Hi,
I am running docker in LSF with over 300GB memory and >=16 cores using a tinker program for small molecules called Poltype2. I am getting a segfault from memory but the log doesn’t even get past the integral section so not sure.
Psi4 input:
molecule {
0 1
O -6.369787488209 0.758212450846 -0.849627614529
N -3.647767587514 0.346041302745 0.200691612299
N -1.327604539555 -0.306119339874 0.192661838416
N 6.472560499215 -0.715748777872 -0.162786953897
N -6.456741296627 2.588032900937 0.526290718055
N 0.212941995780 1.518418143018 -0.195955613549
N 9.127396724275 -1.347766501451 -0.893422154225
N 0.918049412138 -0.699071851876 0.135965102619
N 2.918384947439 -1.767575968563 0.192627516150
C -4.240385575906 -0.976507119452 0.399016865942
C -4.060331454931 -1.880938101936 -0.830552529452
C -3.644863370919 -1.754399121116 1.602318109537
C -3.998726994183 -3.283850791692 -0.230402943414
C -3.133145719845 -3.076378892798 1.015005804156
C -4.319784306597 1.547087309708 0.029047638009
C -2.306132598550 0.597674995440 0.085771223678
C -2.125794393475 1.984494853804 -0.153998843049
C -3.414472784565 2.574974789601 -0.188498172010
C -5.797694505315 1.575739591234 -0.112301589966
C -0.794736407981 2.386256776881 -0.289908639890
C -0.100274259761 0.218220026783 0.037858170427
C 7.096504336050 -1.962791795426 0.269773854776
C 7.032385997558 -0.280093120332 -1.449533726295
C 8.593618862583 -1.746767901239 0.405369562762
C 8.530068357169 -0.082185546003 -1.308834676670
C 5.059740017727 -0.683544283119 -0.116218947369
C -7.881943380461 2.734800874977 0.281134514848
C -5.936687060937 3.346927343826 1.651086244134
C 2.303577347316 -0.584145388598 0.036803644970
C 4.389853387283 0.541733108711 -0.259966094293
C 4.257203571404 -1.809675880242 0.107182846096
C 3.007874809620 0.608618377077 -0.195174448582
H -5.304337733868 -0.798421641579 0.554574269516
H -4.863438814448 -1.720545771601 -1.554666557249
H -3.106142186194 -1.646994848213 -1.312837084609
H -2.858814986670 -1.187984506441 2.105119708711
H -4.438491566846 -1.941047170607 2.333899504712
H -3.589206486951 -4.025675123925 -0.922849730912
H -5.003300788106 -3.619106059073 0.056711784981
H -3.187640405581 -3.905903874494 1.726787880405
H -2.088900931006 -2.955158582958 0.711997452229
H -3.672171947309 3.608157529994 -0.385721969334
H -0.519848426482 3.424355242060 -0.477450102798
H 6.921191307341 -2.787363824769 -0.442618945793
H 6.674110583103 -2.244185641145 1.239423729973
H 6.559384590650 0.659247663904 -1.744988029897
H 6.836527936256 -1.027738045464 -2.236996002192
H 8.767238168175 -0.994517187654 1.194174278332
H 9.071067943037 -2.683586652446 0.711700161664
H 8.707580966365 0.736362299373 -0.589606128111
H 8.953590609762 0.209989261417 -2.275712612652
H 10.139926453214 -1.245088128324 -0.831072651772
H 0.611479247647 -1.652148311440 0.308855779327
H -8.130390724767 2.225544615434 -0.647589222787
H -8.467607624332 2.296407743343 1.097619338650
H -8.124329593117 3.798421184049 0.204971098484
H -6.555140668020 3.159916080289 2.536758599417
H -4.911990779435 3.051550049424 1.862343950577
H -5.961828833470 4.420021126418 1.433307923659
H 4.965128628871 1.454782689009 -0.393539033033
H 4.691697655612 -2.798016989133 0.228555698618
H 2.476346892183 1.544415213137 -0.298967192883
}
memory 392GB
set_num_threads(16)
psi4_io.set_default_path("/scratch1/fs1/bolton/brian/psi4/Psi4-ribociclib")
set maxiter 500
set freeze_core True
set PROPERTIES_ORIGIN ["COM"]
set cubeprop_tasks ['esp']
set basis aug-cc-pVTZ
E, wfn = properties('mp2',properties=['dipole'],return_wfn=True)
cubeprop(wfn)
fchk(wfn, "ribociclib-esp.fchk")
oeprop(wfn,"GRID_ESP","WIBERG_LOWDIN_INDICES","MULLIKEN_CHARGES")
clean()
rrors for Psi4 step with forrtl: severe (174): SIGSEGV, segmentation fault occurred
and here is trace:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libgdma.so 00007FA8EE65B0DC for__signal_handl Unknown Unknown
libpthread-2.27.s 00007FA8F5D1E980 Unknown Unknown Unknown
libc-2.27.so 00007FA8F4FF5C01 fseek Unknown Unknown
core.cpython-38-x 00007FA8F0F65581 _ZN3psi8DFHelper1 Unknown Unknown
core.cpython-38-x 00007FA8F0FE0610 _ZN3psi8DFHelper1 Unknown Unknown
core.cpython-38-x 00007FA8F0FE1274 _ZN3psi8DFHelper1 Unknown Unknown
core.cpython-38-x 00007FA8F121B435 _ZN3psi7MemDFJK13 Unknown Unknown
core.cpython-38-x 00007FA8F3479548 Unknown Unknown Unknown
core.cpython-38-x 00007FA8F34795BB Unknown Unknown Unknown
core.cpython-38-x 00007FA8F3061D69 Unknown Unknown Unknown
python3.8 000055EC0CDF0B94 PyCFunction_Call Unknown Unknown
python3.8 000055EC0CDFFF2E _PyObject_MakeTpC Unknown Unknown
python3.8 000055EC0CE75E1E Unknown Unknown Unknown
python3.8 000055EC0CE96D23 _PyEval_EvalFrame Unknown Unknown
python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown
python3.8 000055EC0CE75807 Unknown Unknown Unknown
python3.8 000055EC0CE93725 _PyEval_EvalFrame Unknown Unknown
python3.8 000055EC0CE74F06 _PyFunction_Vecto Unknown Unknown
python3.8 000055EC0CE929EB _PyEval_EvalFrame Unknown Unknown
python3.8 000055EC0CE74F06 _PyFunction_Vecto Unknown Unknown
python3.8 000055EC0CE929EB _PyEval_EvalFrame Unknown Unknown
python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown
python3.8 000055EC0CE750D8 _PyFunction_Vecto Unknown Unknown
python3.8 000055EC0CDE9DAE PyObject_Call Unknown Unknown
python3.8 000055EC0CE940A8 _PyEval_EvalFrame Unknown Unknown
python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown
python3.8 000055EC0CE750D8 _PyFunction_Vecto Unknown Unknown
python3.8 000055EC0CDE9DAE PyObject_Call Unknown Unknown
python3.8 000055EC0CE940A8 _PyEval_EvalFrame Unknown Unknown
python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown
python3.8 000055EC0CE750D8 _PyFunction_Vecto Unknown Unknown
python3.8 000055EC0CDE9DAE PyObject_Call Unknown Unknown
python3.8 000055EC0CE940A8 _PyEval_EvalFrame Unknown Unknown
python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown
python3.8 000055EC0CE750D8 _PyFunction_Vecto Unknown Unknown
python3.8 000055EC0CE93725 _PyEval_EvalFrame Unknown Unknown
python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown
python3.8 000055EC0CE74D59 PyEval_EvalCodeEx Unknown Unknown
python3.8 000055EC0CF19B5B PyEval_EvalCode Unknown Unknown
python3.8 000055EC0CF19BF3 Unknown Unknown Unknown
python3.8 000055EC0CF335B3 Unknown Unknown Unknown
python3.8 000055EC0CF37E1D PyRun_StringFlags Unknown Unknown
python3.8 000055EC0CF3829F Unknown Unknown Unknown
python3.8 000055EC0CDEDA5B Unknown Unknown Unknown
python3.8 000055EC0CE928CF _PyEval_EvalFrame Unknown Unknown
python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown
python3.8 000055EC0CE74D59 PyEval_EvalCodeEx Unknown Unknown
python3.8 000055EC0CF19B5B PyEval_EvalCode Unknown Unknown
python3.8 000055EC0CF19BF3 Unknown Unknown Unknown
python3.8 000055EC0CF335B3 Unknown Unknown Unknown
python3.8 000055EC0CF385D2 Unknown Unknown Unknown
python3.8 000055EC0CF387B2 PyRun_SimpleFileE Unknown Unknown
python3.8 000055EC0CF38D2D Py_RunMain Unknown Unknown
python3.8 000055EC0CF38EE9 Py_BytesMain Unknown Unknown
libc-2.27.so 00007FA8F4F8FC87 __libc_start_main Unknown Unknown
python3.8 000055EC0CEAC989 Unknown Unknown Unknown