mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-12-22 19:43:32 +01:00
Restored ocaml changes present in dev
This commit is contained in:
parent
f2f82d3f0a
commit
febf89f301
@ -1,3 +1,5 @@
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exception Error of string
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type short_opt = char
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type long_opt = string
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type optional = Mandatory | Optional
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@ -181,15 +183,16 @@ let set_specs specs_in =
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Getopt.parse_cmdline cmd_specs (fun x -> anon_args := !anon_args @ [x]);
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if show_help () then
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(help () ; exit 0);
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help ()
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else
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(* Check that all mandatory arguments are set *)
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List.filter (fun x -> x.short <> ' ' && x.opt = Mandatory) !specs
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|> List.iter (fun x ->
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match get x.long with
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| Some _ -> ()
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| None -> raise (Error ("--"^x.long^" option is missing."))
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)
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(* Check that all mandatory arguments are set *)
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List.filter (fun x -> x.short <> ' ' && x.opt = Mandatory) !specs
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|> List.iter (fun x ->
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match get x.long with
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| Some _ -> ()
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| None -> failwith ("Error: --"^x.long^" option is missing.")
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)
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;;
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@ -59,6 +59,8 @@ let () =
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*)
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exception Error of string
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type short_opt = char
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type long_opt = string
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@ -101,7 +101,7 @@ let to_string_general ~f m =
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|> String.concat "\n"
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let to_string =
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to_string_general ~f:(fun x -> Atom.to_string Units.Angstrom x)
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to_string_general ~f:(fun x -> Atom.to_string ~units:Units.Angstrom x)
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let to_xyz =
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to_string_general ~f:Atom.to_xyz
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@ -113,7 +113,7 @@ let of_xyz_string
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s =
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let l = String_ext.split s ~on:'\n'
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|> List.filter (fun x -> x <> "")
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|> list_map (fun x -> Atom.of_string units x)
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|> list_map (fun x -> Atom.of_string ~units x)
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in
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let ne = ( get_charge {
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nuclei=l ;
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@ -56,3 +56,7 @@ let string_of_string s = s
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let list_map f l =
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List.rev_map f l
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|> List.rev
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let socket_convert socket =
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((Obj.magic (Obj.repr socket)) : [ `Xsub ] Zmq.Socket.t )
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@ -677,12 +677,15 @@ let run ?o b au c d m p cart xyz_file =
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let () =
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try (
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let open Command_line in
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begin
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"Creates an EZFIO directory from a standard xyz file or from a z-matrix file in Gaussian format. The basis set is defined as a single string if all the atoms are taken from the same basis set, otherwise specific elements can be defined as follows:
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-b \"cc-pcvdz | H:cc-pvdz | C:6-31g\"
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-b \"cc-pvtz | 1,H:sto-3g | 3,H:6-31g\"
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If a file with the same name as the basis set exists, this file will be read. Otherwise, the basis set is obtained from the database.
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" |> set_description_doc ;
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set_header_doc (Sys.argv.(0) ^ " - Quantum Package command");
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@ -732,7 +735,7 @@ If a file with the same name as the basis set exists, this file will be read. O
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let basis =
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match Command_line.get "basis" with
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| None -> assert false
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| None -> ""
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| Some x -> x
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in
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@ -771,10 +774,14 @@ If a file with the same name as the basis set exists, this file will be read. O
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let xyz_filename =
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match Command_line.anon_args () with
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| [x] -> x
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| _ -> (Command_line.help () ; failwith "input file is missing")
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| [] -> failwith "input file is missing"
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| x::_ -> x
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in
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run ?o:output basis au charge dummy multiplicity pseudo cart xyz_filename
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)
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with
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| Failure txt -> Printf.eprintf "Fatal error: %s\n%!" txt
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| Command_line.Error txt -> Printf.eprintf "Command line error: %s\n%!" txt
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@ -2,7 +2,7 @@ open Qputils
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open Qptypes
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type ezfio_or_address = EZFIO of string | ADDRESS of string
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type req_or_sub = REQ | SUB
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type req_or_sub = REQ | SUB
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let localport = 42379
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@ -29,7 +29,7 @@ let () =
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end;
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let arg =
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let x =
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let x =
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match Command_line.anon_args () with
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| [x] -> x
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| _ -> begin
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@ -44,7 +44,7 @@ let () =
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in
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let localhost =
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let localhost =
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Lazy.force TaskServer.ip_address
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in
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@ -52,28 +52,28 @@ let () =
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let long_address =
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match arg with
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| ADDRESS x -> x
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| EZFIO x ->
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let ic =
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| EZFIO x ->
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let ic =
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Filename.concat (Qpackage.ezfio_work x) "qp_run_address"
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|> open_in
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in
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let result =
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let result =
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input_line ic
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|> String.trim
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in
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close_in ic;
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result
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in
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let protocol, address, port =
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match String.split_on_char ':' long_address with
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| t :: a :: p :: [] -> t, a, int_of_string p
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| _ -> failwith @@
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| _ -> failwith @@
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Printf.sprintf "%s : Malformed address" long_address
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in
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let zmq_context =
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let zmq_context =
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Zmq.Context.create ()
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in
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@ -105,10 +105,10 @@ let () =
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let create_socket sock_type bind_or_connect addr =
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let socket =
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let socket =
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Zmq.Socket.create zmq_context sock_type
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in
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let () =
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let () =
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try
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bind_or_connect socket addr
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with
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@ -131,37 +131,64 @@ let () =
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Sys.set_signal Sys.sigint handler;
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let new_thread req_or_sub addr_in addr_out =
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let new_thread_req addr_in addr_out =
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let socket_in, socket_out =
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match req_or_sub with
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| REQ ->
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create_socket Zmq.Socket.router Zmq.Socket.bind addr_in,
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create_socket Zmq.Socket.dealer Zmq.Socket.connect addr_out
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| SUB ->
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create_socket Zmq.Socket.sub Zmq.Socket.connect addr_in,
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create_socket Zmq.Socket.pub Zmq.Socket.bind addr_out
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in
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if req_or_sub = SUB then
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Zmq.Socket.subscribe socket_in "";
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let action_in =
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match req_or_sub with
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| REQ -> (fun () -> Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out)
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| SUB -> (fun () -> Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out)
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let action_in =
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fun () -> Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out
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in
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let action_out =
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match req_or_sub with
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| REQ -> (fun () -> Zmq.Socket.recv_all socket_out |> Zmq.Socket.send_all socket_in )
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| SUB -> (fun () -> () )
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let action_out =
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fun () -> Zmq.Socket.recv_all socket_out |> Zmq.Socket.send_all socket_in
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in
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let pollitem =
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Zmq.Poll.mask_of
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[| (socket_in, Zmq.Poll.In) ; (socket_out, Zmq.Poll.In) |]
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[| (socket_convert socket_in, Zmq.Poll.In) ; (socket_convert socket_out, Zmq.Poll.In) |]
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in
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while !run_status do
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let polling =
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Zmq.Poll.poll ~timeout:1000 pollitem
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in
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match polling with
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| [| Some Zmq.Poll.In ; Some Zmq.Poll.In |] -> ( action_out () ; action_in () )
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| [| _ ; Some Zmq.Poll.In |] -> action_out ()
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| [| Some Zmq.Poll.In ; _ |] -> action_in ()
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| _ -> ()
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done;
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Zmq.Socket.close socket_in;
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Zmq.Socket.close socket_out;
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in
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let new_thread_sub addr_in addr_out =
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let socket_in, socket_out =
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create_socket Zmq.Socket.sub Zmq.Socket.connect addr_in,
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create_socket Zmq.Socket.pub Zmq.Socket.bind addr_out
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in
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Zmq.Socket.subscribe socket_in "";
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let action_in =
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fun () -> Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out
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in
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let action_out =
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fun () -> ()
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in
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let pollitem =
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Zmq.Poll.mask_of
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[| (socket_convert socket_in, Zmq.Poll.In) ; (socket_convert socket_out, Zmq.Poll.In) |]
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in
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@ -173,8 +200,8 @@ let () =
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match polling with
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| [| Some Zmq.Poll.In ; Some Zmq.Poll.In |] -> ( action_out () ; action_in () )
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| [| _ ; Some Zmq.Poll.In |] -> action_out ()
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| [| Some Zmq.Poll.In ; _ |] -> action_in ()
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| [| _ ; Some Zmq.Poll.In |] -> action_out ()
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| [| Some Zmq.Poll.In ; _ |] -> action_in ()
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| _ -> ()
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done;
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@ -193,8 +220,8 @@ let () =
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Printf.sprintf "tcp://*:%d" localport
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in
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let f () =
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new_thread REQ addr_in addr_out
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let f () =
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new_thread_req addr_in addr_out
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in
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(Thread.create f) ()
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@ -211,8 +238,8 @@ let () =
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Printf.sprintf "tcp://*:%d" (localport+2)
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in
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let f () =
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new_thread REQ addr_in addr_out
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let f () =
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new_thread_req addr_in addr_out
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in
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(Thread.create f) ()
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in
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@ -227,8 +254,8 @@ let () =
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Printf.sprintf "tcp://*:%d" (localport+1)
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in
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let f () =
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new_thread SUB addr_in addr_out
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let f () =
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new_thread_sub addr_in addr_out
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in
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(Thread.create f) ()
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in
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@ -236,7 +263,7 @@ let () =
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let input_thread =
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let f () =
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let f () =
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let addr_out =
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match arg with
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| EZFIO _ -> None
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@ -248,22 +275,22 @@ let () =
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Printf.sprintf "tcp://*:%d" (localport+9)
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in
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let socket_in =
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let socket_in =
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create_socket Zmq.Socket.rep Zmq.Socket.bind addr_in
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in
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let socket_out =
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match addr_out with
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match addr_out with
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| Some addr_out -> Some (
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create_socket Zmq.Socket.req Zmq.Socket.connect addr_out)
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| None -> None
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in
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let temp_file =
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let temp_file =
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Filename.temp_file "qp_tunnel" ".tar.gz"
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in
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let get_ezfio_filename () =
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let get_ezfio_filename () =
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match arg with
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| EZFIO x -> x
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| ADDRESS _ ->
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@ -277,9 +304,9 @@ let () =
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end
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in
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let get_input () =
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let get_input () =
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match arg with
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| EZFIO x ->
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| EZFIO x ->
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begin
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Printf.sprintf "tar --exclude=\"*.gz.*\" -zcf %s %s" temp_file x
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|> Sys.command |> ignore;
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@ -291,11 +318,11 @@ let () =
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in
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ignore @@ Unix.lseek fd 0 Unix.SEEK_SET ;
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let bstr =
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Unix.map_file fd Bigarray.char
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Unix.map_file fd Bigarray.char
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Bigarray.c_layout false [| len |]
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|> Bigarray.array1_of_genarray
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in
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let result =
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let result =
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String.init len (fun i -> bstr.{i}) ;
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in
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Unix.close fd;
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@ -313,7 +340,7 @@ let () =
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end
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in
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let () =
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let () =
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match socket_out with
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| None -> ()
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| Some socket_out ->
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@ -329,7 +356,7 @@ let () =
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| ADDRESS _ ->
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begin
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Printf.printf "Getting input... %!";
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let ezfio_filename =
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let ezfio_filename =
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get_ezfio_filename ()
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in
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Printf.printf "%s%!" ezfio_filename;
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@ -343,7 +370,7 @@ let () =
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|> Sys.command |> ignore ;
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let oc =
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Filename.concat (Qpackage.ezfio_work ezfio_filename) "qp_run_address"
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|> open_out
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|> open_out
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in
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Printf.fprintf oc "tcp://%s:%d\n" localhost localport;
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close_out oc;
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@ -359,9 +386,9 @@ let () =
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let action () =
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match Zmq.Socket.recv socket_in with
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| "get_input" -> get_input ()
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|> Zmq.Socket.send socket_in
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|> Zmq.Socket.send socket_in
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| "get_ezfio_filename" -> get_ezfio_filename ()
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|> Zmq.Socket.send socket_in
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|> Zmq.Socket.send socket_in
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| "test" -> Zmq.Socket.send socket_in "OK"
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| x -> Printf.sprintf "Message '%s' not understood" x
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|> Zmq.Socket.send socket_in
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@ -372,7 +399,7 @@ On remote hosts, create ssh tunnel using:
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ssh -L %d:%s:%d -L %d:%s:%d -L %d:%s:%d -L %d:%s:%d %s &
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Or from this host connect to clients using:
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ssh -R %d:localhost:%d -R %d:localhost:%d -R %d:localhost:%d -R %d:localhost:%d <host> &
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%!"
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%!"
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(port ) localhost (localport )
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(port+1) localhost (localport+1)
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(port+2) localhost (localport+2)
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@ -392,12 +419,12 @@ Or from this host connect to clients using:
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match polling.(0) with
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| Some Zmq.Poll.In -> action ()
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| None -> ()
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| Some Zmq.Poll.In_out
|
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| Some Zmq.Poll.In_out
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| Some Zmq.Poll.Out -> ()
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done;
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let () =
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let () =
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match socket_out with
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| Some socket_out -> Zmq.Socket.close socket_out
|
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| None -> ()
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@ -415,7 +442,7 @@ Or from this host connect to clients using:
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Thread.join ocaml_thread;
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Zmq.Context.terminate zmq_context;
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Printf.printf "qp_tunnel exited properly.\n"
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