That appears to have been the problem.
Adding the recommended commands to the PBS script produced the following resutls
linux-vdso.so.1 => (0x00007fff2f9ff000)
libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x0000003c9a000000)
libmkl_scalapack_ilp64.so => /opt/intel/mkl/lib/intel64/libmkl_scalapack_ilp64.so (0x00002b3db65ff000)
libmkl_intel_ilp64.so => /opt/intel/mkl/lib/intel64/libmkl_intel_ilp64.so (0x00002b3db6e07000)
libmkl_sequential.so => /opt/intel/mkl/lib/intel64/libmkl_sequential.so (0x00002b3db7508000)
libmkl_core.so => /opt/intel/mkl/lib/intel64/libmkl_core.so (0x00002b3db7ba7000)
libmkl_blacs_intelmpi_ilp64.so => /opt/intel/mkl/lib/intel64/libmkl_blacs_intelmpi_ilp64.so (0x00002b3db8db5000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003c99400000)
libm.so.6 => /lib64/libm.so.6 (0x0000003c99800000)
libmpigf.so.4 => /opt/intel/impi/4.1.0.024/intel64/lib/libmpigf.so.4 (0x00002b3db9023000)
libmpi_ilp64.so.4 => /opt/intel/impi/4.1.0.024/intel64/lib/libmpi_ilp64.so.4 (0x00002b3db9253000)
libmpi.so.4 => /opt/intel/impi/4.1.0.024/intel64/lib/libmpi.so.4 (0x00002b3db947e000)
libibumad.so.3 => /usr/lib64/libibumad.so.3 (0x00002b3db9aa3000)
libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x00002b3db9ca9000)
librt.so.1 => /lib64/librt.so.1 (0x00002b3db9eb7000)
libutil.so.1 => /lib64/libutil.so.1 (0x0000003c9a400000)
libdl.so.2 => /lib64/libdl.so.2 (0x0000003c99000000)
libz.so.1 => /lib64/libz.so.1 (0x0000003c99c00000)
libssl.so.10 => /usr/lib64/libssl.so.10 (0x0000003ca0000000)
libc.so.6 => /lib64/libc.so.6 (0x0000003c98c00000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003c9b800000)
/lib64/ld-linux-x86-64.so.2 (0x0000003c98800000)
libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x0000003c9fc00000)
libkrb5.so.3 => /lib64/libkrb5.so.3 (0x0000003c9ec00000)
libcom_err.so.2 => /lib64/libcom_err.so.2 (0x0000003c9cc00000)
libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x0000003c9f400000)
libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x0000003c9e400000)
libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x0000003c9f000000)
libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x0000003c9f800000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x0000003c9b400000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00002b3dba0c4000)
/opt/openmpi/bin/mpirun
Apparently, the job scheduler was using the OpenMPI version of mpirun rather than the Intel version. I thought I setup the paths correctly... but apparently not.
Providing the PBS script with the full path to the Intel 'mpirun' executable allowed the job to complete successfully, producing an empty 'error' file, and the following output file...
argument 1 = /pathtouserhome/nwchem_test/h2o.nw
============================== echo of input deck ==============================
echo
start h2o
memory global 40 mb stack 23 mb heap 5 mb
geometry units au
O 0 0 0
H 0 1.430 -1.107
H 0 -1.430 -1.107
end
basis
O library 6-31g*
H library 6-31g*
end
scf
rohf
singlet
end
task scf gradient
================================================================================
Northwest Computational Chemistry Package (NWChem) 6.1.1
--------------------------------------------------------
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352
Copyright (c) 1994-2012
Pacific Northwest National Laboratory
Battelle Memorial Institute
NWChem is an open-source computational chemistry package
distributed under the terms of the
Educational Community License (ECL) 2.0
A copy of the license is included with this distribution
in the LICENSE.TXT file
ACKNOWLEDGMENT
--------------
This software and its documentation were developed at the
EMSL at Pacific Northwest National Laboratory, a multiprogram
national laboratory, operated for the U.S. Department of Energy
by Battelle under Contract Number DE-AC05-76RL01830. Support
for this work was provided by the Department of Energy Office
of Biological and Environmental Research, Office of Basic
Energy Sciences, and the Office of Advanced Scientific Computing.
Job information
---------------
hostname = node025.local
program = /share/apps/NWChem/bin/nwchem
date = Wed May 1 13:33:27 2013
compiled = Tue_Apr_23_16:29:12_2013
source = /pathtouserhome/csoft/nwchem-6.1.1-src
nwchem branch = 6.1.1
input = /pathtouserhome/nwchem_test/h2o.nw
prefix = h2o.
data base = ./h2o.db
status = startup
nproc = 16
time left = -1s
Memory information
------------------
heap = 655361 doubles = 5.0 Mbytes
stack = 3014657 doubles = 23.0 Mbytes
global = 5242880 doubles = 40.0 Mbytes (distinct from heap & stack)
total = 8912898 doubles = 68.0 Mbytes
verify = yes
hardfail = no
Directory information
---------------------
0 permanent = .
0 scratch = .
NWChem Input Module
-------------------
C2V symmetry detected
------
auto-z
------
Geometry "geometry" -> ""
-------------------------
Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.)
No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- --------------
1 O 8.0000 0.00000000 0.00000000 0.22140000
2 H 1.0000 -1.43000000 0.00000000 -0.88560000
3 H 1.0000 1.43000000 0.00000000 -0.88560000
Atomic Mass
-----------
O 15.994910
H 1.007825
Effective nuclear repulsion energy (a.u.) 9.1971984402
Nuclear Dipole moment (a.u.)
----------------------------
X Y Z
---------------- ---------------- ----------------
0.0000000000 0.0000000000 0.0000000000
Symmetry information
--------------------
Group name C2v
Group number 16
Group order 4
No. of unique centers 2
Symmetry unique atoms
1 2
Z-matrix (autoz)
--------
Units are Angstrom for bonds and degrees for angles
Type Name I J K L M Value
----------- -------- ----- ----- ----- ----- ----- ----------
1 Stretch 1 2 0.95697
2 Stretch 1 3 0.95697
3 Bend 2 1 3 104.51124
XYZ format geometry
-------------------
3
geometry
O 0.00000000 0.00000000 0.11715984
H -0.75672347 0.00000000 -0.46863937
H 0.75672347 0.00000000 -0.46863937
==============================================================================
internuclear distances
------------------------------------------------------------------------------
center one | center two | atomic units | a.u.
------------------------------------------------------------------------------
2 H | 1 O | 1.80841 | 1.80841
3 H | 1 O | 1.80841 | 1.80841
------------------------------------------------------------------------------
number of included internuclear distances: 2
==============================================================================
==============================================================================
internuclear angles
------------------------------------------------------------------------------
center 1 | center 2 | center 3 | degrees
------------------------------------------------------------------------------
2 H | 1 O | 3 H | 104.51
------------------------------------------------------------------------------
number of included internuclear angles: 1
==============================================================================
library name resolved from: .nwchemrc
library file name is: </share/apps/NWChem/data/libraries/>
Basis "ao basis" -> "" (cartesian)
-----
O (Oxygen)
----------
Exponent Coefficients
-------------- ---------------------------------------------------------
1 S 5.48467170E+03 0.001831
1 S 8.25234950E+02 0.013950
1 S 1.88046960E+02 0.068445
1 S 5.29645000E+01 0.232714
1 S 1.68975700E+01 0.470193
1 S 5.79963530E+00 0.358521
2 S 1.55396160E+01 -0.110778
2 S 3.59993360E+00 -0.148026
2 S 1.01376180E+00 1.130767
3 P 1.55396160E+01 0.070874
3 P 3.59993360E+00 0.339753
3 P 1.01376180E+00 0.727159
4 S 2.70005800E-01 1.000000
5 P 2.70005800E-01 1.000000
6 D 8.00000000E-01 1.000000
H (Hydrogen)
------------
Exponent Coefficients
-------------- ---------------------------------------------------------
1 S 1.87311370E+01 0.033495
1 S 2.82539370E+00 0.234727
1 S 6.40121700E-01 0.813757
2 S 1.61277800E-01 1.000000
Summary of "ao basis" -> "" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
O 6-31g* 6 15 3s2p1d
H 6-31g* 2 2 2s
NWChem SCF Module
-----------------
ao basis = "ao basis"
functions = 19
atoms = 3
closed shells = 5
open shells = 0
charge = 0.00
wavefunction = RHF
input vectors = atomic
output vectors = ./h2o.movecs
use symmetry = T
symmetry adapt = T
Summary of "ao basis" -> "ao basis" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
O 6-31g* 6 15 3s2p1d
H 6-31g* 2 2 2s
Symmetry analysis of basis
--------------------------
a1 10
a2 1
b1 5
b2 3
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Forming initial guess at 0.6s
Superposition of Atomic Density Guess
-------------------------------------
Sum of atomic energies: -75.75081731
Non-variational initial energy
------------------------------
Total energy = -75.919952
1-e energy = -121.737767
2-e energy = 36.620616
HOMO = -0.470482
LUMO = 0.114886
Symmetry analysis of molecular orbitals - initial
-------------------------------------------------
Numbering of irreducible representations:
1 a1 2 a2 3 b1 4 b2
Orbital symmetries:
1 a1 2 a1 3 b1 4 a1 5 b2
6 a1 7 b1 8 b1 9 a1 10 b2
11 a1 12 b1 13 a1 14 a1 15 a2
Starting SCF solution at 0.8s
----------------------------------------------
Quadratically convergent ROHF
Convergence threshold : 1.000E-04
Maximum no. of iterations : 30
Final Fock-matrix accuracy: 1.000E-07
----------------------------------------------
#quartets = 1.009D+03 #integrals = 5.756D+03 #direct = 0.0% #cached =100.0%
Integral file = ./h2o.aoints.00
Record size in doubles = 65536 No. of integs per rec = 43688
Max. records in memory = 2 Max. records in file = 14411335
No. of bits per label = 8 No. of bits per value = 64
File balance: exchanges= 0 moved= 0 time= 0.0
iter energy gnorm gmax time
----- ------------------- --------- --------- --------
1 -75.9747705720 8.31D-01 3.41D-01 0.2
2 -76.0080998407 1.84D-01 1.02D-01 0.3
3 -76.0104204895 4.08D-02 2.40D-02 0.3
4 -76.0105383770 1.63D-03 9.29D-04 0.4
5 -76.0105386160 2.29D-06 9.65D-07 0.5
Final RHF results
------------------
Total SCF energy = -76.010538615956
One-electron energy = -123.058841737821
Two-electron energy = 37.851104681667
Nuclear repulsion energy = 9.197198440198
Time for solution = 0.4s
Symmetry analysis of molecular orbitals - final
-----------------------------------------------
Numbering of irreducible representations:
1 a1 2 a2 3 b1 4 b2
Orbital symmetries:
1 a1 2 a1 3 b1 4 a1 5 b2
6 a1 7 b1 8 b1 9 a1 10 b2
11 a1 12 b1 13 a1 14 a1 15 a2
Final eigenvalues
-----------------
1
1 -20.5603
2 -1.3419
3 -0.7071
4 -0.5711
5 -0.4979
6 0.2108
7 0.3042
8 1.0227
9 1.1318
10 1.1678
11 1.1719
12 1.3809
13 1.4341
14 2.0201
15 2.0337
ROHF Final Molecular Orbital Analysis
-------------------------------------
Vector 2 Occ=2.000000D+00 E=-1.341930D+00 Symmetry=a1
MO Center= -7.8D-17, -1.4D-16, -5.6D-02, r^2= 5.0D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
2 0.475861 1 O s 6 0.439200 1 O s
1 -0.209676 1 O s
Vector 3 Occ=2.000000D+00 E=-7.070590D-01 Symmetry=b1
MO Center= 1.1D-16, -6.1D-18, -1.0D-01, r^2= 7.7D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
3 0.507652 1 O px 7 0.306488 1 O px
16 -0.230979 2 H s 18 0.230979 3 H s
Vector 4 Occ=2.000000D+00 E=-5.710706D-01 Symmetry=a1
MO Center= 8.7D-18, 6.6D-18, 1.7D-01, r^2= 6.9D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
5 0.555445 1 O pz 9 0.403175 1 O pz
6 0.325537 1 O s 2 0.164592 1 O s
Vector 5 Occ=2.000000D+00 E=-4.979252D-01 Symmetry=b2
MO Center= 8.6D-19, -1.1D-16, 9.7D-02, r^2= 6.0D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
4 0.639616 1 O py 8 0.511469 1 O py
Vector 6 Occ=0.000000D+00 E= 2.108019D-01 Symmetry=a1
MO Center= 2.2D-16, -1.1D-18, -6.5D-01, r^2= 2.6D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
6 1.415543 1 O s 17 -1.041448 2 H s
19 -1.041448 3 H s 9 -0.508219 1 O pz
5 -0.217055 1 O pz
Vector 7 Occ=0.000000D+00 E= 3.042325D-01 Symmetry=b1
MO Center= -7.8D-16, 6.1D-17, -6.2D-01, r^2= 2.7D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
17 1.395012 2 H s 19 -1.395012 3 H s
7 0.833804 1 O px 3 0.329272 1 O px
Vector 8 Occ=0.000000D+00 E= 1.022734D+00 Symmetry=b1
MO Center= -6.9D-17, 4.8D-17, -4.7D-02, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
16 0.838912 2 H s 18 -0.838912 3 H s
7 0.662617 1 O px 17 -0.459237 2 H s
19 0.459237 3 H s 12 0.343167 1 O dxz
Vector 9 Occ=0.000000D+00 E= 1.131842D+00 Symmetry=a1
MO Center= 6.7D-17, -3.4D-17, 2.0D-01, r^2= 1.6D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
6 1.636694 1 O s 2 -0.921950 1 O s
9 0.708674 1 O pz 16 0.548807 2 H s
18 0.548807 3 H s 17 -0.474054 2 H s
19 -0.474054 3 H s 5 -0.419234 1 O pz
13 -0.387487 1 O dyy 15 -0.318052 1 O dzz
Vector 10 Occ=0.000000D+00 E= 1.167786D+00 Symmetry=b2
MO Center= -9.1D-17, -8.2D-15, 1.1D-01, r^2= 1.1D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
8 1.036049 1 O py 4 -0.962745 1 O py
Vector 11 Occ=0.000000D+00 E= 1.171944D+00 Symmetry=a1
MO Center= 6.1D-17, 1.0D-14, -3.9D-02, r^2= 1.1D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
5 0.761011 1 O pz 16 0.661200 2 H s
18 0.661200 3 H s 6 -0.462714 1 O s
9 -0.370411 1 O pz 17 -0.357348 2 H s
19 -0.357348 3 H s 10 0.249351 1 O dxx
Vector 12 Occ=0.000000D+00 E= 1.380936D+00 Symmetry=b1
MO Center= -1.2D-16, 2.0D-31, 5.7D-02, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
7 1.537091 1 O px 3 -1.037375 1 O px
17 0.915090 2 H s 19 -0.915090 3 H s
Vector 13 Occ=0.000000D+00 E= 1.434077D+00 Symmetry=a1
MO Center= 1.7D-16, -1.5D-15, -3.9D-01, r^2= 1.4D+00
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
6 3.574399 1 O s 2 -1.418425 1 O s
9 -1.174649 1 O pz 17 -0.784923 2 H s
19 -0.784923 3 H s 10 -0.644454 1 O dxx
5 0.506383 1 O pz 15 -0.402327 1 O dzz
16 -0.323132 2 H s 18 -0.323132 3 H s
Vector 14 Occ=0.000000D+00 E= 2.020054D+00 Symmetry=a1
MO Center= -4.3D-17, -2.1D-16, 1.6D-01, r^2= 6.2D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
15 1.008815 1 O dzz 10 -0.580615 1 O dxx
13 -0.366779 1 O dyy 6 -0.227333 1 O s
Vector 15 Occ=0.000000D+00 E= 2.033721D+00 Symmetry=a2
MO Center= 3.0D-16, -2.0D-16, 1.2D-01, r^2= 6.1D-01
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
----- ------------ --------------- ----- ------------ ---------------
11 1.732051 1 O dxy
center of mass
--------------
x = 0.00000000 y = 0.00000000 z = 0.09751021
moments of inertia (a.u.)
------------------
2.193637940261 0.000000000000 0.000000000000
0.000000000000 6.315440625261 0.000000000000
0.000000000000 0.000000000000 4.121802685000
Mulliken analysis of the total density
--------------------------------------
Atom Charge Shell Charges
----------- ------ -------------------------------------------------------
1 O 8 8.87 2.00 0.90 2.90 0.92 2.07 0.08
2 H 1 0.57 0.46 0.10
3 H 1 0.57 0.46 0.10
Multipole analysis of the density wrt the origin
------------------------------------------------
L x y z total open nuclear
- - - - ----- ---- -------
0 0 0 0 -0.000000 0.000000 10.000000
1 1 0 0 -0.000000 0.000000 0.000000
1 0 1 0 0.000000 0.000000 0.000000
1 0 0 1 -0.875294 0.000000 0.000000
2 2 0 0 -3.071804 0.000000 4.089800
2 1 1 0 -0.000000 0.000000 0.000000
2 1 0 1 -0.000000 0.000000 0.000000
2 0 2 0 -5.372335 0.000000 0.000000
2 0 1 1 -0.000000 0.000000 0.000000
2 0 0 2 -4.444599 0.000000 1.960718
Parallel integral file used 16 records with 0 large values
NWChem Gradients Module
-----------------------
wavefunction = RHF
Using symmetry
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RHF ENERGY GRADIENTS
atom coordinates gradient
x y z x y z
1 O 0.000000 0.000000 0.221400 0.000000 0.000000 0.014490
2 H -1.430000 0.000000 -0.885600 -0.007296 0.000000 -0.007245
3 H 1.430000 0.000000 -0.885600 0.007296 0.000000 -0.007245
----------------------------------------
| Time | 1-e(secs) | 2-e(secs) |
----------------------------------------
| CPU | 0.00 | 0.00 |
----------------------------------------
| WALL | 0.00 | 0.00 |
----------------------------------------
Task times cpu: 0.5s wall: 2.5s
NWChem Input Module
-------------------
Summary of allocated global arrays
-----------------------------------
No active global arrays
GA Statistics for process 0
------------------------------
create destroy get put acc scatter gather read&inc
calls: 313 313 1426 585 1054 0 0 0
number of processes/call 1.71e+00 1.68e+00 1.56e+00 0.00e+00 0.00e+00
bytes total: 9.16e+05 5.34e+05 2.44e+05 0.00e+00 0.00e+00 0.00e+00
bytes remote: 1.58e+05 4.74e+04 8.84e+04 0.00e+00 0.00e+00 0.00e+00
Max memory consumed for GA by this process: 25736 bytes
MA_summarize_allocated_blocks: starting scan ...
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
MA usage statistics:
allocation statistics:
heap stack
---- -----
current number of blocks 0 0
maximum number of blocks 19 29
current total bytes 0 0
maximum total bytes 1059848 22509336
maximum total K-bytes 1060 22510
maximum total M-bytes 2 23
CITATION
--------
Please cite the following reference when publishing
results obtained with NWChem:
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
E. Apra, T.L. Windus, W.A. de Jong
"NWChem: a comprehensive and scalable open-source
solution for large scale molecular simulations"
Comput. Phys. Commun. 181, 1477 (2010)
doi:10.1016/j.cpc.2010.04.018
AUTHORS & CONTRIBUTORS
----------------------
E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski, T. P. Straatsma,
M. Valiev, H. J. J. van Dam, D. Wang, E. Apra, T. L. Windus, J. Hammond,
J. Autschbach, F. Aquino, J. Mullin, P. Nichols, S. Hirata, M. T. Hackler,
Y. Zhao, P.-D. Fan, R. J. Harrison, M. Dupuis, D. M. A. Smith, K. Glaesemann,
J. Nieplocha, V. Tipparaju, M. Krishnan, A. Vazquez-Mayagoitia, L. Jensen,
M. Swart, Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby,
E. Brown, G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao,
R. Kendall, J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell,
D. Bernholdt, P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. Deegan,
K. Dyall, D. Elwood, E. Glendening, M. Gutowski, A. Hess, J. Jaffe,
B. Johnson, J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield,
X. Long, B. Meng, T. Nakajima, S. Niu, L. Pollack, M. Rosing, G. Sandrone,
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. Wong, Z. Zhang.
Total times cpu: 0.6s wall: 3.1s
Should this be the expected result? I believe it's working as it should be now. Is there a better test file for MPI/IB environments?
|