Removing core

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 |> Int.to_string )
+    | Some (a,p) -> a^":"^( (int_of_string p)+4 |> string_of_int )
     | 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 (Byte_units.create `Bytes 0.)
+          ref 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, Byte_units.create `Bytes (Float.of_string bytes))
+                (socket, float_of_string bytes)
-            | _ -> (print_endline msg ; ("", Byte_units.create `Bytes 0.))
+            | _ -> (print_endline msg ; ("", 0.))
           in
-          tot_size := Byte_units.create `Bytes ((Byte_units.bytes !tot_size) +. (Byte_units.bytes bytes));
+          tot_size := !tot_size +. bytes;
-          Printf.printf "%s\n%!" (Byte_units.to_string !tot_size);
+          Printf.printf "%f\n%!" !tot_size;
-          Time.pause (Time.Span.of_sec 1.)
+          Unix.sleep 1
         done
       end
   else
@@ -62,20 +62,29 @@ let run ~t ezfio_filename=
 
 
 
-let spec =
+let () =
-  let open Command.Spec in
+  let open Command_line in
-  empty
+  begin
-  +> flag "t" no_arg 
+    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
-     ~doc:"Measure the throughput"
+    set_description_doc "Debug ZeroMQ communications";
-  +> anon ("ezfio_file" %: string)
+    [ { short='t' ; long="traffic" ; opt=Optional ;
+        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_info.ml

@@ -10,22 +10,22 @@ let run ezfio_filename =
     [| qmcchem_info ; ezfio_filename |]
   in
   ignore @@
-    Unix.exec prog argv 
+    Unix.execv prog argv 
 
+let () =
+  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 spec =
+  let ezfio_file =
-  let open Command.Spec in
+    match Command_line.anon_args () with
-  empty
+    | ezfio_file :: [] -> ezfio_file                                                          
-  +> anon ("ezfio_file" %: string)
+    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
-
+  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.unlink old_name with
+                try Sys.remove old_name with
                 | Sys_error _ -> ();
             end
           in
@@ -87,11 +87,10 @@ let run ?c ?d ~l ~update ezfio_filename =
                 else
                   ""
               in
-              let date = 
+              let date =
-                (Unix.stat filename).Unix.st_mtime
+                let open Unix in
-              in
+                localtime (stat filename).st_mtime 
-              let date = 
+                |> Time.string_of_date
-                Unix.strftime (Unix.localtime date) "%a, %d %b %Y %T %z"
               in
               Printf.printf "%s : %s  %s\n" md5 date this)
     in
@@ -153,6 +152,12 @@ let () =
   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_run.ml

@@ -1,4 +1,3 @@
-open Core
 
 let full_run ?(start_dataserver=true) ezfio_filename  = 
   (* Identify the job scheduler *)
@@ -39,13 +38,13 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
 
 
       (* Start the data server *)
-      let prog, argv = 
+      let prog, args = 
-        qmcchem,  [ qmcchem; "run" ; "-d" ; ezfio_filename]
+        qmcchem,  [| qmcchem; "run" ; "-d" ; ezfio_filename |]
       in
       let pid_dataserver = 
-        Watchdog.fork_exec ~prog ~argv ()
+        Watchdog.fork_exec ~prog ~args ()
       in
-      Printf.printf "%7d : %s\n%!" (Pid.to_int pid_dataserver) (String.concat ~sep:" " argv)
+      Printf.printf "%7d : %s\n%!" pid_dataserver (String.concat " " (Array.to_list args))
     end;
   
 
@@ -87,7 +86,7 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
   | n  -> 
     if (not (test_open_rep_socket ())) then
       begin
-       Time.pause (Time.Span.of_sec 0.5);
+       Unix.sleepf 0.5;
        count (n-1);
       end
     else
@@ -96,32 +95,33 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
   if (not (count 300)) then
     Watchdog.kill ();
   *)
-  Time.pause (Time.Span.of_sec 3.);
+  Unix.sleep 3;
      
 
   (* Start the qmc processes *)
-  let prog, argv =
+  let prog, args_list =
     let launcher =
       Launcher.(find () |> to_string)
     in
     match launcher
-    |> String.split ~on:' '
+    |> String.split_on_char ' '
-    |> List.map ~f:String.strip
+    |> List.map String.trim
-    |> List.filter ~f:(fun x -> x <> "")
+    |> List.filter (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 ~argv ()
+      Watchdog.fork_exec ~prog ~args ()
     with
     | Unix.Unix_error _ ->
         begin
           let command = 
-            String.concat ~sep:" " argv 
+            String.concat " " args_list
           in
           Printf.printf "
 ============================================================
@@ -132,7 +132,7 @@ Error: Unable to run the following command
           Watchdog.kill () 
         end
   in
-  Printf.printf "%7d : %s\n%!" (Pid.to_int pid_qmc) (String.concat ~sep:" " argv);  
+  Printf.printf "%7d : %s\n%!" pid_qmc (String.concat " " args_list);  
 
   (* Wait for processes to finish *)
   Watchdog.join ()
@@ -152,18 +152,19 @@ let run a d ?q ?s ezfio_filename =
   Qputils.set_ezfio_filename ezfio_filename;
 
   (* Signal handler to Kill properly all the processes *)
-  let handler s = 
+  let handler s =
-    Printf.printf "QMC=Chem received the %s signal... killing\n%!" (Signal.to_string s);
+    Printf.printf "QMC=Chem received signal %d... killing\n%!" s;
     Watchdog.kill ();
   in
-  List.iter [
+  List.iter (fun s -> ignore @@ Sys.signal s (Sys.Signal_handle handler))
-     Signal.int  ;
+    [
-     Signal.term ;
+      Sys.sigint  ;
-     Signal.quit ;
+      Sys.sigterm ;
+      Sys.sigquit ;                                                                           
     ]
-    ~f:(fun x -> Signal.Expert.handle x handler)
   ;
 
+
   (* Validate input *)
   Input.validate ();
 (*  Printf.printf "MD5 : %s\n" (Lazy.force Md5.hash) ; *)
@@ -191,30 +192,45 @@ let run a d ?q ?s ezfio_filename =
 
 
 
-let spec =
+let () =
-  let open Command.Spec in
+  let open Command_line in
-  empty
+  begin
-  +> flag "a" no_arg
+    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
-     ~doc:(" Add more resources to a running calculation.")
+    set_description_doc "Run a calculation";
-  +> flag "d" no_arg
+
-     ~doc:(" Start a dataserver process on the local host.")
+    [ { short='a' ; long="add" ; opt=Optional ;
-  +> flag "q" (optional string)
+        doc="Add more resources to a running calculation" ;
-     ~doc:("<dataserver_addr> Start a qmc process on the local host.")
+        arg=Without_arg ; };
-  +> flag "s" (optional string)
+
-     ~doc:("<host> Start a qmc process on <host>.")
+      { short='d' ; long="data-server" ; opt=Optional ;
-  +> anon ("ezfio_file" %: string)
+        doc="Start a dataserver process on the local host" ;
-
+        arg=Without_arg ; };
-
+
-
+      { short='q' ; long="local-qmc" ; opt=Optional ;
-let command =
+        doc="Start a qmc process on the local host attached to the addres given as an argument" ;
-    Command.basic_spec
+        arg=With_arg "<string>" ; };
-    ~summary: "Run a calculation"
+
-    ~readme:(fun () ->
+      { short='s' ; long="remote-qmc" ; opt=Optional ;
-      "
+        doc="Start a qmc process on the remote host as an argument" ;
-Run QMC=Chem
+        arg=With_arg "<string>" ; };
-      ")
+
-    spec
+      anonymous "EZFIO_DIR" Mandatory "EZFIO directory";
-    (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

@@ -3,20 +3,21 @@ let run ezfio_filename =
   Qputils.set_ezfio_filename ezfio_filename;
   Status.write Status.Stopping
 
+let () = 
+  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 spec =
+  let ezfio_file = 
-  let open Command.Spec in
+    match Command_line.anon_args () with
-  empty
+    | ezfio_file :: [] -> ezfio_file
-  +> anon ("ezfio_file" %: string)
+    | _ -> (Command_line.help () ; failwith "Inconsistent command line")
+  in
 
-let command = 
+  run ezfio_file
-    Command.basic_spec
-    ~summary: "Stop a running calculation"
-    ~readme:(fun () ->
-      "
-Stop a running calculation
-      ")
-    spec
-    (fun ezfio_file () ->  run ezfio_file )
 
 

ocaml/Sample.ml

@@ -1,7 +1,9 @@
+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

@@ -20,6 +20,30 @@ 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

@@ -1,16 +1,39 @@
-open Core
+let update_command_line () =
+  let last = Array.length Sys.argv - 1 in
+  for i=1 to last do
+    Sys.argv.(i) <- Sys.argv.(i+1)
+  done;
+  Sys.argv.(last) <- "--"
 
 
-let command =
+let () =
-    Command.group ~summary:"QMC=Chem command" [
+  let open Command_line in
-          "debug" , Qmcchem_debug.command ;
+  begin
-          "edit"  , Qmcchem_edit.command ;
+    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
-          "info"  , Qmcchem_info.command ;
+    set_description_doc "Driver for subcommands.";
-          "md5"   , Qmcchem_md5.command ;
+    [
-          "result", Qmcchem_result.command ;
+      anonymous "COMMAND"   Mandatory "[debug|edit|info|md5|result|run|stop]";
-          "run"   , Qmcchem_run.command ;
+      anonymous "EZFIO_DIR" Mandatory "EZFIO directory";
-          "stop"  , Qmcchem_stop.command ;
     ]
+    |> set_specs
+  end; 
+
+  let command = 
+    match Command_line.anon_args () with
+    | command :: ezfio_file :: [] -> command
+    | _  -> (Command_line.help () ; failwith "Inconsistent command line")
+  in
+
+  update_command_line ();
+
+  match command with
+  | "debug"  -> let open Qmcchem_debug  in ()
+  | "edit"   -> let open Qmcchem_edit   in ()
+  | "info"   -> let open Qmcchem_info   in ()
+  | "md5"    -> let open Qmcchem_md5    in ()
+  | "result" -> let open Qmcchem_result in ()
+  | "run"    -> let open Qmcchem_run    in ()
+  | "stop"   -> let open Qmcchem_stop   in ()
+  | _        -> (Command_line.help () ; failwith "Inconsistent command line")
+
 
-let () = 
-  Command.run command