package lacaml
Install
Dune Dependency
Authors

EEgbert Ammicht <eammicht@lucent.com>

PPatrick Cousot <Patrick.Cousot@ens.fr>

SSam Ehrlichman <sehrlichman@janestreet.com>

FFlorent Hoareau <h.florent@gmail.com>

MMarkus Mottl <markus.mottl@gmail.com>

LLiam Stewart <liam@cs.toronto.edu>

CChristophe Troestler <Christophe.Troestler@umons.ac.be>

OOleg Trott <ot14@columbia.edu>

MMartin Willensdorfer <ma.wi@gmx.at>
Maintainers
Sources
sha256=560e87977d6ed5bbe1d217d653d7aaa08f29199b78621a4645fdee97787e4899
sha512=bda36434ca85590921761ce230fb5fcde2ee2dc5ffa0fe1e5fa26e1457fee98fbc905d008dc759e4182c9d3fffef5a28e27239074ba1f36b6e18edf997e45db2
Description
Lacaml interfaces the BLASlibrary (Basic Linear Algebra Subroutines) and LAPACKlibrary (Linear Algebra routines). It also contains many additional convenience functions for vectors and matrices.
README
Lacaml  Linear Algebra for OCaml
What is Lacaml?
This OCamllibrary interfaces two widely used mathematical FORTRANlibraries:
This allows developers to write highperformance numerical code for applications that require linear algebra.
Features
The BLAS and LAPACKlibraries have evolved over about two decades of time and are therefore extremely mature both in terms of stability and performance.
Lacaml interfaces most of the functions in BLAS and LAPACK (many hundreds!). It supports among other things linear equations, least squares problems, eigenvalue problems, singular value decomposition (SVD), Cholesky and QRfactorization, etc.
Many convenience functions for creating and manipulating matrices.
Powerful printing functions for large vectors and matrices and supplemental information (e.g. row and column headers). Users can specify easily how much context to print. For example, it is usually sufficient to print small blocks of the four corners of a large result matrix to manually verify the correctness of an algorithm. Lacaml uses this approach to limit the output to humanmanageable size.
Integration into the OCamltoplevel allows for easy experimentation for students and researchers as well as demonstration for lecturers. Values of vector and matrix type will be printed automatically without cluttering the screen.
The OCamlinterface was designed in a way to combine both the possibility of gaining optimum efficiency (e.g. by allowing the creation of work arrays outside of loops) with simplicity (thanks to labels and default arguments).
The code is precisionindependent and supports both real and complex transforms in a consistent way. There are four modules that implement the same interface modulo the precision type and specialized real/complex functions. If you refer to elements in this interface only, your code becomes precision and (if meaningful) real/complex independent, too: you can choose at anytime whether you want to use singleprecision or doubleprecision simply by referring to the required module.
You can fully exploit the library within multithreaded programs. Many numerical routines are likely to run for a long time, but they will never block other threads. This also means that you can execute several routines at the same time on several processors if you use POSIXthreads in OCaml.
To make things easy for developers used to the "real" implementation in FORTRAN but also for beginners who need detailed documentation, both function and argument names have been kept compatible to the ones used in the BLAS and LAPACKdocumentation. Only exception: you need not prefix functions with
s
,d
,c
orz
to indicate the precision and type of numbers, because the OCaml module system provides us with a more convenient means of choosing them.(Almost) all errors are handled within OCaml. Typical mistakes like passing nonconforming matrices, parameters that are out of range, etc., will be caught before calling Fortran code and will raise exceptions. These exceptions will explain the error in detail, for example the received illegal parameter and the range of expected legal values.
Using Lacaml
You can make use of this library by referring to the corresponding module for the required precision and number type. E.g.:
open Lacaml.S (* Singleprecision real numbers *)
open Lacaml.D (* Doubleprecision real numbers *)
open Lacaml.C (* Singleprecision complex numbers *)
open Lacaml.Z (* Doubleprecision complex numbers *)
These modules become available if you link the lacaml
library with your application. The widely used OCamltool findlib
will take care of linking lacaml
correctly. If you do not use this tool, you will also have to link in the bigarray
library provided by the OCamldistribution.
The Lacaml.?
modules implement the BLAS/LAPACKinterface. Their corresponding submodules Vec
and Mat
provide for vector and matrix operations that relate to the given precision and number type.
Most functions were implemented using optional arguments (= default arguments). If you do not provide them at the callsite, sane defaults will be used instead. Here is an example of a function call:
let rank = gelss in_mat out_mat in
(* ... *)
This example computes the solution to a general least squares problem (= linear regression) using the SVDalgorithm with in_mat
as the matrix containing the predictor variables and out_mat
as the matrix containing (possibly many) response variables (this function can handle several response variables at once). The result is the rank of the matrix. The matrices provided in the arguments will be overwritten with further results (here: the singular vectors and the solution matrix).
If the above happened in a loop, this would be slightly inefficient, because a workarray would have to be allocated (and later deallocated) at each call. You can hoist the creation of this work array out of the loop, e.g. (m
, n
, nrhs
are problem dependent parameters):
let work = gelss_min_work ~m ~n ~nrhs in
for i = 1 to 1000 do
(* ... *)
let rank = gelss in_mat ~work out_mat in
(* ... *)
done
All matrices can be accessed in a restricted way, i.e. you can specify submatrices for all matrix parameters. For example, if some matrix is called a
in the interface documentation, you can specify the left upper corner of the wanted submatrix for the operation by setting ar
for the row and ac
for the column (1 by default). A vector y
would have an extra optional parameter ofsy
(also 1 by default). Parameters like m
or n
typically specify the numbers of rows or columns.
Printing vectors and matrices
Here is a toplevel example of printing a large random matrix:
# #require "lacaml";;
# open Lacaml.D;;
# let mat = Mat.random 100 200;;
val mat : Lacaml.D.mat =
C1 C2 C3 C198 C199 C200
R1 0.314362 0.530711 0.309887 ... 0.519965 0.230156 0.0479154
R2 0.835658 0.581404 0.161607 ... 0.749358 0.630019 0.858998
R3 0.403421 0.458116 0.497516 ... 0.210811 0.422094 0.589661
... ... ... ... ... ... ...
R98 0.352474 0.878897 0.357842 ... 0.150786 0.74011 0.353253
R99 0.104805 0.984924 0.319127 ... 0.143679 0.858269 0.859059
R100 0.419968 0.333358 0.237761 ... 0.483535 0.0224016 0.513944
Only the corner sections of the matrix, which would otherwise be too large to display readably, are being printed, and ellipses (...
) are used in place of the removed parts of the matrix.
If the user required even less context, the Lacaml.Io.Toplevel.lsc
function, which is also available in each precision module for convenience (here: Lacaml.D
), could be used to indicate how much. In the following example only twobytwo blocks are requested in each corner of the matrix:
# lsc 2;;
 : unit = ()
# mat;;
 : Lacaml.D.mat =
C1 C2 C199 C200
R1 0.314362 0.530711 ... 0.230156 0.0479154
R2 0.835658 0.581404 ... 0.630019 0.858998
... ... ... ... ...
R99 0.104805 0.984924 ... 0.858269 0.859059
R100 0.419968 0.333358 ... 0.0224016 0.513944
Applications can use the standard Format
module in the OCamldistribution together with Lacaml printing functions to output vectors and matrices. Here is an example using labels and showing the high customizability of the printing functions:
open Lacaml.D
open Lacaml.Io
let () =
let rows, cols = 200, 100 in
let a = Mat.random rows cols in
Format.printf "@[<2>This is an indented random matrix:@\n@\n%a@]@."
(Lacaml.Io.pp_lfmat
~row_labels:
(Array.init rows (fun i > Printf.sprintf "Row %d" (i + 1)))
~col_labels:
(Array.init cols (fun i > Printf.sprintf "Col %d" (i + 1)))
~vertical_context:(Some (Context.create 2))
~horizontal_context:(Some (Context.create 3))
~ellipsis:"*"
~print_right:false
~print_foot:false ())
a
The above code might print:
This is an indented random matrix:
Col 1 Col 2 Col 3 Col 98 Col 99 Col 100
Row 1 0.852078 0.316723 0.195646 * 0.513697 0.656419 0.545189
Row 2 0.606197 0.411059 0.158064 * 0.368989 0.2174 0.9001
* * * * * * *
Row 199 0.684374 0.939027 0.000699582 * 0.117598 0.285587 0.654935
Row 200 0.929341 0.823264 0.895798 * 0.198334 0.725029 0.621723
Many other options, e.g. for different padding, printing numbers in other formats or with different precision, etc., are available for output customization.
Error handling
Though Lacaml is quite thorough in checking arguments for consistency with BLAS/LAPACK, an exception to the above is illegal contents of vectors and matrices. This can happen, for example, when freshly allocated matrices are used without initialization. Some LAPACKalgorithms may not be able to deal with floats that correspond to NaNs, infinities, or are subnormal. Checking matrices on every call would seem excessive. Some functions also expect matrices with certain properties, e.g. positivedefiniteness, which would be way too costly to verify beforehand.
Degenerate value shapes, e.g. empty matrices and vectors, and zerosized operations may also be handled inconsistently by BLAS/LAPACK itself. It is rather difficult to detect all such corner cases and to predetermine for all on how they should be handled to provide a sane workaround.
Users are welladvised to to ensure the sanity of the contents of values passed to Lacaml functions and to avoid calling Lacaml with values having degenerate dimensions. User code should either raise exceptions if values seem degenerate or handle unusual corner cases explicitly.
Other sources of usage information
API documentation
Besides the Lacaml interface file, the API documentation can also be found online.
BLAS/LAPACK man pages
BLAS and LAPACK binary packages for Unix operating systems usually come with appropriate manpages. E.g. to quickly look up how to factorize a positivedefinite, complex, single precision matrix, you might enter:
man cpotrf
The corresponding function in Lacaml would be Lacaml.C.potrf
. The naming conventions and additional documentation for BLAS and LAPACK can be found at their respective websites.
Examples
The examples
directory contains several demonstrations of how to use this library for various linear algebra problems.
Improving Performance
It is highly recommended that users install a variant of BLAS (or even LAPACK) that has been optimized for their system. Processor vendors (e.g. Intel) usually sell the most optimized implementations for their CPUarchitectures. Some computer and OSvendors like Apple distribute their own implementations with their products, e.g. vecLib
, which is part of Apple's Accelerate
framework.
There is also ATLAS, a very efficient and compatible substitute for BLAS. It specializes code for the architecture it is compiled on. Binary packages (e.g. RPMs) for Linux should be available from your distribution vendor's site (you must recompile the package to make sure it is suited to your distribution, see the package documentation for more details.).
Another alternative for BLAS is OpenBLAS.
If a nonstandard library or library location is required, the user can override the platformdependent default by setting the following environment variables:
LACAML_CFLAGS
LACAML_LIBS
The first one can be used to add compilation flags, and the second one to override the default linking flags (lblas
and llapack
).
Lacaml already passes O3 march=native ffastmath
as compiler flags to fully exploit SIMD instructions when supported by the used platform. The current Lacaml code base is probably safe with these options.
Contact Information and Contributing
Please submit bugs reports, feature requests, contributions and similar to the GitHub issue tracker.
Uptodate information is available at: https://mmottl.github.io/lacaml
Dependencies (7)
 basebigarray
 basebytes

conflapack
build

confblas
build
 duneconfigurator

ocaml
>= "4.08"

dune
>= "2.7"
Dev Dependencies (1)

odoc
withdoc
Used by (12)

fftw3
>= "0.7.1" & < "0.8.5"

gpr
>= "1.4.0"

lbfgs
>= "0.9"

libsvm
>= "0.9.3"

mesh
>= "0.8.8"
 meshdisplay
 mesheasymesh
 meshtriangle

oml
= "0.0.6"

owl
>= "0.2.0" & < "0.2.2"
 phylogenetics
 pilat