 AM PST - Tue, Nov 5th 2013 by DaniilKh
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