Using petsc - Revision history

Bismg at 12:47, 25 February 2010

2010-02-25T12:47:14Z

2010-02-24T18:23:30Z

2010-02-24T18:22:32Z

2010-02-24T15:57:28Z

2010-02-24T14:58:41Z

2010-02-24T14:52:55Z

2010-02-24T14:41:13Z

2010-02-24T14:33:18Z

2010-02-23T12:23:09Z

2010-02-23T12:21:46Z

← Older revision		Revision as of 12:47, 25 February 2010
Line 409:		Line 409:

	end program main		end program main
		+
		+	</pre>
		+
		+	Extra code to extract '''solution''' from '''PetSc variable'''
		+	<pre>
		+	PetscInt, dimension(:), allocatable :: indx ! array containing the ordering of the elements in soln
		+	real(8), dimension(:), allocatable :: f90solnvec ! solution from the linear solver
		+	real(8), dimension(:,:), allocatable :: answer
		+	integer :: ii,jj
		+
		+	allocate(answer(n,n))
		+	allocate(f90solnvec(ndof))
		+	allocate(indx(ndof))
		+
		+	! Set up the ordering of the PetSc vector to be extracted back to f90
		+	do ii=1,ndof
		+	j=ii-1
		+	indx(ii)=j
		+	end do
		+
		+	! Extract the solution from the PetSc variable
		+	f90solnvec=0.0d0
		+	call VecGetValues(x,ndof,indx,f90solnvec,ierr)
		+
		+	! Put into a 2d array
		+	do j=1,n
		+	do i=1,n
		+	ii=(j-1)*n + i
		+	answer(i,j)=f90solnvec(ii)
		+	end do
		+	end do

	</pre>		</pre>

@@ Line 81: / Line 81: @@
 </pre>
-'''Also, Vicky has noticed that if you use the intel compilers, it appears that the order of command line
+'''Also, Vicky has noticed that if you use the intel compilers, it appears that the order of command line parameters when you come to run programs is important, so, for example, specify -pc_type before -ksp_tye'''
 parameters when you come to run programs is important, so, for example, specify -pc_type before -ksp_tye
 ----

@@ Line 80: / Line 80: @@
 /opt/local/CentOS-64/petsc/petsc-3.0.0-p11
 </pre>
 ----

@@ Line 67: / Line 67: @@
 <pre>
-mpif90 -I /opt/local/CentOS-64/petsc/3.0.0-p11/mpich-1.2.6/intel_fc_10.1/include/ -I /local/include/ -fpp scalar.f90 \
+mpif90 -I $PETSC_DIR/include/ -I /local/include/ -fpp scalar.f90 \
--L /opt/local/CentOS-64/petsc/3.0.0-p11/mpich-1.2.6/intel_fc_10.1/lib/ -L/local/lib  \
+-L $PETSC_DIR/lib/ -L/local/lib  \
 -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -ldmumps -lmumps_common -lparmetis \
 -lmetis -lpord -lscalapack -lblacs -lflapack -lfblas -lX11 -lpthread

@@ Line 83: / Line 83: @@
 ----
-and run (despite compiling using mpif90 etc, the runs below will be '''serial'''):
+and run (despite compiling using mpif90 etc, the runs below will be '''serial'''.  See [[using petsc (parallel)]] for an example of how to run a petsc job on more than one processor):
 <pre>
 >time ./a.out -ksp_monitor

← Older revision		Revision as of 14:52, 24 February 2010
Line 74:		Line 74:

	(There are also a debug versions of the libraries built at /opt/local/CentOS-64/petsc/3.0.0-p11/mpich-1.2.6/intel_fc_10.1/debug/lib/)		(There are also a debug versions of the libraries built at /opt/local/CentOS-64/petsc/3.0.0-p11/mpich-1.2.6/intel_fc_10.1/debug/lib/)
		+
		+	Note that there are '''docs''' and '''tutorials''', which you can copy under:
		+
		+	<pre>
		+	/opt/local/CentOS-64/petsc/petsc-3.0.0-p11
		+	</pre>

	----		----

@@ Line 50: / Line 50: @@
 ----
-On '''the musketeers''', you should first load the mpich module:
+On '''the musketeers''', you should do the following:
 <pre>
-module add mpich/1.2.6
+module add petsc/mpich-1.2.6/intel_fc_10.1/3.0.0-p11
 </pre>
-and then compile (uses ifort) using the command line:
+and then compile using the command line:
 <pre>
-mpif90 -I /opt/local/CentOS-64/petsc/3.0.0-p11/intel_fc_10.1/include/ -I /local/include/ -fpp scalar.f90 \
+mpif90 -I /opt/local/CentOS-64/petsc/3.0.0-p11/mpich-1.2.6/intel_fc_10.1/include/ -I /local/include/ -fpp scalar.f90 \
--L /opt/local/CentOS-64/petsc/3.0.0-p11/intel_fc_10.1/lib/ -L/local/lib  \
+-L /opt/local/CentOS-64/petsc/3.0.0-p11/mpich-1.2.6/intel_fc_10.1/lib/ -L/local/lib  \
 -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -ldmumps -lmumps_common -lparmetis \
 -lmetis -lpord -lscalapack -lblacs -lflapack -lfblas -lX11 -lpthread
 </pre>
-(There are also a debug versions of the libraries built at /opt/local/CentOS-64/petsc/3.0.0-p11/intel_fc_10.1/debug/lib/)
+(There are also a debug versions of the libraries built at /opt/local/CentOS-64/petsc/3.0.0-p11/mpich-1.2.6/intel_fc_10.1/debug/lib/)
 ----

@@ Line 28: / Line 28: @@
 were picked to give the solvers a hard time - if they were all 1, the iterative methods below would beat the direct solver decisively in CPU time. I think the strength of PETSc is the number of solvers and preconditioners you get to try without too much fiddling
 To run this, first you need PETSc, I configured it like this (stuff I compile myself ends up in /local) (petsc is already install on '''the musketeers''', see below)
@@ Line 44: / Line 46: @@
 -L /local/petsc/opt/lib/ -L/local/lib  -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -ldmumps -lmumps_common
 -lparmetis -lmetis -lpord -lscalapack -lblacs -lflapack -lfblas -lX11
-</pre>
+----
 On '''the musketeers''', you should first load the mpich module:
@@ Line 63: / Line 66: @@
 (There are also a debug versions of the libraries built at /opt/local/CentOS-64/petsc/3.0.0-p11/intel_fc_10.1/debug/lib/)
 and run