An Emacs zeromq library using an ffi

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An alternative approach to writing your own dynamic module (which requires some proficiency in c) is to use a foreign function interface (ffi). There is one for emacs at https://github.com/tromey/emacs-ffi, and it is also a dynamic module itself that uses libffi. This lets you use elisp to create functions in Emacs that actually call functions in some other library installed on your system. Here, we use this module to recreate our zeromq bindings that I previously posted.

The emacs-ffi module works fine as it is, but I found it useful to redefine one of the main macros (define-ffi-function) with the following goals in mind:

  1. Allow me to specify the argument names and docstrings for each arg that contain its type and a description of the arg.
  2. Document what each function returns (type and description).
  3. Combine those two things into an overall docstring on the function.

These are important to me because it allows Emacs to work at its fullest potential while writing elisp code, including having the right function signatures in eldoc, and easy access to documentation of each function. You can see the new definition here. For example, here is a docstring for zmq-send using that new macro:

zmq-send is a Lisp function.

(zmq-send *SOCKET *MSG LEN FLAGS)

For more information check the manuals.

send a message part on a socket.
http://api.zeromq.org/4-2:zmq-send

*SOCKET (:pointer) Pointer to a socket.
*MSG (:pointer) Pointer to a C-string to send
LEN (:size_t) Number of bytes to send
FLAGS (:int) 

Returns: Number of bytes sent or -1 on failure. (:int)

That has everything you need to know

(define-ffi-function zmq-send-ori "zmq_send" :int (:pointer :pointer :size_t :int) zmq)
zmq-send-ori

Compare that to this docstring from the original macro.

zmq-send-ori is a Lisp function.

(zmq-send-ori G251 G252 G253 G254)

For more information check the manuals.

You can see the zeromq function definitions in elisp here. Here is a list of the functions we have created:

Type RET on a type label to view its full documentation.

zmq
  Function: Returns a pointer to the libzmq library.
zmq-close
  Function: close ØMQ socket.
zmq-connect
  Function: create outgoing connection from socket.
zmq-ctx-destroy
  Function: terminate a ØMQ context.
zmq-ctx-new
  Function: create new ØMQ context.
zmq-recv
  Function: receive a message part from a socket.
zmq-send
  Function: send a message part on a socket.
zmq-socket
  Function: create ØMQ socket.

Now we can use these to create the client, this time in elisp. Just as in the last post, you need to run the hwserver in a terminal for this to work. Here is the client code.

(let* ((context (zmq-ctx-new))
       (socket (zmq-socket context ZMQ-REQ)))

  (with-ffi-string (endpoint "tcp://localhost:5555")
    (zmq-connect socket endpoint))

  (with-ffi-string (msg "Hi there")
    (zmq-send socket msg 5 0))

  (with-ffi-string (recv (make-string 10 ""))
    (let ((status -1))
      (cl-loop do (setq status (zmq-recv socket recv 10 0)) until (not (= -1 status)))) 
    (print (ffi-get-c-string recv)))

  (zmq-close socket)
  (zmq-ctx-destroy context))

"World     "

This client basically performs the same as the previously one we built. You can see we are mixing some programming styles here. For example, we have to create pointers to string variables in advance that the ffi will be writing to later like we would do in c. We use the with-ffi-string macro which frees the pointer when we are done with it. It basically just avoids me having to create, use, and destroy the pointers myself. So, there it is, a working elisp zeromq client!

1 Summary thoughts

For this example, I feel like the ffi approach here (with my modified function making macro) was much easier than what I previously did with a compiled c-library (although it benefited a lot from my recent work on the c-library). I really like working in elisp, which is a much greater strength of mine than programming in c. It is pretty clear, however, that you have to know how c works to use this, otherwise it isn't so obvious that some functions will return a status, and do something by side effect, e.g. put results in one of the arguments. The signatures of the ffi functions are basically limited by the signatures of the c-functions. If you want to change the signature in Emacs, you have to write wrapper functions to do that.

The macro I used here to create the functions creates really good (the kind I like anyway) docstrings when you use it fully. That isn't a totally new idea, I tried it out here before. In contrast, the original version not only didn't have a docstring, but every arg had a gensym (i.e. practically random) name! I think it would be very difficult to get the same level of documentation when writing c-code to make a module. In the c-code, there is a decoupling of the definition of a c-function (which always has the same signature) that gets data from the Emacs env, e.g. arguments, does stuff with them, and creates data to put back into the env, and the emacs_module_init function where you declare these functions to Emacs and tell it what to call the function in emacs, about how many arguments it takes, etc… The benefit of this is you define what the Emacs signature will look like, and then write the c-function that does the required work. The downside of this is the c-function and Emacs declarations are often far apart in the editor, and there is no easy way to auto-generate docstrings like I can with lisp macros. You would have to manually build them up yourself, and keep them synchronized. Also, I still have not figured out how to get emacs to show the right signature for c-generated functions.

The ffi approach still uses a dynamic module approach, so it still requires a modern Emacs with the module compiled and working. It still requires (in this case) the zeromq library to be installed on the system too. Once you have those, however, the elisp zeromq bindings by this approach is done completely in elisp!

It will be interesting in the coming weeks to see how this approach works with the GNU Scientific Library, particularly with arrays. Preliminary work shows that while the elisp ffi code is much shorter and easier to write than the corresponding c-code for some examples (e.g. a simple mathematical function), it is not as fast. So if performance is crucial, it may still pay off to write the c-code.

2 Modified ffi-define-function macro

Here are two macros I modified to add docstrings and named arguments too.

(defmacro define-ffi-library (symbol name)
  "Create a pointer named to the c library."
  (let ((library (cl-gensym))
        (docstring (format "Returns a pointer to the %s library." name)))
    (set library nil)
    `(defun ,symbol ()
       ,docstring
       (or ,library
           (setq ,library (ffi--dlopen ,name))))))

(defmacro define-ffi-function (name c-name return args library &optional docstring)
  "Create an Emacs function from a c-function.
NAME is a symbol for  the emacs function to create.
C-NAME is a string of the c-function to use.
RETURN is a type-keyword or (type-keyword docstring)
ARGS is a list of type-keyword or (type-keyword name &optional arg-docstring)
LIBRARY is a symbol usually defined by `define-ffi-library'
DOCSTRING is a string for the function to be created.

An overall docstring is created for the function from the arg and return docstrings.
"
  ;; Turn variable references into actual types; while keeping
  ;; keywords the same.
  (let* ((return-type (if (keywordp return)
                          return
                        (car return)))
         (return-docstring (format "Returns: %s (%s)"
                                   (if (listp return)
                                       (second return)
                                     "")
                                   return-type))
         (arg-types (vconcat (mapcar (lambda (arg)
                                       (if (keywordp arg)
                                           (symbol-value arg)
                                         ;; assume list (type-keyword name &optional doc)
                                         (symbol-value (car arg))))
                                     args)))
         (arg-names (mapcar (lambda (arg)
                              (if (keywordp arg)
                                  (cl-gensym)
                                ;; assume list (type-keyword name &optional doc)
                                (second arg)))
                            args))
         (arg-docstrings (mapcar (lambda (arg)
                                   (cond
                                    ((keywordp arg)
                                     "")
                                    ((and (listp arg) (= 3 (length arg)))
                                     (third arg))
                                    (t "")))
                                 args))
         ;; Combine all the arg docstrings into one string
         (arg-docstring (mapconcat 'identity
                                   (mapcar* (lambda (name type arg-doc)
                                              (format "%s (%s) %s"
                                                      (upcase (symbol-name name))
                                                      type
                                                      arg-doc))
                                            arg-names arg-types arg-docstrings)
                                   "\n"))
         (function (cl-gensym))
         (cif (ffi--prep-cif (symbol-value return-type) arg-types)))
    (set function nil)
    `(defun ,name (,@arg-names)
       ,(concat docstring "\n\n" arg-docstring "\n\n" return-docstring)
       (unless ,function
         (setq ,function (ffi--dlsym ,c-name (,library))))
       ;; FIXME do we even need a separate prep?
       (ffi--call ,cif ,function ,@arg-names))))
define-ffi-function

3 The zeromq bindings

These define the ffi functions we use in this post. I use a convention that pointer args start with a * so they look more like the c arguments. I also replace all _ with - so it looks more lispy, and the function names are easier to type.

(add-to-list 'load-path (expand-file-name "."))
(require 'ffi)

(define-ffi-library zmq "libzmq")


(define-ffi-function zmq-ctx-new "zmq_ctx_new"
  (:pointer "Pointer to a context")
  nil zmq
  "create new ØMQ context.
http://api.zeromq.org/4-2:zmq-ctx-new")


(define-ffi-function zmq-ctx-destroy "zmq_ctx_destroy"
  (:int "status")
  ((:pointer *context)) zmq
  "terminate a ØMQ context.
http://api.zeromq.org/4-2:zmq-ctx-destroy")


(define-ffi-function zmq-socket "zmq_socket"
  (:pointer "Pointer to a socket.")
  ((:pointer *context "Created by `zmq-ctx-new '.") (:int type)) zmq
  "create ØMQ socket.
http://api.zeromq.org/4-2:zmq-socket")


(define-ffi-function zmq-close "zmq_close"
  (:int "Status")
  ((:pointer *socket "Socket pointer created by `zmq-socket'")) zmq
  "close ØMQ socket.
http://api.zeromq.org/4-2:zmq-close")


(define-ffi-function zmq-connect "zmq_connect" 
  (:int "Status")
  ((:pointer *socket "Socket pointer created by `zmq-socket'")
   (:pointer *endpoint "Char pointer, e.g. (ffi-make-c-string \"tcp://localhost:5555\")"))
  zmq
  "create outgoing connection from socket.
http://api.zeromq.org/4-2:zmq-connect")


(define-ffi-function zmq-send "zmq_send"
  (:int "Number of bytes sent or -1 on failure.")
  ((:pointer *socket "Pointer to a socket.")
   (:pointer *msg "Pointer to a C-string to send")
   (:size_t len "Number of bytes to send")
   (:int flags)) 
  zmq
   "send a message part on a socket.
http://api.zeromq.org/4-2:zmq-send")


(define-ffi-function zmq-recv "zmq_recv"
  (:int "Number of bytes received or -1 on failure.")
  ((:pointer *socket)
   (:pointer *buf "Pointer to c-string to put result in.")
   (:size_t len "Length to truncate message at.")
   (:int flags)) 
  zmq
   "receive a message part from a socket.
http://api.zeromq.org/4-2:zmq-recv")


;; We cannot get these through a ffi because the are #define'd for the CPP and
;; invisible in the library. They only exist in the zmq.h file.
(defconst ZMQ-REQ 3
  "A socket of type ZMQ_REQ is used by a client to send requests
  to and receive replies from a service. This socket type allows
  only an alternating sequence of zmq_send(request) and
  subsequent zmq_recv(reply) calls. Each request sent is
  round-robined among all services, and each reply received is
  matched with the last issued request.")

Copyright (C) 2017 by John Kitchin. See the License for information about copying.

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Zeromq bindings for Emacs via dynamic modules

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I do a lot of scientific programming, and it is one of the reasons I have been learning to extend Emacs with dynamic modules. They have allowed me to add physical constants, numerical integration, root finding and linear algebra from established c-libraries to Emacs. Today I am taking a break from that and finally getting to another one of the reasons I started playing around with dynamic modules: zeromq. Zeromq is a messaging library that Jupyter uses to communicate with kernels. I thought we might get a smoother integration with Emacs and Jupyter if we could use zeromq directly to communicate between org-mode and the kernel. Currently we have to run a web server that does the communication for us via http requests. We won't solve the Jupyter problem today, but we will look at communicating with a Zeromq server from Emacs.

This might have lots of other useful applications. Suppose Emacs could communicate directly with other zeromq servers to retrieve data from, perhaps scientific data. It might even be possible for Emacs to run its own zeromq server, and other instances of Emacs could then communicate with it. Collaborative editing anyone?

Here we just implement the "Hello world" client example in the zeromq guide. The code for the server, a c-client, the mod-zmq library, a makefile and tests can be found at https://github.com/jkitchin/emacs-modules/tree/master/zeromq. All the server does is receive a string, and then send a response (in this case just the string "World") back to the client.

To run this, make sure to run the hwserver executable in a terminal. I wrapped the zeromq commands required to implement the client into a dynamic module. Since this example focuses on strings, the module returns strings to Emacs. I am not sure if that is always the right thing to do, as zeromq more generically uses bytes, but I will have to wait until I know more about zeromq to know if this is an issue.

This dynamic module uses a new feature that none of the previous posts used, and that is the user_ptr. These allow you to essentially return a reference pointer back to emacs that you can pass back to another function. That way they stay alive between function calls. For example, here we have to create a context and socket and pass these items to functions like zmq_send and zmq_recv.

The directory this library is in is not on my path, so we load it like this:

(add-to-list 'load-path (expand-file-name "."))
(require 'mod-zmq)

Here are the functions and their signatures that have been implemented so far. I only implemented the ones I needed for the client. The signatures may change in the future; this is just a proof of concept for now for the purpose of building the client.

(apropos-command "zmq*" t)
(with-current-buffer "*Apropos*" (buffer-string))
Type RET on a type label to view its full documentation.

zmq-close
  Function: (zmq-close SOCKET)
zmq-connect
  Function: (zmq-connect SOCKET ENDPOINT)
zmq-ctx-destroy
  Function: (zmq-ctx-destroy CONTEXT)
zmq-ctx-new
  Function: (zmq-ctx-new)
zmq-recv
  Function: (zmq-recv SOCKET LEN FLAGS)
zmq-send
  Function: (zmq-send SOCKET BUF FLAGS)
zmq-socket
  Function: (zmq-socket CONTEXT TYPE)

You can see the c code for the client here: hwclient.c . Here is a simple elisp version of the hwclient that basically does the same thing! The main difference is I added a while loop around the zmq-recv because sometimes it returns -1 and no result. So, here we loop until the return result is not -1. That seems to do the right thing.

(let* ((context (zmq-ctx-new))
       (socket (zmq-socket context ZMQ-REQ))
       (recv-ret -1)
       (result))

  (zmq-connect socket "tcp://localhost:5555")
  (zmq-send socket "Hello" 0)

  (while (= recv-ret -1)
    (setq result (zmq-recv socket 10 0)
          recv-ret (second result)))

  (print result)

  (zmq-close socket)
  (zmq-ctx-destroy context))

("World" 5)

Basically this creates the context, then the socket, and connects to it on port 5555 of the localhost where the server is running. Then we send the string "Hello". The server returns the string "World" and tells us it sent 5 bytes. Then we close the socket and destroy the context. There is a lot of code in the module to make this happen. A lot of it is converting args in emacs functions to things we can use in c, running a few lines of zmq commands, and then code to convert those results back to emacs values. Finally, there is code to register each function and define docstrings for them. I am not totally convinced this is the best way to do this, but it does work! An alternative might be emacs-ffi, which might enable most of this to be developed in just elisp.

Copyright (C) 2017 by John Kitchin. See the License for information about copying.

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Adding linear algebra to Emacs with the GSL and dynamic modules

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The goal of this post is to be able to solve equations like this one:

\[\left(\begin{array}{cccc} 0.18& 0.60& 0.57& 0.96 \\ 0.41& 0.24& 0.99& 0.58 \\ 0.14& 0.30& 0.97& 0.66 \\ 0.51& 0.13& 0.19& 0.85 \end{array} \right ) \left ( \begin{array}{c} x_0 \\ x_1 \\ x_2 \\ x_3 \end{array} \right ) = \left ( \begin{array}{c} 1.0 \\ 2.0 \\ 3.0 \\ 4.0 \end{array} \right ) \]

The answer is given as

\[x = \left ( \begin{array}{c} -4.05205 \\ -12.6056 \\ 1.66091 \\ 8.69377 \end{array} \right ) \]

The syntax we want to use is shown below, and we want it to return a vector containing the solution:

(let ((A [[0.18 0.60 0.57 0.96]
          [0.41 0.24 0.99 0.58]
          [0.14 0.30 0.97 0.66]
          [0.51 0.13 0.19 0.85]])
      (b [1.0 2.0 3.0 4.0]))
  (gsl-linalg-LU-solve A b))

Rather than put all the code in here like I have for the past several posts, I started a git repo at https://github.com/jkitchin/emacs-modules that contains this code.

The module for this post can be found here: https://github.com/jkitchin/emacs-modules/blob/master/gsl-linalg.c. There are a few notable features in it. First, I started writing/collecting some helper functions to make these modules simpler to write. For example, look how nice this looks to declare the functions and provide the feature.

int emacs_module_init(struct emacs_runtime *ert)
{
  emacs_env *env = ert->get_environment(ert);
  
  DEFUN("gsl-linalg-LU-solve", Fgsl_linalg_LU_solve, 2, 2,
        "(gsl-linalg-LU-solve A b).\n" \
        "Solve A x = b for x.\n" \
        "Returns a vector containing the solution x.",
        NULL);
  provide(env, "gsl-linalg");
  
  return 0;
}

The DEFUN and provide function are defined in https://github.com/jkitchin/emacs-modules/blob/master/emacs-module-helpers.c.

Within the module itself, we have to loop over the inputs to create the arrays that GSL wants to solve this problem. Second, after the solution is obtained, we have to build up a vector to return. The solution is in a gsl_vector, and we need to create an array of emacs_value elements containing each element of the gsl_vector as a float, and then create a vector to return to emacs. I use vectors here because it was easy to get the size of the b vector, which is also related to the size of the A matrix.

The repo has a Makefile in it, so we can build this module with:

make gsl-linalg.so

Once it is compiled, we load it like this. In this post we are in the emacs-modules directory where the gsl-linalg.so library is, and it is not on my load-path, so I add it here.

(add-to-list 'load-path (expand-file-name "."))
(require 'gsl-linalg)
gsl-linalg

Here is one function in the module:

(describe-function 'gsl-linalg-LU-solve)
gsl-linalg-LU-solve is a Lisp function.

(gsl-linalg-LU-solve &rest ARGS)

For more information check the manuals.

(gsl-linalg-LU-solve A b).
Solve A x = b for x.
Returns a vector containing the solution x.

Now, we can solve linear equations like this:

(gsl-linalg-LU-solve
 [[0.18 0.60 0.57 0.96]
  [0.41 0.24 0.99 0.58]
  [0.14 0.30 0.97 0.66]
  [0.51 0.13 0.19 0.85]]
 [1.0 2.0 3.0 4.0])
[-4.052050229573973 -12.605611395906903 1.6609116267088417 8.693766928795227]

We have a limited ability to confirm this answer. I have written a function that uses blas for multiplication of 2d vectors. You can see from this:

(gsl-blas-dgemm [[0.18 0.60 0.57 0.96]
                 [0.41 0.24 0.99 0.58]
                 [0.14 0.30 0.97 0.66]
                 [0.51 0.13 0.19 0.85]]
                [[-4.052050229573973]
                 [-12.605611395906903]
                 [1.6609116267088417]
                 [8.693766928795227]])
[[1.0] [1.9999999999999991] [2.9999999999999996] [4.0]]

That within float that indeed \(A x = b\).

The main limitation of this module at the moment is that you have to use vectors; you cannot put in a list of numbers. It is possible to make it take lists and vectors, but for now I am leaving it at vectors. Also, it only produces solutions of float numbers (not integers).

The module does not handle 1d vectors well,, e.g. in gsl-linalg-LU-solve example, the right hand side is implied to be a column vector, and we don't have the array broadcasting features of Python yet. Those are doable things for some future day perhaps. For now I am happy to have figured out how to handle arrays!

Copyright (C) 2017 by John Kitchin. See the License for information about copying.

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Adding GSL constants to Emacs in a dynamic module

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The GNU Scientific Library defines a lot of physical constants. Since we are exploring how to make Emacs a more scientific environment to work in, it would be nice to import these constants to elisp. We do that through a dynamic module. This turned out to be tricky. I thought we could just use a funcall to defconst or defvar, but these are special forms and you cannot funcall them. @polizta on Stackoverflow pointed me to the path that led to success: You make a list like '(defconst sym val doc) and then eval it. That can be funcall'd, and it works nicely in the module below. It is a growing theme that it takes much hacking around to figure out how to do things like this.

The only other notable feature of this module is that I created a defconst function to make adding multiple constants less verbose. Here I only add two constants. There are about 408 constants defined in gsl_const_*.h, so brevity might be a good idea! Here is the module.

#include <gsl/gsl_const_mksa.h>
#include <string.h>
#include "emacs-module.h"

int plugin_is_GPL_compatible;

// I assume here that all values will be double. I can't think of any that would
// be ints
static void defconst (emacs_env *env, const char *name, double value, const char *doc)
{
  // These are functions we will call
  emacs_value eval = env->intern(env, "eval");  
  emacs_value list = env->intern(env, "list");

  // These will make up the list we will eventally eval
  emacs_value fdefconst = env->intern(env, "defconst");
  emacs_value sym = env->intern(env, name);
  emacs_value val = env->make_float(env, value);
  emacs_value sdoc = env->make_string(env, doc, strlen(doc));

  // make a list of (defconst sym val doc)
  emacs_value largs[] = {fdefconst, sym, val, sdoc};
  emacs_value qlist = env->funcall(env, list, 4, &largs);   

  // now eval the list of symbols
  emacs_value args[] = { qlist };  
  env->funcall(env, eval, 1, &args);
}

int emacs_module_init(struct emacs_runtime *ert)
{
  emacs_env *env = ert->get_environment(ert);

  defconst(env, "GSL-CONST-MKSA-SPEED-OF-LIGHT",
           GSL_CONST_MKSA_SPEED_OF_LIGHT,
           "Speed of light in vacuum (m/s).");
  
  defconst(env, "GSL-CONST-MKSA-PLANCKS-CONSTANT-H",
           GSL_CONST_MKSA_PLANCKS_CONSTANT_H,
           "Plank's constant, h");

  // This is what allows the shared library to provide a feature 
  emacs_value provide = env->intern(env, "provide");
  emacs_value provide_args[] = { env->intern(env, "gsl-constants") };
  env->funcall(env, provide, 1, provide_args);
  
  return 0;
}

Regular gcc will work to compile this module.

rm -f gsl-constants.so gsl-constants.o
gcc -Wall -I/usr/local/include -fPIC -c gsl-constants.c
gcc -shared -L/usr/local/include -lgsl -o gsl-constants.so gsl-constants.o

Here is in action.

(add-to-list 'load-path "/Users/jkitchin/vc/blogofile-jkitchin.github.com/_blog/dynamic-module/")
(require 'gsl-constants)
GSL-CONST-MKSA-SPEED-OF-LIGHT
299792458.0

We can see there is a docstring on that constant:

(describe-variable 'GSL-CONST-MKSA-SPEED-OF-LIGHT)
GSL-CONST-MKSA-SPEED-OF-LIGHT's value is 299792458.0


  This variable can be risky when used as a file-local variable.

Documentation:
Speed of light in vacuum (m/s).

For more information check the manuals.

It is worth thinking about what we accomplished here. The value of each constant in GSL is stored in a header file. The units are stored in a comment next to the value, and the documentation is in an html page somewhere. It is not easy to introspect that! Getting it all into an Emacs variable makes that more introspectable, and findable. That means while typing elisp code you will get completion on these variables. Check this out:

(apropos-variable "GSL-*")
(with-current-buffer "*Apropos*" (buffer-string))
Type RET on a type label to view its full documentation.

GSL-CONST-MKSA-PLANCKS-CONSTANT-H
  Variable: Plank's constant, h
GSL-CONST-MKSA-SPEED-OF-LIGHT
  Variable: Speed of light in vacuum (m/s).

It seems like it might be possible to partially automate creation of this module by parsing the gsl_const*.h files. There is no automating adding the doc strings though, I am pretty sure that will have to be done by hand ;(

Copyright (C) 2017 by John Kitchin. See the License for information about copying.

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Adding a GSL integration function to Emacs with a dynamic module

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Here we work out how to run this program: https://www.gnu.org/software/gsl/doc/html/integration.html#adaptive-integration-example in a dynamic module in emacs. The goal is to be able to evaluate \(\int_0^1 x^{-1/2} \log(x) dx\). According to the example page the answer is -4. We will define an integration function that takes at least a function and integration bounds as arguments, and several optional arguments to specify tolerances and limits. In other words we want to evaluate integrals of the form:

\(\int_a^b f(x; params) dx\)

I want that to happen in an elisp function with a signature like:

(gsl-integration-qags (lambda (x params) body) a b &optional params epsabs epsrel limit)

And that function will return a list containing (result error-estimate). Here is the C-code that makes this happen. It is more complex that the last example, and only compiles with gcc that allows nested functions. I don't know how to write this without that feature. This is more complex also because you have to create a workspace to do the integration inside the function that does the integration. The C-module also has extra code in it to allow for optional arguments.

#include <gsl/gsl_integration.h>
#include "emacs-module.h"

int plugin_is_GPL_compatible;

static emacs_value F_gsl_integrate (emacs_env *env, ptrdiff_t nargs, emacs_value args[], void *data)
{
  // nested function - only supported as an extension in gcc
  double f (double x, void *params) 
  {
    emacs_value fn = args[0];  // function we will integrate
    emacs_value x2[] = { env->make_float(env, x), params };
    emacs_value y = env->funcall(env, fn, 2, &x2);   
    
    return env->extract_float (env, y);
  }

  double a = env->extract_float (env, args[1]);
  double b = env->extract_float (env, args[2]);

  // default values for optional arguments
  double epsabs = 0.0;
  double epsrel = 1e-7;
  size_t limit = 1000;
  double result, error; 

  // Here is how I handle the optional arguments
  // (gsl-integrate func a b params epsabs epsrel limit)
  gsl_function F;
  F.function = &f;
  if (nargs >= 4) {F.params = args[3];}
  if (nargs >= 5 && env->is_not_nil(env, args[4])) {epsabs = env->extract_float(env, args[4]);}
  if (nargs >= 6 && env->is_not_nil(env, args[5])) {epsrel = env->extract_float(env, args[5]);}
  if (nargs >= 7 && env->is_not_nil(env, args[6])) {limit = env->extract_integer(env, args[6]);}

  gsl_integration_workspace * w = gsl_integration_workspace_alloc (limit);

  gsl_integration_qags (&F, // gsl_function pointer
                        a, // lower integration bound
                        b, // upper integration bound
                        epsabs, // absolute error tolerance
                        epsrel, // relative error tolerance
                        limit, // max number of subintervals for integration
                        w, // the workspace
                        // pointers to put results and error in
                        &result, &error);

  gsl_integration_workspace_free (w);
    
  // make a list of (result error) to return
  emacs_value Qlist = env->intern(env, "list");
  emacs_value Qresult = env->make_float (env, result);
  emacs_value Qerror = env->make_float (env, error);
  emacs_value list_args[] = { Qresult, Qerror };
  return env->funcall(env, Qlist, 2, list_args);
}

int emacs_module_init(struct emacs_runtime *ert)
{
  emacs_env *env = ert->get_environment(ert);
  
  // Here we create the function.
  emacs_value fset = env->intern(env, "fset");
  emacs_value args[2];
  args[0] = env->intern(env, "gsl-integration-qags"); // symbol to create for function
  // The function we set that symbol to.
  args[1] = env->make_function(env,
                               3, // min nargs
                               7, // max nargs
                               F_gsl_integrate,
                               "(gsl-integration-qags F A B &optional PARAMS EPSABS EPSREL LIMIT)\n" \
                               "Integrate F(x; params) from A to B.\n" \
                               "F is a function of a single variable and parameters.\n" \
                               "A is the lower bound of integration\n"  \
                               "B is the upper bound of integration.\n" \
                               "Optional parameters:\n"\
                               "PARAMS is a list of params to pass to F.\n" \
                               "EPSABS is a float (default 0.0) and is the absolute error tolerance.\n" \
                               "EPSREL is a float (default 1e-7) and is the relative error tolerance.\n" \
                               "LIMIT is the maximum number of subintervals for the integration (default 1000).\n" \
                               "Returns (list result error-estimate).\n" \
                               "See https://www.gnu.org/software/gsl/manual/html_node/QAGS-adaptive-integration-with-singularities.html.",
                               0);
  // This is basically (fset 'gsl-integration-qags (lambda func))
  env->funcall(env, fset, 2, args);
  
  // This is what allows the shared library to provide a feature 
  emacs_value provide = env->intern(env, "provide");
  emacs_value provide_args[] = { env->intern(env, "gsl-integration") };
  env->funcall(env, provide, 1, provide_args);
  
  return 0;
}

Building this was moderately tricky. It appears the first gcc on my path uses clang which does not support nested functions in C. I don't know enough C to figure out how to do this without a nested function though, since the function has to be defined at run-time based on the emacs env and args. gcc does support inline functions, so the code below uses a gcc that does compile it.

rm -f gsl-integration.so gsl-integration.o
/usr/local/Cellar/gcc/6.1.0/bin/gcc-6 -Wall -I/usr/local/include -fPIC -c gsl-integration.c
/usr/local/Cellar/gcc/6.1.0/bin/gcc-6  -shared -L/usr/local/include -lgsl -o gsl-integration.so gsl-integration.o

Now we add this directory to our path since it is not on it and require our new module.

(add-to-list 'load-path "/Users/jkitchin/vc/blogofile-jkitchin.github.com/_blog/dynamic-module/")
(require 'gsl-integration)
gsl-integration

Let us see our new function in action. We evaluate \(\int_0^1 x^{-1/2} \log(x) dx\). According to the example page the answer is -4. Here is an example where we ignore the parameters. You have to be careful; Emacs sometimes segfaults and crashes if you use an integer or float argument when it expects the other type.

(gsl-integration-qags (lambda (x params) (/ (log x) (sqrt x))) 0.0 1.0)
-4.000000000000085 1.354472090042691e-13

Here are some optional arguments.

(gsl-integration-qags (lambda (x params) (/ (log x) (sqrt x))) 0.0 1.0 nil nil 0.01)
-4.000000000000075 0.019526557540360034

Nice, with a larger epsrel argument we get a larger error. Note the arguments are positional, so we have to include them all just to set the epsrel argument. How about an easier example with parameters that we actually use. Here we integrate a constant, and set the value of the constant from the params arg. The integral should be the area of a rectangle of length 1 and width of the param we use.

(list
 (gsl-integration-qags (lambda (x params) (first params)) 0.0 1.0 '(1.0))
 (gsl-integration-qags (lambda (x params) (first params)) 0.0 1.0 '(0.5)))
1.0 1.1102230246251565e-14
0.5 5.551115123125783e-15

Wow! It actually works!!! That was harder won success than usual for me. I am claiming victory for now and leaving the following notes to future me:

  1. It would be nice to have optional keyword arguments. This would take some handling of the arguments beyond what I know how to do for now, unless it is possible to pull in something like plist-get the way we pull in fset, provide and list in this example.
  2. Error checking on types would be helpful. It is not good for Emacs to crash because 0 is not 0.0!
  3. In numpy there is often a feature to get full_output. Here, the workspace created in the function has more information available in a struct that might be helpful to have access to at times. It seems like it might be possible to get that here too.

Copyright (C) 2017 by John Kitchin. See the License for information about copying.

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