submit
Submitting a job
Using splash
, you can easily submit an ORCA
job on Nimbus using only an ORCA
input file and a single terminal command.
To best demonstrate the use of splash
, lets look at the example of a geometry optimisation and frequency calculation for a benzene molecule.
!PBE def2-svp OPT FREQ
%PAL NPROCS 16 END
%maxcore 2000
*xyzfile 0 1 benzene.xyz
In this example the structure is located in a separate .xyz
file - benzene.xyz
, though
splash
does support input file coordinate specification.
12
Benzene
H 1.2194 -0.1652 2.1600
C 0.6825 -0.0924 1.2087
C -0.7075 -0.0352 1.1973
H -1.2644 -0.0630 2.1393
C -1.3898 0.0572 -0.0114
H -2.4836 0.1021 -0.0204
C -0.6824 0.0925 -1.2088
H -1.2194 0.1652 -2.1599
C 0.7075 0.0352 -1.1973
H 1.2641 0.0628 -2.1395
C 1.3899 -0.0572 0.0114
H 2.4836 -0.1022 0.0205
To submit a job for this calculation, simply run
splash submit benzene.inp
You should then see an message informing you that a submission script was created and subsequently submitted.
The job will be given the same name as your input file, and the output file for this calculation should appear in the current directory when the job starts running - for example
user@nimbus-1-login-1 ~/benzene $ ls
benzene.6718675.e benzene.6718675.o benzene.inp benzene.out benzene.slm benzene.xyz
When the calculation has finished, been evicted, timed-out, or otherwise halted, you should see a new directory in the same location as your input and .xyz
files.
This directory will be named <jobname>_results
and will contain all the files ORCA
creates.
user@nimbus-1-login-1 ~/benzene $ ls
benzene.6718675.e benzene.6718675.o benzene.inp benzene.out benzene.slm benzene.xyz benzene_results
Submitting multiple jobs
You can submit more than one calculation at once by providing more than one input file to splash. For example
splash submit input_1.inp input_2.inp
You can even use a wildcard to submit jobs without typing each filename out
splash submit input_*.inp
Note that this will run all jobs in the current directory, and so can produce a large number of files in the same directory.
Providing coordinates within the input file
Instead of providing a separate .xyz
file, it is possible to specify coordinates within the ORCA
input file.
This feature is supported by splash
and requires no additional effort on the part of the user.
Providing input orbitals
From the current calculation
When resuming a job, ORCA
automatically searches for a .gbw
file with the same name as your input file.
To support this, splash
checks for a <jobname>_results
directory whenever you run splash submit
and
copies the <jobname>.gbw
file to the compute node’s scratch space. This feature can be disabled with the
--no_guess
argument, e.g.
splash submit benzene.inp --no_guess
From another calculation
To provide ORCA
with a guess set of orbitals to ORCA
from another calculation, make sure you have both the MORead
keyword and the %moinp "<gbw_filename>"
line in
your input file. Note that ORCA
will not allow your specified file to have the same name-head as the input file.
For the benzene example in the previous section, a correct input file would be
!PBE def2-svp OPT FREQ MORead
%moinp "new_orbs.gbw"
%PAL NPROCS 16 END
%maxcore 2000
*xyzfile 0 1 benzene.xyz
The file <gbw_filename>
can be located either in <jobname>_results
or in the same directory as the input file - splash
will look for this file in both locations.
Selecting a compute instance
Specific Nimbus compute instances can be requested using the --node_type
option.
The full list of ORCA
compatible instances currently known to splash are
spot-fsv2-2
spot-fsv2-4
spot-fsv2-8
spot-fsv2-16
spot-fsv2-32
spot-hc-44
spot-hb-60
spot-hbv2-120
spot-hbv3-120
paygo-fsv2-2
paygo-fsv2-4
paygo-fsv2-8
paygo-fsv2-16
paygo-fsv2-32
paygo-hc-44
paygo-hb-66
paygo-hbv2-120
paygo-hbv3-120
Note
You can only use instances to which you have been granted access.
This is usually indicated by a QOS
error at submission time. To resolve this, modify your access
on the RCAM portal.
By default, splash
submits to spot-fsv2-16
which has 16 cores and 2GB RAM per core, to change this default for your account
add the following to your ~/.bash_rc
file, where <node_name>
is one of those given above
export DEF_COMP_INST=<node_name>
More
Additional command line arguments for splash submit
can be listed by running
splash submit -h