diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/global.patch b/global.patch new file mode 100644 index 0000000..006edb4 --- /dev/null +++ b/global.patch @@ -0,0 +1,378 @@ +diff --git a/scripts/python3/pretel/extract_contour.py b/scripts/python3/pretel/extract_contour.py +index 9572723dc..e4473075d 100644 +--- a/scripts/python3/pretel/extract_contour.py ++++ b/scripts/python3/pretel/extract_contour.py +@@ -2,6 +2,8 @@ + import numpy as np + import matplotlib.path as mpltPath + from data_manip.extraction.telemac_file import TelemacFile ++from utils.progressbar import ProgressBar ++ + + def detecting_boundaries(connectivity_table, npoints): + """ +@@ -17,69 +19,36 @@ def detecting_boundaries(connectivity_table, npoints): + @return bnd_points (np.array of shape (number of boundary points, 1)) a + numpy array wich contains indexes of all boundary points of the mesh + """ ++ # Building adjacency list from connectivity table ++ adjacency_list = {i: [] for i in range(npoints)} ++ for row in connectivity_table: ++ for i in range(3): ++ adjacency_list[row[i]].extend(row[np.arange(3) != i]) ++ + buf = [] + connectivity_bnd_elt = [] + +- div = (npoints - npoints % 10) // 10 +- if div == 0: +- div = 1 +- +- if np.__version__ < '1.19.0': +- import collections +- +- for i in range(npoints): +- if i % div == 0: +- print(i // div * 10, '%') +- +- connectivity_rows = collections.Counter( +- connectivity_table[ +- np.where((connectivity_table[:, 0] == i) +- + (connectivity_table[:, 1] == i) +- + (connectivity_table[:, 2] == i)) +- ].flatten()) +- +- +- temp = np.array( +- list(connectivity_rows.keys()))[np.where( +- np.array(list(connectivity_rows.values())) == 1)].tolist() +- buf.extend(temp) +- +- if temp != []: +- #to handle overconstrained element +- if i in temp: +- temp.remove(i) +- temp.append(i) +- connectivity_bnd_elt.append(temp) +- +- else: +- for i in range(npoints): +- if i % div == 0: +- print(i // div * 10, '%') +- +- connectivity_rows = connectivity_table[ +- np.where((connectivity_table[:, 0] == i) +- + (connectivity_table[:, 1] == i) +- + (connectivity_table[:, 2] == i)) +- ].flatten() +- +- uniq, count = np.unique(connectivity_rows, return_counts=True) +- temp = uniq[np.where(count == 1)].tolist() +- buf.extend(temp) ++ pbar = ProgressBar(npoints) ++ for i in range(npoints): ++ pbar.update(i) ++ # Directly accessing the connections for each point ++ connections = adjacency_list[i] + +- if temp != []: +- #to handle overconstrained element +- if i in temp: +- temp.remove(i) +- temp.append(i) +- connectivity_bnd_elt.append(temp) ++ uniq, count = np.unique(connections, return_counts=True) ++ temp = uniq[count == 1].tolist() ++ buf.extend(temp) + ++ if temp: ++ if i in temp: ++ temp.remove(i) ++ temp.append(i) ++ connectivity_bnd_elt.append(temp) + +- buf = np.array(buf) +- connectivity_bnd_elt = np.array(connectivity_bnd_elt) +- ++ pbar.finish() + bnd_points = np.unique(buf) + +- return connectivity_bnd_elt, bnd_points ++ return np.array(connectivity_bnd_elt), bnd_points ++ + + def detecting_boundaries_with_bnd_file(connectivity_bnd_table, bnd_points): + """ +@@ -215,7 +184,45 @@ def sorting_boundary(tel, first_pt_idx, connectivity_bnd_elt, clockwise=True): + + return bnd + +-def sorting_boundaries(tel, bnd_points, connectivity_bnd_elt): ++def create_shifted_paths(path): ++ """ ++ Duplicate paths across the -180/180 meridian. ++ This allows to find right inside / outside points in sorting_boundary function ++ ++ @param path (mpltPath.Path) a mpltPath.Path object ++ @return left_path (mpltPath.Path) a mpltPath.Path object ++ @return right_path (mpltPath.Path) a mpltPath.Path object ++ """ ++ left_path_vertices = path.vertices.copy() ++ right_path_vertices = path.vertices.copy() ++ ++ # Shift for the left path ++ left_path_vertices[:, 0] = np.where(left_path_vertices[:, 0] >= -50, ++ left_path_vertices[:, 0] - 360, ++ left_path_vertices[:, 0]) ++ # Shift for the right path ++ right_path_vertices[:, 0] = np.where(right_path_vertices[:, 0] < -50, ++ right_path_vertices[:, 0] + 360, ++ right_path_vertices[:, 0]) ++ # -50 because of Eurasia: we don't want to have a path that jumps across the -180/180° ++ # so we choose a meridian that does not touch separate the left from the right part ++ left_path = mpltPath.Path(left_path_vertices) ++ right_path = mpltPath.Path(right_path_vertices) ++ ++ return left_path, right_path ++ ++def has_meridian_crossing(path): ++ """ ++ Check if the path crosses the -180/180 meridian. ++ Returns True if it crosses, False otherwise. ++ """ ++ for point1, point2 in zip(path.vertices[:-1], path.vertices[1:]): ++ if abs(point1[0] - point2[0]) > 180: ++ return True ++ return False ++ ++ ++def sorting_boundaries(tel, bnd_points, connectivity_bnd_elt, global_ = False): + """ + Sort boundaries in the case there is islands and detect + the case of separated domains +@@ -242,7 +249,6 @@ def sorting_boundaries(tel, bnd_points, connectivity_bnd_elt): + first_pt_idx = get_first_point(tel, bnd_points) + boundaries.append(sorting_boundary(tel, first_pt_idx, connectivity_bnd_elt)) + if len(boundaries[0]) - 1 == len(bnd_points): +- print("No islands") + return boundaries, np.array([]), np.array([]) + + left_bnd_elt = connectivity_bnd_elt +@@ -250,6 +256,7 @@ def sorting_boundaries(tel, bnd_points, connectivity_bnd_elt): + + poly = np.column_stack((tel.meshx[boundaries[0]], tel.meshy[boundaries[0]])) + path = mpltPath.Path(poly) ++ + for i in range(len(boundaries[j])): + left_bnd_elt = np.delete(left_bnd_elt, np.where( + (left_bnd_elt[:, 0] == boundaries[0][i]) | +@@ -261,10 +268,23 @@ def sorting_boundaries(tel, bnd_points, connectivity_bnd_elt): + left_pts = np.column_stack((tel.meshx[left_pts_idx], + tel.meshy[left_pts_idx])) + +- left_pts_idx_inside = left_pts_idx[path.contains_points(left_pts)] ++ if global_ and has_meridian_crossing(path): ++ # For inside points: Union of left and right points ++ left_path, right_path = create_shifted_paths(path) ++ left_pts_idx_inside1 = left_pts_idx[left_path.contains_points(left_pts)] ++ left_pts_idx_inside2 = left_pts_idx[right_path.contains_points(left_pts)] ++ left_pts_idx_inside = np.append(left_pts_idx_inside1, left_pts_idx_inside2) ++ ++ # For outside points: Intersection of left and right points ++ left_pts_idx_outside_left = left_pts_idx[~left_path.contains_points(left_pts)] ++ left_pts_idx_outside_right = left_pts_idx[~right_path.contains_points(left_pts)] ++ left_pts_idx_outside = np.intersect1d(left_pts_idx_outside_left, left_pts_idx_outside_right) ++ else: ++ left_pts_idx_inside = left_pts_idx[ ++ path.contains_points(left_pts)] ++ left_pts_idx_outside = left_pts_idx[ ++ np.invert(path.contains_points(left_pts))] + +- left_pts_idx_outside = left_pts_idx[ +- np.invert(path.contains_points(left_pts))] + if left_pts_idx_outside.size > 0: + left_bnd_elt_outside = left_bnd_elt[ + np.where(left_bnd_elt[:, 2] == left_pts_idx_outside)] +@@ -298,11 +318,8 @@ def sorting_boundaries(tel, bnd_points, connectivity_bnd_elt): + left_pts_idx_inside = left_bnd_elt_inside[:, 2] + + +- +- + return boundaries, left_pts_idx_outside, left_bnd_elt_outside + +- print("No Islands") + + return boundaries, left_pts_idx_outside, left_bnd_elt_outside + +diff --git a/scripts/python3/pretel/generate_atm.py b/scripts/python3/pretel/generate_atm.py +index 4a77bc00b..cf4e7261e 100644 +--- a/scripts/python3/pretel/generate_atm.py ++++ b/scripts/python3/pretel/generate_atm.py +@@ -30,8 +30,9 @@ from utils.exceptions import TelemacException + from data_manip.conversion.convert_utm import to_latlon + from data_manip.formats.selafin import Selafin + from data_manip.extraction.parser_selafin import \ +- subset_variables_slf, get_value_history_slf ++ subset_variables_slf + from pretel.meshes import xys_locate_mesh ++from utils.geometry import get_weights, interp + + # _____ ________________________________________________ + # ____/ MAIN CALL /_______________________________________________/ +@@ -77,7 +78,6 @@ def generate_atm(geo_file, slf_file, atm_file, ll2utm): + 'seem to exist: {}\n\n'.format(geo_file)) + + # Find corresponding (x,y) in corresponding new mesh +- print(' +> getting hold of the GEO file') + geo = Selafin(geo_file) + if ll2utm is not None: + zone = int(ll2utm[:-1]) +@@ -98,7 +98,6 @@ def generate_atm(geo_file, slf_file, atm_file, ll2utm): + slf.set_kd_tree() + slf.set_mpl_tri() + +- print(' +> support extraction') + # Extract triangles and weights in 2D + support2d = [] + ibar = 0 +@@ -153,7 +152,6 @@ def generate_atm(geo_file, slf_file, atm_file, ll2utm): + atm.npoin3 = geo.npoin2*atm.nplan + atm.nelem2 = geo.nelem2 + +- print(' +> setting connectivity') + if atm.nplan > 1: + atm.nelem3 = geo.nelem2*(atm.nplan-1) + atm.ikle2 = geo.ikle2 +@@ -181,7 +179,9 @@ def generate_atm(geo_file, slf_file, atm_file, ll2utm): + atm.meshx = geo.meshx + atm.meshy = geo.meshy + +- print(' +> writing header') ++ in_xy = np.vstack((slf.meshx,slf.meshy)).T ++ out_xy = np.vstack((atm.meshx,atm.meshy)).T ++ vert, wgts, u_x, g_x = get_weights(in_xy, out_xy) + # Write header + atm.datetime = slf.datetime + atm.append_header_slf() +@@ -189,7 +189,6 @@ def generate_atm(geo_file, slf_file, atm_file, ll2utm): + # <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + # ~~~~ writes ATM core ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- print(' +> setting variables') + # TIME and DATE extraction + atm.tags['times'] = slf.tags['times'] + # VARIABLE extraction +@@ -199,10 +198,10 @@ def generate_atm(geo_file, slf_file, atm_file, ll2utm): + # Read / Write data, one time step at a time to support large files + pbar = ProgressBar(maxval=len(slf.tags['times'])).start() + for time in range(len(slf.tags['times'])): +- +- data = get_value_history_slf(slf.file, slf.tags, [time], support3d, +- slf.nvar, slf.npoin3, slf.nplan, vrs) +- # special cases ? ++ tmp = slf.get_values(time) ++ data = [] ++ for i, v in zip(*vrs): ++ data = np.append(data,[interp(tmp[i], vert, wgts, u_x, g_x)]) + atm.append_core_time_slf(time) + atm.append_core_vars_slf(np.reshape(np.transpose(\ + np.reshape(np.ravel(data), +diff --git a/scripts/python3/utils/geometry.py b/scripts/python3/utils/geometry.py +index bb1a8abb4..c9b04c245 100644 +--- a/scripts/python3/utils/geometry.py ++++ b/scripts/python3/utils/geometry.py +@@ -32,6 +32,8 @@ r""" + # ~~> dependencies towards standard python + import math + import numpy as np ++from scipy.spatial import Delaunay ++from scipy.spatial import cKDTree + + # _____ __________________________________________ + # ____/ Global Variables /_________________________________________/ +@@ -41,6 +43,66 @@ import numpy as np + # ____/ General Toolbox /__________________________________________/ + # + ++def get_weights(in_xy, out_xy, d = 2): ++ """ ++ Triangulate an output mesh based on a set of input points and return the ++ corresponding barycentric weights. ++ ++ Parameters ++ ---------- ++ @param in_xy (np.ndarray): Nx2 array of input point coordinates. ++ @param out_xy (np.ndarray): Nx2 array of output point coordinates. ++ @param d (int): Dimension of the input points, by default 2. ++ ++ @returns (4-uple): (vert, wgts, out_idx_out, in_idx_out), with: ++ vert (np.ndarray): Nx3 array of triangle vertices. ++ wgts (np.ndarray): Nx3 array of barycentric weights. ++ out_idx_out (np.ndarray): Boolean array indicating which points ++ are outside the input mesh. ++ in_idx_out (np.ndarray): Index array of the nearest input points ++ for points outside the input mesh. ++ ++ """ ++ t = Delaunay(in_xy) # triangulate output mesh ++ s = t.find_simplex(out_xy) ++ vert = np.take(t.simplices, np.maximum(s, 0), axis=0) # Use max to avoid negative indices ++ t_ = np.take(t.transform, np.maximum(s, 0), axis=0) ++ delta = out_xy - t_[:, d] ++ bary = np.einsum('njk,nk->nj', t_[:, :d, :], delta) ++ wgts = np.hstack((bary, 1 - bary.sum(axis=1, keepdims=True))) ++ # Points outside the out_xy ++ out_idx_out = s < 0 ++ if np.any(out_idx_out): ++ # For points outside, find nearest neighbors ++ tree = cKDTree(in_xy) ++ _, in_idx_out = tree.query(out_xy[out_idx_out]) ++ else : ++ in_idx_out = None ++ return vert, wgts, out_idx_out, in_idx_out ++ ++ ++def interp(values, vtx, wts, out_idx_out, in_idx_out): ++ """ ++ Interpolate values using barycentric coordinates and weights ++ ++ Parameters ++ ---------- ++ @param values (np.ndarray): Array of values to be interpolated. ++ @param vtx (np.ndarray): Array of vertex indices. ++ @param wts (np.ndarray): Array of barycentric weights. ++ @param out_idx_out (np.ndarray): Boolean array indicating which points ++ are outside the input mesh. ++ @param in_idx_out (np.ndarray): Index array of the nearest input points ++ for points outside the input mesh. ++ ++ @return (np.ndarray): Interpolated values ++ ++ """ ++ res = np.einsum('nj,nj->n', np.take(values, vtx), wts) ++ if in_idx_out is not None: ++ res[out_idx_out] = values[in_idx_out] ++ return res ++ + + def is_ccw(t_1, t_2, t_3): + """@brief Checks if the element is conterclockwise oriented or not +diff --git a/sources/utils/partel/partel.F b/sources/utils/partel/partel.F +index b6c0ab0c0..6f276802e 100644 +--- a/sources/utils/partel/partel.F ++++ b/sources/utils/partel/partel.F +@@ -637,6 +637,13 @@ + CALL HASH_TABLE_INSERT(GELEGL,EF,I,NELEM_P(I)) + ENDIF + ENDDO ++! ++ DO I = 1, NPOIN ++ IRAND(I) = 0 ++ ENDDO ++ DO I = 1, NPTFR ++ IRAND(NBOR(I)) = 1 ++ ENDDO! + ! + CALL COMPUTE_BOUNDARY_AND_INTERFACE(NPARTS,NDP_2D,NPOIN_P, + & NPTFR_P, ELELG, diff --git a/matrix_build.sh b/matrix_build.sh index 1676306..927e8c7 100755 --- a/matrix_build.sh +++ b/matrix_build.sh @@ -1,23 +1,33 @@ # Define your matrices -python_versions=("3.8" "3.9" "3.10" "3.11" "3.12") +python_versions=("3.8" "3.9" "3.10" "3.11") numpy_versions=("1.19" "1.20" "1.21" "1.22" "1.23" "1.24" "1.25" "1.26") -mpi_versions=("openmpi" ) - -# File to store the build results +mpi_types=("openmpi" "mpich") +openmpi_versions=("4.1.2" "4.1.3" "4.1.4" "4.1.5" "4.1.6" "5.0.0" "5.0.1") +mpich_versions=("4.0.2" "4.0.3" "4.1.2" "4.2.0" "5.0.1") results_file="build_results.txt" # Loop over each configuration for py in "${python_versions[@]}"; do for np in "${numpy_versions[@]}"; do - for mpi in "${mpi_versions[@]}"; do - echo "Building for Python $py, NumPy $np, and MPI $mpi" - # Run conda build and check the result - if conda build recipe --variants="{mpi: '$mpi', python: '$py', numpy: '$np'}" -c tomsail; then - # If build succeeds - echo "SUCCESS: Python $py, NumPy $np, MPI $mpi" >> "$results_file" - else - # If build fails - echo "FAIL: Python $py, NumPy $np, MPI $mpi" >> "$results_file" + for mpi in "${mpi_types[@]}"; do + if [ "$mpi" == "openmpi" ]; then + for mpi_version in "${openmpi_versions[@]}"; do + echo "Building for Python $py, NumPy $np, MPI $mpi $mpi_version" + if conda build recipe --variants="{mpi: '$mpi', mpi_ver: '$mpi_version', python: '$py', numpy: '$np'}" -c tomsail; then + echo "SUCCESS: Python $py, NumPy $np, MPI $mpi $mpi_version" >> "$results_file" + else + echo "FAIL: Python $py, NumPy $np, MPI $mpi $mpi_version" >> "$results_file" + fi + done + elif [ "$mpi" == "mpich" ]; then + for mpi_version in "${mpich_versions[@]}"; do + echo "Building for Python $py, NumPy $np, MPI $mpi $mpi_version" + if conda build recipe --variants="{mpi: '$mpi', mpi_ver: '$mpi_version', python: '$py', numpy: '$np'}" -c tomsail; then + echo "SUCCESS: Python $py, NumPy $np, MPI $mpi $mpi_version" >> "$results_file" + else + echo "FAIL: Python $py, NumPy $np, MPI $mpi $mpi_version" >> "$results_file" + fi + done fi done done diff --git a/recipe/configs/systel.linux.cfg b/recipe/configs/systel.linux.cfg index cba6cd6..4ebb605 100644 --- a/recipe/configs/systel.linux.cfg +++ b/recipe/configs/systel.linux.cfg @@ -6,7 +6,8 @@ # ____/ TELEMAC Project Definitions /______________________________/ # [Configurations] -configs: gnu.dynamic gnu.dynamic.debug +configs: gnu.dynamic # not using debug +# configs: gnu.dynamic gnu.dynamic.debug # _____ ____________________________________ # ____/ General /___________________________________/ # Global declaration used for all configurations diff --git a/recipe/fix981.patch b/recipe/fix981.patch new file mode 100644 index 0000000..5fb513b --- /dev/null +++ b/recipe/fix981.patch @@ -0,0 +1,53 @@ +diff --git a/documentation/telemac2d/user/latex/chap6.tex b/documentation/telemac2d/user/latex/chap6.tex +index b99003eb0..482512b08 100644 +--- a/documentation/telemac2d/user/latex/chap6.tex ++++ b/documentation/telemac2d/user/latex/chap6.tex +@@ -458,7 +458,8 @@ common with \waqtel, see \waqtel user manual) are among WINDX, WINDY, WINDS, + WINDD, PATM, TAIR. + The name of the variables can be changed in the + \telkey{BINARY ATMOSPHERIC DATA FILE} by running:\\ +-run\_telfile.py alter --rename 'old name var=new name var' name\_bin\_meteo\_file \\ ++run\_telfile.py alter --rename 'old name var=new name var' ++name\_bin\_meteo\_file\_old name\_bin\_meteo\_file\_new \\ + one variable by one variable e.g. + Reference times are to be added in the keywords + \telkey{ORIGINAL DATE OF TIME} and \telkey{ORIGINAL HOUR OF TIME} +diff --git a/documentation/telemac3d/user/latex/physical_setup.tex b/documentation/telemac3d/user/latex/physical_setup.tex +index cc298e702..0cadf2926 100644 +--- a/documentation/telemac3d/user/latex/physical_setup.tex ++++ b/documentation/telemac3d/user/latex/physical_setup.tex +@@ -532,7 +532,8 @@ common with \waqtel, see \waqtel user manual) are among WINDX, WINDY, WINDS, + WINDD, PATM, TAIR. + The name of the variables can be changed in the + \telkey{BINARY ATMOSPHERIC DATA FILE} by running:\\ +-run\_telfile.py alter --rename 'old name var=new name var' name\_bin\_meteo\_file \\ ++run\_telfile.py alter --rename 'old name var=new name var' ++name\_bin\_meteo\_file\_old name\_bin\_meteo\_file\_new \\ + one variable by one variable e.g. + Reference times are to be added in the keywords + \telkey{ORIGINAL DATE OF TIME} and \telkey{ORIGINAL HOUR OF TIME} +diff --git a/scripts/python3/pretel/generate_atm.py b/scripts/python3/pretel/generate_atm.py +index 4a77bc00b..2370701aa 100644 +--- a/scripts/python3/pretel/generate_atm.py ++++ b/scripts/python3/pretel/generate_atm.py +@@ -126,14 +126,14 @@ def generate_atm(geo_file, slf_file, atm_file, ll2utm): + atm.title = '' + atm.varnames = [] + atm.varunits = [] +- if 'WIND VELOCITY U ' in slf.varnames: +- atm.varnames.append('WIND VELOCITY U ') ++ if ('WIND VELOCITY U ' in slf.varnames) or ('WINDX ' in slf.varnames): ++ atm.varnames.append('WINDX ') + atm.varunits.append('M/S ') +- if 'WIND VELOCITY V ' in slf.varnames: +- atm.varnames.append('WIND VELOCITY V ') ++ if ('WIND VELOCITY V ' in slf.varnames) or ('WINDY ' in slf.varnames): ++ atm.varnames.append('WINDY ') + atm.varunits.append('M/S ') +- if 'SURFACE PRESSURE' in slf.varnames: +- atm.varnames.append('SURFACE PRESSURE') ++ if 'PATM ' in slf.varnames: ++ atm.varnames.append('PATM ') + atm.varunits.append('UI ') + if 'AIR TEMPERATURE ' in slf.varnames: + atm.varnames.append('AIR TEMPERATURE ') diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 5b9877f..c3c964e 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -3,7 +3,8 @@ {% set build = 0 %} {% set python = python or '3.10' %} # Default to 3.10 if not specified {% set numpy = numpy or '1.21' %} # Default to 1.21 if not specified -{% set mpi = "openmpi" %} # Default to "openmpi" if not specified +{% set mpi = mpi or "openmpi" %} # Default to "openmpi" if not specified +{% set mpi_ver = mpi_ver or "4.1.6" %} # Default version if not specified package: name: {{ name|lower }} @@ -15,9 +16,10 @@ source: sha256: 45468b850c8271c21f7d6ef7017945c297dfc3b670c3cde706d71124189d6396 patches: - global.patch + - fix981.patch build: - {% set mpi_prefix = "mpi_" + mpi %} + {% set mpi_prefix = mpi + "_" + mpi_ver %} {% set py_prefix = "py_" + python %} {% set np_prefix = "np_" + numpy %} string: {{ mpi_prefix }}_{{ py_prefix }}_{{ np_prefix }}_{{ build }} @@ -29,15 +31,17 @@ build: - "*/notebooks/*" outputs: - - name: {{ name }}-examples - build: - script: "%RECIPE_DIR%/build-examples.bat" # [win] - script: "$RECIPE_DIR/build-examples.sh" # [not win] + ## we only need to build exemples and docs once # # # # # # # # + # - name: {{ name }}-examples + # build: + # script: "%RECIPE_DIR%/build-examples.bat" # [win] + # script: "$RECIPE_DIR/build-examples.sh" # [not win] - - name: {{ name }}-documentation - build: - script: "%RECIPE_DIR%/build-documentation.bat" # [win] - script: "$RECIPE_DIR/build-documentation.sh" # [not win] + # - name: {{ name }}-documentation + # build: + # script: "%RECIPE_DIR%/build-documentation.bat" # [win] + # script: "$RECIPE_DIR/build-documentation.sh" # [not win] + ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # - name: {{ name }} requirements: @@ -52,7 +56,7 @@ outputs: - scalapack-otm # [win] # Linux / MacOS - {{ compiler('fortran') }} # [not win] - - {{ mpi }} # [not win] + - {{ mpi }} {{ mpi_ver }} # [not win] - {{ mpi }}-mpifort # [not win] - {{ compiler('gcc') }} # [not win] - {{ compiler('gxx') }} # [not win] @@ -83,7 +87,7 @@ outputs: - scalapack-otm # [win] # Linux / MacOS - {{ compiler('fortran') }} # [not win] - - {{ mpi }} # [not win] + - {{ mpi }} {{ mpi_ver }} # [not win] - {{ mpi }}-mpifort # [not win] - {{ compiler('gcc') }} # [not win] - {{ compiler('gxx') }} # [not win] diff --git a/recipe/scripts/activate.sh b/recipe/scripts/activate.sh index 78782f2..5305f00 100644 --- a/recipe/scripts/activate.sh +++ b/recipe/scripts/activate.sh @@ -1,6 +1,21 @@ # Path to telemac root dir export HOMETEL=$CONDA_PREFIX/opentelemac -# Adding python scripts to PATH + +# Backup original environment variables if not already done +if [[ -z "${OLD_PATH}" ]]; then + export OLD_PATH="${PATH}" +fi +if [[ -z "${OLD_PYTHONPATH}" ]]; then + export OLD_PYTHONPATH="${PYTHONPATH}" +fi +if [[ -z "${OLD_LD_LIBRARY_PATH}" ]]; then + export OLD_LD_LIBRARY_PATH="${LD_LIBRARY_PATH}" +fi + +# Optional: Echo the variables to ensure they are correctly restored +echo "Stored PATH: ${OLD_PATH}" +echo "Stored PYTHONPATH: ${OLD_PYTHONPATH}" +echo "Stored LD_LIBRARY_PATH: ${OLD_LD_LIBRARY_PATH}" # Configuration file if [[ $(uname) == Linux ]]; then export SYSTELCFG=$HOMETEL/configs/systel.cfg @@ -12,13 +27,12 @@ elif [[ $(uname) == Darwin ]]; then # Name of the configuration to use export USETELCFG=gfort-mpich fi -### Python -# To force python to flush its output + +# Adding python scripts and TELEMAC libs to PATH/LD_LIBRARY_PATH export PATH=$HOMETEL/scripts/python3:$PATH -export PYTHONPATH=$HOMETEL/scripts/python3 +export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH export PYTHONPATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$PYTHONPATH -export LD_LIBRARY_PATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$HOMETEL/builds/$USETELCFG/lib:$CONDA_PREFIX/lib -export PYTHONUNBUFFERED='true' +export LD_LIBRARY_PATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$HOMETEL/builds/$USETELCFG/lib:$LD_LIBRARY_PATH telemac-debug() { if [[ "$1" == "on" ]]; then diff --git a/recipe/scripts/deactivate.sh b/recipe/scripts/deactivate.sh index c024354..eab96d1 100644 --- a/recipe/scripts/deactivate.sh +++ b/recipe/scripts/deactivate.sh @@ -1,6 +1,17 @@ -unset HOMETEL -unset SYSTELCFG -unset USETELCFG -unset PYTHONUNBUFFERED -unset PYTHONPATH -unset LD_LIBRARY_PATH \ No newline at end of file +# Restore the original environment variables +export PATH="${OLD_PATH}" +export PYTHONPATH="${OLD_PYTHONPATH}" +export LD_LIBRARY_PATH="${OLD_LD_LIBRARY_PATH}" + +# Clear the backup variables +unset OLD_PATH +unset OLD_PYTHONPATH +unset OLD_LD_LIBRARY_PATH + +# $CONDA_PREFIX/bin remains in OLD_PATH and needs to be manually removed +export PATH=$(echo "$PATH" | sed "s|:$CONDA_PREFIX/bin||g; s|^$CONDA_PREFIX/bin:||g; s|:$CONDA_PREFIX/bin:|:|g") +# Optional: Echo the variables to ensure they are correctly restored +echo "Restored PATH: ${PATH}" +echo "Removed ${CONDA_PREFIX}/bin from PATH" +echo "Restored PYTHONPATH: ${PYTHONPATH}" +echo "Restored LD_LIBRARY_PATH: ${LD_LIBRARY_PATH}"