Commit f221dfb7 authored by Josef Hrabal's avatar Josef Hrabal
Browse files

Software ORCA updated

parent 08c02106
......@@ -2,65 +2,132 @@
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
## Making ORCA Available
## ORCA Available on the Cluster
The following module command makes the latest version of orca available to your session
Many versions of ORCA is available on our clusters. You can list all versions by `ml av` command.
```console
$ module load ORCA/3_0_3-linux_x86-64
$ ml av orca
-------------------------- /apps/modules/chem --------------------------
ORCA/4_0_0-linux_x86-64 ORCA/4_0_1-linux_x86-64 ORCA/4.0.1.2 (D)
Where:
D: Default Module
```
## Serial Computation With ORCA
You can test serial computation with this simple input file. Create a file called orca_serial.inp and fill it with following ORCA commands.
```bash
# Taken from the Orca manual
# https://orcaforum.cec.mpg.de/OrcaManual.pdf
! HF SVP
* xyz 0 1
C 0 0 0
O 0 0 1.13
*
```
Next, create a PBS submission file (interactive job can be used too).
```bash
#!/bin/bash
#PBS -S /bin/bash
#PBS -N ORCA_SERIAL
#PBS -l select=1
#PBS -q qexp
ml ORCA/4.0.1.2
${EBROOTORCA}orca orca_serial.inp
```
### Dependency
Submit the job to the queue and wait before it ends. Then you can find an output log in your working directory.
```console
$ module list
Currently Loaded Modulefiles:
1) /opt/modules/modulefiles/oscar-modules/1.0.3(default)
2) GCC/4.9.3-binutils-2.25
3) binutils/2.25-GCC-4.9.3-binutils-2.25
4) GNU/4.9.3-2.25
5) icc/2015.3.187-GNU-4.9.3-2.25
6) ifort/2015.3.187-GNU-4.9.3-2.25
7) iccifort/2015.3.187-GNU-4.9.3-2.25
8) numactl/2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25
9) hwloc/1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25
10) OpenMPI/1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25
11) ORCA/3_0_3-linux_x86-64
$ qsub submit_serial.pbs
1417552.dm2
$ ll ORCA_SERIAL.*
-rw------- 1 hra0031 hra0031 0 Aug 21 12:24 ORCA_SERIAL.e1417552
-rw------- 1 hra0031 hra0031 20715 Aug 21 12:25 ORCA_SERIAL.o1417552
$ cat ORCA_SERIAL.o1417552
*****************
* O R C A *
*****************
--- An Ab Initio, DFT and Semiempirical electronic structure package ---
#######################################################
# -***- #
# Department of molecular theory and spectroscopy #
# Directorship: Frank Neese #
# Max Planck Institute for Chemical Energy Conversion #
# D-45470 Muelheim/Ruhr #
# Germany #
# #
# All rights reserved #
# -***- #
#######################################################
Program Version 4.0.1.2 - RELEASE -
...
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 0 minutes 1 seconds 47 msec
```
## Example Single Core Job
## Running ORCA in Parallel
Create a file called orca_serial.inp that contains the following orca commands
Your serial computation can be converted to parallel in a very simple way. You simply have to specify the number of parallel processes by directive **%pal**. In this example, 4 nodes, 16 cores each are used.
```cpp
# My first ORCA calculation :-)
#
!!! warning
Don't use **! PAL** directive as only PAL2 to PAL8 is recognized!
```bash
# Taken from the Orca manual
# https://orcaforum.cec.mpg.de/OrcaManual.pdf
! HF SVP
%pal
nprocs 64 # 4 nodes, 16 cores each
end
* xyz 0 1
C 0 0 0
O 0 0 1.13
*
```
Create a Sun Grid Engine submission file called submit_serial.sh that looks like this
You also need to edit the previously used PBS submission file. You have to specify number of nodes, cores and MPI-processes to run.
```console
!/bin/bash
```bash
#!/bin/bash
#PBS -S /bin/bash
#PBS -N ORCA_PARALLEL
#PBS -l select=4:ncpus=16:mpiprocs=16
#PBS -q qexp
module load ORCA/3_0_3-linux_x86-64
orca orca_serial.inp
ml ORCA/4.0.1.2
${EBROOTORCA}/orca orca_parallel.inp
```
Submit the job to the queue with the command
!!! note
When running ORCA in parallel, ORCA should **NOT** be started with mpirun: e.g. mpirun -np 4 orca etc. like many MPI programs and has to be called with full pathname.
Submit this job to the queue and see the output file.
```console
$ qsub -q qexp -I -l select=1
qsub: waiting for job 196821.isrv5 to start
qsub: job 196821.isrv5 ready
[username@r37u04n944 ~]$ ./submit_serial.sh
$ qsub submit_parallel.pbs
1417598.dm2
$ ll ORCA_PARALLEL.*
-rw------- 1 hra0031 hra0031 0 Aug 21 13:12 ORCA_PARALLEL.e1417598
-rw------- 1 hra0031 hra0031 23561 Aug 21 13:13 ORCA_PARALLEL.o1417598
$ cat ORCA_PARALLEL.o1417598
*****************
* O R C A *
......@@ -80,19 +147,44 @@ qsub: job 196821.isrv5 ready
# -***- #
#######################################################
Program Version 4.0.1.2 - RELEASE -
...
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 0 minutes 2 seconds 796 msec
[username@r37u04n944 orca]$ logout
************************************************************
* Program running with 64 parallel MPI-processes *
* working on a common directory *
************************************************************
qsub: job 196821.isrv5 completed
...
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 0 minutes 11 seconds 859 msec
```
You can see, that the program was running with 64 parallel MPI-processes. In version 4.0.1.2, only the following modules are parallelized:
* ANOINT
* CASSCF / NEVPT2
* CIPSI
* CIS/TDDFT
* CPSCF
* EPRNMR
* GTOINT
* MDCI (Canonical-, PNO-, DLPNO-Methods)
* MP2 and RI-MP2 (including Gradient and Hessian)
* MRCI
* PC
* ROCIS
* SCF
* SCFGRAD
* SCFHESS
* SOC
* Numerical Gradients and Frequencies
## Register as a User
You are encouraged to register as a user of Orca at [Here](https://orcaforum.cec.mpg.de/) in order to take advantage of updates, announcements and also of the users forum.
You are encouraged to register as a user of ORCA at [Here](https://orcaforum.cec.mpg.de/) in order to take advantage of updates, announcements and also of the users forum.
## Documentation
A comprehensive [.pdf](https://orcaforum.cec.mpg.de/OrcaManual.pdf) manual is available online.
A comprehensive [PDF](https://orcaforum.cec.mpg.de/OrcaManual.pdf) manual is available online.
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