LCPQ/qmcchem
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Fixing Ocaml

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This commit is contained in:
Anthony Scemama 2019-07-23 17:27:02 +02:00
parent 5e25738f53
commit 380169d219
24 changed files with 121 additions and 225 deletions
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4
build.ninja
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@ -28,7 +28,7 @@ rule compile_ocaml_dep
pool = console
rule compile_ocaml
command = cd ocaml ; ninja $target
command = cd ocaml ; make $target
description = Compiling OCaml tools
pool = console
@ -77,7 +77,7 @@ build ocaml/qmcchem : compile_ocaml | EZFIO/Ocaml/ezfio.ml ocaml/Property.ml
build bin/qmc: copy_to_bin src/MAIN/qmc
build bin/qmcchem_info: copy_to_bin src/MAIN/qmcchem_info
build bin/qmc_create_walkers: copy_to_bin src/MAIN/qmc_create_walkers
build bin/qmcchem: copy_to_bin ocaml/qmcchem
build bin/qmcchem: copy_to_bin ocaml/qmcchem
default bin/qmc bin/qmcchem_info bin/qmc_create_walkers bin/qmcchem

12
ezfio_config/qmc.config
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@ -8,12 +8,12 @@ ao_basis
ao_expo real (ao_basis_ao_num,ao_basis_ao_prim_num_max)
mo_basis
mo_tot_num integer
mo_coef real (ao_basis_ao_num,mo_basis_mo_tot_num)
mo_classif character (mo_basis_mo_tot_num)
mo_energy real (mo_basis_mo_tot_num)
mo_occ real (mo_basis_mo_tot_num)
mo_symmetry character*(8) (mo_basis_mo_tot_num)
mo_num integer
mo_coef real (ao_basis_ao_num,mo_basis_mo_num)
mo_classif character (mo_basis_mo_num)
mo_energy real (mo_basis_mo_num)
mo_occ real (mo_basis_mo_num)
mo_symmetry character*(8) (mo_basis_mo_num)
electrons
elec_alpha_num integer

2
ocaml/Block.ml
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@ -86,7 +86,7 @@ let update_raw_data ?(locked=true) () =
in
let files =
let result =
if Sys.is_directory dir_name then
if Sys.file_exists dir_name && Sys.is_directory dir_name then
begin
Sys.readdir dir_name
|> Array.map (fun x -> dir_name^x)

15
ocaml/Command_line.ml
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@ -166,7 +166,7 @@ let help () =
let set_specs specs_in =
let set_specs ?(no_help=false) specs_in =
specs := { short='h' ;
long ="help" ;
doc ="Prints the help message." ;
@ -188,11 +188,20 @@ let set_specs specs_in =
)
in
Getopt.parse_cmdline cmd_specs (fun x -> anon_args := !anon_args @ [x]);
let cmdline =
Sys.argv
|> Array.to_list
|> List.filter (fun x -> x <> "")
|> Array.of_list
in
Getopt.parse cmd_specs (fun x -> anon_args := !anon_args @ [x])
cmdline 1 (Array.length cmdline -1);
if show_help () then
if not no_help && (show_help ()) then
(help () ; exit 0);
(* Check that all mandatory arguments are set *)
List.filter (fun x -> x.short <> ' ' && x.opt = Mandatory) !specs
|> List.iter (fun x ->

2
ocaml/Command_line.mli
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@ -117,7 +117,7 @@ val help : unit -> unit
(** Sets the specification list as a list of tuples:
( short option, long option, documentation, argument ) *)
val set_specs : description list -> unit
val set_specs : ?no_help:bool -> description list -> unit
(** Returns the list of anonymous arguments *)

2
ocaml/Input.ml
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@ -788,7 +788,7 @@ end = struct
let doc = "Type of Jastrow factor [ None | Core | Simple ]"
let of_string s =
match String.capitalize (String.trim s) with
match String.capitalize_ascii (String.trim s) with
| "Core" -> Core
| "Simple" -> Simple
| "None" -> None

1
ocaml/Makefile
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@ -24,7 +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)

149
ocaml/Md5.ml
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@ -1,149 +0,0 @@
open Core
(** Directory containing the list of input files. The directory is created is inexistant. *)
let input_directory = lazy (
let ezfio_filename =
Lazy.force Qputils.ezfio_filename
in
let dirname =
Filename.concat ezfio_filename "input"
in
begin
match ( Sys.is_directory dirname ) with
| `No -> Unix.mkdir dirname
| _ -> ()
end ;
dirname
)
(** List of files responsible for the MD5 key of the input *)
let files_to_track = [
"ao_basis/ao_coef.gz" ;
"ao_basis/ao_expo.gz" ;
"ao_basis/ao_nucl.gz" ;
"ao_basis/ao_num" ;
"ao_basis/ao_power.gz" ;
"ao_basis/ao_prim_num.gz" ;
"electrons/elec_alpha_num" ;
"electrons/elec_beta_num" ;
"electrons/elec_walk_num" ;
"jastrow/jast_type" ;
"mo_basis/mo_coef.gz" ;
"mo_basis/mo_tot_num" ;
"nuclei/nucl_charge.gz" ;
"nuclei/nucl_coord.gz" ;
"nuclei/nucl_num" ;
"simulation/ci_threshold" ;
"simulation/nucl_fitcusp_factor" ;
"simulation/jast_a_up_dn" ;
"simulation/jast_a_up_up" ;
"simulation/jast_b_up_dn" ;
"simulation/jast_b_up_up" ;
"simulation/jast_core_a1" ;
"simulation/jast_core_a2" ;
"simulation/jast_core_b1" ;
"simulation/jast_core_b2" ;
"simulation/jast_een_e_a.gz" ;
"simulation/jast_een_e_b.gz" ;
"simulation/jast_een_n.gz" ;
"simulation/jast_pen.gz" ;
"simulation/method" ;
"simulation/time_step" ;
"simulation/dmc_projection_time" ;
"spindeterminants/bit_kind" ;
"spindeterminants/n_det" ;
"spindeterminants/n_det_alpha" ;
"spindeterminants/n_det_beta" ;
"spindeterminants/n_int" ;
"spindeterminants/n_states" ;
"spindeterminants/psi_coef_matrix_columns.gz" ;
"spindeterminants/psi_coef_matrix_rows.gz" ;
"spindeterminants/psi_coef_matrix_values.gz" ;
"spindeterminants/psi_det_alpha.gz" ;
"spindeterminants/psi_det_beta.gz" ;
"/pseudo/do_pseudo" ;
"/pseudo/mo_pseudo_grid.gz" ;
"/pseudo/pseudo_dz_kl.gz";
"/pseudo/pseudo_klocmax" ;
"/pseudo/pseudo_n_k.gz" ;
"/pseudo/pseudo_v_kl.gz" ;
"/pseudo/pseudo_grid_rmax" ;
"/pseudo/pseudo_kmax" ;
"/pseudo/pseudo_n_kl.gz" ;
"/pseudo/pseudo_dz_k.gz" ;
"/pseudo/pseudo_grid_size" ;
"/pseudo/pseudo_v_k.gz" ;
]
(** Get an MD5 ke from the content of a file. *)
let hash_file filename =
match Sys.is_file filename with
| `Yes ->
begin
In_channel.with_file filename ~f:(fun ic ->
Cryptokit.hash_channel (Cryptokit.Hash.md5 ()) ic
|> Cryptokit.transform_string (Cryptokit.Hexa.encode ()) )
end
| _ -> ""
(** Cache containing the current value of the MD5 hash. *)
let _hash =
ref None
(** Get the hash correcponding to the EZFIO file. *)
let hash () =
let compute_hash () =
let ezfio_filename =
Lazy.force Qputils.ezfio_filename
in
let old_md5 =
if Ezfio.has_simulation_md5_key () then
Ezfio.get_simulation_md5_key ()
else
""
in
let md5_string =
files_to_track
|> List.map ~f:(fun x -> Printf.sprintf "%s/%s" ezfio_filename x)
|> List.map ~f:hash_file
|> String.concat
in
let new_md5 =
md5_string
|> Cryptokit.hash_string (Cryptokit.Hash.md5 ())
|> Cryptokit.transform_string (Cryptokit.Hexa.encode ())
in
if (new_md5 <> old_md5) then
begin
Printf.eprintf "Info : MD5 key changed\n %s\n-> %s\n%!" old_md5 new_md5 ;
Ezfio.set_simulation_md5_key new_md5
end
;
new_md5
in
match (!_hash) with
| Some key -> key
| None ->
begin
let key =
compute_hash ()
in
_hash := Some key ;
key
end
(** Reset the cache of the MD5 hash. *)
let reset_hash () =
_hash := None;
ignore (hash ())

2
ocaml/QmcMd5.ml
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@ -10,7 +10,7 @@ let input_directory = lazy (
in
begin
if not (Sys.is_directory dirname) then
if not (Sys.file_exists dirname && Sys.is_directory dirname) then
Unix.mkdir dirname 0o777
end ;

9
ocaml/Qmcchem_dataserver.ml
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@ -36,13 +36,12 @@ let run ?(daemon=true) ezfio_filename =
Printf.printf "Generating initial walkers...\n%!";
match Unix.fork () with
| 0 ->
Unix.execv
Unix.execvp
(Lazy.force Qmcchem_config.qmc_create_walkers)
[|"qmc_create_walkers" ; ezfio_filename|]
| pid ->
begin
let pid', status = Unix.waitpid [] pid in
assert (status = Unix.WEXITED 0);
ignore @@ Unix.waitpid [] pid;
Printf.printf "Initial walkers ready\n%!"
end
end
@ -348,8 +347,8 @@ let run ?(daemon=true) ezfio_filename =
Lazy.force Block.dir_name
in
let () =
if not (Sys.is_directory dirname) then
Unix.mkdir dirname 0o600
if not ( Sys.file_exists dirname && Sys.is_directory dirname ) then
Unix.mkdir dirname 0o755
in
Filename.concat dirname (
hostname ^ "." ^ (string_of_int dataserver_pid)

4
ocaml/Qmcchem_edit.ml
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@ -252,12 +252,12 @@ let run ~c ?f ?t ?l ?m ?e ?et ?s ?ts ?w ?wt ?n ?j ?p ?input ezfio_filename =
Filename.concat (Filename.concat ezfio_filename "blocks") (QmcMd5.hash ())
in
let rec clean_dir y =
if Sys.is_directory y then
if Sys.file_exists y && Sys.is_directory y then
begin
Sys.readdir y
|> Array.map (fun x -> Filename.concat y x)
|> Array.iter (function x ->
if Sys.is_directory x then
if Sys.file_exists x && Sys.is_directory x then
clean_dir x
else
Sys.remove x

4
ocaml/Qmcchem_forwarder.ml
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@ -48,7 +48,7 @@ let run ezfio_filename dataserver =
*)
let () =
try
Unix.mkdir tmpdir 0o600;
Unix.mkdir tmpdir 0o755;
Unix.chdir tmpdir
with
| Unix.Unix_error _ ->
@ -69,7 +69,7 @@ let run ezfio_filename dataserver =
| pid ->
try
Unix.kill pid 0 ;
ignore @@ Unix.execv prog argv
ignore @@ Unix.execvp prog argv
with
| Unix.Unix_error (Unix.ESRCH, _, _) -> ()
end

2
ocaml/Qmcchem_info.ml
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@ -10,7 +10,7 @@ let run ezfio_filename =
[| qmcchem_info ; ezfio_filename |]
in
ignore @@
Unix.execv prog argv
Unix.execvp prog argv
let command () =
let open Command_line in

2
ocaml/Qmcchem_result.ml
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@ -224,7 +224,7 @@ let command () =
doc="Display the convergence of the error of the property by merging blocks";
arg=With_arg "<string>"; };
{ short='h' ; long="histogram" ; opt=Optional ;
{ short='i' ; long="histogram" ; opt=Optional ;
doc="Display the histogram of the property blocks" ;
arg=With_arg "<string>"; };

4
ocaml/Qmcchem_run.ml
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@ -48,7 +48,6 @@ let full_run ?(start_dataserver=true) ezfio_filename =
end;
(*
(* Check if the Zmq Rep socket is open *)
let test_open_rep_socket () =
let zmq_context =
@ -86,7 +85,7 @@ let full_run ?(start_dataserver=true) ezfio_filename =
| n ->
if (not (test_open_rep_socket ())) then
begin
Unix.sleepf 0.5;
Unix.sleep 2;
count (n-1);
end
else
@ -94,7 +93,6 @@ let full_run ?(start_dataserver=true) ezfio_filename =
in
if (not (count 300)) then
Watchdog.kill ();
*)
Unix.sleep 3;

23
ocaml/Qputils.ml
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@ -13,7 +13,7 @@ let set_ezfio_filename ezfio_filename =
failwith (ezfio_filename^" does not exist")
in
let () =
if Sys.is_directory ezfio_filename then
if Sys.file_exists ezfio_filename && Sys.is_directory ezfio_filename then
Ezfio.set_file ezfio_filename
else
failwith ("Error : "^ezfio_filename^" is not a directory")
@ -34,13 +34,30 @@ let ezfio_filename = lazy (
match f with
| "EZFIO_File" ->
begin
if (Array.length Sys.argv = 1) then
let args =
Command_line.anon_args ()
|> Array.of_list
in
if (Array.length args < 1) then
failwith "Error : EZFIO directory not specified on the command line\n";
Sys.argv.(1)
args.(0)
end
| f -> f
in
set_ezfio_filename full_path;
(*
(* Check if input directory is present *)
let dirname = Filename.concat full_path "input" in
if not (Sys.file_exists dirname) then
Unix.mkdir dirname 0o755;
(* Check if blocks directory is present *)
let dirname = Filename.concat full_path "blocks" in
if not (Sys.file_exists dirname) then
Unix.mkdir dirname 0o755;
*)
!Ezfio.ezfio_filename
)

2
ocaml/Random_variable.ml
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@ -686,7 +686,7 @@ let compress_files () =
Filename.concat "qmc" rand_num
in
try
Unix.mkdir tmp_dir 0o600;
Unix.mkdir tmp_dir 0o755;
tmp_dir
with _ -> raise (Sys_error "Cannot create temp dir")
in

25
ocaml/Watchdog.ml
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@ -1,16 +1,16 @@
let _list = ref [] ;;
let _running = ref false;;
let _threads = ref [] ;;
let _list = ref []
let _running = ref false
let _threads = ref []
(** Kill the current process and all children *)
let kill () =
let kill pid =
Unix.kill pid Sys.sigint;
Unix.kill pid Sys.sigkill;
Printf.printf "Killed %d\n%!" pid
in
List.iter kill (!_list);
exit 1
;;
(** Start watchdog *)
@ -50,7 +50,7 @@ let start () =
in
_threads := ( (Thread.create f) () ) :: (!_threads)
end
;;
(** Stop watchdog *)
let stop () =
@ -58,14 +58,14 @@ let stop () =
_running := false
else
failwith "Watchdog error: Already stopped"
;;
(** Add a PID to tracking *)
let add pid =
if (not !_running) then
start ();
_list := pid :: (!_list)
;;
(** Remove a PID from tracking *)
let del pid =
@ -82,14 +82,13 @@ let del pid =
match (!_list) with
| [] -> if (!_running) then stop ()
| _ -> ()
;;
(** Fork and exec a new process *)
let fork_exec ~prog ~args () =
let pid =
match Unix.fork () with
| 0 -> (* Chile process *)
let _ = Unix.execv prog args in 0
| 0 -> Unix.execvp prog args
| pid -> pid
in
@ -111,11 +110,11 @@ let fork_exec ~prog ~args () =
in
_threads := ( (Thread.create f) () ) :: (!_threads);
pid
;;
(** Wait for threads to finish *)
let join () =
(* if (!_running) then stop (); *)
List.iter Thread.join (!_threads);
assert (not !_running)
;;

72
ocaml/qmcchem.ml
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@ -1,36 +1,60 @@
let update_command_line () =
let last = (Array.length Sys.argv) - 2 in
Sys.argv.(0) <- Sys.argv.(0) ^ " " ^ Sys.argv.(1);
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) <- "--"
Sys.argv.(last+1) <- ""
let help () =
Printf.printf "
qmcchem - QMC=Chem command
Usage:
qmcchem [-h] COMMAND
Arguments:
COMMAND QMC=Chem command to run :
[run|edit|stop|result|md5|info|debug]
Options:
-h --help Prints the help message.
Description:
Driver for subcommands.
"
let () =
let open Command_line in
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")
(help (); failwith "Inconsistent command line") ;
match String.trim Sys.argv.(1) with
| "-h" | "--help" ->
begin
help () ;
exit 0
end
| _ ->
begin
let command =
Sys.argv.(1)
in
update_command_line ();
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 ()
| _ -> (help () ; failwith "Inconsistent command line")
end

2
ocaml/qptypes_generator.ml
View File

@ -296,7 +296,7 @@ let input_lines filename =
let create_ezfio_handler () =
let lines =
input_lines "ezfio.ml"
|> List.mapi (fun i l -> if i > 470 then Some l else None)
|> List.mapi (fun i l -> if i > 474 then Some l else None)
|> List.filter (fun x -> x <> None)
|> List.map (fun x ->
match x with

2
scripts/clean.sh
View File

@ -1,7 +1,7 @@
#!/bin/bash
# This script is supposed to run in $QMCCHEM_PATH
ninja -C ocaml clean
make -C ocaml clean
if [[ -d src/IRPF90_temp ]]
then
ninja -C src/IRPF90_temp -t clean

2
scripts/compile_ocaml.sh
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@ -8,4 +8,4 @@ fi
cd ${QMCCHEM_PATH}/ocaml || exit -1
exec ninja -f generated.ninja ${@} || exit -1
exec make

2
src/ezfio_interface.irp.f
View File

@ -52,7 +52,7 @@ data = [ \
]
data_no_set = [\
("mo_basis_mo_tot_num" , "integer" , ""),
("mo_basis_mo_num" , "integer" , ""),
("pseudo_ao_pseudo_grid" , "double precision" , "(ao_num,pseudo_lmax+pseudo_lmax+1,pseudo_lmax-0+1,nucl_num,pseudo_grid_size)"),
("pseudo_mo_pseudo_grid" , "double precision" , "(ao_num,pseudo_lmax+pseudo_lmax+1,pseudo_lmax-0+1,nucl_num,pseudo_grid_size)"),
("pseudo_pseudo_dz_k" , "double precision" , "(nucl_num,pseudo_klocmax)"),

2
src/mo.irp.f
View File

@ -410,7 +410,7 @@ BEGIN_PROVIDER [ integer, mo_tot_num ]
END_DOC
mo_tot_num = -1
call get_mo_basis_mo_tot_num(mo_tot_num)
call get_mo_basis_mo_num(mo_tot_num)
if (mo_tot_num <= 0) then
call abrt(irp_here,'Total number of MOs can''t be <0')
endif