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[[Category:Software]] | [[Category:Software]] | ||
The General Atomic and Molecular Electronic Structure System (GAMESS)<ref name="homepage">GAMESS | The General Atomic and Molecular Electronic Structure System (GAMESS) | ||
is a general | <ref name="homepage">GAMESS Homepage: http://www.msg.ameslab.gov/gamess/</ref> | ||
is a general ''ab initio'' quantum chemistry package. | |||
== Running GAMESS == | == Running GAMESS == | ||
Our Clusters are using the Slurm scheduler; for details about submitting jobs, see [[Running jobs]]. | === Job Submission === | ||
Our Clusters are using the Slurm scheduler; for details about submitting jobs, | |||
see [[Running jobs]]. | |||
First step is to prepare a GAMESS input file containing the molecular geometry and run parameters. | First step is to prepare a GAMESS input file containing the molecular geometry | ||
Please refer to the GAMESS Documentation<ref name="gamess-docs"> | and run parameters. Please refer to the GAMESS Documentation | ||
and particularly Chapter 2 "Input Description"<ref name="gamess-input"> | <ref name="gamess-docs">Documentation: http://www.msg.ameslab.gov/gamess/documentation.html</ref> | ||
and particularly Chapter 2 "Input Description"<ref name="gamess-input">Input | |||
Description (PDF): http://www.msg.ameslab.gov/gamess/GAMESS_Manual/input.pdf</ref> | |||
for a description the file format and all available keywords. | |||
Besides your input file (in our example name.inp), you have to prepare a job script to define the compute resources for the job; both input file and job script must be in the same directory. | Besides your input file (in our example name.inp), you have to prepare a job | ||
script to define the compute resources for the job; both input file and job | |||
script must be in the same directory. | |||
{{File | {{File | ||
| Line 21: | Line 29: | ||
|contents= | |contents= | ||
#!/bin/bash | #!/bin/bash | ||
#SBATCH --cpus-per-task= | #SBATCH --cpus-per-task=1 # Number of CPUs | ||
#SBATCH --mem-per-cpu=2000M # memory per CPU in MB | #SBATCH --mem-per-cpu=2000M # memory per CPU in MB | ||
#SBATCH --time=0-00:30 # time (DD-HH:MM) | #SBATCH --time=0-00:30 # time (DD-HH:MM) | ||
export SLURM_CPUS_PER_TASK | |||
## uncomment the following 2 lines to use network $SCRATCH | |||
#export USRSCR="$SCRATCH/gamess_${SLURM_JOB_ID}/" | |||
#mkdir -p $USRSCR | |||
module load gamess-us/20170420-R1 | module load gamess-us/20170420-R1 | ||
| Line 29: | Line 42: | ||
rungms name.inp &> name.out | rungms name.inp &> name.out | ||
}} | }} | ||
=== Running GAMESS on multiple CPUs === | |||
GAMESS calculations can make use of more than one CPU. The number of CPUs | |||
used for a calculation is controlled by the <code>--cpus-per-task</code> | |||
setting in the submission script. | |||
As GAMESS has been built using the "sockets" parallelization, it can only | |||
use CPU cores that are located on the same compute node and therefore | |||
the maximum number of CPU cores that can be used for a job is dictated by | |||
the node configuraion of the system (e.g. 32 CPU cores per node on Graham). | |||
Quantum chemistry calculations are known to not scale as well across | |||
many CPUs as compared to e.g. classical molecular mechanics, which means | |||
that they can't use large numbers of CPUs efficiently. Exactly how many | |||
CPUs can be utilized efficiently, depends on the size of a system (i.e. | |||
number of atoms, number of basis functions and level of theory). | |||
To determine a reasonable number of CPUs to use, one needs to run a scaling | |||
test - that is running the same input file using different numbers of CPUs | |||
and comparing the execution time. Ideally the exection time should be half | |||
as long when using twice as many CPUs (= 100% speedup). | |||
Obviously it is not a good use of resources when a calculation runs only 30% | |||
faster when doubling the number of CPUs and in extreme cases calculations | |||
can become even slower when further increasing the number of CPUs. | |||
== References == | == References == | ||
<references /> | <references /> | ||