iOpenShell » Q-Chem specific questions » hanging job during constrained dihedral scans

hanging job during constrained dihedral scans

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Author Post
Member
Registered: Feb 2008
Posts: 33
Hello All,

I am performing constrained scans at the M08-SO/(varying basis set) level of theory for oxygenated hydrocarbon species. I am running a couple dozen jobs and noticed that only about a half successfully finished, which leads me to believe this might be a job handler (sun grid engine, in this case) problem, but I wanted to bring it up here anyway. The ones that do fail print to the qchem.out file up to some like :

A total of 1 constraints

1
1 3.0100000
2 12.0100000
3 10.0100000
4 13.0100000
5 14.0100000
6 180.0000000
7-180.0000000
8 15.0000000
9 0.0000000
10 0.0000000

There are no error messages. It also doesn't seem to matter if I'm running these jobs in parallel or serial. I've also checked the scratch files and it seems these failing jobs just 'run' for a few min and then take up their allotted walltime, and finally abort. Any suggestions? Thanks.
Member
Registered: Nov 2007
Posts: 110
Location: Q-Chem Inc.
Can you provide the Q-Chem input file?
Member
Registered: Feb 2008
Posts: 33
Sure, an example is below. I've provided the complete output as well.

$i]j5]=Wo\Grem
JOBTYPE pes_scan
EXCHANGE M062X
BASIS gen
GUI=2
UNRESTRICTED TRUE
CORRELATION NONE
$i]j5]=Wo\Gend

$i]j5]=Wo\Gscan
tors 4 3 5 7 180 -180 15
$i]j5]=Wo\Gend

$i]j5]=Wo\Gcomment
c5h11o-1
$i]j5]=Wo\Gend

$i]j5]=Wo\Gmolecule
READ c5h11o-3MG3S.out
$i]j5]=Wo\Gend

$i]j5]=Wo\Gbasis
H 0
S 3 1.00
3.386500000000E+01 2.549380000000E-02
5.094790000000E+00 1.903730000000E-01
1.158790000000E+00 8.521610000000E-01
S 1 1.00
3.258400000000E-01 1.000000000000E+00
S 1 1.00
1.027410000000E-01 1.000000000000E+00
S 1 1.00
3.600000000000E-02 1.000000000000E+00
P 1 1.00
1.500000000000E+00 1.000000000000E+00
P 1 1.00
3.750000000000E-01 1.000000000000E+00
****
C 0
S 6 1.00
4.563240000000E+03 1.966650000000E-03
6.820240000000E+02 1.523060000000E-02
1.549730000000E+02 7.612690000000E-02
4.445530000000E+01 2.608010000000E-01
1.302900000000E+01 6.164620000000E-01
1.827730000000E+00 2.210060000000E-01
S 3 1.00
2.096420000000E+01 1.146600000000E-01
4.803310000000E+00 9.199990000000E-01
1.459330000000E+00 -3.030680000000E-03
S 1 1.00
4.834560000000E-01 1.000000000000E+00
S 1 1.00
1.455850000000E-01 1.000000000000E+00
S 1 1.00
4.380000000000E-02 1.000000000000E+00
P 3 1.00
2.096420000000E+01 4.024870000000E-02
4.803310000000E+00 2.375940000000E-01
1.459330000000E+00 8.158540000000E-01
P 1 1.00
4.834560000000E-01 1.000000000000E+00
P 1 1.00
1.455850000000E-01 1.000000000000E+00
P 1 1.00
4.380000000000E-02 1.000000000000E+00
D 1 1.00
1.252000000000E+00 1.000000000000E+00
D 1 1.00
3.130000000000E-01 1.000000000000E+00
F 1 1.00
8.000000000000E-01 1.000000000000E+00
****
O 0
S 6 1.00
8.588500000000E+03 1.895150000000E-03
1.297230000000E+03 1.438590000000E-02
2.992960000000E+02 7.073200000000E-02
8.737710000000E+01 2.400010000000E-01
2.567890000000E+01 5.947970000000E-01
3.740040000000E+00 2.808020000000E-01
S 3 1.00
4.211750000000E+01 1.138890000000E-01
9.628370000000E+00 9.208110000000E-01
2.853320000000E+00 -3.274470000000E-03
S 1 1.00
9.056610000000E-01 1.000000000000E+00
S 1 1.00
2.556110000000E-01 1.000000000000E+00
S 1 1.00
8.450000000000E-02 1.000000000000E+00
P 3 1.00
4.211750000000E+01 3.651140000000E-02
9.628370000000E+00 2.371530000000E-01
2.853320000000E+00 8.197020000000E-01
P 1 1.00
9.056610000000E-01 1.000000000000E+00
P 1 1.00
2.556110000000E-01 1.000000000000E+00
P 1 1.00
8.450000000000E-02 1.000000000000E+00
D 1 1.00
2.584000000000E+00 1.000000000000E+00
D 1 1.00
6.460000000000E-01 1.000000000000E+00
F 1 1.00
1.400000000000E+00 1.000000000000E+00
****
$i]j5]=Wo\Gend


Output:

Running Job 1 of 1 c5h11o3scan2.in
qchem c5h11o3scan2.in_19500.0 /tmp/qchem19500/ 4
/opt/qchem/bin/mpi/mpirun_qchem -machinefile /tmp/281341.1.normal1/hostfile -np 4 /opt/qchem/exe/qcprog.exe c5h11o3scan2.in_19500.0 /tmp/qchem19500/

Process 0 of 4 is on node07.cluster - thread support 0
Process 2 of 4 is on node07.cluster - thread support 0
Process 1 of 4 is on node07.cluster - thread support 0
Process 3 of 4 is on node07.cluster - thread support 0
initial socket setup ...start
initial socket setup ...done
now start server 0 ...
Welcome to Q-Chem
A Quantum Leap Into The Future Of Chemistry

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R. A. DiStasio Jr., R. C. Lochan, T. Wang, G. J. O. Beran, N. A. Besley,
J. M. Herbert, C. Y. Lin, T. Van Voorhis, S. H. Chien, A. Sodt, R. P. Steele,
V. A. Rassolov, P. E. Maslen, P. P. Korambath, R. D. Adamson, B. Austin,
J. Baker, E. F. C. Byrd, H. Dachsel, R. J. Doerksen, A. Dreuw, B. D. Dunietz,
A. D. Dutoi, T. R. Furlani, S. R. Gwaltney, A. Heyden, S. Hirata, C.-P. Hsu,
G. Kedziora, R. Z. Khaliullin, P. Klunzinger, A. M. Lee, M. S. Lee, W. Liang,
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F. J. Keil, A. Warshel, W. J. Hehre, H. F. Schaefer III, J. Kong,
A. I. Krylov, P. M. W. Gill, M. Head-Gordon

Additional authors for Version 3.1:
Z. Gan, Y. Zhao, N. E. SchultzD. Truhlar, E. Epifanovsky, M. Oana

Additional authors for Version 3.2:
R. Baer, B. R. Brooks, D. Casanova, J.-D. Chai, C.-L. Cheng, C. Cramer,
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D. Neuhauser, R. Olson, M. A. Rohrdanz, K. S. Thanthiriwatte, A. J. W. Thom,
V. Vanovschi, C. F. Williams, Q. Wu, Z.-Q. You

Additional authors for Version 4.0:
A. Aspuru-Guzik, Y. Bernard, C. Chang, J. Deng, A. Dreuw, M. Diedenhofen,
R. G. Edgar, D. Ghosh, W. A. Goddard III, M. Goldey, L. D. Jacobson,
M. Gordon, B. Kaduk, I. Kaliman, K. Khistyaev, R. King, A. Klamt,
D. Kosenkov, T. Kus, D. Lambrecht, A. Landau, A. W. Lange, K. Lawler, F. Liu,
J. Liu, R. Olivares-Amaya, S. P. Mao, J. Parkhill, N. Russ, M. Schmidt,
N. Shenvi, D. Small, Y. C. Su, E. Sundstrom, L. Vogt, O. Vydrov, M. Watson,
M. Wormit, X. Xu, S. Yeganeh, I. Y. Zhang, D. Zuev

Additional authors for Version 4.1:
X. Feng, M. W. D. Hanson-Heine, P. Horn, H. Ji, A. Laurent, R. Peverati,
N. Mardirossian, N. Sergueev, S. Sharada, P. Zimmerman


Q-Chem, Version 4.1, Q-Chem, Inc., Pittsburgh, PA (2013).

Intel X86 Linux Version 4.1.0.1

Q-chem begins on Wed Apr 9 16:37:14 2014

Host:
0

Scratch files written to /tmp/qchem19500.0//
Oct1213 14483_epif 4150
Parallel job on 4 processors
Processing $i]j5]=Wo\Grem in /opt/qchem/config/preferences.
MEM_TOTAL 2000
Warning: disabling incdft.
Q-Chem warning in module /home/scratch/svnadmin/14483_epif/qchem/forms1/BasisType.C, line 1125:

Setting pure/cartesian flag to 2111 for general basis


Finally everything over in PARseQInput

--------------------------------------------------------------
User input:
--------------------------------------------------------------
$i]j5]=Wo\Grem
JOBTYPE pes_scan
EXCHANGE M062X
BASIS gen
GUI=2
UNRESTRICTED TRUE
CORRELATION NONE
$i]j5]=Wo\Gend

$i]j5]=Wo\Gscan
tors 4 3 5 7 180 -180 15
$i]j5]=Wo\Gend

$i]j5]=Wo\Gcomment
c5h11o-1
$i]j5]=Wo\Gend

$i]j5]=Wo\Gmolecule
READ c5h11o-3MG3S.out
$i]j5]=Wo\Gend

$i]j5]=Wo\Gbasis
H 0
S 3 1.00
3.386500000000E+01 2.549380000000E-02
5.094790000000E+00 1.903730000000E-01
1.158790000000E+00 8.521610000000E-01
S 1 1.00
3.258400000000E-01 1.000000000000E+00
S 1 1.00
1.027410000000E-01 1.000000000000E+00
S 1 1.00
3.600000000000E-02 1.000000000000E+00
P 1 1.00
1.500000000000E+00 1.000000000000E+00
P 1 1.00
3.750000000000E-01 1.000000000000E+00
****
C 0
S 6 1.00
4.563240000000E+03 1.966650000000E-03
6.820240000000E+02 1.523060000000E-02
1.549730000000E+02 7.612690000000E-02
4.445530000000E+01 2.608010000000E-01
1.302900000000E+01 6.164620000000E-01
1.827730000000E+00 2.210060000000E-01
S 3 1.00
2.096420000000E+01 1.146600000000E-01
4.803310000000E+00 9.199990000000E-01
1.459330000000E+00 -3.030680000000E-03
S 1 1.00
4.834560000000E-01 1.000000000000E+00
S 1 1.00
1.455850000000E-01 1.000000000000E+00
S 1 1.00
4.380000000000E-02 1.000000000000E+00
P 3 1.00
2.096420000000E+01 4.024870000000E-02
4.803310000000E+00 2.375940000000E-01
1.459330000000E+00 8.158540000000E-01
P 1 1.00
4.834560000000E-01 1.000000000000E+00
P 1 1.00
1.455850000000E-01 1.000000000000E+00
P 1 1.00
4.380000000000E-02 1.000000000000E+00
D 1 1.00
1.252000000000E+00 1.000000000000E+00
D 1 1.00
3.130000000000E-01 1.000000000000E+00
F 1 1.00
8.000000000000E-01 1.000000000000E+00
****
O 0
S 6 1.00
8.588500000000E+03 1.895150000000E-03
1.297230000000E+03 1.438590000000E-02
2.992960000000E+02 7.073200000000E-02
8.737710000000E+01 2.400010000000E-01
2.567890000000E+01 5.947970000000E-01
3.740040000000E+00 2.808020000000E-01
S 3 1.00
4.211750000000E+01 1.138890000000E-01
9.628370000000E+00 9.208110000000E-01
2.853320000000E+00 -3.274470000000E-03
S 1 1.00
9.056610000000E-01 1.000000000000E+00
S 1 1.00
2.556110000000E-01 1.000000000000E+00
S 1 1.00
8.450000000000E-02 1.000000000000E+00
P 3 1.00
4.211750000000E+01 3.651140000000E-02
9.628370000000E+00 2.371530000000E-01
2.853320000000E+00 8.197020000000E-01
P 1 1.00
9.056610000000E-01 1.000000000000E+00
P 1 1.00
2.556110000000E-01 1.000000000000E+00
P 1 1.00
8.450000000000E-02 1.000000000000E+00
D 1 1.00
2.584000000000E+00 1.000000000000E+00
D 1 1.00
6.460000000000E-01 1.000000000000E+00
F 1 1.00
1.400000000000E+00 1.000000000000E+00
****
$i]j5]=Wo\Gend

--------------------------------------------------------------
----------------------------------------------------
Standard Nuclear Orientation (Angstroms)
I Atom X Y Z
----------------------------------------------------
1 C -1.006298 0.036412 -0.332290
2 H -1.007588 0.092267 -1.432760
3 C 0.292381 0.589152 0.163904
4 H 0.314624 1.225868 1.045789
5 C 1.583610 0.297786 -0.519747
6 H 1.984159 1.184943 -1.026325
7 H 1.428577 -0.472446 -1.292421
8 O 2.617231 -0.094442 0.378395
9 H 2.258861 -0.775016 0.967239
10 C -2.198994 0.837609 0.191043
11 H -2.120734 1.893002 -0.087267
12 H -3.141047 0.444953 -0.205471
13 H -2.244349 0.779121 1.285115
14 C -1.147211 -1.450786 0.044761
15 H -0.300797 -2.038713 -0.325390
16 H -2.064690 -1.877680 -0.376478
17 H -1.185796 -1.561795 1.134788
----------------------------------------------------
Molecular Point Group C1 NOp = 1
Largest Abelian Subgroup C1 NOp = 1
Nuclear Repulsion Energy = 243.6222714792 hartrees
There are 25 alpha and 24 beta electrons
Requested basis set is non-standard
There are 138 shells and 314 basis functions

Total QAlloc Memory Limit 2000 MB
Mega-Array Size 61 MB
MEM_STATIC part 62 MB
A total of 1 constraints

1
1 3.0100000
2 4.0100000
3 3.0100000
4 5.0100000
5 7.0100000
6 180.0000000
7-180.0000000
8 15.0000000
9 0.0000000
10 0.0000000
Member
Registered: Nov 2007
Posts: 110
Location: Q-Chem Inc.
Can you try changing the line
tors 4 3 5 7 180 -180 15
to
tors 4 3 5 7 -180 180 15
where the first value of the torsional angle is put before the last value?
Member
Registered: Feb 2008
Posts: 33
That seems to do the trick. Thanks Yihan.
Member
Registered: Jul 2016
Posts: 2
Hello,

I also have problem to scan the 1D-PES via dihedral angle.

This is my setting

tors 6 4 1 2 0 180 15

But the output cannot stop at the final dihedral angle (180), and then it shows the wrong angle (-18).

I extract the dihedral angle data from the output.

Dihedral: 6 4 1 2 0.000 0.000
Dihedral: 6 4 1 2 0.000 0.000
Dihedral: 6 4 1 2 0.000 0.000
Dihedral: 6 4 1 2 -0.000 0.000
Dihedral: 6 4 1 2 0.000 0.000
Dihedral: 6 4 1 2 -0.000 15.000
Dihedral: 6 4 1 2 14.517 15.000
Dihedral: 6 4 1 2 15.000 15.000
Dihedral: 6 4 1 2 15.000 15.000
Dihedral: 6 4 1 2 15.000 30.000
Dihedral: 6 4 1 2 29.506 30.000
Dihedral: 6 4 1 2 30.000 30.000
Dihedral: 6 4 1 2 30.000 30.000
Dihedral: 6 4 1 2 30.000 45.000
Dihedral: 6 4 1 2 44.486 45.000
Dihedral: 6 4 1 2 45.000 45.000
Dihedral: 6 4 1 2 45.000 45.000
Dihedral: 6 4 1 2 45.000 45.000
Dihedral: 6 4 1 2 45.000 60.000
Dihedral: 6 4 1 2 59.438 60.000
Dihedral: 6 4 1 2 60.000 60.000
Dihedral: 6 4 1 2 60.000 60.000
Dihedral: 6 4 1 2 60.000 60.000
Dihedral: 6 4 1 2 60.000 60.000
Dihedral: 6 4 1 2 60.000 75.000
Dihedral: 6 4 1 2 74.398 75.000
Dihedral: 6 4 1 2 75.000 75.000
Dihedral: 6 4 1 2 75.000 75.000
Dihedral: 6 4 1 2 75.000 75.000
Dihedral: 6 4 1 2 75.000 75.000
Dihedral: 6 4 1 2 75.000 90.000
Dihedral: 6 4 1 2 89.358 90.000
Dihedral: 6 4 1 2 89.999 90.000
Dihedral: 6 4 1 2 90.000 90.000
Dihedral: 6 4 1 2 90.000 90.000
Dihedral: 6 4 1 2 90.000 90.000
Dihedral: 6 4 1 2 90.000 90.000
Dihedral: 6 4 1 2 90.000 105.000
Dihedral: 6 4 1 2 104.320 105.000
Dihedral: 6 4 1 2 104.999 105.000
Dihedral: 6 4 1 2 105.000 105.000
Dihedral: 6 4 1 2 105.000 105.000
Dihedral: 6 4 1 2 105.000 105.000
Dihedral: 6 4 1 2 105.000 105.000
Dihedral: 6 4 1 2 105.000 120.000
Dihedral: 6 4 1 2 119.286 120.000
Dihedral: 6 4 1 2 119.999 120.000
Dihedral: 6 4 1 2 120.000 120.000
Dihedral: 6 4 1 2 120.000 120.000
Dihedral: 6 4 1 2 120.000 120.000
Dihedral: 6 4 1 2 120.000 120.000
Dihedral: 6 4 1 2 120.000 120.000
Dihedral: 6 4 1 2 120.000 135.000
Dihedral: 6 4 1 2 134.258 135.000
Dihedral: 6 4 1 2 134.999 135.000
Dihedral: 6 4 1 2 134.999 135.000
Dihedral: 6 4 1 2 135.000 135.000
Dihedral: 6 4 1 2 135.000 135.000
Dihedral: 6 4 1 2 135.000 135.000
Dihedral: 6 4 1 2 135.000 135.000
Dihedral: 6 4 1 2 135.000 150.000
Dihedral: 6 4 1 2 149.241 150.000
Dihedral: 6 4 1 2 149.998 150.000
Dihedral: 6 4 1 2 149.999 150.000
Dihedral: 6 4 1 2 150.000 150.000
Dihedral: 6 4 1 2 150.000 150.000
Dihedral: 6 4 1 2 150.000 150.000
Dihedral: 6 4 1 2 150.000 150.000
Dihedral: 6 4 1 2 150.000 150.000
Dihedral: 6 4 1 2 150.000 165.000
Dihedral: 6 4 1 2 164.242 165.000
Dihedral: 6 4 1 2 164.998 165.000
Dihedral: 6 4 1 2 164.999 165.000
Dihedral: 6 4 1 2 165.000 165.000
Dihedral: 6 4 1 2 165.000 165.000
Dihedral: 6 4 1 2 165.000 165.000
Dihedral: 6 4 1 2 165.000 165.000
Dihedral: 6 4 1 2 165.000 165.000
Dihedral: 6 4 1 2 165.000 180.000
Dihedral: 6 4 1 2 179.300 180.000
Dihedral: 6 4 1 2 179.998 180.000
Dihedral: 6 4 1 2 179.995 180.000
Dihedral: 6 4 1 2 179.998 180.000
Dihedral: 6 4 1 2 179.996 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000
Dihedral: 6 4 1 2 -18.043 180.000

Thanks for your patient to read this question.

Page: 1

iOpenShell » Q-Chem specific questions » hanging job during constrained dihedral scans