Documentation of Xg_t and XgBlock_t for abinit

Written on: 2018/09/07
Updated on:

Introduction and motivation

For the last decade, computers and more precisely processors have evolved a lot. To answer the issue of renewal, a new set of functions has been written to ease and adapt abinit to new architectures. This abstract layer is still a prototype and proof of concept. The true library should be written in an Oriented Object way to allow to switch during runtime between different libraries, or accelerators.

This current state of the code is stable. It is designed for 2D arrays of complex or real It is Fortran2003 compliant and without any OOP. Here is a list of what you can do

• Memory management

  • Allocate memory
  • Free memory
  • Block and sub-blocks
  • Map an object to an already allocated memory space
  • Get a Fortran90 array from an object
  • Get/Set values from/to Fortran90 array
  • Copy an object to an other one.
  • Pack a matrix to Upper/Lower Triangular Matrix
  • Reshape

• BLAS operations

  • POTRF
  • TRSM
  • GEMM
  • ADD
  • Scale

• LAPACK operations

  • HEEV
  • HEEVD
  • HPEV
  • HPEVD
  • HEGV
  • HEGVX
  • HPGVX
  • HPGVD

• ScaLAPACK

  • PHEEV
  • PHEGV

• Custom extensions

  • Array Shift
  • Colwise Norm 2
  • Colwise $Y-aX$
  • Set to 0
  • Set to Identity
  • Set the diagonal
  • Set the diagonal and zero off-diagonal terms
  • Get average
  • Get deviation
  • Print

• Tools

  • Get size
  • Get space

Each function is explained in detail below.

Memory management

In this section, two types are explained. The first one, xg_t, is for allocating memory whereas the second one, xgBlock_t works on an already allocated object or pointer. I did not find an other way of doing thing in Fortran. Of course, in C, both types would be the same.

Allocate memory

To create a new xg_t, one has to declare a xg_t and allocate its memory through the xg_init function:

type(xg_t) :: xg1
call xg_init(xg1,space,rows,cols,comm)

space can either be SPACE_C, SPACE_R or SPACE_CR. SPACE_C is for true complex numbers, SPACE_R is for real numbers taken from only the real part of complex numbers whereas SPACE_CR is consider both the real and imaginary parts of complex numbers as independent real numbers. The difference between SPACE_R and SPACE_CR is only visible for getting and setting the values. See the Get/Set values section for more details.

rows would be the number of rows to consider and cols the number of columns. comm is optional and is use if reductions are needed for algebra operations, and even ScaLAPACK if available.

Free memory

Once you do not need an array anymore, or you do not need the memory anymore, you can free it with xg_free:

call xg_free(xg1)

Block and sub block

It may happen that you do not want to work on the full array but only a part of the array. This is the main motivation to introduce the block notion. A block is a part of an array on which you can work. The main thing to remember is that a block work on an already allocated memory. Therefore there is no check allocation nor freeing of block. The Fortran90 type for this object is xgBlock_t and you can create it with

type(xgBlock_t) :: xgblockA

Basically, this is the main object you will use. Even if you created a xg_t object to allocate memory, you cannot work on xg_t but rather on its own block that you can access with xg%self. xg%self is of type xgBlock_t and represents the full array you allocated.

To work on a subarray, you will need a xgBlock_t object, and build it with the xg_setBlock function

type(xg_t)::xg1
type(xgBlock_t)::xgblockA
call xg_init(xg1,SPACE_C,maxRows,maxCols)
call xg_setBlock(xg1,xgblockA,firstColumn,rows,cols)

xgblockA represents a subarray of xg1 starting from the first column firstColumn (the very first one is 1) of xg1 and has rows rows and cols columns.

Map an object to an already allocated memory space

Usually, you will have a Fortran90 array that you may want to plug in an xgBlock_t or vice versa you have a xgBlock_t object and want to get a Fortran90 array variable. You can achieve this operation with what is called mapping and reverse mapping. From Fortran90 array to xgBlock_t it is mapping On a regular cpu, this should be free, no allocations, no memory transfer, nothing. But keep in mind that if you xgBlock_t represent an array on a GPU or other coprocessor unit, this will allocate memory and transfer it!

double precision :: array(2,10)
type(xgBlock_t) :: xgblockA
! if array represents complex numbers, it has 10 complex numbers
call xgBlock_map(xgblockA,array,SPACE_C,rows,cols,comm)
! if array represents real numbers, it has 20 real numbers (SPACE_CR)
call xgBlock_map(xgblockA,array,SPACE_CR,rows,cols,comm)

rows and cols are the number of rows and columns for the representation inside the xgBlock_t. It takes into account the space: regardless the space you chose, row*cols is the size of elements. Example: array if Fortran90

1	2	3	4	5	6	7	8	9	10
a	c	e	g	i	k	m	o	q	s
b	d	f	h	j	l	n	p	r	t

call xgBlock_map(xgblockA,array,SPACE_C,5,2,comm)

gives

1	2
(a,b)	(k,l)
(c,d)	(m,n)
(e,f)	(o,p)
(g,h)	(q,r)
(i,j)	(s,t)

(a,b) is the complex number at position (1,1)

call xgBlock_map(xgblockA,array,SPACE_CR,5,2,comm)

gives

1	2
a	f
b	g
c	h
d	i
e	j

a is the real number at position (1,1)

Get a Fortran90 array from an object

From xgBlock_t to Fortran90 array is a reverse mapping. This is exactly the opposite operation as the mapping.

double precision :: array(2,10)
type(xgBlock_t) :: xgblockA
! if array represents complex numbers, we take only the 10 first complex numbers
call xgBlock_reverseMap(xgblockA,array,rows,cols)
! if array represents real numbers, it has 20 real numbers (SPACE_CR) to put in a (2,10) array.
call xgBlock_reverseMap(xgblockA,array,rows,cols)

Be careful! If you work with complex, the array(2,10) has 10 complex numbers, only one row of complex numbers, not 2!!!
Example: xgBlock_t is (complex)

1	2
(a,b)	(k,l)
(c,d)	(m,n)
(e,f)	(o,p)
(g,h)	(q,r)
(i,j)	(s,t)

call xgBlock_reverseMap(xgblockA,array,1,10)

gives

1	2	3	4	5	6	7	8	9	10
a	c	e	g	i	k	m	o	q	s
b	d	f	h	j	l	n	p	r	t

and xgBlock_t is (real)

1	2
a	f
b	g
c	h
d	i
e	j

call xgBlock_reverseMap(xgblockA,array,2,5)

gives

1	2	3	4	5
a	c	e	g	i
b	d	f	h	j

call xgBlock_reverseMap(xgblockA,array,1,10)

gives

1	2	3	4	5	6	7	8	9	10
a	b	c	d	e	f	g	h	i	j

You can access the space of an xgBlock_t and the dimensions with

! depending on the version it can be space(xgblockA)
space = getSpace(xgblockA)
! depending on the version it can be cols(xgblockA)
cols = getCols(xgBlock1)
! In a next version there will be a getRows(xgblockA) function too
call xgBlock_getSize(xgBlock1,rows,cols)

Get/Set values from/to Fortran90 array

Those are old functions that should not be used that much. Before the mapping and reverse mapping processes, on had to copy values from Fortran90 array to xgBlock_t and vice versa Here it is very import to take care of the declared space for the xgBlock_t. Furthermore, for abinit compliance, a Fortran90 array is here always a 2D array with the first dimension equals to 2 double precision :: array(2,:). Each setter/getter exist for xg_t and xgBlock_t. Only the xgBlock_t version follows.

double precision :: array(2,10)
type(xgBlock_t) :: xgblockA
... Manage memory
call xgBlock_set(xgblockA,array,shiftCol,rows)

Let’s say array is

1	2	3	4	5	6	7	8	9	10
a	c	e	g	i	k	m	o	q	s
b	d	f	h	j	l	n	p	r	t

shiftCol = 1 and rows = 5.
The result array in xgblockA will be * if SPACE_C

1	2	3
xxxxx	(a,b)	(k,l)
xxxxx	(c,d)	(m,n)
xxxxx	(e,f)	(o,p)
xxxxx	(g,h)	(q,r)
xxxxx	(i,j)	(s,t)

• if SPACE_CR Here we set 5 rows of complex numbers so there are 5*2=10 rows of reals

1	2	3
xxxxx	a	b
xxxxx	c	d
xxxxx	e	f
xxxxx	g	h
xxxxx	i	j
xxxxx	k	l
xxxxx	m	n
xxxxx	o	p
xxxxx	q	r
xxxxx	s	t

Just to be clear, the first half columns are the real parts and the second half parts are the imaginary parts. This is absolutely not important since both are decoupled.

• if SPACE_R

Here we only take the reals parts of the number so there is actually 5 rows.

1	2	3
xxxxx	a	k
xxxxx	c	m
xxxxx	e	o
xxxxx	g	q
xxxxx	i	s

The getter works to reverse the set operation.

Copy an object to an other one.

If you want to copy a xgBlock_t into an other one, then you can use this functions. As in the BLAS copy function, you can specify the incrementation for each object

call xgBlock_copy(xgblockA,xgblockB,inc1,inc2)

This will copy xgblockA by incrementation of inc1 into xgblockB by incrementation of inc2

Pack a matrix to Upper/Lower Triangular Matrix

Packing is only usefull if you intent to use LAPACK functions that need packing. Both upper and lower triangular packing are implemented.

call xgBlock_pack(xgblockA,xgblockB,uplo)

xgblockA will be packed into xgblockB according to the value of uplo: l or L for lower packing and u or U for upper packing (See BLAS documentation for more explanations).

Reshape

This tool is only here if the shape of the block should be changed.

call xgBlock_reshape(xgblockA,newShape)

newShape is a 2 values array, the first one for the number of rows and the second one for the number of columns.

Here were presented the tools to allocate, free and manage memory blocks. The next part will focus on BLAS functions and ease of use compare to bare BLAS functions.

BLAS operations

All Blas functions have input variable names identical to real BLAS calls. Missing arguments are not needed with this library. Please refer to blas documentation at Netlib documentation

POTRF

TRSM

GEMM

ADD

Scale

LAPACK operations

All Lapack functions have input variable names identical to real Lapack calls. Missing arguments are not needed with this library. Please refer to blas documentation at Netlib documentation

HEEV

HEEVD

HPEV

HPEVD

HEGV

HEGVX

HPGVX

HPGVD

ScaLAPACK

Warning

At the present time (2018/10), none of scalapack implementation is thread safe. ELPA should work but requires MPI_THREAD_MULTIPLE to work which is not yet available on our architectures! So it is not tested and for security, scalapack/elpa is disabled at runtime with threads.

---

Before using a ScaLAPACK function, one has to check if it is possible or not (or event efficient). The xgScalapack_init function is design for this purpose and is very similar to what was already done in the old implementation but in a more flexible way.

use m_xgScalapack
type(xgScalapack_t) :: xgScalapack
integer :: comm
integer :: maxDim
integer :: verbosity
logical :: usable

call xgScalapack_init(xgScalapack,comm,maxDim,verbosity,usable)

comm is the MPI communicator to use. Note that not all of the processes available will be used. maxDim is the maximum dimension of a matrix that will be used with this xgScalapack object. verbosity is 0 or positive value. If 0 then nothing is printed. If positive, then the number of processes inside the communicator comm is displayed.

To configure the number of processus that will be selected, you must invoke the function xgScalapack_config before calling xgScalapack_init.

call xgScalapack_config(config,rankpp)

where config is one of {SLK_AUTO,SLK_DISABLED} or any positive value. A positive value will force scalapack to use exactly config processes. In SLK_AUTO mode, maxDim will drive the number of processes to use on the fly. Basically it is the maximum size of a matrix that a processes can hold. For instance, if the full matrix is 2000x2000 and maxDim=500, then scalapack will use at most 4 processes. When config=SLK_DISABLED, scalapack will not be used and usable will be set to false. In addition, if the matrix is too small with respect to the configuration of the moddule, usable is set to false. usable is set to true only if scalapack can be used. In this case, subcommincators are created in the xgScalapack object. Do not forget to call xgScalapack_free(xgScalapack) to free memory and destroy communicators.

With threads, usable is always set to false

Calling the following functions when usable=false is not tested and will crash (I think) or give trash results !

PHEEV

This is equivalent to HEEV to solve matrixA*X=eigenvalues*X

call xgScalapack_heev(xgScalapack,matrixA,eigenvalues)

xgScalapack is a previously initialized xgScalapac_t object, matrixA is the matrix to diagonalize and eigenvalues the eigenvalues. Eigenvectors are placed in matrixA at the end.

PHEGV

This is equivalent to HEGV to solve matrixA*X=eigenvalues*matrixB*X

call xgScalapack_hegv(xgScalapack,matrixA,matrixB,eigenvalues)

Eigenvectors are placed in matrixA at the end.

Custom extensions

Array Shift

This function is the same as the standard fortran cshift function. It is just an interface.

  integer :: nshift
  integer :: shiftdim
  call xgBlock_cshift(xgBlock,nshift,shiftdim)

nshift is the shift to perform along the shiftdim dimension. See fortran documentation for more information.

Colwise Norm 2

This function is usefull to compute the square L2 norm – meaning dot product – of each column. The function also provide information on min and max if there are present.

  call xgBlock_colwiseNorm2(xgBlock,dot,max_val,max_elt,min_val,min_elt)

dot is the resulting dot product (BLAS call) for each column of xgBlock. Therefore dot is a SPACE_R column vector with xgBlock%cols rows. max_val, min_val are the maximal and minimal values of the dot vector and max_elt, min_elt are the indices of maximal and minimal values. All those 4 variables are optional.

Colwise $<span><span class="MathJax_Preview">Y-aX</span><script type="math/tex">Y-aX$

The colwise operation done here is done column by columns. It is a useful function to compute residuals for eigen problems. Let suppose you solve HX=eX or HX=eBX, then calling this function will compute HX-eX or HX-eBX for each eigenvector of the matrix X.

  call xgBlock_colwiseCymax(xgBlockA, da, xgBlockB,xgBlockW)

Here the operation is xgBlockA(:,i) = xgBlockW(:,i)-da(i)*xgBlockB(:,i). da is a xgBlock_t colum vector of xgBlockA%cols rows. In our example, xgBlockA is HX and xgBlockW is X or BX and da is the eigenvalues vector. Note: this function is very similar to the BLAS saxpy function by the last one is not used because the minus operation would require an array copy that I want to avoid.

Set to 0

Nullify –set to 0– all coefficient of the block.

  call xgBlock_zero(xgBlock)

Set to Identity

This function just set the diagonal to ones. The off-diagonal coefficients are not modified. If you want to build the identity matrix, first call the xgBlock_zero function.

  call xgBlock_one(xgBlock)

Set the diagonal

Impose the diagonal of a matrix.

  call xgBlock_diagonal(xgBlock,diag)

diag is of type xgBlock_t is is a column vector. It is the diagonal to impose to xgBlock object.

Set the diagonal and zero off-diagonal terms

Only keep the diagonal termes and set the off-diagonal terms to 0.

  call xgBlock_diagonalOnly(xgBlock)

Get average

Compute the average of the full block

  call xgBlock_average(xgBlock,average)

average is the resulting real number.

Get deviation

Compute the deviation of the full block.

  call xgBlock_deviation(xgBlock,deviation)

deviation is the resulting real number.

Print

As obvious as it seems, this function just print in a convenient way the data inside the block.

  call xgBlock_print(xgBlock,outunit)

xgBlock is the block to print and outunit is the unit number in which the data will be written.