Author Topic: faults in run with jobbsse (Read 8332 times)

Jandir · « **on:** March 23, 2014, 10:28:19 PM »

I have tried run jobbsse but I haven`t sucess yet. My system has 102 atoms. This is my output after did run defien:

1_ghosts auxbasis coord.init define.out.supermol GEO_OPT_CONVERGED job.start monomer3 original SGE_turbo_SMP_local slave1.output slave5.output slave9.output
2_ghosts basis define_input dscf.out gradient master mos outfile.2406484 slave10.output slave2.output slave6.output supermol
3_ghosts control define_input.supermol energy hessapprox monomer1 not.converged ridft.out.supermol slave11.output slave3.output slave7.output tmp
adc2.out coord define.out f.temp job.last monomer2 options runcalcs slave12.output slave4.output slave8.output

OUTPUT AFTER RUN JOBBSSE:

data group $actual step is not empty
due to the abend of dscf

check reason for abend ...

use the command 'actual -r' to get rid of that
========================
internal module stack:
------------------------
bsseenergy
========================
CONTRL dead = actual step
bsseenergy ended abnormally
bsseenergy ended abnormally
program stopped.
error in initial setup step... aborting

After type "actual -r"

dscf step seems to have been in serious trouble

My jobex is

##########################################
echo "STARTING AT " `date`

# jobex -ri -c 10
# aoforce > freq.out
## ********** GEOMETRY OPTIMIZATION CC2 ********************************
jobex -ri -c 700
# jobex -ri -level mp2 -c 700
jobbsse -ri –opt
## *********************************************************************
## ********** SINGLE POINT CC2 *****************************************
# dscf > dscf.out
# aoforce > aoforce.out
dscf> dscf.out
ricc2 > adc2.out
# jobex -c 4000 > jobex.out

## *********************************************************************
echo "FINISHED AT " `date`
##########################################

Any help is welcome.

Jandir

antti_karttunen · « **Reply #1 on:** March 24, 2014, 08:45:56 AM »

Hi,

please post the contents of dscf.out and slave1.output. The actual error message should be in there.

Antti

Jandir · « **Reply #2 on:** March 24, 2014, 12:15:25 PM »

slave.1.output

operating system is UNIX !
hostname is r28n24

OpenMP run-time library returned nthreads = 12

dscf (r28n24) : TURBOMOLE V6.4 3 Apr 2012 at 09:58:30
Copyright (C) 2012 TURBOMOLE GmbH, Karlsruhe

2014-03-21 14:56:07.840

Program dscf can not use the RI-J approximation.
Please either use the ridft program or delete the option $rij
from your control file.

MODTRACE: no modules on stack

Option $rij found!
dscf ended abnormally

ridft (r28n24) : TURBOMOLE V6.4 4 May 2012 at 11:14:21
Copyright (C) 2012 TURBOMOLE GmbH, Karlsruhe
2014-03-21 14:47:59.482

r i d f t

DFT program with RI approximation
for coulomb part

References:
6,1 Top

par_setmem: 39321600 1310720 F
MA: Allocated stack: 10.00000 MB/processor
SHM: Allocated heap : 300.0000 MB/processor
********** GlobalArray OPTION SETTINGS : **********
default distributed memory heap/proc = 39321600
default distributed memory stack/proc = 1310720
*****************************************************
Distributing input file(s)

+--------------------------------------------------+
| general information about current run |
+--------------------------------------------------+

SCF run will be profiled !

PBE functional
exchange: LDA + PBE
correlation: LDA (PW) + PBE
A DFT calculation using the RI-J approximation will be carried out.
Allocatable memory for RI due to $ricore (MB): 0
Multipole approximation for Coulomb integrals is used

+--------------------------------------------------+
| Atomic coordinate, charge and isotop information |
+--------------------------------------------------+

+--------------------------------------------------+
| Atomic coordinate, charge and isotop information |
+--------------------------------------------------+

atomic coordinates atom shells charge pseudo isotop
-12.12127448 -3.01799476 -1.97120476 c 11 6.000 0 0
-10.18663832 -2.09010464 -0.44540631 c 11 6.000 0 0
-11.17541909 0.64369696 1.10393693 s 14 16.000 0 0
-14.15322743 0.53046313 -0.29048713 c 11 6.000 0 0
-14.33049683 -1.55876588 -1.88493565 c 11 6.000 0 0
-16.01451136 2.42439695 0.25356511 c 11 6.000 0 0
-18.97510395 2.35104682 -1.18005674 s 14 16.000 0 0
-19.96028422 5.07769499 0.38511864 c 11 6.000 0 0
-18.03692048 5.97338869 1.94409101 c 11 6.000 0 0
-15.83989481 4.49632941 1.87099091 c 11 6.000 0 0
-7.69099501 -3.07402668 -0.07155944 c 11 6.000 0 0
-6.70636943 -5.78873519 -1.63681191 s 14 16.000 0 0
-3.71455941 -5.65316635 -0.24255106 c 11 6.000 0 0
-3.55607007 -3.55565226 1.36721081 c 11 6.000 0 0
-5.76415458 -2.11954223 1.46591042 c 11 6.000 0 0
-22.43648975 6.09942079 -0.01381672 c 11 6.000 0 0
-23.37629747 8.84742977 1.52091536 s 14 16.000 0 0
-26.35787167 8.76676609 0.10178480 c 11 6.000 0 0
-26.54737784 6.65965564 -1.49181086 c 11 6.000 0 0
-24.37043525 5.17414001 -1.56037527 c 11 6.000 0 0
-1.70715538 -7.37676317 -0.65232373 c 11 6.000 0 0
-1.59091289 -9.49380561 -2.17499988 c 11 6.000 0 0
-3.64775272 -10.33888052 -3.68726647 c 11 6.000 0 0
-5.34334233 -11.02224231 -4.92437680 n 11 7.000 0 0
-28.32214878 10.54839428 0.47273287 c 11 6.000 0 0
-28.38977063 12.68893917 1.96460071 c 11 6.000 0 0
-30.61080472 14.21144889 2.02668747 c 11 6.000 0 0
-32.43661545 15.44878477 2.06515434 n 11 7.000 0 0
-26.32183330 13.49208296 3.48485677 c 11 6.000 0 0
-24.61852980 14.14161134 4.72946365 n 11 7.000 0 0
0.68065781 -10.93710995 -2.28556208 c 11 6.000 0 0
2.55458989 -12.09880169 -2.36366594 n 11 7.000 0 0
-28.25945613 6.25754921 -2.56162286 h 6 1.000 0 0
-1.83903996 -3.11978885 2.41601341 h 6 1.000 0 0
-16.03229506 -2.00060933 -2.95451529 h 6 1.000 0 0
-5.98488583 -0.42534326 2.61221813 h 6 1.000 0 0
-18.24155635 7.66103123 3.10429209 h 6 1.000 0 0
0.01183732 -6.94535553 0.40871916 h 6 1.000 0 0
-14.14909234 4.91107020 2.96841058 h 6 1.000 0 0
-30.04445634 10.15332056 -0.59641408 h 6 1.000 0 0
-24.17616286 3.46705369 -2.69223514 h 6 1.000 0 0
-11.91666673 -4.71622472 -3.11584619 h 6 1.000 0 0
9.75587657 -0.04167243 -6.54208920 c 11 6.000 0 0
9.54284914 2.41892183 -5.60032926 c 11 6.000 0 0
7.78670738 -1.88350298 -6.02846940 c 11 6.000 0 0
12.17294124 -1.33926037 -6.45790902 c 11 6.000 0 0
7.35229568 3.13202189 -4.10879747 c 11 6.000 0 0
11.73851752 3.67605143 -4.53804163 c 11 6.000 0 0
5.67598233 -1.19611463 -4.59512774 c 11 6.000 0 0
11.69727810 -3.98279342 -5.89285246 c 11 6.000 0 0
8.19456510 4.82918441 -2.12259092 c 11 6.000 0 0
14.28741951 -0.12815559 -5.43429774 c 11 6.000 0 0
8.98653778 -4.31901207 -5.62631485 c 11 6.000 0 0
5.45505264 1.35842006 -3.61603978 c 11 6.000 0 0
14.06595440 2.42608853 -4.45602534 c 11 6.000 0 0
10.90506436 5.16578359 -2.38819654 c 11 6.000 0 0
4.68837788 -2.91904182 -2.70129827 c 11 6.000 0 0
13.35323156 -5.31689307 -4.32424254 c 11 6.000 0 0
7.10920381 4.69220309 0.28335465 c 11 6.000 0 0
16.00773202 -1.51445693 -3.80624850 c 11 6.000 0 0
8.03392056 -5.97853941 -3.80516311 c 11 6.000 0 0
4.32860577 1.21543879 -1.11667152 c 11 6.000 0 0
15.65020007 2.61897975 -2.22244421 c 11 6.000 0 0
12.43043318 5.35115102 -0.23706176 c 11 6.000 0 0
3.85525695 -1.42851076 -0.55192220 c 11 6.000 0 0
5.84549728 -5.26312468 -2.31339951 c 11 6.000 0 0
12.36298113 -7.03951895 -2.43156591 c 11 6.000 0 0
15.54904543 -4.05973215 -3.26185023 c 11 6.000 0 0
8.69261140 4.88368549 2.51628626 c 11 6.000 0 0
5.14078412 2.84955137 0.79633208 c 11 6.000 0 0
16.84963596 0.18358655 -1.82126223 c 11 6.000 0 0
9.75332704 -7.36464486 -2.17706187 c 11 6.000 0 0
14.84876931 4.05422674 -0.15275042 c 11 6.000 0 0
11.30302118 5.20665416 2.26104627 c 11 6.000 0 0
4.20674844 -2.33986593 1.90659404 c 11 6.000 0 0
6.21112739 -6.20953456 0.23686278 c 11 6.000 0 0
13.94675008 -6.84731393 -0.19878657 c 11 6.000 0 0
15.91571681 -5.00556260 -0.71183833 c 11 6.000 0 0
7.70279151 3.16136675 4.40953245 c 11 6.000 0 0
5.50726638 1.90406908 3.34678126 c 11 6.000 0 0
17.20254342 -0.72699410 0.63499172 c 11 6.000 0 0
8.62707756 -7.50914291 0.32073977 c 11 6.000 0 0
15.21408779 3.10811435 2.39764895 c 11 6.000 0 0
13.02373664 3.82043031 3.88908703 c 11 6.000 0 0
5.40643983 -4.77721864 2.30825627 c 11 6.000 0 0
5.04870957 -0.64169657 3.89267102 c 11 6.000 0 0
12.86219746 -6.98646848 2.20703175 c 11 6.000 0 0
16.72766356 -3.37064780 1.19991517 c 11 6.000 0 0
9.35942881 1.82576774 5.97667706 c 11 6.000 0 0
16.36849021 0.76262693 2.78395530 c 11 6.000 0 0
10.15145958 -7.32217875 2.47135542 c 11 6.000 0 0
12.07050331 2.16199194 5.71186950 c 11 6.000 0 0
6.98933081 -4.58384846 4.54336447 c 11 6.000 0 0
6.76878437 -2.02943012 5.52015286 c 11 6.000 0 0
13.70411059 -5.28844253 4.19198202 c 11 6.000 0 0
15.60052276 -3.51457740 3.69849740 c 11 6.000 0 0
8.88393078 -0.81768145 6.54314688 c 11 6.000 0 0
15.37858766 -0.95951060 4.67699318 c 11 6.000 0 0
9.31807683 -5.83176451 4.62145537 c 11 6.000 0 0
13.27015110 -0.27276071 6.11412981 c 11 6.000 0 0
11.51327493 -4.57470559 5.68367959 c 11 6.000 0 0
11.30059947 -2.11479864 6.62742938 c 11 6.000 0 0

center of nuclear mass : 0.27437892 -0.02777331 -0.00026015

center of nuclear charge: 0.15013709 -0.01519766 -0.00059189

+--------------------------------------------------+
| basis set information |
+--------------------------------------------------+

we will work with the 1s 3p 5d 7f 9g ... basis set
...i.e. with spherical basis functions...

type atoms prim cont basis
---------------------------------------------------------------------------
c 84 46 31 def2-TZVPP [5s3p2d1f|11s6p2d1f]
s 4 63 42 def2-TZVPP [5s5p3d1f|14s9p3d1f]
n 4 46 31 def2-TZVPP [5s3p2d1f|11s6p2d1f]
h 10 16 14 def2-TZVPP [3s2p1d|5s2p1d]
---------------------------------------------------------------------------
total: 102 4460 3036
---------------------------------------------------------------------------

total number of primitive shells : 75
total number of contracted shells : 1084
total number of cartesian basis functions : 3510
total number of SCF-basis functions : 3036

integral neglect threshold : 0.95E-11
integral storage threshold THIZE : 0.10E-04
integral storage threshold THIME : 5

RI-J AUXILIARY BASIS SET information:

we will work with the 1s 3p 5d 7f 9g 11h 13i auxiliary basis set
...i.e. with spherical basis functions...

type atoms prim cont basis
---------------------------------------------------------------------------
c 84 70 49 def2-TZVPP [6s4p3d1f1g|12s5p4d2f1g]
s 4 77 51 def2-TZVPP [8s4p3d1f1g|14s5p5d2f1g]
n 4 70 49 def2-TZVPP [6s4p3d1f1g|12s5p4d2f1g]
h 10 16 11 def2-TZVPP [3s1p1d|5s2p1d]
---------------------------------------------------------------------------
total: 102 6628 4626
---------------------------------------------------------------------------

total number of primitive shells : 83
total number of contracted shells : 1438
total number of cartesian basis functions : 5740
total number of SCF-basis functions : 4626

symmetry group of the molecule : c1

the group has the following generators :
c1(z)
1 symmetry operations found

there are 1 real representations : a

maximum number of shells which are related by symmetry : 1

mo occupation :
irrep mo's occupied
a 3036 303

number of basis functions : 3036
number of occupied orbitals : 303

------------------
density functional
------------------
PBE functional
exchange: LDA + PBE
correlation: LDA (PW) + PBE
iterations will be done with small grid

spherical integration : Lebedev's spherical grid
spherical gridsize : 4
i.e. gridpoints : 434
value for diffuse not defined
radial integration : Chebyshev 2nd kind (scaling 3)
radial gridsize : 6
integration cells : 102
partition function : becke
partition sharpness : 3

biggest AO integral is expected to be 9.804440325

------------------------
RI-J - INFORMATION
------------------------
+---------------- Multipole Accelerated RI-J ---------------+
-------------------------------------------------------------
Number of bins for density partition : 8
Maximum multipole moment used : 14
Multipole precision parameter : 1.0000E-08
Threshold for moment summation : 1.0000E-24
Minimum separation between boxes : 0.0000E+00
Maximum allowed extent : 2.0000E+01
+-----------------------------------------------------------+

Extensions and centers of shell-pairs:
number of shells with a single center: 191709
number of shells with double centers: 14543
Memory core needed for (P|Q) and Cholesky 82 MByte on GA
Memory core minimum needed except 9 MByte

****************************************
Memory allocated for RI-J 9 MByte
plus additional 0 MByte (integrals) (GA)
plus additional 82 MByte (pqmatrix) (GA)
****************************************
PQ decomposition by par_ichol 4626

------------------------
nuclear repulsion energy : 15168.6065892
------------------------

-----------------
-S,T+V- integrals
-----------------

1e-integrals will be neglected if expon. factor < 0.952126E-12

Difference densities algorithm switched on.
The maximal number of linear combinations of
difference densities is 20 .

automatic virtual orbital shift switched on
shift if e(lumo)-e(homo) < 0.10000000

DIIS switched on: error vector is FDS-SDF
Max. Iterations for DIIS is : 4
DIIS matrix (see manual)
Scaling factor of diagonals : 1.200
threshold for scaling factor : 0.000

scf convergence criterion : increment of total energy < .1000000D-05
and increment of one-electron energy < .1000000D-02

MOs are in ASCII format !

reading orbital data $scfmo from file mos .

orbital characterization : scfconv=6

mo-orthogonalization by Cholesky decomposition

DSCF restart information will be dumped onto file mos

Starting SCF iterations

Multipoles:
mktayshl: transb used 2667 times; moments skipped 0
mktayaux: transb used 33239 times; moments skipped 0
non-zero weights= 32253
Overall gridpoints after grid construction = 332867

ITERATION ENERGY 1e-ENERGY 2e-ENERGY NORM[dD(SAO)] TOL
1 -5014.9544354648 -37067.644903 16884.083879 0.000D+00 0.950D-11
Exc = -585.865814621 Coul = 17469.9496934
N = 605.99906094
current damping = 0.700

max. resid. norm for Fia-block= 2.151D-03 for orbital 211a
max. resid. fock norm = 6.701D-03 for orbital 631a
irrep a : virtual orbitals shifted by 0.02065
Multipoles:
mktayshl: transb used 2667 times; moments skipped 0
mktayaux: transb used 33239 times; moments skipped 0

Jandir · « **Reply #3 on:** March 24, 2014, 12:16:58 PM »

dscf.out

operating system is UNIX !
hostname is r28n24

OpenMP run-time library returned nthreads = 12

dscf (r28n24) : TURBOMOLE V6.4 3 Apr 2012 at 09:58:30
Copyright (C) 2012 TURBOMOLE GmbH, Karlsruhe

2014-03-21 14:56:07.840

Program dscf can not use the RI-J approximation.
Please either use the ridft program or delete the option $rij
from your control file.

MODTRACE: no modules on stack

Option $rij found!
dscf ended abnormally

antti_karttunen · « **Reply #4 on:** March 24, 2014, 02:12:04 PM »

Hmm, one reason could be that jobbsse somehow neglects your -ri switch and runs normal dscf (which then crashes due to the presence of $rij keyword). I don't know if version 6.5 could fix this. But I'm also a bit confused by your SGE script. While running both jobex -ri and jobbsse -ri in the same script might be OK from a technical point of view, it surely complicates troubleshooting, especially if you are running jobbsse for the first time. Perhaps it's best to create a new (clean) directory, run define and then execute just jobbsse -ri to see if everything goes OK.

Antti

Jandir · « **Reply #5 on:** March 24, 2014, 02:46:01 PM »

Ok. Right now I`m making another attempt with following structure:

# jobex -ri -c 10
# aoforce > freq.out
jobbsse -opt -energy -level dft -setup &
dscf > dscf.out

## ********** GEOMETRY OPTIMIZATION CC2 ********************************
# jobex -ri -level cc2 -c 700
# jobex -ri -level mp2 -c 700
## *********************************************************************
## ********** SINGLE POINT CC2 *****************************************
# dscf > dscf.out
# aoforce > aoforce.out
# ricc2 > adc2.out
# jobex -c 4000 > jobex.out

TURBOMOLE Users Forum

Author Topic: faults in run with jobbsse (Read 8332 times)

Jandir

faults in run with jobbsse

antti_karttunen

Re: faults in run with jobbsse

Jandir

Re: faults in run with jobbsse

Jandir

Re: faults in run with jobbsse

antti_karttunen

Re: faults in run with jobbsse

Jandir

Re: faults in run with jobbsse