Problems with Resonance Raman Calculation
Clicked A Few Times
3:37:03 AM PDT - Fri, Oct 16th 2015
Hi all,


I optimised the geometry of the molecule using B3LYP/6-31g* with another package, and am interested in the response near the electronic excitation at 5.4976991E-2 Hartrees (calculated separately using linear response TDDFT). My input file was as follows:

title "3DPP-TT-T trans - Geom from b3lyp/6-31g* Gaussian job. B3LYP sp."
echo "3DPP-TT-T wiggly snake"
memory stack 300 mb heap 300 mb global 600 mb
echo
geometry noautoz units angstroms
H 30.556636 1.116992 0.025631
C 29.511828 0.835426 0.025243
C 28.995938 -0.432741 0.031124
C 27.573987 -0.403253 0.028372
C 27.027208 0.881127 0.020466
C 25.618705 0.922735 0.017654
H 29.603458 -1.329951 0.037065
H 25.006092 1.819794 0.011675
S 26.323949 -1.610170 0.032573
S 28.291320 2.087486 0.016291
C 25.061907 -0.350750 0.023477
C 23.648388 -0.610297 0.022190
C 21.367632 -0.325869 0.016325
C 21.605981 -1.750074 0.024210
C 22.621453 0.338113 0.015274
C 22.383571 1.762551 0.007195
O 23.125497 2.743450 0.003362
O 20.864283 -2.731330 0.027853
N 20.953825 1.875220 0.003858
N 23.036158 -1.862378 0.027566
C 20.340412 0.622657 0.009295
C 23.648257 -3.179355 0.035762
H 24.257668 -3.333535 0.931884
H 22.823586 -3.894779 0.037747
H 24.261467 -3.342891 -0.856093
C 20.342258 3.192244 -0.004594
H 21.167404 3.907187 -0.006859
H 19.733052 3.347071 -0.900850
H 19.729470 3.356922 0.887451
C 18.929385 0.362829 0.007965
C 18.371195 -0.913274 0.013211
C 16.967159 -0.871827 0.010516
C 16.417263 0.413861 0.003353
C 15.006384 0.447487 0.000681
H 18.984939 -1.809606 0.018755
H 14.409559 1.352388 -0.004735
S 15.708095 -2.081865 0.014042
S 17.667148 1.622218 -0.000337
C 14.456621 -0.823707 0.005769
C 13.065307 -1.192698 0.004930
C 12.502233 -2.456887 0.009556
C 11.091491 -2.453842 0.006964
S 11.802288 0.030367 -0.002820
H 13.094702 -3.365522 0.014697
H 10.495158 -3.359975 0.009912
C 10.533869 -1.187251 0.000333
C 9.144321 -0.812264 -0.003805
C 8.600175 0.461522 -0.010088
C 7.189366 0.434173 -0.012620
C 6.633535 -0.849250 -0.008359
C 5.229734 -0.884459 -0.010823
H 9.201074 1.363722 -0.012639
H 4.611919 -1.778028 -0.008258
S 5.945087 1.648252 -0.019933
S 7.887308 -2.064906 -0.001023
C 4.676918 0.394488 -0.017124
C 3.267887 0.660331 -0.020673
C 0.985803 0.384734 -0.022977
C 1.229946 1.808461 -0.028804
C 2.235598 -0.284168 -0.018244
C 1.991418 -1.707934 -0.012447
O 2.729946 -2.691566 -0.007117
O 0.491462 2.792151 -0.034258
N 0.561800 -1.814788 -0.014146
N 2.659563 1.915322 -0.027022
C -0.046521 -0.559805 -0.020347
C 3.276784 3.229835 -0.032245
H 3.889643 3.382645 -0.926324
H 2.454885 3.948457 -0.036630
H 3.887258 3.390868 0.862009
C -0.055577 -3.129228 -0.009268
H 0.766204 -3.847988 -0.005515
H -0.668122 -3.282352 0.884971
H -0.666444 -3.289718 -0.903354
C -1.455462 -0.293837 -0.023266
C -2.007867 0.985316 -0.029378
C -3.411599 0.950648 -0.030594
C -3.968019 -0.332542 -0.025654
C -5.378865 -0.359211 -0.026813
H -1.389763 1.878687 -0.032553
H -5.980248 -1.261083 -0.023791
S -4.664737 2.166916 -0.036578
S -2.724162 -1.547128 -0.019161
C -5.922386 0.914896 -0.032543
C -7.311560 1.291059 -0.034832
C -7.867663 2.558321 -0.043720
C -9.278316 2.563180 -0.043277
S -8.581543 0.075008 -0.025030
H -7.270216 3.463702 -0.050860
H -9.869661 3.472524 -0.050283
C -9.843057 1.299684 -0.034037
C -11.234896 0.933069 -0.030954
C -11.787375 -0.337045 -0.030404
C -13.198110 -0.300531 -0.026636
C -13.745360 0.986374 -0.024419
C -15.149170 1.031061 -0.020815
H -11.192372 -1.243168 -0.033218
H -15.760888 1.928780 -0.018457
S -14.450859 -1.506161 -0.024294
S -12.483865 2.193808 -0.026528
C -15.710413 -0.243863 -0.020165
C -17.121722 -0.500484 -0.016240
C -19.401948 -0.210095 -0.008216
C -19.167769 -1.635016 -0.011229
C -18.147176 0.450547 -0.011788
C -18.381923 1.875835 -0.008177
O -17.637016 2.854662 -0.009676
O -19.912503 -2.614181 -0.010933
N -19.810928 1.992265 -0.002091
N -17.738534 -1.751425 -0.015931
C -20.427601 0.741540 -0.001847
C -17.130300 -3.069967 -0.019760
H -16.516958 -3.232542 0.872300
H -17.957232 -3.782849 -0.018277
H -16.522348 -3.229939 -0.915980
C -20.419446 3.310841 0.001557
H -19.592931 4.024128 -0.002857
H -21.035258 3.471611 -0.889043
H -21.025248 3.471451 0.899049
C -21.838962 0.486069 0.003799
C -22.400600 -0.788355 0.000612
C -23.805023 -0.743456 0.010893
C -24.351010 0.542968 0.021133
C -25.764120 0.580243 0.019389
H -21.789224 -1.686325 -0.007665
H -26.360535 1.485206 0.005035
S -25.069193 -1.948847 0.017601
S -23.098783 1.748245 0.017945
C -26.314610 -0.687730 0.012074
C -27.712626 -1.056445 0.005343
C -28.283491 -2.280645 -0.278533
C -29.703014 -2.279555 -0.192318
S -28.961529 0.116324 0.396883
H -27.700065 -3.151161 -0.559150
H -30.318391 -3.150775 -0.387757
C -30.213676 -1.058520 0.155334
H -31.249298 -0.775701 0.287540
end

basis
 * library 6-31g*
end


dft
 iterations 100
 print kinetic_energy
[[Media:
 xc B3LYP
 direct

 decomp
end
task dft energy]]



property
 response  1 5.4976991E-2
 damping 0.007
end
raman
 resonance
 lorentzian
end
task dft raman


The DFT energy calculation works, but the resonance raman calculation fails with the following few lines:

------------------------------------------------------------------------
 hess_init: could not allocate g_rhs      555
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
  current input line :
   171: task dft raman
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 For more information see the NWChem manual at
 http://nwchemgit.github.io/index.php/NWChem_Documentation


 For further details see manual section:




0:0:hess_init: could not allocate g_rhs:: 555
Last System Error Message from Task 0:: Inappropriate ioctl for device
[cli_0]: aborting job:
application called MPI_Abort(comm=0x84000001, 555) - process 0
(rank:0 hostname:cx1-1-19-4.cx1.hpc.ic.ac.uk pid:32574):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/armci.c:ARMCI_Error():208 cond:0
 hess_init: could not allocate g_rhs      555
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
  current input line :
     0:
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 For more information see the NWChem manual at
 http://nwchemgit.github.io/index.php/NWChem_Documentation


If anyone has any advice, I would be very grateful! Thanks in advance.

Forum Regular
9:14:36 AM PDT - Fri, Oct 16th 2015
You do not have enough memory to allocate the needed array. That array has dimensions (number of basis functions)x(number of basis functions)x(3 times the number of atoms). It is a global array so you would need to increase the global memory in order to perform this calculation.

Best,
Sean

Clicked A Few Times
2:04:30 AM PDT - Mon, Oct 19th 2015
Thanks, Sean. I will try with higher global memory.

Best,

Sheridan

Clicked A Few Times
11:59:25 PM PDT - Fri, Oct 23rd 2015
Hi,

I retried the same calculation with a significantly higher allocation of memory:

memory total 127000 mb stack 31750 mb heap 31750 mb global 63500 mb


The got a little further, but unfortunately still failed, albeit with a different error message, and with the following lines after the DFT energy calculation:

  stpr_wrt_fd_from_sq: overwrite of existing file:
 ./3DPP_TT_T_trans_ResRaman.hess
 stpr_wrt_fd_dipole: overwrite of existing file
 ./3DPP_TT_T_trans_ResRaman.fd_ddipole

 HESSIAN: the one electron contributions are done in     384.6s


 HESSIAN: 2-el 1st deriv. term done in                 15857.4s


 HESSIAN: 2-el 2nd deriv. term done in                  2744.5s

  stpr_wrt_fd_from_sq: overwrite of existing file:
 ./3DPP_TT_T_trans_ResRaman.hess
 stpr_wrt_fd_dipole: overwrite of existing file
 ./3DPP_TT_T_trans_ResRaman.fd_ddipole

 HESSIAN: the two electron contributions are done in   19384.2s

0:CreateSharedRegion:kr_malloc failed KB=: 20528
(rank:0 hostname:cx1-11-4-3.cx1.hpc.ic.ac.uk pid:22026):ARMCI DASSERT fail. ../../ga-5-1/armci/src/memory/shmem.c:Create_Shared_Region():1188 cond:0
Last System Error Message from Task 0:: Inappropriate ioctl for device
[cli_0]: aborting job:
application called MPI_Abort(comm=0x84000001, 20528) - process 0
rank 0 in job 1  cx1-11-4-3.cx1.hpc.ic.ac.uk_59624   caused collective abort of all ranks
  exit status of rank 0: return code 48
Job terminated normally


I would be very grateful for any advice.

Forum Regular
8:17:08 AM PDT - Mon, Oct 26th 2015
It looks like another out of memory problem. You don't need much memory allocated to heap, so I would suggest cutting the heap allocation to only about 300 mb and redistributing the rest of the allocation to stack and global.

Best,
Sean

Clicked A Few Times
11:19:46 AM PDT - Tue, Oct 27th 2015
Thanks, I am trying that now.

Clicked A Few Times
7:15:02 AM PDT - Thu, Oct 29th 2015
I tried the same job with two different memory allocations, one with significantly more global memory:

 memory total 127000 mb stack 26700 mb heap 300 mb global 100000 mb


and

 memory total 127000 mb stack 63350 mb heap 300 mb global 63350 mb


Unfortunately both failed at a same stage as the previously reported job (although each stage completed more quickly with the highest global memory allocation).

Perhaps the molecule is simply too large (137 atoms) to calculate Resonance Raman with available resources?

Thanks again,

Sheridan


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