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Apwillis: /* Typical setup commands */

2024-12-03T17:23:08Z

Typical setup commands

← Older revision		Revision as of 10:23, 3 December 2024
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	>		>
	> [Run!...]		> [Run!...]
	> nohup ./main.out > OUT 2> OUT.err & [run serial]		> nohup ./main.out > OUT 2> OUT.err & [run serial]
	> nohup mpirun -np 8 ./main.out > OUT~~.err~~ 2> OUT.err & [run parallel]		> nohup mpirun -np 8 ./main.out > OUT 2> OUT.err & [run parallel]
	>		>
	> head OUT [check for warnings/errors]		> head OUT [check for warnings/errors]

Apwillis: /* Serial and parallel use */

2020-07-15T09:06:52Z

Serial and parallel use

← Older revision		Revision as of 02:06, 15 July 2020
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	==== Serial and parallel use ====		==== Serial and parallel use ====

			* To launch a serial job
			> nohup ./main.out > OUT 2> OUT.err &
	* The number of cores is set in <tt>parallel.h</tt> (all other parameters are in <tt>program/parameters.f90</tt>).		* The number of cores is set in <tt>parallel.h</tt> (all other parameters are in <tt>program/parameters.f90</tt>).
	* For serial use ~~set~~ both <tt>_Nr</tt> and <tt>_Ns</tt> to <tt>1</tt> in <tt>parallel.h</tt>.		* For serial use, both <tt>_Nr</tt> and <tt>_Ns</tt> should be <tt>1</tt> in <tt>parallel.h</tt>.
	* MPI is required if, and only if, <tt>_Np=_Nr*_Ns</tt> is greater than <tt>1</tt>.
	* For modest parallelisation, <tt>_Np</tt><=32, it is recommended to change <tt>_Nr</tt> only~~, and leave~~ <tt>_Ns</tt> set to <tt>1</tt> (i.e. <tt>_Np==_Nr</tt>).		* For parallel use, in <tt>Makefile</tt> the <tt>COMPILER</tt> needs to be changed to e.g. <tt>mpif90</tt>.
			* MPI is required if, and only if, <tt>_Np=_Nr*_Ns</tt> is greater than <tt>1</tt> in <tt>parallel.h</tt>.
			* For modest parallelisation, <tt>_Np</tt><=32, it is recommended to change <tt>_Nr</tt> only. Leave <tt>_Ns</tt> set to <tt>1</tt> (i.e. <tt>_Np==_Nr</tt>).
	* For high parallelisation, <tt>_Nr</tt> and <tt>_Ns</tt> should be of the same order.		* For high parallelisation, <tt>_Nr</tt> and <tt>_Ns</tt> should be of the same order.
	* ~~In <tt~~>~~Makefile<~~/tt> ~~the~~ <tt>COMPILER</tt> ~~might need to be changed~~ when switching between parallel and serial use, or it may be more convenient to ~~use the parallel compiler for all cases, an to replace the serial~~ launch ~~command~~ with ~~the parallel launch command~~		* To launch a parallel job on 8 cores
	> ~~nohup mpirun~~ -np 1 ./~~main.out~~ > ~~OUT 2> OUT~~.~~err &~~		> nohup mpirun -np 8 ./main.out > OUT 2> OUT.err &
			* Note that, rather than keep changing <tt>COMPILER</tt> when switching between parallel and serial use, it may be more convenient to simply launch with <tt>-np 1</tt> in the parallel launch command.

	==== Initial conditions ====		==== Initial conditions ====

Apwillis: /* Makefile */

2020-07-15T08:48:41Z

Makefile

← Older revision		Revision as of 01:48, 15 July 2020
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	#COMPFLAGS = -cpp -c -O3 -OPT:Ofast -march=opteron -fno-second-underscore		#COMPFLAGS = -cpp -c -O3 -OPT:Ofast -march=opteron -fno-second-underscore

	COMPILER = gfortran [*CHANGE TO mpif90 FOR PARALLEL USE*]		COMPILER = gfortran [*CHANGE TO mpif90 FOR PARALLEL USE*]
	COMPFLAGS = -ffree-line-length-none -x f95-cpp-input -c -O3 \		COMPFLAGS = -ffree-line-length-none -x f95-cpp-input -c -O3 \
	-I/usr/include \ [*MIGHT NEED TO UPDATE INCLUDE PATH*]		-I/usr/include \ [*MIGHT NEED TO UPDATE INCLUDE PATH*]

Apwillis: /* Installation */

2020-07-15T08:46:43Z

Installation

← Older revision		Revision as of 01:46, 15 July 2020
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	:~> make clean		:~> make clean

	'''NOTE: If you wish to run in parallel, then you will need an mpi-fortran compiler. BUT, the code is sufficiently parallelized that it does NOT require parallel versions of LAPACK, netCDF or FFTW3. Each thread ~~can~~ calls the serial implementation.'''		'''NOTE: If you wish to run in parallel, then you will need an mpi-fortran compiler. BUT, the code is sufficiently parallelized that it does NOT require parallel versions of LAPACK, netCDF or FFTW3. Each thread calls the serial implementation of each library.'''

	'''Next''' try the [[Tutorial]], or take a look below if there were problems with libraries.		'''Next''' try the [[Tutorial]], or take a look below if there were problems with libraries.

Apwillis: /* Installation */

2020-07-15T08:45:50Z

Installation

← Older revision		Revision as of 01:45, 15 July 2020
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	:~> sudo apt-get install libnetcdf-dev		:~> sudo apt-get install libnetcdf-dev
	:~> sudo apt-get install libnetcdff-dev		:~> sudo apt-get install libnetcdff-dev
	# ~~and~~ for parallel MPI use:		# optionally, for parallel MPI use:
	:~> sudo apt-get install libopenmpi-dev		:~> sudo apt-get install libopenmpi-dev

Apwillis: /* Libraries */

2020-07-14T16:14:51Z

Libraries

← Older revision		Revision as of 09:14, 14 July 2020
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	If you get something like		If you get something like
	~~Missing~~ 'mpif.h'		Error: Can't open included file 'mpif.h'
	it is possible that <tt>_Np (=_Nr*_Ns)</tt> is not <tt>1</tt> in <tt>parallel.h</tt>, but the <tt>COMPILER</tt> has not been changed to <tt>mpif90</tt> in <tt>Makefile</tt>.		it is possible that <tt>_Np (=_Nr*_Ns)</tt> is not <tt>1</tt> in <tt>parallel.h</tt>, but the <tt>COMPILER</tt> has not been changed to <tt>mpif90</tt> in <tt>Makefile</tt>.

Apwillis: /* Libraries */

2020-07-14T16:13:03Z

Libraries

← Older revision		Revision as of 09:13, 14 July 2020
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	If you get something like		If you get something like
	Missing 'mpif.h'		Missing 'mpif.h'
	it is possible that <tt>_Np (=_Nr*_Ns)</tt> is not <tt>1</tt> in <tt>parallel.h</tt>, but the ~~compiler~~ has not been changed to <tt>mpif90</tt>.		it is possible that <tt>_Np (=_Nr*_Ns)</tt> is not <tt>1</tt> in <tt>parallel.h</tt>, but the <tt>COMPILER</tt> has not been changed to <tt>mpif90</tt> in <tt>Makefile</tt>.

Apwillis: /* Precompiled binaries */

2020-07-14T16:11:25Z

Precompiled binaries

← Older revision		Revision as of 09:11, 14 July 2020
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	If using a linux environment, install the LAPACK, FFTW3 and netCDF packages with your package manager or 'software center'. If you have sudo privileges, it may be sufficient to try		If using a linux environment, install the LAPACK, FFTW3 and netCDF packages with your package manager or 'software center'. If you have sudo privileges, it may be sufficient to try
	:~> sudo apt-get install ~~liblapack-dev~~		:~> sudo apt-get install ...
	~~:~> sudo apt-get install libfftw3-dev~~		commands listed at the top of this page. Then
	~~:~> sudo apt-get install libnetcdf-dev~~
	Then
	:~> cd openpipeflow-x.xx/		:~> cd openpipeflow-x.xx/
	:~> make		:~> make

Apwillis: /* Libraries */

2020-07-14T16:08:34Z

Libraries

← Older revision		Revision as of 09:08, 14 July 2020
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	If you get something like		If you get something like
	Missing 'mpif.h'		Missing 'mpif.h'
	it is possible that <tt>_Np</tt> is not <tt>1</tt>, but the compiler has not been changed to <tt>mpif90</tt>.		it is possible that <tt>_Np (=_Nr*_Ns)</tt> is not <tt>1</tt> in <tt>parallel.h</tt>, but the compiler has not been changed to <tt>mpif90</tt>.

Apwillis: /* Libraries */

2020-07-14T16:06:19Z

Libraries

← Older revision		Revision as of 09:06, 14 July 2020
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	/usr/bin/ld: cannot find -llapack		/usr/bin/ld: cannot find -llapack
	/usr/bin/ld: cannot find -lfftw3		/usr/bin/ld: cannot find -lfftw3

			If you get something like
			Missing 'mpif.h'
			it is possible that <tt>_Np</tt> is not <tt>1</tt>, but the compiler has not been changed to <tt>mpif90</tt>.


	=== Precompiled binaries ===		=== Precompiled binaries ===