olympe: compil pyscf interface with ifort

.gitignore

@@ -1,3 +1,8 @@
 *.o
 *.
 *.so
+*.mod
+*.slurm
+__pycache__
+int/
+.ninja_deps

config/env.sh

@@ -0,0 +1,24 @@
+#!/bin/env
+
+CURRENT_HOSTNAME=$(hostname)
+echo "Current machine: $CURRENT_HOSTNAME"
+
+export QUACK_ROOT=/users/p18005/ammar/tmpdir/QuAcK
+
+case $CURRENT_HOSTNAME in
+        *turpan*)
+        ;;
+        *olympe*)
+		module purge
+		module load python/3.9.5
+		module load intel/18.2.199
+		export PATH=$PATH:/users/p18005/ammar/qp2/bin
+		export LD_LIBRARY_PATH=/usr/local/miniconda/4.9.2/envs/python-3.9.5/lib:$LD_LIBRARY_PATH
+		export LD_LIBRARY_PATH=$QUACK_ROOT/lib:$LD_LIBRARY_PATH
+		export PYTHONPATH=$QUACK_ROOT/src/pyscf:$PYTHONPATH
+        ;;
+        *)
+                echo "Unknown hostname: $CURRENT_HOSTNAME. No modules loaded."
+        ;;
+esac
+

src/QuAcK/QuAcK.f90

@@ -1,5 +1,7 @@
 program QuAcK
 
+  use pyscf_module
+
   implicit none
   include 'parameters.h'
 
@@ -68,6 +70,27 @@ program QuAcK
 
   logical                       :: dotest,doRtest,doUtest,doGtest
 
+  ! test pyscf interface
+  character(len = 50) :: xyz, input_basis, unit_type
+  integer :: charge, multiplicity, cartesian
+  integer :: natoms, nalpha, nbeta
+  xyz = '/users/p18005/ammar/tmpdir/QuAcK/mol/H2O.xyz' // c_null_char
+  input_basis = 'sto-3g' // c_null_char
+  unit_type = 'Angstrom' // c_null_char
+  charge = 0
+  multiplicity = 1
+  cartesian = 0
+
+  call call_mol_prop(xyz, input_basis, charge, multiplicity, unit_type, cartesian, &
+                     natoms, nalpha, nbeta, Enuc)
+
+  print *, "Number of atoms:", natoms
+  print *, "Number of alpha electrons:", nalpha
+  print *, "Number of beta electrons:", nbeta
+  print *, "Nuclear energy:", Enuc
+  stop
+
+
 !-------------!
 ! Hello World !
 !-------------!
@@ -130,7 +153,8 @@ program QuAcK
 ! nBas = number of basis functions (see below)   !
 !------------------------------------------------!
 
-  call read_molecule(nNuc,nO,nC,nR)
+  call read_molecule(nNuc, nO, nC, nR)
+
   allocate(ZNuc(nNuc),rNuc(nNuc,ncart))
 
 ! Read geometry

src/make_ninja.py

@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 import os
 import sys
+import subprocess
+
 
 DEBUG=False
 try:
@@ -46,7 +48,7 @@ FIX_ORDER_OF_LIBS=-Wl,--start-group
     compile_ifort_linux = """
 FC = ifort -mkl=parallel -qopenmp
 AR = ar crs
-FFLAGS = -I$IDIR -g -Ofast -traceback
+FFLAGS = -I$IDIR -module $IDIR -g -Ofast -traceback
 CC = icc
 CXX = icpc
 LAPACK=
@@ -79,7 +81,7 @@ FIX_ORDER_OF_LIBS=-Wl,--start-group
 compile_olympe = """
 FC = ifort -mkl=parallel -qopenmp
 AR = ar crs
-FFLAGS = -I$IDIR -Ofast -traceback -xCORE-AVX512
+FFLAGS = -I$IDIR -module $IDIR -Ofast -traceback -xCORE-AVX512
 CC = icc
 CXX = icpc
 LAPACK=
@@ -119,13 +121,25 @@ rule fc
 
 """
 
-rule_build_so = """
+rule_cctoso = """
-rule build_so
+rule cctoso
-  command = $AR $out $in 
+  command = $CC $CFLAGS $PYINC $in -o $out $LDFLAGS $PYLDF
-  description = Linking $out
 
 """
 
+def rule_cctoso_flags():
+
+    PYTHON_VERSION = "{}.{}".format(sys.version_info.major, sys.version_info.minor)
+    PYINC = subprocess.run(['python{}-config'.format(PYTHON_VERSION), '--includes'], stdout=subprocess.PIPE, text=True)
+    PYLDF = subprocess.run(['python{}-config'.format(PYTHON_VERSION), '--ldflags'], stdout=subprocess.PIPE, text=True)
+
+    return """
+LDFLAGS = -shared -fPIC -L$LDIR -Wl,-rpath=$LDIR
+PYINC = {}
+PYLDF = {} -lpython{}
+        
+""".format(PYINC.stdout.strip(), PYLDF.stdout.strip(), PYTHON_VERSION)
+
 rule_build_lib = """
 rule build_lib
   command = $AR $out $in 
@@ -137,7 +151,7 @@ rule_build_exe = """
 LIBS = {0} $LAPACK $STDCXX
 
 rule build_exe
-  command = $FC $FIX_ORDER_OF_LIBS $in $LIBS -o $out
+  command = $FC $FFLAGS $FIX_ORDER_OF_LIBS $PYINC $in $LIBS -o $out -L$LDIR -lpyscf_wrapper $PYLDF
   pool = console
   description = Linking $out
 
@@ -156,11 +170,12 @@ rule git_clone
 
 """
 
-build_in_so_dir = "\n".join([
+build_in_py_dir = "\n".join([
 	header,
 	compiler,
+        rule_cctoso_flags(),
+	rule_cctoso,
 	rule_fortran,
-	rule_build_so,
 ])
 
 build_in_lib_dir = "\n".join([
@@ -174,6 +189,7 @@ build_in_lib_dir = "\n".join([
 build_in_exe_dir = "\n".join([
 	header,
 	compiler,
+        rule_cctoso_flags(),
 	rule_fortran,
 	rule_build_exe,
 ])
@@ -193,40 +209,14 @@ lib_dirs = list(filter(lambda x: os.path.isdir(x) and \
 
 def create_makefile_in_pydir(directory):
 
-    PYTHON_VERSION = "{}.{}".format(sys.version_info.major, sys.version_info.minor)
-    CC = "gcc"
-    CCFLAGS = "$(shell python$(PYTHON_VERSION)-config --includes)"
-    LDFLAGS = "-shared -fPIC -L$(LDIR) -Wl,-rpath=$(LDIR) $(shell python$(PYTHON_VERSION)-config --ldflags)"
-
     lib_pydir = "lib{}_wrapper.so".format(directory)
     c_pydir = "{}_wrapper.c".format(directory)
+    with open(os.path.join(directory, "build.ninja"), "w") as f:
+        f.write(build_in_py_dir)
+        f.write("build $LDIR/{}: cctoso {}\n\n".format(lib_pydir, c_pydir))
+        f.write("build {}_module.o: fc {}_module.f90\n".format(directory, directory))
 
-    with open(os.path.join(directory, "Makefile"), "w") as f:
-        f.write("# This file was automatically generated. Do not modify this file.\n\n")
 
-        f.write("IDIR = {}/include\n".format(QUACK_ROOT))
-        f.write("LDIR = {}/lib\n".format(QUACK_ROOT))
-        f.write("BDIR = {}/bin\n".format(QUACK_ROOT))
-        f.write("SDIR = {}/src\n\n".format(QUACK_ROOT))
-
-        f.write("CC = gcc\n")
-        f.write("PYTHON_VERSION = {}\n".format(PYTHON_VERSION))
-        f.write("CCFLAGS = {}\n".format(CCFLAGS))
-        f.write("LDFLAGS = {}\n\n".format(LDFLAGS))
-
-        f.write("TARGETS = $(LDIR)/{} {}_module.o\n\n".format(lib_pydir, directory))
-
-        f.write("all: $(TARGETS)\n\n")
-
-        f.write("$(LDIR)/{}: {}\n".format(lib_pydir, c_pydir))
-        f.write("\t$(CC) $(CCFLAGS) {} -o $(LDIR)/{} $(LDFLAGS)\n\n".format(c_pydir, lib_pydir))
-
-        f.write("{}_module.o: {}_module.f90\n".format(directory, directory))
-        f.write("\tgfortran -c {}_module.f90 -o {}_module.o -J.\n\n".format(directory, directory))
-
-        f.write(".PHONY: clean\n")
-        f.write("clean:\n")
-        f.write("\trm -f ../../lib/{} *.mod *.o\n\n".format(lib_pydir))
 
 
 def create_ninja_in_libdir(directory):
@@ -244,8 +234,8 @@ def create_ninja_in_libdir(directory):
                    obj_file = write_rule(f, filename, suffix)
                    objects.append(obj_file)
         objects = " ".join(objects)
-        f.write("build $LDIR/lib{}.a: build_lib {}\n".format(directory, objects))
+        f.write("build $LDIR/{}.a: build_lib {}\n".format(directory, objects))
-        f.write("default $LDIR/lib{}.a\n".format(directory))
+        f.write("default $LDIR/{}.a\n".format(directory))
 
 
 def create_ninja_in_exedir(directory):
@@ -273,6 +263,8 @@ def create_ninja_in_exedir(directory):
 def create_main_ninja():
 
     libs = " ".join([ "$LDIR/{0}.a".format(x) for x in lib_dirs]) + " "+LIBS
+    for py_dir in py_dirs:
+        libs += "$LDIR/lib{0}_wrapper.so".format(py_dir)
     with open("build.ninja","w") as f:
         f.write(build_main)
         f.write("""
@@ -290,6 +282,8 @@ rule build_lib
             sources = [ "$SDIR/{0}/{1}".format(exe_dir,x) for x in  os.listdir(exe_dir) ]
             sources = filter(lambda x: x.endswith(".f") or x.endswith(".f90"), sources)
             sources = " ".join(sources)
+            for py_dir in py_dirs:
+                sources += " $SDIR/{0}/{0}_wrapper.c $SDIR/{0}/{0}_module.f90".format(py_dir)
             f.write("build $BDIR/{0}: build_exe {1} {2}\n".format(exe_dir,libs,sources))
             f.write("  dir = {0} \n".format(exe_dir) )
 
@@ -298,6 +292,10 @@ rule build_lib
             sources = filter(lambda x: x.endswith(".f") or x.endswith(".f90"), sources)
             sources = " ".join(sources)
             f.write("build $LDIR/{0}.a: build_lib {1} \n  dir = $SDIR/{0}\n".format(libname, sources))
+
+        for py_dir in py_dirs:
+            f.write("build $LDIR/lib{0}_wrapper.so: build_lib $SDIR/{0}/{0}_wrapper.c $SDIR/{0}/{0}_module.f90 \n  dir = $SDIR/{0}\n".format(py_dir))
+
         f.write("build all: phony $BDIR/QuAcK\n")
         f.write("default all\n")
 
@@ -318,6 +316,7 @@ debug:
 def main():
     for py_dir in py_dirs:
        create_makefile_in_pydir(py_dir)
+       create_makefile(py_dir)
 
     for lib_dir in lib_dirs:
        create_ninja_in_libdir(lib_dir)

src/pyscf/pyscf_module.py

@@ -1,11 +1,14 @@
 
+import warnings
+warnings.filterwarnings("ignore", category=UserWarning, module="numpy.core.getlimits")
 import numpy as np
 from pyscf import gto
 
 
+
 def read_xyz(xyz):
 
-    f = open(xyz + '.xyz', 'r')
+    f = open(xyz, 'r')
 
     lines = f.read().splitlines()
 

src/pyscf/pyscf_wrapper.c

@@ -1,5 +1,8 @@
 #include <Python.h>
 #include <stdio.h>
+#include <limits.h>
+#include <unistd.h>
+#include <string.h>
 
 
 void call_mol_prop(const char *xyz, const char *input_basis, int charge, int multiplicity, 
@@ -13,12 +16,27 @@ void call_mol_prop(const char *xyz, const char *input_basis, int charge, int mul
     // Initialize the Python interpreter
     Py_Initialize();
 
-    printf("Python version: %s\n", Py_GetVersion());
+    //printf("Python version: %s\n", Py_GetVersion());
+    //printf("xyz: %s\n", xyz);
+    //printf("input_basis: %s\n", input_basis);
+    //printf("charge: %d\n", charge);
+    //printf("multiplicity: %d\n", multiplicity);
+    //printf("unit: %s\n", unit);
+    //printf("cartesian: %d\n", cartesian);
 
-    PyRun_SimpleString("import sys");
+    char exe_path[PATH_MAX];
-    PyRun_SimpleString("sys.path.append('.')");
+    ssize_t len = readlink("/proc/self/exe", exe_path, sizeof(exe_path) - 1);
-
+    if (len != -1) {
-    // Import the Python module
+        exe_path[len] = '\0'; // Null-terminate the string
+        dirname(exe_path); // Get directory part
+        char sys_path_command[PATH_MAX + 30];
+        snprintf(sys_path_command, sizeof(sys_path_command), "sys.path.append('%s')", exe_path);
+        PyRun_SimpleString("import sys");
+        PyRun_SimpleString(sys_path_command);
+    } else {
+        PyRun_SimpleString("import sys");
+        PyRun_SimpleString("sys.path.append('.')");
+    }
     pName = PyUnicode_DecodeFSDefault("pyscf_module");
     pModule = PyImport_Import(pName);
     Py_XDECREF(pName);

src/pyscf/test_python_call.f90

@@ -8,16 +8,19 @@ program test_python_call
     integer :: natoms, nalpha, nbeta
     double precision :: Enuc
 
-    xyz = "../../mol/H2O"
+    xyz = '/users/p18005/ammar/tmpdir/QuAcK/mol/H2O.xyz' // C_NULL_CHAR
-    input_basis = "sto-3g"
+    input_basis = 'sto-3g' // C_NULL_CHAR
     charge = 0
     multiplicity = 1
-    unit_type = "Angstrom"
+    unit_type = 'Angstrom' // C_NULL_CHAR
     cartesian = 0
 
-    call call_mol_prop(trim(adjustl(xyz)), trim(adjustl(input_basis)), charge, multiplicity, trim(adjustl(unit_type)), cartesian, &
+    call call_mol_prop(xyz, input_basis, charge, multiplicity, unit_type, cartesian, &
                        natoms, nalpha, nbeta, Enuc)
 
+    !call call_mol_prop(trim(adjustl(xyz)), trim(adjustl(input_basis)), charge, multiplicity, trim(adjustl(unit_type)), cartesian, &
+    !                   natoms, nalpha, nbeta, Enuc)
+
     print *, "Number of atoms:", natoms
     print *, "Number of alpha electrons:", nalpha
     print *, "Number of beta electrons:", nbeta