James at 20:12, 27 October 2022

2022-10-27T20:12:38Z

← Older revision		Revision as of 20:12, 27 October 2022
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	is also available on ANDY server. The current license is group-limited and allows for up to 32 cores of simultaneous ADF		is also available on ANDY server. The current license is group-limited and allows for up to 32 cores of simultaneous ADF
	use and 8 cores of simultaneous BAND use. This is a floating license limited to the DDR side of ANDY		use and 8 cores of simultaneous BAND use. This is a floating license limited to the DDR side of ANDY
	and the ~~PBS~~ 'production' queue. Users not currently in the ADF group should inquire about access by sending		and the SLURM 'production' queue. Users not currently in the ADF group should inquire about access by sending
	an email to 'hpchelp@csi.cuny.edu'.		an email to 'hpchelp@csi.cuny.edu'.

	Here is a simple ADF input deck that compute the SCF wave function for HCN. This example can be run		Here is a simple ADF input deck that compute the SCF wave function for HCN. This example can be run
	with the ~~PBS~~ script shown below on from 1 to 4 cores.		with the SLURM script shown below on from 1 to 4 cores.

	<pre>		<pre>
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	</pre>		</pre>

	A ~~PBS~~ script ('adf_4.job') configured to use 4 cores is shown here. Note that ADF does not use the		A SLURM script ('adf_4.job') configured to use 4 cores is shown here. Note that ADF does not use the
	version of MPI that the HPC Center supports by default. ADF used the proprietary version		version of MPI that the HPC Center supports by default. ADF used the proprietary version
	of MPI from SGI that is part of SGI's MPT parallel library package. This script includes special		of MPI from SGI that is part of SGI's MPT parallel library package. This script includes special
	lines to configure the run for this. A side effect of this fact is that ADF jobs will not clock		lines to configure the run for this. A side effect of this fact is that ADF jobs will not clock
	time in ~~PBS~~ as shown under the 'Time' column when your job is being checked with 'qstat'		time in SLURM as shown under the 'Time' column when your job is being checked with 'qstat'

	To include all required environmental variables and the path to the ADF executable		To include all required environmental variables and the path to the ADF executable
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	# with these resources, although this computation is really		# with these resources, although this computation is really
	# too small to make full use of them. To increase or decrease		# too small to make full use of them. To increase or decrease
	# the resources ~~PBS~~ requests (cpus, memory, or disk) change the		# the resources SLURM requests (cpus, memory, or disk) change the
	# '-l select' line below and the parameter values in the input deck.		# '-l select' line below and the parameter values in the input deck.
	#		#
	#~~PBS~~ -q production		#SLURM -q production
	#~~PBS~~ -N adf_4P_job		#SLURM -N adf_4P_job
	#~~PBS~~ -l select=1:ncpus=4:mem=11520mb:lscratch=400gb		#SLURM -l select=1:ncpus=4:mem=11520mb:lscratch=400gb
	#~~PBS~~ -l place=free		#SLURM -l place=free
	#~~PBS~~ -V		#SLURM -V

	# Find out name of master execution host (compute node)		# Find out name of master execution host (compute node)
	echo -n ">>>> ~~PBS~~ Master compute node is: "		echo -n ">>>> SLURM Master compute node is: "
	hostname		hostname

	# You must explicitly change to the working directory in ~~PBS~~		# You must explicitly change to the working directory in SLURM
	cd $~~PBS_O_WORKDIR~~		cd $SLURM_O_WORKDIR

	# set environment up to use SGI's MPT version of MPI rather		# set environment up to use SGI's MPT version of MPI rather
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	environment to use the SGI proprietary version of MPI for parallel runs. Next is the NSCM environmental		environment to use the SGI proprietary version of MPI for parallel runs. Next is the NSCM environmental
	variable which defines the number of cores to use along with the '-n' option on the command		variable which defines the number of cores to use along with the '-n' option on the command
	line. Both of these (along with the number of cpus on the ~~PBS~~ '-l select' line at the beginning		line. Both of these (along with the number of cpus on the SLURM '-l select' line at the beginning
	of the script) must be adjusted to control the number of cores used by the job.		of the script) must be adjusted to control the number of cores used by the job.

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	run in parallel.		run in parallel.

	With the HCN input file and ~~PBS~~ script above, you can submit an ADF job on ANDY with:		With the HCN input file and SLURM script above, you can submit an ADF job on ANDY with:

	<pre>		<pre>

James: Created page with "===ADF (Amsterdam Density Functional Theory)=== ADF (Amsterdam Density Functional) is a Fortran program for calculations on atoms and molecules (in gas phase or solution) from first principles. It can be used for the study of such diverse fields as molecular spectroscopy, organic and inorganic chemistry, crystallography and pharmacochemistry. Some of its key strengths include high accuracy supported by its use of Slater-type orbitals, all-electron relativistic treatment..."

2022-10-17T17:43:02Z

Created page with "===ADF (Amsterdam Density Functional Theory)=== ADF (Amsterdam Density Functional) is a Fortran program for calculations on atoms and molecules (in gas phase or solution) from first principles. It can be used for the study of such diverse fields as molecular spectroscopy, organic and inorganic chemistry, crystallography and pharmacochemistry. Some of its key strengths include high accuracy supported by its use of Slater-type orbitals, all-electron relativistic treatment..."

New page

===ADF (Amsterdam Density Functional Theory)===
ADF (Amsterdam Density Functional) is a Fortran program for calculations on atoms and molecules
(in gas phase or solution) from first principles. It can be used for the study of such diverse fields as
molecular spectroscopy, organic and inorganic chemistry, crystallography and pharmacochemistry. Some
of its key strengths include high accuracy supported by its use of Slater-type orbitals, all-electron relativistic
treatment of the heavier elements, and fast parameterized DFT-based semi-empirical methods. A separate
program BAND is available for the study of periodic systems: crystals, surfaces, and polymers. The
COSMO-RS program is used for calculating thermodynamic properties of (mixed) fluids.

The underlying theory is the Kohn-Sham approach to Density-Functional Theory (DFT). This implies
a one-electron picture of the many-electron systems, but yields in principle the exact electron density
(and related properties) and the total energy. If ADF is a new program for you, we recommend that you
carefully read Chapter 1, section 1.3 'Technical remarks, Terminology', which presents a discussion of
a few ADF-typical aspects and terminology. This will help you to understand and appreciate the output
of an ADF calculation. The ADF Manual is located on the web here: [http://www.scm.com/Doc/Doc2013/ADF/ADFUsersGuide/page1.html]

ADF 2013 (and SCM's other programs) is installed on ANDY and PENZIAS at the CUNY HPC Center. The older 2012 version
is also available on ANDY server. The current license is group-limited and allows for up to 32 cores of simultaneous ADF
use and 8 cores of simultaneous BAND use. This is a floating license limited to the DDR side of ANDY
and the PBS 'production' queue. Users not currently in the ADF group should inquire about access by sending
an email to 'hpchelp@csi.cuny.edu'.

Here is a simple ADF input deck that compute the SCF wave function for HCN. This example can be run
with the PBS script shown below on from 1 to 4 cores.

<pre>
Title HCN Linear Transit, first part
NoPrint SFO, Frag, Functions, Computation

Atoms Internal
1 C 0 0 0 0 0 0
2 N 1 0 0 1.3 0 0
3 H 1 2 0 1.0 th 0
End

Basis
Type DZP
End

Symmetry NOSYM

Integration 6.0 6.0

Geometry
Branch Old
LinearTransit 10
Iterations 30 4
Converge Grad=3e-2, Rad=3e-2, Angle=2
END

Geovar
th 180 0
End

End Input
</pre>

A PBS script ('adf_4.job') configured to use 4 cores is shown here. Note that ADF does not use the
version of MPI that the HPC Center supports by default. ADF used the proprietary version
of MPI from SGI that is part of SGI's MPT parallel library package. This script includes special
lines to configure the run for this. A side effect of this fact is that ADF jobs will not clock
time in PBS as shown under the 'Time' column when your job is being checked with 'qstat'

To include all required environmental variables and the path to the ADF executable
run the modules load command (the modules utility is discussed in detail above):

<pre>
module load adf
</pre>

<pre>
#!/bin/bash
# This script runs a 4-cpu (core) ADF job using the group
# license of Dr. Vittadello, Dr. Birke, and the CUNY HPC
# Center. This script requests only one half of the resources
# on an ANDY compute node (4 cores, 1 half its memory).
#
# The HCN_4P.inp deck in this directory is configured to work
# with these resources, although this computation is really
# too small to make full use of them. To increase or decrease
# the resources PBS requests (cpus, memory, or disk) change the
# '-l select' line below and the parameter values in the input deck.
#
#PBS -q production
#PBS -N adf_4P_job
#PBS -l select=1:ncpus=4:mem=11520mb:lscratch=400gb
#PBS -l place=free
#PBS -V

# Find out name of master execution host (compute node)
echo -n ">>>> PBS Master compute node is: "
hostname

# You must explicitly change to the working directory in PBS
cd $PBS_O_WORKDIR

# set environment up to use SGI's MPT version of MPI rather
# than the CUNY default which is OpenMPI
BASEPATH=/opt/sgi/mpt/mpt-2.02

export PATH=${BASEPATH}/bin:${PATH}
export CPATH=${BASEPATH}/include:${CPATH}
export FPATH=${BASEPATH}/include:${FPATH}
export LD_LIBRARY_PATH=${BASEPATH}/lib:${LD_LIBRARY_PATH}
export LIBRARY_PATH=${BASEPATH}/lib:${LIBRARY_PATH}
export MPI_ROOT=${BASEPATH}

# set the ADF root directory
export ADFROOT=/share/apps/adf
export ADFHOME=${ADFROOT}/2013.01

# point ADF to the ADF license file
export SCMLICENSE=${ADFHOME}/license.txt

# set up ADF scratch directory
export MY_SCRDIR=`whoami;date '+%m.%d.%y_%H:%M:%S'`
export MY_SCRDIR=`echo $MY_SCRDIR | sed -e 's; ;_;'`
export SCM_TMPDIR=/home/adf/adf_scr/${MY_SCRDIR}_$$

mkdir -p $SCM_TMPDIR

echo ""
echo "The ADF scratch files for this job are in: ${SCM_TMPDIR}"
echo ""

# check important paths
#type mpirun
#type adf

# set the number processors to use in this job to 4
export NSCM=4

# run the ADF job
echo "Starting ADF job ... "
echo ""

adf -n 4 < HCN_4P.inp > HCN_4P.out 2>&1

# name output files
mv logfile HCN_4P.logfile

echo ""
echo "ADF job finished ... "

# clean up scratch directory files
/bin/rm -r $SCM_TMPDIR
</pre>

Much of this script is similar to the script that runs Gaussian jobs, but the differences should
should be described in some detail. First, ADF must be submitted to the 'production' queue
which is where its floating license has been limited, and where it can only use 32 cores at one
for ADF and 8 cores at a time for BAND. Second, there is a block in the script that sets up the
environment to use the SGI proprietary version of MPI for parallel runs. Next is the NSCM environmental
variable which defines the number of cores to use along with the '-n' option on the command
line. Both of these (along with the number of cpus on the PBS '-l select' line at the beginning
of the script) must be adjusted to control the number of cores used by the job.

Note the 'adf' command is actually a script that generates and runs another script that
actually runs the 'adf.exe' executable. This script (called 'runscript') is built and placed
in the users working directory. It typically includes some preliminary steps that are NOT
run in parallel.

With the HCN input file and PBS script above, you can submit an ADF job on ANDY with:

<pre>
qsub adf_4.job
</pre>

All users of ADF must be licensed and placed in the 'gadf' Unix group by HPC Center staff.

Applications Environment/ADF - Revision history

James at 20:12, 27 October 2022