PETSc - Revision history

Lothar.brendel: /* Debian (like merope, asterope, and electra) */ no comma!

2025-07-01T14:46:43Z

Debian (like merope, asterope, and electra): no comma!

← Older revision		Revision as of 16:46, 1 July 2025
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	# L.B. 2024		# L.B. 2024

	declare -A inc=(["openmpi"]="/usr/lib/x86_64-linux-gnu/openmpi/include",		declare -A inc=(["openmpi"]="/usr/lib/x86_64-linux-gnu/openmpi/include"
	["mpich"]="/usr/include/x86_64-linux-gnu/mpich")		["mpich"]="/usr/include/x86_64-linux-gnu/mpich")

	declare -A lib=(["openmpi"]="[/usr/lib/x86_64-linux-gnu/libmpi.so,/usr/lib/x86_64-linux-gnu/libmpi_mpifh.so]",		declare -A lib=(["openmpi"]="[/usr/lib/x86_64-linux-gnu/libmpi.so,/usr/lib/x86_64-linux-gnu/libmpi_mpifh.so]"
	["mpich"]="[/usr/lib/x86_64-linux-gnu/libmpich.so,/usr/lib/x86_64-linux-gnu/libmpichfort.so]")		["mpich"]="[/usr/lib/x86_64-linux-gnu/libmpich.so,/usr/lib/x86_64-linux-gnu/libmpichfort.so]")

	~~# On Debian 12, the MPICH libraries are actually called~~
	~~# "libmpich.so.12" and "libmpichfort.so.12", and the standard links~~
	~~# .so -> .so.12 are missing. Ask your admin to fix that. Specifying~~
	~~# the suffix ".12" doesn't work, it confuses the configure.py.~~

	export PETSC_DIR=$PWD		export PETSC_DIR=$PWD

Lothar.brendel: /* Version 3.1-p8 */ +MPI_Comm_f2c()

2025-06-13T15:21:02Z

Version 3.1-p8: +MPI_Comm_f2c()

← Older revision		Revision as of 17:21, 13 June 2025
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	* PETSc 3.1-p8 uses deprecated objects: MPI_Attr_get, MPI_Attr_put, MPI_Attr_delete, MPI_Keyval_create, MPI_Keyval_free, OMPI_C_MPI_NULL_COPY_FN, OMPI_C_MPI_NULL_DELETE_FN (deprecated since MPI-2.0) and MPI_Errhandler_create, MPI_Errhandler_set, MPI_Type_struct (''removed'' in MPI-3.0)		* PETSc 3.1-p8 uses deprecated objects: MPI_Attr_get, MPI_Attr_put, MPI_Attr_delete, MPI_Keyval_create, MPI_Keyval_free, OMPI_C_MPI_NULL_COPY_FN, OMPI_C_MPI_NULL_DELETE_FN (deprecated since MPI-2.0) and MPI_Errhandler_create, MPI_Errhandler_set, MPI_Type_struct (''removed'' in MPI-3.0)
	* Pluto4.1 itself uses deprecated objects (in Parallel/al_subarray_.c): MPI_Type_extent, MPI_Type_hvector, MPI_Type_struct (''removed'' in MPI-3.0)		* Pluto4.1 itself uses deprecated objects (in Parallel/al_subarray_.c): MPI_Type_extent, MPI_Type_hvector, MPI_Type_struct (''removed'' in MPI-3.0)
			* The configurator checks the existence of the function <code>MPI_Comm_f2c()</code> by calling it as <code>MPI_Comm_f2c(MPI_COMM_WORLD)</code> (in function <code>configureConversion()</code> in petsc-3.1-p8/config/BuildSystem/config/packages/MPI.py), but <code>MPI_COMM_WORLD</code> is [https://linux.die.net/man/3/mpi_comm_world not an integer]. The failing check may finally result in "mpi.h" allegedly not being found. [[PETSc/config/BuildSystem/config/packages/MPI.py\|Patching MPI.py]] works.

	OpenMPI is (at least on Debian) hardwired to reject removed functions (<code>#define OMPI_ENABLE_MPI1_COMPAT 0</code> in /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h and /usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/openmpi/mpi.h). Changing 0 → 1 (by the admin) works, the compiler flag <code>-Wno-deprecated-declarations</code> is recommended, then. A script like the following for configuring PETSc is advisable:		OpenMPI is (at least on Debian) hardwired to reject removed functions (<code>#define OMPI_ENABLE_MPI1_COMPAT 0</code> in /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h and /usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/openmpi/mpi.h). Changing 0 → 1 (by the admin) works, the compiler flag <code>-Wno-deprecated-declarations</code> is recommended, then. A script like the following for configuring PETSc is advisable:

Lothar.brendel: /* Debian (like merope, asterope, and electra) */ +python2

2024-04-12T08:45:57Z

Debian (like merope, asterope, and electra): +python2

← Older revision		Revision as of 10:45, 12 April 2024
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	Necessary packages:		Necessary packages:
	* make		* make, python2-minimal
	* libopenmpi-dev or libmpich-dev		* libopenmpi-dev or libmpich-dev
	* libblas-dev, liblapack-dev		* libblas-dev, liblapack-dev

Lothar.brendel: /* Debian (like merope, asterope, and electra) */ +make

2024-04-10T12:00:39Z

Debian (like merope, asterope, and electra): +make

← Older revision		Revision as of 14:00, 10 April 2024
Line 21:		Line 21:

	Necessary packages:		Necessary packages:
			* make
	* libopenmpi-dev or libmpich-dev		* libopenmpi-dev or libmpich-dev
	* libblas-dev, liblapack-dev		* libblas-dev, liblapack-dev

Lothar.brendel: /* Debian (merope, asterope, electra) */ packages

2024-04-09T15:33:14Z

Debian (merope, asterope, electra): packages

← Older revision		Revision as of 17:33, 9 April 2024
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	OpenMPI is (at least on Debian) hardwired to reject removed functions (<code>#define OMPI_ENABLE_MPI1_COMPAT 0</code> in /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h and /usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/openmpi/mpi.h). Changing 0 → 1 (by the admin) works, the compiler flag <code>-Wno-deprecated-declarations</code> is recommended, then. A script like the following for configuring PETSc is advisable:		OpenMPI is (at least on Debian) hardwired to reject removed functions (<code>#define OMPI_ENABLE_MPI1_COMPAT 0</code> in /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h and /usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/openmpi/mpi.h). Changing 0 → 1 (by the admin) works, the compiler flag <code>-Wno-deprecated-declarations</code> is recommended, then. A script like the following for configuring PETSc is advisable:

	== Debian (merope, asterope, electra) ==		== Debian (like merope, asterope, and electra) ==

			Necessary packages:
			* libopenmpi-dev or libmpich-dev
			* libblas-dev, liblapack-dev

	<syntaxhighlight lang="shell">		<syntaxhighlight lang="shell">

Lothar.brendel: Link 3.1-p8

2024-04-09T08:28:46Z

Link 3.1-p8

← Older revision		Revision as of 10:28, 9 April 2024
Line 1:		Line 1:
	[https://petsc.org/release PETSc] is the ''Portable, Extensible Toolkit for Scientific Computation''.		[https://petsc.org/release PETSc] is the ''Portable, Extensible Toolkit for Scientific Computation''.

	= Version 3.1-p8 =		= [https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-3.1-p8.tar.gz Version 3.1-p8] =

	(March 25, 2010)		(March 25, 2010)

Lothar.brendel: /* magnitude */ downloads on magnitude

2024-03-22T11:08:04Z

magnitude: downloads on magnitude

← Older revision		Revision as of 13:08, 22 March 2024
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	</syntaxhighlight>		</syntaxhighlight>

	In your script or shell, where you do the actual <code>make</code> (as given in the last line of output of the configure script), you need first to load above modules, too.		'''Attention:'''

			* In your script or shell, where you do the actual <code>make</code> (as given in the last line of output of the configure script), you need first to load above modules, too.
			* On magnitude, downloading extra packages (like ''hypre'') is not possible, you have to copy the source from a computer in our local network to magnitude.

Lothar.brendel: /* magnitude */ +make

2024-03-21T10:29:33Z

magnitude: +make

← Older revision		Revision as of 12:29, 21 March 2024
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	# 32-bit integer type.		# 32-bit integer type.
	</syntaxhighlight>		</syntaxhighlight>

			In your script or shell, where you do the actual <code>make</code> (as given in the last line of output of the configure script), you need first to load above modules, too.

Lothar.brendel: /* Version 3.1-p8 */ +magnitude_intel

2024-03-21T10:26:42Z

Version 3.1-p8: +magnitude_intel

@@ Line 17: / Line 17: @@
 OpenMPI is (at least on Debian) hardwired to reject removed functions (<code>#define OMPI_ENABLE_MPI1_COMPAT 0</code> in /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h and /usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/openmpi/mpi.h). Changing 0 → 1 (by the admin) works, the compiler flag <code>-Wno-deprecated-declarations</code> is recommended, then. A script like the following for configuring PETSc is advisable:
 <syntaxhighlight lang="shell">
@@ Line 44: / Line 46: @@
          --with-x=0 --with-debugging=0 --download-hypre=1 \
          --with-mpi-include="${inc[$mpi]}" --with-mpi-lib="${lib[$mpi]}"
 </syntaxhighlight>

Lothar.brendel: /* Version 3.1-p8 */ openmpi, opt

2024-02-15T13:56:34Z

Version 3.1-p8: openmpi, opt

← Older revision		Revision as of 15:56, 15 February 2024
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	export PETSC_DIR=$PWD		export PETSC_DIR=$PWD

	mpi=~~mpich~~		opt=-O3 # Some prefer -O2.
			mpi=openmpi

	python2 ./config/configure.py PETSC_ARCH=debian_$mpi \		python2 ./config/configure.py PETSC_ARCH=debian_$mpi \
	--with-cc=mpicc.$mpi --with-cxx=mpicxx.$mpi --with-fc=mpif90.$mpi --with-mpiexec=mpirun.$mpi \		--with-cc=mpicc.$mpi --with-cxx=mpicxx.$mpi --with-fc=mpif90.$mpi --with-mpiexec=mpirun.$mpi \
	--CFLAGS=-Wno-deprecated-declarations --COPTFLAGS=~~-O3~~ --FOPTFLAGS=~~-O3~~ \		--CFLAGS=-Wno-deprecated-declarations --COPTFLAGS=$opt --FOPTFLAGS=$opt \
	--with-x=0 --with-debugging=0 --download-hypre=1 \		--with-x=0 --with-debugging=0 --download-hypre=1 \
	--with-mpi-include="${inc[$mpi]}" --with-mpi-lib="${lib[$mpi]}"		--with-mpi-include="${inc[$mpi]}" --with-mpi-lib="${lib[$mpi]}"
	</syntaxhighlight>		</syntaxhighlight>