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Usage of ORCA in FGI requires registration at the ORCA site: Once you have registered yourself, send an email stating that to heldesk@csc.fi for ORCA to be enabled for you in the FGI.

Interface definition

The runtime environment sets the following environment variables:

  • PATH is set so that the ORCA bin directory is included in the path
  • A compatibility version of openMPI is loaded with command: module add compat-openmpi-x86_64

Examples

Serial ORCA job

orca.xrsl

&
(executable=runserial.sh)
(jobname=orca-test)
(stdout=std.out)
(stderr=std.err)
(gmlog=gridlog_1)
(walltime=1h)
(memory=1000)
(disk=1000)
(runtimeenvironment="APPS/CHEM/ORCA-3.0.1"
)
(inputfiles= 
( "test.inp" "test.inp" )
)
(outputfiles= 
( "output.tar" "output.tar" )

 

And the corresponding run script runserial.sh :

 

#!/bin/sh
echo "Hello ORCA!"
$ORCA_PATH/orca test.inp > test.out
tar cf output.tar ./*
echo "Bye ORCA!"
exit

 

test.inp i.e. an example serial input file

#!/bin/sh
# Test a simple serial DFT calculation 
! RKS BLYP SVP Grid4
* xyz 0 1
C -0.79263 0.55338 -1.58694
C 0.68078 0.13314 -1.72622
C 1.50034 0.61020 -0.52199
C 1.01517 -0.06749 0.77103
C -0.49095 -0.38008 0.74228
C -1.24341 0.64080 -0.11866
H 1.10490 0.53546 -2.67754
H 0.76075 -0.97866 -1.78666
H -0.95741 1.54560 -2.07170
H -1.42795 -0.17916 -2.14055
H -2.34640 0.48232 -0.04725
H -1.04144 1.66089 0.28731
H -0.66608 -1.39636 0.31480
H -0.89815 -0.39708 1.78184
H 1.25353 0.59796 1.63523
H 1.57519 -1.01856 0.93954
H 2.58691 0.40499 -0.67666
H 1.39420 1.71843 -0.44053
*

 

Parallel ORCA job

The file runMPI.xrsl describes that the amber job using 6 cores (count=6) with MPI. In the case of parallel jobs, the memory requirement is set for one core. So in this case the reservation is 500 MB * 6 cores = 1200 MB. For most parallel jobs it is advantageous to have all computing cores that the job uses in the same cluster node. To ensure this ENV/ONENODE runtime environment can be used. Please note that this runtime environment limits the maximum number of cores to 12.

orcaMPI.xrsl

&
(executable=runMPI.sh)
(jobname=ORCA-test)
(stdout=std.out)
(stderr=std.err)
(gmlog=gridlog_1)
(walltime=1h)
(memory=500)
(disk=1000)
(count=6)
(runtimeenvironment="ENV/ONENODE")
(runtimeenvironment="APPS/CHEM/ORCA-3.0.1")
(inputfiles=
 ( "testMPI.inp" "testMPI.inp" )
)
(outputfiles=
   ( "output.tar" "output.tar" )
)

 

And the corresponding run script runMPI.sh :

 

#!/bin/sh
echo "Hello ORCA!"
$ORCA_PATH/orca testMPI.inp > testMPI.out
tar cf output.tar ./*
echo "Bye ORCA!"
exit

"testMPI.inp" i.e. an example serial input file. NOTE, that you need to specify the NUMBER OF CORES on the second line!

#!/bin/sh
%pal nprocs 6 end
# Test a simple serial DFT calculation
! RKS BLYP SVP Grid4
* xyz 0 1
C -0.79263 0.55338 -1.58694
C 0.68078 0.13314 -1.72622
C 1.50034 0.61020 -0.52199
C 1.01517 -0.06749 0.77103
C -0.49095 -0.38008 0.74228
C -1.24341 0.64080 -0.11866
H 1.10490 0.53546 -2.67754
H 0.76075 -0.97866 -1.78666
H -0.95741 1.54560 -2.07170
H -1.42795 -0.17916 -2.14055
H -2.34640 0.48232 -0.04725
H -1.04144 1.66089 0.28731
H -0.66608 -1.39636 0.31480
H -0.89815 -0.39708 1.78184
H 1.25353 0.59796 1.63523
H 1.57519 -1.01856 0.93954
H 2.58691 0.40499 -0.67666
H 1.39420 1.71843 -0.44053
*

 

Commands to submit the sample job in linux and MacOSX machines

Copy and paste the sample job(s) and the scripts to corresponding files.

Set up grid environment and submit the job

 

arcproxy
arcsub orca.xrsl
 or
arcsub orcaMPI.xrsl

 

Follow the progress of the job and retrieve the result when the job is finished,

 

arcstat job_id
arcget job_id

 

In the commands above, job_id should be replaced with the job identifier given by the the arcsub command

for example:

 

arcstat gsiftp://grid.triton.aalto.fi:2811/jobs/2864513391466861182312366
arcget gsiftp://grid.triton.aalto.fi:2811/jobs/2864513391466861182312366

 

The arcget command will retrieve the results of the job to a new directory named according to the job ID number.

System administrator guide for installing the RE

To be added.

More information

ORCA manual can be downloaded from the ORCA site (after registration)

For help at CSC, contact helpdesk@csc.fi

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