ocaml/Command_line.ml

@@ -12,22 +12,12 @@ type description   = {
   arg  : argument ;
   }
 
-(* Mutable variables *)
 let anon_args  = ref []
 and header_doc = ref ""
 and description_doc = ref ""
 and footer_doc = ref ""
 and specs      = ref []
 
-let reset () = 
-    anon_args  := [];
-    header_doc := "";
-    description_doc := "";
-    footer_doc := "";
-    specs      := []
-
-(* End mutable variables *)
-
 let set_header_doc s = header_doc := s
 let set_description_doc s = description_doc := s
 let set_footer_doc s = footer_doc := s

ocaml/Command_line.mli

@@ -124,6 +124,3 @@ val set_specs : description list -> unit
 val anon_args : unit -> string list
 
 
-(** Reset the internal state *)
-val reset : unit -> unit
-

ocaml/Makefile

@@ -24,8 +24,6 @@ ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml)) qmcchem.native
 
 
 default: $(ALL_EXE) 
-	mv qmcchem.native $(QMCCHEM_PATH)/bin/qmcchem
-
 tests: $(ALL_TESTS) 
 
 

ocaml/Qmcchem_debug.ml

@@ -19,7 +19,7 @@ let run ~t ezfio_filename=
     match (Ezfio.get_simulation_http_server ()
         |> String_ext.rsplit2 ~on:':' )
     with
-    | Some (a,p) -> a^":"^( (int_of_string p)+4 |> string_of_int )
+    | Some (a,p) -> a^":"^( (Int.of_string p)+4 |> Int.to_string )
     | None -> failwith "Badly formed address"
   in
   Zmq.Socket.connect socket address;
@@ -31,7 +31,7 @@ let run ~t ezfio_filename=
            Str.regexp " *: *"
         in
         let tot_size = 
-          ref 0.
+          ref (Byte_units.create `Bytes 0.)
         in
         while true
         do
@@ -41,12 +41,12 @@ let run ~t ezfio_filename=
           let (socket, bytes)  =
             match Str.split re_split msg with
             |  socket :: bytes :: _ ->
-                (socket, float_of_string bytes)
+                (socket, Byte_units.create `Bytes (Float.of_string bytes))
-            | _ -> (print_endline msg ; ("", 0.))
+            | _ -> (print_endline msg ; ("", Byte_units.create `Bytes 0.))
           in
-          tot_size := !tot_size +. bytes;
+          tot_size := Byte_units.create `Bytes ((Byte_units.bytes !tot_size) +. (Byte_units.bytes bytes));
-          Printf.printf "%f\n%!" !tot_size;
+          Printf.printf "%s\n%!" (Byte_units.to_string !tot_size);
-          Unix.sleep 1
+          Time.pause (Time.Span.of_sec 1.)
         done
       end
   else
@@ -62,29 +62,20 @@ let run ~t ezfio_filename=
 
 
 
-let command () =
+let spec =
-  let open Command_line in
+  let open Command.Spec in
-  begin
+  empty
-    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
+  +> flag "t" no_arg 
-    set_description_doc "Debug ZeroMQ communications";
+     ~doc:"Measure the throughput"
-    [ { short='t' ; long="traffic" ; opt=Optional ;
+  +> anon ("ezfio_file" %: string)
-        doc="Print traffic in bytes" ;
-        arg=Without_arg } ;
-
-        anonymous "EZFIO_DIR" Mandatory "EZFIO directory" ]
-    |> set_specs
-  end;
-
-  let t = Command_line.get_bool "traffic" in
-  let ezfio_file =
-    match Command_line.anon_args () with
-    | ezfio_file :: [] -> ezfio_file
-    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
-  in
-
-  run t ezfio_file
 
 
+let command = 
+  Command.basic_spec
+  ~summary: "Debug ZeroMQ communications"
+  ~readme:(fun () -> "Gets debug information from the Zmq debug sockets.")
+  spec
+  (fun t ezfio_file () -> run t ezfio_file)
 
 
 

ocaml/Qmcchem_edit.ml

@@ -274,7 +274,7 @@ let run ~c ?f ?t ?l ?m ?e ?et ?s ?ts ?w ?wt ?n ?j ?p ?input ezfio_filename =
   write_input_in_ezfio ezfio_filename fields
 
 
-let command () = 
+let () = 
   let open Command_line in
   begin
     set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");

ocaml/Qmcchem_info.ml

@@ -10,22 +10,22 @@ let run ezfio_filename =
     [| qmcchem_info ; ezfio_filename |]
   in
   ignore @@
-    Unix.execv prog argv 
+    Unix.exec prog argv 
 
-let command () =
-  let open Command_line in
-  begin
-    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
-    set_description_doc "Display info on an EZFIO database";
-    [ anonymous "EZFIO_DIR" Mandatory "EZFIO directory" ]
-    |> set_specs
-  end;
 
-  let ezfio_file =
+let spec =
-    match Command_line.anon_args () with
+  let open Command.Spec in
-    | ezfio_file :: [] -> ezfio_file                                                          
+  empty
-    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
+  +> anon ("ezfio_file" %: string)
-  in
+
+let command = 
+    Command.basic_spec
+    ~summary: "Display info on an EZFIO database"
+    ~readme:(fun () ->
+      "
+Display info on an EZFIO database
+      ")
+    spec
+    (fun ezfio_file () ->  run ezfio_file )
 
-  run ezfio_file
 

ocaml/Qmcchem_md5.ml

@@ -52,7 +52,7 @@ let run ?c ?d ~l ~update ezfio_filename =
                   String.concat "/" [ ezfio_filename; "input"; old_key ]
                 in
                 Printf.printf "Removing %s\n%!" old_name;
-                try Sys.remove old_name with
+                try Sys.unlink old_name with
                 | Sys_error _ -> ();
             end
           in
@@ -88,9 +88,10 @@ let run ?c ?d ~l ~update ezfio_filename =
                   ""
               in
               let date = 
-                let open Unix in
+                (Unix.stat filename).Unix.st_mtime
-                localtime (stat filename).st_mtime 
+              in
-                |> Time.string_of_date
+              let date = 
+                Unix.strftime (Unix.localtime date) "%a, %d %b %Y %T %z"
               in
               Printf.printf "%s : %s  %s\n" md5 date this)
     in
@@ -120,7 +121,7 @@ let run ?c ?d ~l ~update ezfio_filename =
   | _ -> handle_options ()
 
 
-let command () =
+let () =
   let open Command_line in
   begin
     set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
@@ -152,12 +153,6 @@ let command () =
   let d = Command_line.get "diff" in
   let l = Command_line.get_bool "list" in
 
-  let ezfio_file =
-    match Command_line.anon_args () with
-    | ezfio_file :: [] -> ezfio_file
-    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
-  in
-
   run ?c ?d ~l ~update ezfio_file 
 
 

ocaml/Qmcchem_result.ml

@@ -206,7 +206,7 @@ let run ?a ?c ?e ?h ?t ?p ?rmin ?rmax ezfio_file =
     display_summary ~range
 
 
-let command () = 
+let () = 
   let open Command_line in
   begin
     set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");

ocaml/Qmcchem_run.ml

@@ -1,3 +1,4 @@
+open Core
 
 let full_run ?(start_dataserver=true) ezfio_filename  = 
   (* Identify the job scheduler *)
@@ -38,13 +39,13 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
 
 
       (* Start the data server *)
-      let prog, args = 
+      let prog, argv = 
-        qmcchem,  [| qmcchem; "run" ; "-d" ; ezfio_filename |]
+        qmcchem,  [ qmcchem; "run" ; "-d" ; ezfio_filename]
       in
       let pid_dataserver = 
-        Watchdog.fork_exec ~prog ~args ()
+        Watchdog.fork_exec ~prog ~argv ()
       in
-      Printf.printf "%7d : %s\n%!" pid_dataserver (String.concat " " (Array.to_list args))
+      Printf.printf "%7d : %s\n%!" (Pid.to_int pid_dataserver) (String.concat ~sep:" " argv)
     end;
   
 
@@ -86,7 +87,7 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
   | n  -> 
     if (not (test_open_rep_socket ())) then
       begin
-       Unix.sleepf 0.5;
+       Time.pause (Time.Span.of_sec 0.5);
        count (n-1);
       end
     else
@@ -95,33 +96,32 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
   if (not (count 300)) then
     Watchdog.kill ();
   *)
-  Unix.sleep 3;
+  Time.pause (Time.Span.of_sec 3.);
      
 
   (* Start the qmc processes *)
-  let prog, args_list =
+  let prog, argv =
     let launcher =
       Launcher.(find () |> to_string)
     in
     match launcher
-    |> String.split_on_char ' '
+    |> String.split ~on:' '
-    |> List.map String.trim
+    |> List.map ~f:String.strip
-    |> List.filter (fun x -> x <> "")
+    |> List.filter ~f:(fun x -> x <> "")
     with
     | launcher_exe::launcher_flags -> 
        launcher_exe, launcher_exe :: launcher_flags @ qmc @ [ 
          Ezfio.get_simulation_http_server () ; ezfio_filename ] 
     | _ -> failwith "Error in launcher"
   in
-  let args = Array.of_list args_list in
   let pid_qmc = 
     try 
-      Watchdog.fork_exec ~prog ~args ()
+      Watchdog.fork_exec ~prog ~argv ()
     with
     | Unix.Unix_error _ ->
         begin
           let command = 
-            String.concat " " args_list
+            String.concat ~sep:" " argv 
           in
           Printf.printf "
 ============================================================
@@ -132,7 +132,7 @@ Error: Unable to run the following command
           Watchdog.kill () 
         end
   in
-  Printf.printf "%7d : %s\n%!" pid_qmc (String.concat " " args_list);  
+  Printf.printf "%7d : %s\n%!" (Pid.to_int pid_qmc) (String.concat ~sep:" " argv);  
 
   (* Wait for processes to finish *)
   Watchdog.join ()
@@ -153,18 +153,17 @@ let run a d ?q ?s ezfio_filename =
 
   (* Signal handler to Kill properly all the processes *)
   let handler s = 
-    Printf.printf "QMC=Chem received signal %d... killing\n%!" s;
+    Printf.printf "QMC=Chem received the %s signal... killing\n%!" (Signal.to_string s);
     Watchdog.kill ();
   in
-  List.iter (fun s -> ignore @@ Sys.signal s (Sys.Signal_handle handler))
+  List.iter [
-    [
+     Signal.int  ;
-      Sys.sigint  ;
+     Signal.term ;
-      Sys.sigterm ;
+     Signal.quit ;
-      Sys.sigquit ;                                                                           
     ]
+    ~f:(fun x -> Signal.Expert.handle x handler)
   ;
 
-
   (* Validate input *)
   Input.validate ();
 (*  Printf.printf "MD5 : %s\n" (Lazy.force Md5.hash) ; *)
@@ -192,45 +191,30 @@ let run a d ?q ?s ezfio_filename =
 
 
 
-let command () =
+let spec =
-  let open Command_line in
+  let open Command.Spec in
-  begin
+  empty
-    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
+  +> flag "a" no_arg
-    set_description_doc "Run a calculation";
+     ~doc:(" Add more resources to a running calculation.")
-
+  +> flag "d" no_arg
-    [ { short='a' ; long="add" ; opt=Optional ;
+     ~doc:(" Start a dataserver process on the local host.")
-        doc="Add more resources to a running calculation" ;
+  +> flag "q" (optional string)
-        arg=Without_arg ; };
+     ~doc:("<dataserver_addr> Start a qmc process on the local host.")
-
+  +> flag "s" (optional string)
-      { short='d' ; long="data-server" ; opt=Optional ;
+     ~doc:("<host> Start a qmc process on <host>.")
-        doc="Start a dataserver process on the local host" ;
+  +> anon ("ezfio_file" %: string)
-        arg=Without_arg ; };
+
-
+
-      { short='q' ; long="local-qmc" ; opt=Optional ;
+
-        doc="Start a qmc process on the local host attached to the addres given as an argument" ;
+let command =
-        arg=With_arg "<string>" ; };
+    Command.basic_spec
-
+    ~summary: "Run a calculation"
-      { short='s' ; long="remote-qmc" ; opt=Optional ;
+    ~readme:(fun () ->
-        doc="Start a qmc process on the remote host as an argument" ;
+      "
-        arg=With_arg "<string>" ; };
+Run QMC=Chem
-
+      ")
-      anonymous "EZFIO_DIR" Mandatory "EZFIO directory";
+    spec
-    ]
+    (fun a d q s ezfio_file () -> run a d ?q ?s ezfio_file )
-    |> set_specs
-  end;
-
-  let a = Command_line.get_bool "add" in
-  let d = Command_line.get_bool "data-server" in
-  let q = Command_line.get "local-qmc" in
-  let s = Command_line.get "remote-qmc" in
-
-  let ezfio_file =
-    match Command_line.anon_args () with
-    | ezfio_file :: [] -> ezfio_file                                                          
-    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
-  in
-
-  run a d ?q ?s ezfio_file 
 
 
 

ocaml/Qmcchem_stop.ml

@@ -3,21 +3,20 @@ let run ezfio_filename =
   Qputils.set_ezfio_filename ezfio_filename;
   Status.write Status.Stopping
 
-let command () = 
-  let open Command_line in
-  begin
-    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
-    set_description_doc "Stop a running calculation";
-    [ anonymous "EZFIO_DIR" Mandatory "EZFIO directory" ]
-    |> set_specs
-  end;
 
-  let ezfio_file = 
+let spec =
-    match Command_line.anon_args () with
+  let open Command.Spec in
-    | ezfio_file :: [] -> ezfio_file
+  empty
-    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
+  +> anon ("ezfio_file" %: string)
-  in
 
-  run ezfio_file
+let command = 
+    Command.basic_spec
+    ~summary: "Stop a running calculation"
+    ~readme:(fun () ->
+      "
+Stop a running calculation
+      ")
+    spec
+    (fun ezfio_file () ->  run ezfio_file )
 
 

ocaml/Sample.ml

@@ -1,9 +1,7 @@
-open Sexplib.Std
-
 type t = 
   | One_dimensional  of float
   | Multidimensional of (float array * int)
-[@@deriving sexp]
+[@ deriving sexp]
 
 let dimension = function
   | One_dimensional _ -> 1

ocaml/Sample.mli

@@ -1,4 +1,4 @@
-type t [@@deriving sexp]
+type t [@@ deriving sexp]
 val to_float        : ?idx:int -> t -> float
 val to_float_array  : t -> float array
 val of_float        : float -> t

ocaml/Time.ml

@@ -20,30 +20,6 @@ let string_of_t t =
   in
   Printf.sprintf "%2d:%2d:%2d" hour min sec
 
-let string_of_date t = 
-  let year = 1900 + t.Unix.tm_year in
-  let mon  = t.Unix.tm_mon  in
-  let mday = t.Unix.tm_mday in
-  let sec  = t.Unix.tm_sec
-  and min  = t.Unix.tm_min
-  and hour = t.Unix.tm_hour 
-  in
-  let month = 
-    match mon with 
-      | 0  -> "Jan" | 1  -> "Feb" | 2  -> "Mar" | 3  -> "Apr"
-      | 4  -> "May" | 5  -> "Jun" | 6  -> "Jul" | 7  -> "Aug"
-      | 8  -> "Sep" | 9  -> "Oct" | 10 -> "Nov" | 11 -> "Dec"
-      | _ -> assert false
-  in
-  Printf.sprintf "%2d %3s %4d - %2.2d:%2.2d:%2.2d" mday month year hour min sec
-
-
-let string_of_now () = 
-  Unix.time ()
-  |> Unix.localtime 
-  |> string_of_date
-
-
 let string_of_sec s = 
   of_sec s 
   |> string_of_t 

ocaml/qmcchem.ml

@@ -1,36 +1,16 @@
-let update_command_line () =
+open Core
-  let last = (Array.length Sys.argv) - 2 in
-  Sys.argv.(0) <- Sys.argv.(0) ^ " " ^ Sys.argv.(1);
-  for i=1 to last do
-    Sys.argv.(i) <- Sys.argv.(i+1)
-  done;
-  Sys.argv.(last+1) <- "--"
 
 
+let command =
+    Command.group ~summary:"QMC=Chem command" [
+          "debug" , Qmcchem_debug.command ;
+          "edit"  , Qmcchem_edit.command ;
+          "info"  , Qmcchem_info.command ;
+          "md5"   , Qmcchem_md5.command ;
+          "result", Qmcchem_result.command ;
+          "run"   , Qmcchem_run.command ;
+          "stop"  , Qmcchem_stop.command ;
+    ]
 
 let () = 
-  let open Command_line in
+  Command.run command
-  begin
-    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
-    set_description_doc "Driver for subcommands.";
-    set_specs []
-  end; 
-
-  if Array.length Sys.argv < 2 then
-    (Command_line.help (); failwith "Inconsistent command line");
-
-  let command = Sys.argv.(1) in
-  update_command_line ();
-  Command_line.reset ();
-
-  match command with
-  | "debug"  -> let open Qmcchem_debug  in command ()
-  | "edit"   -> let open Qmcchem_edit   in command ()
-  | "info"   -> let open Qmcchem_info   in command ()
-  | "md5"    -> let open Qmcchem_md5    in command ()
-  | "result" -> let open Qmcchem_result in command ()
-  | "run"    -> let open Qmcchem_run    in command ()
-  | "stop"   -> let open Qmcchem_stop   in command ()
-  | _        -> (Command_line.help () ; failwith "Inconsistent command line")
-
-