Dear All, I tried to perform a TDDFT calculation on a molecule of 124 atoms with 488 electrons at b3lyp/6-31g* level (1158 AOs). The task has been running on a workstation equipped with 4-cpu/48-cores and 128 GB of RAM (and also 5 HDDs of 2 TB each). This is the input deck I used:
echo
START PB_166
TITLE "TDDFT B3LYP/6-31G* PB_166"
memory heap 100 mb stack 1000 mb global 1000 mb
geometry units angstroms
CARBON 3.2593623488 -1.8892593764 -0.0894787160
CARBON -3.2593623488 1.8892593764 -0.0894787160
CARBON -2.7926481739 0.5667699406 -0.2553721756
CARBON 2.7926481739 -0.5667699406 -0.2553721756
CARBON -1.3944736870 0.2917225452 -0.1570899000
CARBON 1.3944736870 -0.2917225452 -0.1570899000
CARBON 0.4695910920 -1.3813690147 -0.0063436639
CARBON -0.4695910920 1.3813690147 -0.0063436639
CARBON 0.9773255072 -2.6733511057 0.2570667557
CARBON -0.9773255072 2.6733511057 0.2570667557
CARBON 2.3692061833 -2.8995829680 0.1993350845
CARBON -2.3692061833 2.8995829680 0.1993350845
CARBON -0.9589992126 -1.0752484664 -0.2194695571
CARBON 0.9589992126 1.0752484664 -0.2194695571
CARBON -3.7127238835 -0.4700449582 -0.5234397154
CARBON 3.7127238835 0.4700449582 -0.5234397154
CARBON -3.2563500645 -1.7634899097 -0.6915626710
CARBON 3.2563500645 1.7634899097 -0.6915626710
CARBON -1.9002769128 -2.0634516737 -0.5278175573
CARBON 1.9002769128 2.0634516737 -0.5278175573
CARBON -4.6985971253 2.2158772668 -0.1773315252
CARBON 4.6985971253 -2.2158772668 -0.1773315252
NITROGEN -5.5640030722 1.1437720602 -0.4611081692
NITROGEN 5.5640030722 -1.1437720602 -0.4611081692
CARBON -5.1616118913 -0.2042474749 -0.6488670978
CARBON 5.1616118913 0.2042474749 -0.6488670978
CARBON -6.9901907994 1.4291743262 -0.5696580305
CARBON 6.9901907994 -1.4291743262 -0.5696580305
CARBON -7.5226614334 1.7756191846 -1.8232994341
CARBON 7.5226614334 -1.7756191846 -1.8232994341
CARBON -8.8970755269 2.0263340006 -1.9099279667
CARBON 8.8970755269 -2.0263340006 -1.9099279667
CARBON -9.7109450781 1.9358613719 -0.7835536110
CARBON 9.7109450781 -1.9358613719 -0.7835536110
CARBON -9.1611152029 1.6059619342 0.4527283456
CARBON 9.1611152029 -1.6059619342 0.4527283456
CARBON -7.7918634839 1.3459009154 0.5818634389
CARBON 7.7918634839 -1.3459009154 0.5818634389
CARBON 0.1428367894 -3.8409708502 0.6659093569
CARBON -0.1428367894 3.8409708502 0.6659093569
CARBON 0.1747853200 -5.0403770944 -0.0687302078
CARBON -0.1747853200 5.0403770944 -0.0687302078
CARBON -0.5658948364 -6.1416651146 0.3379799031
CARBON 0.5658948364 6.1416651146 0.3379799031
CARBON -1.3510424808 -6.0815073593 1.4994059874
CARBON 1.3510424808 6.0815073593 1.4994059874
CARBON -1.3754632525 -4.8970247768 2.2456454811
CARBON 1.3754632525 4.8970247768 2.2456454811
CARBON -0.6353726211 -3.7916743849 1.8292129681
CARBON 0.6353726211 3.7916743849 1.8292129681
CARBON -7.1802943259 1.0744724459 1.9550249719
CARBON 7.1802943259 -1.0744724459 1.9550249719
CARBON -6.9922187839 2.4291238870 2.6916012476
CARBON 6.9922187839 -2.4291238870 2.6916012476
CARBON -8.0153384136 0.0888412047 2.8027367733
CARBON 8.0153384136 -0.0888412047 2.8027367733
CARBON -6.6213059790 1.9719338033 -3.0408348761
CARBON 6.6213059790 -1.9719338033 -3.0408348761
CARBON -7.2188988461 1.3782266105 -4.3361458258
CARBON 7.2188988461 -1.3782266105 -4.3361458258
CARBON -6.3321915977 3.4897769504 -3.2029782515
CARBON 6.3321915977 -3.4897769504 -3.2029782515
OXYGEN -2.0487336823 -7.2306317435 1.8148895163
OXYGEN 2.0487336823 7.2306317435 1.8148895163
CARBON -2.8862683489 -7.2244397281 3.0125202682
CARBON 2.8862683489 7.2244397281 3.0125202682
OXYGEN -5.9868713061 -1.0894713451 -0.8999664913
OXYGEN 5.9868713061 1.0894713451 -0.8999664913
OXYGEN 5.1306971980 -3.3698489594 -0.0115046054
OXYGEN -5.1306971980 3.3698489594 -0.0115046054
HYDROGEN 2.7610226683 -3.8910556460 0.3887768618
HYDROGEN -2.7610226683 3.8910556460 0.3887768618
HYDROGEN -3.9739725269 -2.5377333729 -0.9313730981
HYDROGEN 3.9739725269 2.5377333729 -0.9313730981
HYDROGEN -1.5777173701 -3.0864013999 -0.6291200936
HYDROGEN 1.5777173701 3.0864013999 -0.6291200936
HYDROGEN -9.3303033301 2.2988264405 -2.8642220154
HYDROGEN 9.3303033301 -2.2988264405 -2.8642220154
HYDROGEN -10.7738923321 2.1319777109 -0.8674824826
HYDROGEN 10.7738923321 -2.1319777109 -0.8674824826
HYDROGEN -9.7989108611 1.5547033918 1.3263264928
HYDROGEN 9.7989108611 -1.5547033918 1.3263264928
HYDROGEN 0.7737081962 -5.0979816565 -0.9705805093
HYDROGEN -0.7737081962 5.0979816565 -0.9705805093
HYDROGEN -0.5581945138 -7.0665670931 -0.2230100521
HYDROGEN 0.5581945138 7.0665670931 -0.2230100521
HYDROGEN -1.9611691692 -4.8275038497 3.1521817279
HYDROGEN 1.9611691692 4.8275038497 3.1521817279
HYDROGEN -0.6615299883 -2.8791033556 2.4126597947
HYDROGEN 0.6615299883 2.8791033556 2.4126597947
HYDROGEN -6.1919261949 0.6310951637 1.8034301693
HYDROGEN 6.1919261949 -0.6310951637 1.8034301693
HYDROGEN -6.4820413902 2.2767312976 3.6503269121
HYDROGEN 6.4820413902 -2.2767312976 3.6503269121
HYDROGEN -6.4043222673 3.1117586012 2.0713120330
HYDROGEN 6.4043222673 -3.1117586012 2.0713120330
HYDROGEN -7.9694465516 2.8860288974 2.8843527574
HYDROGEN 7.9694465516 -2.8860288974 2.8843527574
HYDROGEN -7.4954764107 -0.1188951546 3.7450872602
HYDROGEN 7.4954764107 0.1188951546 3.7450872602
HYDROGEN -8.9960342771 0.5102250480 3.0481768046
HYDROGEN 8.9960342771 -0.5102250480 3.0481768046
HYDROGEN -8.1638216525 -0.8546151965 2.2673842319
HYDROGEN 8.1638216525 0.8546151965 2.2673842319
HYDROGEN -5.6722477685 1.4646077386 -2.8454093509
HYDROGEN 5.6722477685 -1.4646077386 -2.8454093509
HYDROGEN -6.4988451482 1.4822194466 -5.1558116842
HYDROGEN 6.4988451482 -1.4822194466 -5.1558116842
HYDROGEN -7.4520691544 0.3164879704 -4.2060273377
HYDROGEN 7.4520691544 -0.3164879704 -4.2060273377
HYDROGEN -8.1339532424 1.9056419745 -4.6259165433
HYDROGEN 8.1339532424 -1.9056419745 -4.6259165433
HYDROGEN -5.6227350238 3.6592272990 -4.0218459547
HYDROGEN 5.6227350238 -3.6592272990 -4.0218459547
HYDROGEN -7.2627913122 4.0217761026 -3.4307826487
HYDROGEN 7.2627913122 -4.0217761026 -3.4307826487
HYDROGEN -5.9187339480 3.8925177666 -2.2738657114
HYDROGEN 5.9187339480 -3.8925177666 -2.2738657114
HYDROGEN -3.3307439871 -8.2188446571 3.0482985312
HYDROGEN 3.3307439871 8.2188446571 3.0482985312
HYDROGEN -2.2922203656 -7.0516634523 3.9177694867
HYDROGEN 2.2922203656 7.0516634523 3.9177694867
HYDROGEN -3.6767177395 -6.4675081919 2.9461738576
HYDROGEN 3.6767177395 6.4675081919 2.9461738576
end
BASIS
* library 6-31G*
END
DFT
direct
iterations 100
XC B3LYP
vectors input PB_166.movecs
END
TDDFT
NROOTS 30
notriplet
thresh 1.0d-05
maxiter 200
END
task tddft energy
permanent_dir /media/DSK_1/pernwc
scratch_dir /media/DSK_2/scrnwc
After the completion of the scf cycles, as soon as the the code enters the TDDFT procedure, the following error occurs:
ARMCI INFO
The application attempted to allocate a shared memory segment of 5045551104 bytes in size. This might be in addition to segments that were allocated succesfully previously. The current system configuration does not allow enough shared memory to be allocated to the application.
This is most often caused by:
1) system parameter SHMMAX (largest shared memory segment) being too small or
2) insufficient swap space.
Please ask your system administrator to verify if SHMMAX matches the amount of memory needed by your application and the system has sufficient amount of swap space. Most UNIX systems can be easily reconfigured to allow larger shared memory segments,
see http://www.emsl.pnl.gov/docs/global/support.html
In some cases, the problem might be caused by insufficient swap space.
0:allocate: failed to create shared region : -1
(rank:0 hostname:gundam pid:10579):ARMCI DASSERT fail. ../../ga-5-1/armci/src/memory/shmem.c:armci_allocate():1117 cond:0
I was running the task using 24 cores having specified kernel.shmmax = 8589934592 (8192 MB)
and ARMCI_DEFAULT_SHMMAX=4096 (I also tried with ARMCI_DEFAULT_SHMMAX=8192 but nothing changes).
If someone can put me in the right direction, I really appreciate.
Thanks a lot,
Davide
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