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Contents
- 5 Running Gaussian on the cluster
Gaussian
Gaussian is a widely-used computational quantum-chemistry program. It does electronic-structure calculations and standard quantum chemical calculations. Among the methods available are simple molecular mechanics (such as Amber force field), semi-empirical methods (such as CNDO), Hartree-Fock (restricted and unrestricted), MPn (Mollar-Plesset perturbation theory of order n=2,3,4), CI (Configuration-Interaction), CC (Coupled-Cluster), Multi-configurational SCF (such as CAS-SCF) and various DFT (Density-Functional Theory) methods. Specific to Gaussian are high-accuracy energy methods (G2, CBS). It can be used to obtain electronic properties, molecular geometries, vibrational frequencies, orbitals, reaction profiles, and much more. For a more complete list see this Overview.
GaussView: Graphical User Interface for Gaussian
GaussView establishes an interactive visual environment toimport or build the molecular structures that interest you; set up, launch, monitor and control Gaussian calculations,; and, retrieve and view the results, all without ever leaving the application.
GaussView 5 reference materials provide tutorials and detailed documentation to access the full capabilities of the interface. Guidance to use GaussView 5 in an interactive session with Gaussian appears below.
GaussView 6 is now available for use with Gaussian 16.
Important Notes
- Due to licensing restrictions, you must make a specific request to [email protected] to be able to use Gaussian.
- Don't copy checkpoint files from other users. You may run into ownership and file permission issues
- Match the number of processor (ppn) to the value for the field '%NProcShared' in the input file
- You may get out-of-memory error & may need to change the value of %mem in your input file
- For better visualization experience, please use X2Go (HPC Guide to X2Go)
Installed Versions
All the available versions of Gaussian for use can be viewed by issuing the following command. This applies for other applications as well.output:
---------------------- /usr/local/share/modulefiles -------------------------
gaussian/09(D) gaussian/16-avx gaussian/16-avx2 gaussian/16-sse
The default version is identified by '(default)' behind the module name and can be loaded as:
Then run a script that adds additional environmental variables:
Running Gaussian on the cluster
Running Gaussian 16
Gaussian 16 is now available on the cluster. The Gaussian 16 release notes at gaussian.com/relnotes include a tab that specifically deals with changes from G09. Gaussian also refers users to http://expchem3.com/ for instructional materials associated with a textbook making use of Gaussian 16.
The g16 executable is available in three versions, which feature support for extended instruction sets appropriate for sse-, avx- and avx2-enabled cpus. There are therefore three separate modules installed for Gaussian 16. Use 'module spider gaussian' to list the appropriate module names. The table indicates the nodes on Rider that support each version:
Module Name | Instruction Set | Runs in this node range |
g16-sse | sse | comp001t - comp252t |
g16-avx | avx | comp145t - comp252t |
g16-avx2 | avx2 | comp194t - comp252t |
Running a serial job
To run a Gaussian batch job on the cluster, you need to create a slurm script for it. The sample script below includes a request for one processor in a single compute node and imposes a limit of 1 hour of wall time. Note that the script includes the command to load the Gaussian module as pointed out previously.
#SBATCH --time=1:00:00
#SBATCH --ntasks-per-node=1
# Change working group to 'gaussian'
newgrp gaussian
# Load the Gaussian module
module load gaussian/16-sse
# Run Gaussian
g16 water09.com
# copy results back to directory from which the job was submitted
cp -u *.* $SLURM_SUBMIT_DIR
Note that the script specifies that the Gaussian input file is located in the file 'water09.com', which should contain the following lines:
%chk=water09.chk
#N B3LYP/6-311+G(3df,2p) opt freq
Gaussian test file
0 1
o
h 1 r
h 1 r 2 a
r=0.98
a=109.
If the job runs successfully the slurm output file should be empty and water09.log will end in lines similar to the following:
Job cpu time: 0 days 0 hours 0 minutes 10.9 seconds.
File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1
Normal termination of Gaussian 09 at Tue May 18 14:28:36 2010.
Running a parallel job
This example runs a geometry calculation using the Hartree-Fock method and 3-21G basis set on Cr hexacarbonyl.
%NProcShared=6
%Chk=hexacarbonyl.chk
%Mem=1GB
# RHF/3-21G Opt Test SCF=NoVarAcc
Cr(CO)6 3-21G Optimization
0 1
Cr 0.00 0.00 0.00
C 1.93 0.00 0.00
C -1.93 0.00 0.00
C 0.00 1.93 0.00
C 0.00 -1.93 0.00
C 0.00 0.00 1.93
C 0.00 0.00 -1.93
O 3.07 0.00 0.00
O -3.07 0.00 0.00
O 0.00 3.07 0.00
O 0.00 -3.07 0.00
O 0.00 0.00 3.07
O 0.00 0.00 -3.07
slurm script file: hexacarbonyl.slurm
#!/bin/bash
#SBATCH --job-name=hexacarbonyl_job
#SBATCH --time=1:00:00
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=6
#SBATCH -o hexacarbonyl.o%j
# Load the Gaussian module
module load gaussian
# Change to working directory
cd $PFSDIR
# Run Gaussian
g09 hexacarbonyl.com
# copy results back to directory from which the job was submitted
cp -u *.* $SLURM_SUBMIT_DIR
The final 3 lines of hexacarbonyl.log:
Job cpu time: 0 days 0 hours 1 minutes 4.7 seconds.
File lengths (MBytes): RWF= 15 Int= 0 D2E= 0 Chk= 2 Scr= 1
Normal termination of Gaussian 09 at Tue May 18 22:33:38 2010.
Troubleshooting (Input file has been included):
i. You may encounter 'out-of-memory error' like the one below or similar errors as explained in [2]:
Out-of-memory error in routine RdGeom-1 (IEnd= 7750001 MxCore= 6291456)
Use %Mem=8MW to provide the minimum amount of memory required to complete this step.
Error termination via Lnk1e in /usr/local/gaussian/g09/l101.exe at Mon Jul 26 14:30:54 2010.
Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds.
File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1
Solution: You need to change the value of %Mem in your input file; let's say 10MW, ...16MW.
ii. You may also encounter the following error:
Error termination request processed by link 9999.
Error termination via Lnk1e in /usr/local/gaussian/g09/l9999.exe at Tue Jul 27 08:13:24 2010.
Solution: I replaced gdiis with gediis in the input file following the troubleshoot document [2]
# opt=(calcfc,gediis) freq=raman hf/6-31g(d) geom=connectivity
iii. Now, you may encounter convergence problem as shown:
>>>>>>>>>> Convergence criterion not met.
SCF Done: E(RHF) = -2727.91297847 A.U. after 129 cycles
Convg = 0.3800D-05 -V/T = 1.9982
Convergence failure -- run terminated.
Error termination via Lnk1e in /usr/local/gaussian/g09/l502.
Solution: Again, the documentation [2] recommends using alternatives like SCF=QC in the input file as shown:
#T SCF=QC
With this alternative, the input file looks like this:
%chk=gtp.chk
%mem=10MW
%nproc=6
# opt=(calcfc,gediis) freq=raman hf/6-31g(d) geom=connectivity
#T SCF=QC
GTP calculation
0 1
O
C 1 B1
H 2 B2 1 A1
H 2 B3 1 A2 3 D1
C 2 B4 1 A3 4 D2
H 5 B5 2 A4 1 D3
O 5 B6 2 A5 1 D4
C 7 B7 5 A6 2 D5
H 8 B8 7 A7 5 D6
N 8 B9 7 A8 5 D7
C 10 B10 8 A9 7 D8
H 11 B11 10 A10 8 D9
N 11 B12 10 A11 8 D10
C 13 B13 11 A12 10 D11
C 14 B14 13 A13 11 D12
O 15 B15 14 A14 13 D13
N 15 B16 14 A15 13 D14
H 17 B17 15 A16 14 D15
C 17 B18 15 A17 14 D16
N 19 B19 17 A18 15 D17
H 20 B20 19 A19 17 D18
H 20 B21 19 A20 17 D19
N 19 B22 17 A21 15 D20
C 14 B23 13 A22 11 D21
C 5 B24 2 A23 1 D22
H 25 B25 5 A24 2 D23
C 25 B26 5 A25 2 D24
H 27 B27 25 A26 5 D25
O 27 B28 25 A27 5 D26
H 29 B29 27 A28 25 D27
O 25 B30 5 A29 2 D28
P 27 B31 25 A30 5 D29
P 32 B32 27 A31 25 D30
P 33 B33 32 A32 27 D31
O 32 B34 27 A33 25 D32
H 35 B35 32 A34 27 D33
O 34 B36 33 A35 32 D34
H 37 B37 34 A36 33 D35
O 33 B38 32 A37 27 D36
H 39 B39 33 A38 32 D37
O 34 B40 33 A39 32 D38
O 33 B41 32 A40 27 D39
O 27 B42 25 A41 5 D40
O 34 B43 33 A42 32 D41
O 32 B44 27 A43 25 D42
O 34 B45 33 A44 32 D43
H 46 B46 34 A45 33 D44
H 29 B47 27 A46 25 D45
B1 1.43056902
B2 1.06955851
B3 1.07046097
B4 1.54031674
B5 1.07010151
B6 1.46840658
B7 1.47007917
B8 1.07005874
B9 1.47011310
B10 1.35545048
B11 1.07044273
B12 1.31050107
B13 1.46205563
B14 1.38182535
B15 1.25761005
B16 1.46859879
B17 0.99997377
B18 1.35583886
B19 1.33744823
B20 0.99985865
B21 1.00005231
B22 1.35654227
B23 1.31732863
B24 1.51943573
B25 1.06965602
B26 1.50125317
B27 1.06944237
B28 1.42996911
B29 0.96016210
B30 1.42968822
B31 1.63100314
B32 2.87130655
B33 2.87570438
B34 1.75970810
B35 0.95952062
B36 1.76007760
B37 0.96015967
B38 1.75965642
B39 0.96032546
B40 1.54911358
B41 1.54884316
B42 0.70648760
B43 1.75995567
B44 1.76009893
B45 1.75980326
B46 0.95981859
B47 2.64631418
A1 109.45224357
A2 109.40285704
A3 109.61150174
A4 108.71231964
A5 108.69992694
A6 104.01129474
A7 108.55257593
A8 112.87856128
A9 125.49540865
A10 124.57043883
A11 110.86259595
A12 103.58529086
A13 129.93276533
A14 122.19804326
A15 115.62124211
A16 120.38046311
A17 119.22050751
A18 119.48707269
A19 120.01560517
A20 119.97612269
A21 121.02784872
A22 108.59730431
A23 107.89111538
A24 114.00513935
A25 96.94977639
A26 111.00675875
A27 115.17288953
A28 109.42082407
A29 112.09565479
A30 97.47447408
A31 139.46241123
A32 163.96800507
A33 129.42045232
A34 109.49060082
A35 157.41397598
A36 109.46698294
A37 51.41468767
A38 109.44217924
A39 71.87768308
A40 118.68799717
A41 73.08396098
A42 35.21530827
A43 109.50919465
A44 111.28216657
A45 109.47445748
A46 74.47676289
D1 -119.97064757
D2 -119.99570299
D3 -179.98455212
D4 -56.88644394
D5 97.71528610
D6 97.46134183
D7 -141.81353358
D8 89.22034817
D9 0.03245328
D10 -179.95448380
D11 -0.00291670
D12 179.96712331
D13 -0.13613317
D14 179.86514373
D15 -179.92804397
D16 0.06936121
D17 -179.93008288
D18 -0.05508633
D19 179.94093438
D20 0.07303913
D21 -0.02946423
D22 56.56226532
D23 51.45515738
D24 -69.93532182
D25 62.94040237
D26 -174.68382510
D27 175.52864832
D28 173.85937740
D29 94.14816650
D30 -172.81184323
D31 169.02057425
D32 25.23696255
D33 -161.63986614
D34 132.13735633
D35 -39.52658803
D36 179.63891316
D37 113.05054969
D38 145.28258473
D39 -48.77427493
D40 161.33161000
D41 40.11845102
D42 163.66668587
D43 8.86659290
D44 108.39271826
D45 24.17670460
1 2 1.0 32 1.0
2 3 1.0 4 1.0 5 1.0
3
4
5 6 1.0 7 1.0 25 1.0
6
7 8 1.0
8 9 1.0 10 1.0 27 1.0
9
10 11 1.5 24 1.5
11 12 1.0 13 2.0
12
13 14 1.0
14 15 1.5 24 2.0
15 16 2.0 17 1.0
16
17 18 1.0 19 1.5
18
19 20 1.5 23 1.5
20 21 1.0 22 1.0
21
22
23 24 1.5
24
25 26 1.0 27 1.0 31 1.0
26
27 28 1.0 29 1.0
28
29 30 1.0
30
31 48 1.0
32 35 1.0 43 2.0 45 1.0
33 39 1.0 42 2.0 45 1.0 44 1.0
34 41 2.0 44 1.0 37 1.0 46 1.0
35 36 1.0
36
37 38 1.0
38
39 40 1.0
40
41
42
43
44
45
46 47 1.0
47
48
The excerpt of the output is included below:
...
...
ScaDFX= 1.000000 1.000000 1.000000 1.000000
FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0
NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T
Omega= 0.000000 0.000000 1.000000 0.000000 0.000000 ICntrl= 500 IOpCl= 0
NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
I1Cent= 4 NGrid= 0.
Petite list used in FoFCou.
Gradient too large for Newton-Raphson -- use scaled steepest descent instead.
Gradient too large for Newton-Raphson -- use scaled steepest descent instead.
Gradient too large for Newton-Raphson -- use scaled steepest descent instead.
Gradient too large for Newton-Raphson -- use scaled steepest descent instead.
LinEq1: Iter= 0 NonCon= 1 RMS=1.91D-05 Max=8.94D-04
Estimated number of processors is: 3
AX will form 1 AO Fock derivatives at one time.
LinEq1: Iter= 1 NonCon= 1 RMS=1.35D-05 Max=6.04D-04
Estimated number of processors is: 3
LinEq1: Iter= 2 NonCon= 1 RMS=1.96D-06 Max=8.19D-05
Estimated number of processors is: 3
LinEq1: Iter= 3 NonCon= 1 RMS=1.15D-06 Max=4.09D-05
Estimated number of processors is: 3
LinEq1: Iter= 4 NonCon= 1 RMS=1.51D-07 Max=5.89D-06
Estimated number of processors is: 3
LinEq1: Iter= 5 NonCon= 1 RMS=8.59D-08 Max=3.10D-06
Estimated number of processors is: 3
LinEq1: Iter= 6 NonCon= 1 RMS=1.99D-08 Max=7.21D-07
Estimated number of processors is: 3
LinEq1: Iter= 7 NonCon= 0 RMS=1.00D-08 Max=3.19D-07
Linear equations converged to 3.233D-08 3.233D-07 after 7 iterations.
LinEq1: Iter= 0 NonCon= 1 RMS=1.13D-07 Max=3.67D-06
Estimated number of processors is: 3
LinEq1: Iter= 1 NonCon= 1 RMS=4.93D-08 Max=2.47D-06
Estimated number of processors is: 3
LinEq1: Iter= 2 NonCon= 1 RMS=1.39D-08 Max=6.08D-07
Estimated number of processors is: 3
LinEq1: Iter= 3 NonCon= 1 RMS=5.89D-09 Max=2.10D-07
Estimated number of processors is: 3
LinEq1: Iter= 4 NonCon= 1 RMS=2.03D-09 Max=8.03D-08
Estimated number of processors is: 3
LinEq1: Iter= 5 NonCon= 1 RMS=8.83D-10 Max=2.80D-08
Estimated number of processors is: 3
LinEq1: Iter= 6 NonCon= 1 RMS=3.24D-10 Max=1.48D-08
Estimated number of processors is: 3
LinEq1: Iter= 7 NonCon= 0 RMS=1.26D-10 Max=3.49D-09
Linear equations converged to 4.914D-10 4.914D-09 after 7 iterations.
SCF Done: E(RHF) = -2730.29360378 a.u. after 8 cycles
Convg = 0.1199D-06 38 Fock formations.
S**2 = 0.0000 -V/T = 2.0017
PrsmSu: requested number of processors reduced to: 2 ShMem 1 Linda.
PrsmSu: requested number of processors reduced to: 5 ShMem 1 Linda.
Calling FoFJK, ICntrl= 2127 FMM=F ISym2X=0 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0.
GaussView Interactive Session
Start a visual interface session on a compute node by performing the following steps:
- Establish a visual connection to the cluster (e.g. x2go-client, mobaXterm). All methods rely on underlying X11 forwarding.
- Obtain a session on a compute node using srun on a head node. For example, request 12 processors on 1 node to enhance visualization throughput:
'srun --x11 --nodes=1 --ntasks=12 --time=2:00:00 --pty /bin/bash' - load modules gaussian and gaussview; start gaussview
- module load gaussian
- module load gaussview
- gview
- (Optional) Run gaussview alone for visualization work.
Tutorials are available. Youtube may be consulted for useful introductory and advanced user instruction.
References:
[1] Home: http://computing.chem.wisc.edu/software/g98.php
[2] Troubleshooting: http://docs.notur.no/application-support/chemistry-applications/gaussian-1/gaussian-03-1/troubleshooting-gaussian-calculations
[3] http://chemistry.ncssm.edu/book/Chap18Gaussian.pdf
[4] http://chemistry.umeche.maine.edu/Modeling/GGGauss.html
[5] http://superbeton.wordpress.com/2007/07/08/gaussian-error-messages/
[1] Home: http://computing.chem.wisc.edu/software/g98.php
[2] Troubleshooting: http://docs.notur.no/application-support/chemistry-applications/gaussian-1/gaussian-03-1/troubleshooting-gaussian-calculations
[3] http://chemistry.ncssm.edu/book/Chap18Gaussian.pdf
[4] http://chemistry.umeche.maine.edu/Modeling/GGGauss.html
[5] http://superbeton.wordpress.com/2007/07/08/gaussian-error-messages/