NWChem - Revision history

Kwbent@uab.edu at 23:20, 28 September 2015

2015-09-28T23:20:01Z

← Older revision		Revision as of 23:20, 28 September 2015
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	#The make.log file contains tons of useful information, and is hard to dig through, but there is useful information in there if things go badly		#The make.log file contains tons of useful information, and is hard to dig through, but there is useful information in there if things go badly
	#You may have noticed that the MPI_LOC directory was never explicitly set in the "build_nwchem" script. It's defined as an environment variable once we load the openmpi/openmpi-gnu module.		#You may have noticed that the MPI_LOC directory was never explicitly set in the "build_nwchem" script. It's defined as an environment variable once we load the openmpi/openmpi-gnu module.
			#The environment variable DFLT_TOT_MEM=475000000 in the "build_nwchem" script represents how many 'doubles' (8 bytes) to give each processor by default. I used ~4GB per node here, based on the information available about the gen3 Cheaha hardware. This can be overridden in the NWChem input file by using the 'memory' keyword to allocate more or less memory per core.

	==Loadable module for NWChem==		==Loadable module for NWChem==
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	Submit this job to the queue with qsub, and wait for the results. Once it starts, it shouldn't be more than a few minutes with this input file.		Submit this job to the queue with qsub, and wait for the results. Once it starts, it shouldn't be more than a few minutes with this input file.
	<pre> qsub nwchem_test </pre>		<pre> qsub nwchem_test </pre>

			=Final Thoughts=
			#With any large software package, the setup is tedious and much can go wrong, especially when it depends on many previous steps. Make sure to run tests at each step of the way, and verify them before moving on.
			#NWChem scales very well with the number of cores used. The more the merrier!
			#Google has been, and shall always be your friend when it comes to compile errors, and NWChem input files.

	=References=		=References=
	{{Reflist}}		{{Reflist}}

Kwbent@uab.edu: /* Testing the NWChem Package */

2015-09-28T23:13:33Z

Testing the NWChem Package

← Older revision		Revision as of 23:13, 28 September 2015
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	#$ -N test_job		#$ -N test_job
	#$ -pe rr_openmpi 8		#$ -pe rr_openmpi 8
	#$ -l h_rt=00:10:00,h_vmem=1.25G,vf=1G		#$ -l h_rt=00:20:00,h_vmem=1.25G,vf=1G
	#$ -M $USER@uab.edu		#$ -M $USER@uab.edu
	#$ -m eas		#$ -m eas
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	mpiexec -np $NSLOTS nwchem $INPUT.nw >& $INPUT.out		mpiexec -np $NSLOTS nwchem $INPUT.nw >& $INPUT.out
	</pre>		</pre>

			Submit this job to the queue with qsub, and wait for the results. Once it starts, it shouldn't be more than a few minutes with this input file.
			<pre> qsub nwchem_test </pre>

	=References=		=References=
	{{Reflist}}		{{Reflist}}

Kwbent@uab.edu: /* Testing the NWChem Package */

2015-09-28T23:11:56Z

Testing the NWChem Package

@@ Line 517: / Line 517: @@
 <pre> cp $HOME/src/nwchem-6.5/examples/pspw/C6.nw $HOME </pre>
 Refer to the getting started <ref name="STARTMEUP"> [[https://docs.uabgrid.uab.edu/wiki/Cheaha_GettingStarted#Submitting_Jobs Getting Started]] </ref> guide for more information on submitting jobs.  Below is an example SGE script that will run the NWChem test file, and place the results back in the home directory.
 =References=
 {{Reflist}}

Kwbent@uab.edu: /* Testing the NWChem Package */

2015-09-28T23:03:03Z

Testing the NWChem Package

← Older revision		Revision as of 23:03, 28 September 2015
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	Though they should all be ran and verified, copy one of the examples to the $HOME directory.		Though they should all be ran and verified, copy one of the examples to the $HOME directory.
	<pre> cp $HOME/src/nwchem-6.5/examples/pspw/C6.nw $HOME </pre>		<pre> cp $HOME/src/nwchem-6.5/examples/pspw/C6.nw $HOME </pre>
			Refer to the getting started <ref name="STARTMEUP"> [[https://docs.uabgrid.uab.edu/wiki/Cheaha_GettingStarted#Submitting_Jobs Getting Started]] </ref> guide for more information on submitting jobs. Below is an example SGE script that will run the NWChem test file, and place the results back in the home directory.

	=References=		=References=
	{{Reflist}}		{{Reflist}}

Kwbent@uab.edu at 22:59, 28 September 2015

2015-09-28T22:59:51Z

← Older revision		Revision as of 22:59, 28 September 2015
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	NWChem/nwchem-6.5		NWChem/nwchem-6.5
	</pre>		</pre>

			=Testing the NWChem Package=
			NWChem includes its own set of example input files. In the $HOME/src/nwchem-6.5/example directory there are 5 tests of different types of calculations.
			<pre>dirdyvtst md pspw qmd rimp2 tcepolar</pre>
			Though they should all be ran and verified, copy one of the examples to the $HOME directory.
			<pre> cp $HOME/src/nwchem-6.5/examples/pspw/C6.nw $HOME </pre>

	=References=		=References=
	{{Reflist}}		{{Reflist}}

Kwbent@uab.edu: /* Loadable module for NWChem */

2015-09-28T22:52:23Z

Loadable module for NWChem

← Older revision		Revision as of 22:52, 28 September 2015
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	prepend-path PATH $HOME/NWChem/bin		prepend-path PATH $HOME/NWChem/bin
	prepend-path LD_LIBRARY_PATH $HOME/OpenBLAS/lib		prepend-path LD_LIBRARY_PATH $HOME/OpenBLAS/lib
			</pre>

			In order to use this newly created module, you have to first load the module 'use.own'. Then you should be able to see it in when running 'module avail'. It will be at the very bottom of the list.
			<pre>
			module load use.own
			module load NWChem/nwchem-6.5
			module list
			</pre>
			<pre>
			-------------- /home/kwbent/privatemodules -----------
			NWChem/nwchem-6.5
	</pre>		</pre>

	=References=		=References=
	{{Reflist}}		{{Reflist}}

Kwbent@uab.edu at 22:48, 28 September 2015

2015-09-28T22:48:20Z

@@ Line 471: / Line 471: @@
 #The make.log file contains tons of useful information, and is hard to dig through, but there is useful information in there if things go badly
 #You may have noticed that the MPI_LOC directory was never explicitly set in the "build_nwchem" script.  It's defined as an environment variable once we load the openmpi/openmpi-gnu module.
 =References=
 {{Reflist}}

Kwbent@uab.edu: /* Notes on Compiling and Installing NWChem */

2015-09-28T22:37:29Z

Notes on Compiling and Installing NWChem

← Older revision		Revision as of 22:37, 28 September 2015
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	#More recent versions of OpenMPI do not usually build libmpi_f77 and libmpi_f90. If in the future NWChem is recompiled with a newer version of OpenMPI, the appropriate library is just libmpi_mpifh. The appropriate compiler is just mpifort, as opposed to having both mpif77 and mpif90.		#More recent versions of OpenMPI do not usually build libmpi_f77 and libmpi_f90. If in the future NWChem is recompiled with a newer version of OpenMPI, the appropriate library is just libmpi_mpifh. The appropriate compiler is just mpifort, as opposed to having both mpif77 and mpif90.
	#The make.log file contains tons of useful information, and is hard to dig through, but there is useful information in there if things go badly		#The make.log file contains tons of useful information, and is hard to dig through, but there is useful information in there if things go badly
	#You may have noticed that the ~~MPI_ROOT~~ directory was never explicitly set in the "build_nwchem" script. It's defined as an environment variable once we load the openmpi/openmpi-gnu module.		#You may have noticed that the MPI_LOC directory was never explicitly set in the "build_nwchem" script. It's defined as an environment variable once we load the openmpi/openmpi-gnu module.

	=References=		=References=
	{{Reflist}}		{{Reflist}}

Kwbent@uab.edu: /* Notes on Compiling and Installing NWChem */

2015-09-28T22:37:02Z

Notes on Compiling and Installing NWChem

← Older revision		Revision as of 22:37, 28 September 2015
Line 470:		Line 470:
	#More recent versions of OpenMPI do not usually build libmpi_f77 and libmpi_f90. If in the future NWChem is recompiled with a newer version of OpenMPI, the appropriate library is just libmpi_mpifh. The appropriate compiler is just mpifort, as opposed to having both mpif77 and mpif90.		#More recent versions of OpenMPI do not usually build libmpi_f77 and libmpi_f90. If in the future NWChem is recompiled with a newer version of OpenMPI, the appropriate library is just libmpi_mpifh. The appropriate compiler is just mpifort, as opposed to having both mpif77 and mpif90.
	#The make.log file contains tons of useful information, and is hard to dig through, but there is useful information in there if things go badly		#The make.log file contains tons of useful information, and is hard to dig through, but there is useful information in there if things go badly
			#You may have noticed that the MPI_ROOT directory was never explicitly set in the "build_nwchem" script. It's defined as an environment variable once we load the openmpi/openmpi-gnu module.

	=References=		=References=
	{{Reflist}}		{{Reflist}}

Kwbent@uab.edu: /* Notes on Compiling and Installing NWChem */

2015-09-28T22:35:09Z

Notes on Compiling and Installing NWChem

← Older revision		Revision as of 22:35, 28 September 2015
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	checking whether SCALAPACK implements pdsyevr... yes		checking whether SCALAPACK implements pdsyevr... yes
	configure:		configure:

	</pre>		</pre>
			#The openmpi/openmpi-gnu module uses mpi 1.4, which is a little more dated than I would have liked, but it was 'infiniband aware', which kept me from needing to specify the IB libs and include directory in the NWChem environment variables inside the "build_nwchem" script.
			#More recent versions of OpenMPI do not usually build libmpi_f77 and libmpi_f90. If in the future NWChem is recompiled with a newer version of OpenMPI, the appropriate library is just libmpi_mpifh. The appropriate compiler is just mpifort, as opposed to having both mpif77 and mpif90.
			#The make.log file contains tons of useful information, and is hard to dig through, but there is useful information in there if things go badly

	=References=		=References=
	{{Reflist}}		{{Reflist}}