science/neko: New port: Framework for high-order spectral element flow simulations

8 files changed, 864 insertions, 0 deletions

diff --git a/science/Makefile b/science/Makefile
index 0b3aa4567874..cf0c3d2e9269 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -205,6 +205,7 @@
     SUBDIR += mutationpp
     SUBDIR += namd
     SUBDIR += ncrystal
+    SUBDIR += neko
     SUBDIR += nest
     SUBDIR += netcdf
     SUBDIR += netcdf-cxx
diff --git a/science/neko/Makefile b/science/neko/Makefile
new file mode 100644
index 000000000000..142120520018
--- /dev/null
+++ b/science/neko/Makefile
@@ -0,0 +1,48 @@
+PORTNAME=	neko
+DISTVERSION=	1.0.3
+CATEGORIES=	science
+MASTER_SITES=	https://github.com/ExtremeFLOW/neko/releases/download/v${DISTVERSION}/
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Framework for high-order spectral element flow simulations
+WWW=		https://neko.cfd/ \
+		https://github.com/ExtremeFLOW/neko
+
+LICENSE=	BSD3CLAUSE
+LICENSE_FILE=	${WRKSRC}/COPYING
+
+LIB_DEPENDS=	libjsonfortran.so:devel/json-fortran \
+		libopenblas.so:math/openblas
+TEST_DEPENDS=	bash:shells/bash \
+		${PYTHON_PKGNAMEPREFIX}pytest>=0:devel/py-pytest@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numpy>=0:math/py-numpy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}json5>=0:devel/py-json5@${PY_FLAVOR}
+
+USES=		fortran gmake libtool mpi:mpich pkgconfig python:test shebangfix
+
+SHEBANG_GLOB=	*.sh
+
+GNU_CONFIGURE=	yes
+
+BINARY_ALIAS=	python=${PYTHON_CMD}
+
+do-test:
+	@${MKDIR} ${WRKSRC}/contrib/neko_log_parser
+	@${CP} ${FILESDIR}/neko_log_parser.py ${WRKSRC}/contrib/neko_log_parser/
+	@${CHMOD} +x ${WRKSRC}/makeneko
+	@${REINPLACE_CMD} -e 's|^prefix=.*|prefix=${WRKSRC}|' \
+		-e 's|^includedir_pkg=.*|includedir_pkg=${WRKSRC}/src|' \
+		-e 's|^libdir=.*|libdir=${WRKSRC}/src/.libs|' \
+		${WRKSRC}/makeneko ${WRKSRC}/neko.pc
+	@cd ${WRKSRC}/tests/integration && ${SETENV} ${TEST_ENV} \
+		PKG_CONFIG_PATH=${WRKSRC} \
+		NEKO_EXEC=${WRKSRC}/src/neko \
+		MAKENEKO_EXEC=${WRKSRC}/makeneko \
+		PYTHONNOUSERSITE=1 \
+		${PYTHON_CMD} -m pytest -p no:xdist -p no:parallel \
+		--launcher-script=${WRKSRC}/tests/integration/default_cpu_launcher.sh \
+		tests
+
+# tests as of 1..3: 14 passed in 38.37s
+
+.include <bsd.port.mk>
diff --git a/science/neko/distinfo b/science/neko/distinfo
new file mode 100644
index 000000000000..ae06a4291a86
--- /dev/null
+++ b/science/neko/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1778249730
+SHA256 (neko-1.0.3.tar.gz) = 29f01e671c4eccc919ed4e3cb912d0b0d1345d73a5c66f2c237ca342ac35e61b
+SIZE (neko-1.0.3.tar.gz) = 14517977
diff --git a/science/neko/files/neko_log_parser.py b/science/neko/files/neko_log_parser.py
new file mode 100644
index 000000000000..06afc506347f
--- /dev/null
+++ b/science/neko/files/neko_log_parser.py
@@ -0,0 +1,192 @@
+import re
+import argparse
+from pprint import pprint
+import json
+import os
+
+
+def parse_neko_log(log_lines):
+    data = {}
+    step_data = {}
+    current_step = None
+
+    for line in log_lines:
+        # Step and time value
+        step_match = re.match(r"\s*Step\s*=\s*(\d+)\s*t\s*=\s*([\d.Ee+-]+)", line)
+
+        # CFL and dt
+        cfl_match = re.match(r"\s*CFL:\s*([\d.Ee+-]+)\s+dt:\s*([\d.Ee+-]+)", line)
+
+        # Field residuals
+        field_match = re.match(
+            r"\s*(\d+)\s+\|\s+(\S+)\s+(\d+)\s+([\d.Ee+-]+)\s+([\d.Ee+-]+)", line
+        )
+
+        # Total time for step
+        total_step_time_match = re.match(
+            r"\s*Total time for step\s+\d+\s+\(s\):\s+([\d.Ee+-]+)", line
+        )
+
+        if step_match:
+            if current_step is not None:
+                data[current_step] = step_data
+            current_step = int(step_match.group(1))
+            time_value = float(step_match.group(2))
+            step_data = {
+                "time": time_value,
+                "CFL": None,
+                "dt": None,
+                "total_step_time": None,
+                "fields": {},
+            }
+
+        elif cfl_match and current_step is not None:
+            step_data["CFL"] = float(cfl_match.group(1))
+            step_data["dt"] = float(cfl_match.group(2))
+
+        elif total_step_time_match and current_step is not None:
+            step_data["total_step_time"] = float(total_step_time_match.group(1))
+
+        elif field_match:
+            _, field_name, iters, start_res, final_res = field_match.groups()
+            field_info = {
+                "iters": int(iters),
+                "start_residual": float(start_res),
+                "final_residual": float(final_res),
+            }
+            step_data["fields"][field_name.lower()] = field_info
+
+    if current_step is not None:
+        data[current_step] = step_data
+
+    return data
+
+
+def flatten_parsed_data(parsed_data):
+    import numpy as np
+
+    first_step = next(iter(parsed_data.values()))
+    all_fields = sorted(first_step["fields"].keys())
+
+    # Define the full list of column names
+    columns = ["step", "time", "CFL", "dt", "total_step_time"]
+    for field in all_fields:
+        columns += [
+            f"{field}_iters",
+            f"{field}_start_residual",
+            f"{field}_final_residual",
+        ]
+
+    # Create rows
+    rows = []
+    for step_num, step in sorted(parsed_data.items()):
+        row = [
+            step_num,
+            step.get("time"),
+            step.get("CFL"),
+            step.get("dt"),
+            step.get("total_step_time"),
+        ]
+        for field in all_fields:
+            field_data = step["fields"].get(field)
+            if field_data:
+                row.extend(
+                    [
+                        field_data["iters"],
+                        field_data["start_residual"],
+                        field_data["final_residual"],
+                    ]
+                )
+            else:
+                row.extend([np.nan, np.nan, np.nan])
+        rows.append(row)
+
+    # Create and return the structured array
+    return np.array(rows), columns
+
+
+def save_as_csv(array, columns, output_file):
+    import numpy as np
+
+    header = ",".join(columns)
+    np.savetxt(
+        output_file, array, delimiter=",", header=header, comments="", fmt="%.17e"
+    )
+    print(f"Saved CSV to {output_file}")
+
+
+def save_as_hdf5(parsed_data, output_file):
+    import h5py
+
+    array, columns = flatten_parsed_data(parsed_data)
+    num_rows = array.shape[0]
+
+    # Separate root-level and field-level columns
+    root_keys = {"step", "time", "CFL", "dt", "total_step_time"}
+    field_data = {}  # {field: {subkey: col_index}}
+
+    for i, col in enumerate(columns):
+        if col in root_keys:
+            continue
+        parts = col.split("_")
+        if len(parts) == 2:
+            field, dataset = parts
+        elif (
+            len(parts) == 3
+            and parts[1] in {"start", "final"}
+            and parts[2] == "residual"
+        ):
+            field = parts[0]
+            dataset = f"{parts[1]}_residual"
+        else:
+            raise ValueError(f"Unrecognized column format: {col}")
+        field_data.setdefault(field, {})[dataset] = i
+
+    with h5py.File(output_file, "w") as f:
+        # Write root-level datasets
+        for i, col in enumerate(columns):
+            if col in root_keys and col != "step":
+                f.create_dataset(col, data=array[:, i])
+
+        # Write field-specific groups and datasets
+        for field, subfields in field_data.items():
+            grp = f.create_group(field)
+            for subkey, col_index in subfields.items():
+                # Dataset names: iters, start_residual, final_residual
+                dataset_name = subkey
+                grp.create_dataset(dataset_name, data=array[:, col_index])
+
+    print(f"Saved HDF5 to {output_file}")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Parse a Neko log file.")
+    parser.add_argument("logfile", help="Path to the Neko log file")
+    parser.add_argument(
+        "-o",
+        "--output",
+        help="Output filename (supports .json, .csv, or .hdf5)",
+        required=True,
+    )
+
+    args = parser.parse_args()
+    output_ext = os.path.splitext(args.output)[1].lower()
+
+    with open(args.logfile, "r") as f:
+        log_lines = f.readlines()
+
+    parsed_data = parse_neko_log(log_lines)
+
+    if output_ext == ".json":
+        with open(args.output, "w") as f:
+            json.dump(parsed_data, f, indent=2)
+        print(f"Saved JSON to {args.output}")
+
+    elif output_ext == ".csv":
+        array, columns = flatten_parsed_data(parsed_data)
+        save_as_csv(array, columns, args.output)
+    elif output_ext == ".hdf5" or output_ext == ".h5":
+        save_as_hdf5(parsed_data, args.output)
+
+    else:
+        print(f"Unsupported output format: {args.output} (use .json or .csv)")
diff --git a/science/neko/files/patch-tests_integration_tests_test__demo_test__suite.py b/science/neko/files/patch-tests_integration_tests_test__demo_test__suite.py
new file mode 100644
index 000000000000..51299f73b0a3
--- /dev/null
+++ b/science/neko/files/patch-tests_integration_tests_test__demo_test__suite.py
@@ -0,0 +1,13 @@
+-- Fix cylinder example path in demo test
+-- This patch is needed to ensure tests pass on FreeBSD
+--- tests/integration/tests/test_demo/test_suite.py.orig	2026-05-08 17:08:44 UTC
++++ tests/integration/tests/test_demo/test_suite.py
+@@ -24,7 +24,7 @@ def test_demo(launcher_script, request, log_file, tmp_
+ 
+     # Either specify a case, or load it here into a json, manipulate
+     # and save a new case file.
+-    case_file = join(neko_dir, "examples", "cylinder", "cylinder.case")
++    case_file = join(neko_dir, "tests", "integration", "tests", "test_cylinder", "cylinder_part1.case")
+ 
+     # Read the case file. We use json5 to allow comments in the case file.
+     with open(case_file, "r") as f:
diff --git a/science/neko/files/patch-tests_integration_tests_test__examples_test__examples.py b/science/neko/files/patch-tests_integration_tests_test__examples_test__examples.py
new file mode 100644
index 000000000000..ecb2df1173e2
--- /dev/null
+++ b/science/neko/files/patch-tests_integration_tests_test__examples_test__examples.py
@@ -0,0 +1,41 @@
+-- Filter examples to only those present in the distribution and use gmake
+-- This patch is needed to ensure tests pass on FreeBSD
+-- Filter examples to only those present in the distribution and use gmake
+-- This patch is needed to ensure tests pass on FreeBSD
+--- tests/integration/tests/test_examples/test_examples.py.orig	2026-05-08 17:08:44 UTC
++++ tests/integration/tests/test_examples/test_examples.py
+@@ -20,7 +20,7 @@ examples_dir = join(neko_dir, "examples")
+ 
+ examples_dir = join(neko_dir, "examples")
+ 
+-examples = {
++all_examples = {
+     "2d_cylinder": NekoTestCase(
+         case_file=join(examples_dir, "2d_cylinder", "2d_cylinder.case"),
+         user_file=join(examples_dir, "2d_cylinder", "2d_cylinder.f90"),
+@@ -123,6 +123,7 @@ examples = {
+         user_file=join(examples_dir, "programming", "user_file_template.f90")
+     ),
+ }
++examples = {k: v for k, v in all_examples.items() if k in ['2d_cylinder', 'cyl_boundary_layer', 'hemi', 'lid', 'rayleigh_benard', 'rayleigh_benard_cylinder', 'tgv', 'turb_channel', 'turb_pipe']}
+ 
+ 
+ def manipulate_case(example, case, tmp_path):
+@@ -149,7 +150,7 @@ def manipulate_case(example, case, tmp_path):
+     case_object["output_directory"] = str(tmp_path)
+ 
+ 
+-@pytest.mark.parametrize("example", ["hemi", "rayleigh_benard", "cylinder"])
++@pytest.mark.parametrize("example", ["hemi", "rayleigh_benard", "2d_cylinder"])
+ #@pytest.mark.parametrize("example", examples.keys())
+ def test_example_smoke(example, launcher_script, request, log_file, tmp_path):
+     """Run a smoke test for the specified Neko example.
+@@ -222,7 +223,7 @@ def test_example_poisson(log_file):
+     """
+ 
+     result = subprocess.run(
+-            ["make", "-C", join(examples_dir, "poisson")],
++            ["gmake", "-C", join(examples_dir, "poisson")],
+             stdout=subprocess.PIPE,
+             stderr=subprocess.STDOUT,
+             text=True)
diff --git a/science/neko/pkg-descr b/science/neko/pkg-descr
new file mode 100644
index 000000000000..2b26292904f3
--- /dev/null
+++ b/science/neko/pkg-descr
@@ -0,0 +1,7 @@
+Gemmi is a library, accompanied by a set of programs, developed primarily for
+use in macromolecular crystallography (MX). For working with:
+* macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),
+* refinement restraints (CIF files),
+* reflection data (MTZ and mmCIF formats),
+* data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
+* crystallographic symmetry.
diff --git a/science/neko/pkg-plist b/science/neko/pkg-plist
new file mode 100644
index 000000000000..730d3eddbe05
--- /dev/null
+++ b/science/neko/pkg-plist
@@ -0,0 +1,559 @@
+bin/adios2_to_nek5000
+bin/average_field_in_space
+bin/average_fields_in_time
+bin/calc_lift_from_field
+bin/genmeshbox
+bin/makeneko
+bin/map_to_equidistant_1d
+bin/mesh_checker
+bin/neko
+bin/postprocess_fluid_stats
+bin/prepart
+bin/psnr
+bin/rea2nbin
+include/neko.h
+include/neko/COMM.mod
+include/neko/CUDA_INTF.mod
+include/neko/CURVE.mod
+include/neko/DATADIST.mod
+include/neko/DEVICE.mod
+include/neko/DISTDATA.mod
+include/neko/ELEMENT.mod
+include/neko/ENTITY.mod
+include/neko/FACET_ZONE.mod
+include/neko/HEX.mod
+include/neko/HIP_INTF.mod
+include/neko/HTABLE.mod
+include/neko/JSON_UTILS.mod
+include/neko/LOGGER.mod
+include/neko/MATH.mod
+include/neko/MESH.mod
+include/neko/NEKO_CONFIG.mod
+include/neko/NMSH.mod
+include/neko/NUM_TYPES.mod
+include/neko/OPENCL_INTF.mod
+include/neko/OPENCL_PRGM_LIB.mod
+include/neko/POINT.mod
+include/neko/QUAD.mod
+include/neko/STACK.mod
+include/neko/STRUCTS.mod
+include/neko/TUPLE.mod
+include/neko/USET.mod
+include/neko/UTILS.mod
+include/neko/aabb.mod
+include/neko/aabb_el_finder.mod
+include/neko/aabb_pe_finder.mod
+include/neko/aabb_tree.mod
+include/neko/ab_time_scheme.mod
+include/neko/adv_dealias.mod
+include/neko/adv_dummy.mod
+include/neko/adv_no_dealias.mod
+include/neko/adv_oifs.mod
+include/neko/advection.mod
+include/neko/ax_helm.mod
+include/neko/ax_helm_cpu.mod
+include/neko/ax_helm_device.mod
+include/neko/ax_helm_full.mod
+include/neko/ax_helm_full_cpu.mod
+include/neko/ax_helm_full_device.mod
+include/neko/ax_helm_sx.mod
+include/neko/ax_helm_xsmm.mod
+include/neko/ax_product.mod
+include/neko/bc.mod
+include/neko/bc/bcknd/device/cuda/bc_utils.h
+include/neko/bc/bcknd/device/cuda/dirichlet_kernel.h
+include/neko/bc/bcknd/device/cuda/dong_outflow_kernel.h
+include/neko/bc/bcknd/device/cuda/facet_normal_kernel.h
+include/neko/bc/bcknd/device/cuda/inflow_kernel.h
+include/neko/bc/bcknd/device/cuda/inhom_dirichlet_kernel.h
+include/neko/bc/bcknd/device/cuda/neumann_kernel.h
+include/neko/bc/bcknd/device/cuda/symmetry_kernel.h
+include/neko/bc/bcknd/device/cuda/zero_dirichlet_kernel.h
+include/neko/bc/bcknd/device/hip/bc_utils.h
+include/neko/bc/bcknd/device/hip/dirichlet_kernel.h
+include/neko/bc/bcknd/device/hip/dong_outflow_kernel.h
+include/neko/bc/bcknd/device/hip/facet_normal_kernel.h
+include/neko/bc/bcknd/device/hip/inflow_kernel.h
+include/neko/bc/bcknd/device/hip/inhom_dirichlet_kernel.h
+include/neko/bc/bcknd/device/hip/neumann_kernel.h
+include/neko/bc/bcknd/device/hip/symmetry_kernel.h
+include/neko/bc/bcknd/device/hip/zero_dirichlet_kernel.h
+include/neko/bc/bcknd/device/opencl/bc_utils.h
+include/neko/bc/bcknd/device/opencl/dirichlet_kernel.cl
+include/neko/bc/bcknd/device/opencl/dong_outflow_kernel.cl
+include/neko/bc/bcknd/device/opencl/facet_normal_kernel.cl
+include/neko/bc/bcknd/device/opencl/inflow_kernel.cl
+include/neko/bc/bcknd/device/opencl/inhom_dirichlet_kernel.cl
+include/neko/bc/bcknd/device/opencl/neumann_kernel.cl
+include/neko/bc/bcknd/device/opencl/symmetry_kernel.cl
+include/neko/bc/bcknd/device/opencl/zero_dirichlet_kernel.cl
+include/neko/bc_list.mod
+include/neko/bdf_time_scheme.mod
+include/neko/bicgstab.mod
+include/neko/blasius.mod
+include/neko/boussinesq_source_term.mod
+include/neko/boussinesq_source_term_cpu.mod
+include/neko/boussinesq_source_term_device.mod
+include/neko/box_point_zone.mod
+include/neko/bp_file.mod
+include/neko/brinkman_source_term.mod
+include/neko/buffer.mod
+include/neko/buffer_1d.mod
+include/neko/buffer_4d.mod
+include/neko/buffer_4d_npar.mod
+include/neko/cacg.mod
+include/neko/cartesian_el_finder.mod
+include/neko/cartesian_pe_finder.mod
+include/neko/case.mod
+include/neko/centrifugal_source_term.mod
+include/neko/centrifugal_source_term_cpu.mod
+include/neko/centrifugal_source_term_device.mod
+include/neko/cg.mod
+include/neko/cg_cpld.mod
+include/neko/cg_cpld_device.mod
+include/neko/cg_device.mod
+include/neko/cg_sx.mod
+include/neko/cheby.mod
+include/neko/cheby_device.mod
+include/neko/checkpoint.mod
+include/neko/chkp_file.mod
+include/neko/chkp_output.mod
+include/neko/coefs.mod
+include/neko/combine_point_zone.mod
+include/neko/comm.mod
+include/neko/comm/comm.h
+include/neko/comm/comm_nccl.h
+include/neko/common/bcknd/device/cuda/makebdf_kernel.h
+include/neko/common/bcknd/device/cuda/makeext_kernel.h
+include/neko/common/bcknd/device/cuda/makeoifs_kernel.h
+include/neko/common/bcknd/device/cuda/projection_kernel.h
+include/neko/common/bcknd/device/cuda/sumab_kernel.h
+include/neko/common/bcknd/device/hip/makebdf_kernel.h
+include/neko/common/bcknd/device/hip/makeext_kernel.h
+include/neko/common/bcknd/device/hip/makeoifs_kernel.h
+include/neko/common/bcknd/device/hip/projection_kernel.h
+include/neko/common/bcknd/device/hip/sumab_kernel.h
+include/neko/common/bcknd/device/opencl/rhs_maker_kernel.cl
+include/neko/common/neko_log.h
+include/neko/compressible_ops_cpu.mod
+include/neko/compressible_ops_device.mod
+include/neko/const_source_term.mod
+include/neko/const_source_term_cpu.mod
+include/neko/const_source_term_device.mod
+include/neko/coriolis_source_term.mod
+include/neko/coriolis_source_term_cpu.mod
+include/neko/coriolis_source_term_device.mod
+include/neko/cpr.mod
+include/neko/craypat.mod
+include/neko/csv_file.mod
+include/neko/cuda_intf.mod
+include/neko/cuda_mappings.mod
+include/neko/cuda_math.mod
+include/neko/curl_simcomp.mod
+include/neko/curve.mod
+include/neko/cylinder_point_zone.mod
+include/neko/data_streamer.mod
+include/neko/datadist.mod
+include/neko/derivative_simcomp.mod
+include/neko/device.mod
+include/neko/device/cuda/check.h
+include/neko/device/device_config.h
+include/neko/device/hip/check.h
+include/neko/device/opencl/check.h
+include/neko/device/opencl/jit.h
+include/neko/device/opencl/prgm_lib.h
+include/neko/device_coef.mod
+include/neko/device_dirichlet.mod
+include/neko/device_dong_outflow.mod
+include/neko/device_dynamic_smagorinsky_nut.mod
+include/neko/device_facet_normal.mod
+include/neko/device_gradient_jump_penalty.mod
+include/neko/device_identity.mod
+include/neko/device_inflow.mod
+include/neko/device_inhom_dirichlet.mod
+include/neko/device_jacobi.mod
+include/neko/device_local_interpolation.mod
+include/neko/device_math.mod
+include/neko/device_mathops.mod
+include/neko/device_neumann.mod
+include/neko/device_projection.mod
+include/neko/device_schwarz.mod
+include/neko/device_sigma_nut.mod
+include/neko/device_smagorinsky_nut.mod
+include/neko/device_symmetry.mod
+include/neko/device_tree_amg_smoother.mod
+include/neko/device_vreman_nut.mod
+include/neko/device_wale_nut.mod
+include/neko/device_zero_dirichlet.mod
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