Integrated anydsl-md repository

apps/CMakeLists.txt

@@ -22,6 +22,8 @@ else ()
     add_subdirectory ( tutorials EXCLUDE_FROM_ALL )
 endif()
 
+add_subdirectory ( anydsl )
+
 
 # Python module
 if ( WALBERLA_BUILD_WITH_PYTHON )

apps/impala/CMakeLists.txt → apps/anydsl/CMakeLists.txt

@@ -6,12 +6,13 @@ include_directories(${ANYDSL_RUNTIME_DIR}/src)
 set(CLANG_FLAGS -O3 -march=native)
 set(IMPALA_FLAGS --log-level info)
 
+
 # examples based on the "mapping"
 anydsl_runtime_wrap(IMPALA_OBJECT_FILE
     CLANG_FLAGS ${CLANG_FLAGS}
     IMPALA_FLAGS ${IMPALA_FLAGS}
-    FILES intrinsics/intrinsics_cpu.impala common.impala datastructures/linked_cell/cpu.impala utilities/linked_cell/cpu.impala algorithm/linked_cell/cpu.impala initialization/test.impala potential/lennard_jones.impala integration/verlet.impala boundary/rigid_walls.impala time_integration/cpu.impala run/cpu.impala)
+    FILES anydsl-md/impala/intrinsics/intrinsics_cpu.impala anydsl-md/impala/common.impala anydsl-md/impala/datastructures/linked_cell/cpu.impala anydsl-md/impala/utilities/linked_cell/cpu.impala anydsl-md/impala/algorithm/linked_cell/cpu.impala anydsl-md/impala/initialization/test.impala anydsl-md/impala/potential/lennard_jones.impala anydsl-md/impala/integration/verlet.impala anydsl-md/impala/boundary/rigid_walls.impala anydsl-md/impala/time_integration/cpu.impala anydsl-md/impala/run/cpu.impala)
 
 waLBerla_add_executable ( NAME md_simulation
-    FILES md_simulation.cpp ${IMPALA_OBJECT_FILE} clib/fileIO.c clib/allocate.c
+    FILES md_simulation.cpp ${IMPALA_OBJECT_FILE} anydsl-md/impala/clib/fileIO.c anydsl-md/impala/clib/allocate.c
     DEPENDS core blockforest pe domain_decomposition vtk)

apps/impala/algorithm/array/cpu.impala

-
-fn compute_force(P: ParticleSystem, force: fn(Particle, Particle, Constants) -> ()) -> ()
-{
-    let start = 0 as size_t;
-    let lut = P.lut();
-    for i in par_loop(start, P.np()) {
-        let p = P.getParticle(i);
-        p.setForces(get_null_vector());
-    }
-    /*
-    initialize(lut.data, lut.rows()*lut.cols()*sizeof[u8]() as size_t, 0i32); 
-    
-    for i in par_loop(start, P.np()){
-        for j in loop(start, P.np()) {
-            if(i != j)
-            {
-                let mut row = i;
-                let mut col = j; 
-                if (i > j) {
-                    row = j; 
-                    col = i;
-                } 
-                
-                if(row >= lut.rows()) {
-                    let tmp = col;
-                    col = row;
-                    row = tmp;
-                    col -= lut.rows();
-                    row -= lut.rows();
-
-                }
-                let flag = cmpxchg(&mut bitcast[&mut[u8]](lut.data)(row*lut.cols() + col), 0u8, 1u8);
-                if (flag(1) == true)
-                {
-                    force(P.getParticle(i), P.getParticle(j), P.constants());
-                }
-            }
-        }
-    }*/
-    
-    for i in loop(start, P.np()) {
-        for j in loop(i+(1 as size_t), P.np()) {
-            let p1 = P.getParticle(i);
-            let p2 = P.getParticle(j);
-            force(p1, p2, P.constants());
-        }
-    }
-}
-
-fn update(P: ParticleSystem, dt: real, f: fn(Particle, real) -> ()) -> () {
-    for i in loop(0 as size_t, P.np()) {
-        f(P.getParticle(i), dt);
-    }
-}
-
-fn move_particles(P: ParticleSystem) -> () {
-    for i in loop(0 as size_t, P.np()) {
-        boundary(P.getParticle(i), P.l());
-    }
-}
-
-
-fn fprint_particle_system(fname: &[u8], step: size_t, P: ParticleSystem) -> ()
-{
-    let start = 0 as size_t;
-    let fp = open_file(fname);
-    let N = P.np();
-
-    fprint_line(fp, "# vtk DataFile Version 2.0");
-    fprint_string(fp, "Step ");
-    fprint_size_t(fp, step);
-    fprint_line(fp, " data");
-    fprint_line(fp, "ASCII");
-    fprint_line(fp, "DATASET UNSTRUCTURED_GRID");
-    fprint_string(fp, "POINTS ");
-    fprint_size_t(fp, N);
-    fprint_line(fp, " double");
-    loop(start, N, |i| {
-        let p = P.getParticle(i);
-        p.getCoordinates().fprint(fp);
-        fprint_string(fp, "\n");
-    });
-    fprint_string(fp, "\n\n");
-    fprint_string(fp, "CELLS ");
-    fprint_size_t(fp, N);
-    fprint_string(fp, " ");
-    fprint_size_t(fp, (2 as size_t)*N);
-
-    fprint_string(fp, "\n");
-    loop(start, N, |i| {
-        fprint_string(fp, "1 ");
-        fprint_size_t(fp, i);
-        fprint_string(fp, "\n");
-    });
-    fprint_string(fp, "\n\n");
-
-
-    fprint_string(fp, "CELL_TYPES ");
-    fprint_size_t(fp, N);
-    fprint_string(fp, "\n");
-    loop(start, N, |i| {
-        fprint_string(fp, "1");
-        fprint_string(fp, "\n");
-    });
-
-    fprint_string(fp, "\n\n");
-
-
-    fprint_string(fp, "POINT_DATA ");
-    fprint_size_t(fp, N);
-    fprint_string(fp, "\n");
-    @loop(start, DIM, |d| {
-        fprint_string(fp, "SCALARS velocity_dim_");
-        fprint_size_t(fp, d);
-        fprint_line(fp, " double");
-        fprint_line(fp, "LOOKUP_TABLE default");
-        $loop(start, N, |i| {
-
-            let p = P.getParticle(i);
-            let v = p.getVelocities();
-            let x = v.x();
-            fprint_double(fp, x(d));
-            fprint_string(fp, "\n");
-        });
-        fprint_string(fp, "\n");
-    });
-
-    @loop(start, DIM, |d| {
-        fprint_string(fp, "SCALARS force_dim_");
-        fprint_size_t(fp, d);
-        fprint_line(fp, " double");
-        fprint_line(fp, "LOOKUP_TABLE default");
-        $loop(start, N, |i| {
-
-            let p = P.getParticle(i);
-            let v = p.getForces();
-            let x = v.x();
-            fprint_double(fp, x(d));
-            fprint_string(fp, "\n");
-        });
-        fprint_string(fp, "\n");
-    });
-
-
-    fprint_string(fp, "SCALARS mass");
-    fprint_line(fp, " double");
-    fprint_line(fp, "LOOKUP_TABLE default");
-    loop(start, N, |i| {
-        let p = P.getParticle(i);
-        let m = p.getMass();
-        fprint_double(fp, m);
-        fprint_string(fp, "\n");
-    });
-    fprint_string(fp, "\n");
-
-
-    close_file(fp);
-}
-
-
-fn print_statistics(P: ParticleSystem, t: real) -> ()
-{
-
-    let sqr = |x : real| {x*x};
-    let mut e : real = 0.0;
-    loop(0 as size_t, P.np(), |i| {
-        let p = P.getParticle(i);
-        let v = p.getVelocities().reduce(sqr, |x,y|{x+y}, 0.0);
-        e += 0.5 * p.getMass() * v;
-    });
-    print_string("t: ");
-    print_double(t);
-    print_string("\tE: ");
-    print_double(e);
-    print_char('\n');
-}

apps/impala/algorithm/linked_cell/cpu.impala

-
-fn compute_force(P: ParticleSystem, force: fn(Particle, Particle, Constants) -> ()) -> ()
-{
-    let z = 0 as size_t;
-    let ic_start = [z,z,z];
-    let ic_end = P.nc();
-    for ic, pl1 in @iterate_over_particle_system(ic_start, ic_end, P) {
-        let p1 = get_particle_from_node(*pl1);
-        p1.setForces(get_null_vector());
-    }
-    for ic, pl1 in @iterate_over_particle_system(ic_start, ic_end, P) {
-        let p1 = get_particle_from_node(*pl1);
-        let jc_start = [if(ic(0) > z) {ic(0) - 1 as size_t} else {ic(0)}, 
-                        if(ic(1) > z) {ic(1) - 1 as size_t} else{ic(1)}, 
-                        if(ic(2) > z) {ic(2) - 1 as size_t} else {ic(2)}];
-        let jc_end =   [if(ic(0) + 1 as size_t < ic_end(0)) {ic(0) + 2 as size_t} else {ic_end(0)}, 
-                        if(ic(1) + 1 as size_t < ic_end(1)) {ic(1) + 2 as size_t} else {ic_end(1)}, 
-                        if(ic(2) + 1 as size_t < ic_end(2)) {ic(2) + 2 as size_t} else {ic_end(2)}];
-        for jc, pl2 in iterate_over_particle_system(jc_start, jc_end, P) {
-            if((pl1 as ptr_t < pl2 as ptr_t)) {
-                let p2 = get_particle_from_node(*pl2);
-                force(p1, p2, P.constants());   
-            }
-        }
-    }
-}
-
-fn update(P: ParticleSystem, dt: real, f: fn(Particle, real) -> ()) -> ()
-{
-    let z = 0 as size_t;
-    let ic_start = [z,z,z];
-    let ic_end = P.nc();
-    for ic, pl in @iterate_over_particle_system(ic_start, ic_end, P) {
-        let p = get_particle_from_node(*pl);
-        f(p, dt);
-    }
-}
-
-fn move_particles(P: ParticleSystem) -> () {
-    let z = 0 as size_t;
-    let ic_start = [z,z,z];
-    let ic_end = P.nc();
-    for ic, root in @iterate_over_particle_cells(ic_start, ic_end, P) {
-        let mut q : &mut &ParticleList = root;
-        let mut i : &ParticleList = *q;
-        
-        while(i != 0 as &ParticleList) {    
-            let p = get_particle_from_node(*i); 
-            boundary(p, P.l());
-            let kc = compute_cell_position(p, P.nc(), P.l());
-            let mut moving_node : &mut ParticleList;
-            if(ic(0) != kc(0) || ic(1) != kc(1) || ic(2) != kc(2)) {
-                moving_node = remove(q);
-                insert(P.head(index(kc, P.nc())), moving_node);
-            }
-            else {
-                q = (&(*i).next) as &mut& ParticleList;
-            }
-            i = (*q);
-        }
-    }
-
-}
-fn fprint_particle_system(fname: &[u8], step: size_t, P: ParticleSystem) -> ()
-{
-    let start = 0 as size_t;
-    let fp = open_file(fname);
-    let N = P.np();
-
-    fprint_line(fp, "# vtk DataFile Version 2.0");
-    fprint_string(fp, "Step ");
-    fprint_size_t(fp, step);
-    fprint_line(fp, " data");
-    fprint_line(fp, "ASCII");
-    fprint_line(fp, "DATASET UNSTRUCTURED_GRID");
-    fprint_string(fp, "POINTS ");
-    fprint_size_t(fp, N);
-    fprint_line(fp, " double");
-    
-    let addresses = P.addresses();
-
-    for i in loop(start, N) {
-        let p = get_particle(addresses.get(i));
-        p.getCoordinates().fprint(fp);
-        fprint_string(fp, "\n");
-    }
-    fprint_string(fp, "\n\n");
-    fprint_string(fp, "CELLS ");
-    fprint_size_t(fp, N);
-    fprint_string(fp, " ");
-    fprint_size_t(fp, (2 as size_t)*N);
-
-    fprint_string(fp, "\n");
-    for i in loop(start, N){
-        fprint_string(fp, "1 ");
-        fprint_size_t(fp, i);
-        fprint_string(fp, "\n");
-    }
-    fprint_string(fp, "\n\n");
-
-
-    fprint_string(fp, "CELL_TYPES ");
-    fprint_size_t(fp, N);
-    fprint_string(fp, "\n");
-    for i in loop(start, N) {
-        fprint_string(fp, "1");
-        fprint_string(fp, "\n");
-    }
-
-    fprint_string(fp, "\n\n");
-
-
-    fprint_string(fp, "POINT_DATA ");
-    fprint_size_t(fp, N);
-    fprint_string(fp, "\n");
-    for d in loop(start, DIM) {
-        fprint_string(fp, "SCALARS velocity_dim_");
-        fprint_size_t(fp, d);
-        fprint_line(fp, " double");
-        fprint_line(fp, "LOOKUP_TABLE default");
-        for i in loop(start, N) {
-            let p = get_particle(addresses.get(i));
-            let v = p.getVelocities();
-            let x = v.x();
-            fprint_double(fp, x(d));
-            fprint_string(fp, "\n");
-        }
-        fprint_string(fp, "\n");
-    }
-    for d in loop(start, DIM) {
-        fprint_string(fp, "SCALARS force_dim_");
-        fprint_size_t(fp, d);
-        fprint_line(fp, " double");
-        fprint_line(fp, "LOOKUP_TABLE default");
-        for i in loop(start, N) {
-            let p = get_particle(addresses.get(i));
-            let v = p.getForces();
-            let x = v.x();
-            fprint_double(fp, x(d));
-            fprint_string(fp, "\n");
-        }
-        fprint_string(fp, "\n");
-    }
-
-    fprint_string(fp, "SCALARS mass");
-    fprint_line(fp, " double");
-    fprint_line(fp, "LOOKUP_TABLE default");
-    for i in loop(start, N) {
-        let p = get_particle(addresses.get(i));
-        let m = p.getMass();
-        fprint_double(fp, m);
-        fprint_string(fp, "\n");
-    }
-    fprint_string(fp, "\n");
-    close_file(fp);
-}
-
-/*
-fn fprint_particle_system(fname: &[u8], step: size_t, P: ParticleSystem) -> ()
-{
-    let start = 0 as size_t;
-    let fp = open_file(fname);
-    let N = P.np();
-
-    let z = 0 as size_t;
-    let ic_start = [z,z,z];
-    let ic_end = P.nc();
-
-    fprint_line(fp, "# vtk DataFile Version 2.0");
-    fprint_string(fp, "Step ");
-    fprint_size_t(fp, step);
-    fprint_line(fp, " data");
-    fprint_line(fp, "ASCII");
-    fprint_line(fp, "DATASET UNSTRUCTURED_GRID");
-    fprint_string(fp, "POINTS ");
-    fprint_size_t(fp, N);
-    fprint_line(fp, " double");
-
-    for ic, pl in iterate_over_particle_system(ic_start, ic_end, P) {
-        let p = get_particle_from_cell(*pl);
-        p.getCoordinates().fprint(fp);
-        fprint_string(fp, "\n");
-    }
-    fprint_string(fp, "\n\n");
-    fprint_string(fp, "CELLS ");
-    fprint_size_t(fp, N);
-    fprint_string(fp, " ");
-    fprint_size_t(fp, (2 as size_t)*N);
-
-    fprint_string(fp, "\n");
-    for i in loop(start, N){
-        fprint_string(fp, "1 ");
-        fprint_size_t(fp, i);
-        fprint_string(fp, "\n");
-    }
-    fprint_string(fp, "\n\n");
-
-
-    fprint_string(fp, "CELL_TYPES ");
-    fprint_size_t(fp, N);
-    fprint_string(fp, "\n");
-    for i in loop(start, N) {
-        fprint_string(fp, "1");
-        fprint_string(fp, "\n");
-    }
-
-    fprint_string(fp, "\n\n");
-
-
-    fprint_string(fp, "POINT_DATA ");
-    fprint_size_t(fp, N);
-    fprint_string(fp, "\n");
-    for d in loop(start, DIM) {
-        fprint_string(fp, "SCALARS velocity_dim_");
-        fprint_size_t(fp, d);
-        fprint_line(fp, " double");
-        fprint_line(fp, "LOOKUP_TABLE default");
-        for ic, pl in iterate_over_particle_system(ic_start, ic_end, P) {
-            let p = get_particle_from_cell(*pl);
-            let v = p.getVelocities();
-            let x = v.x();
-            fprint_double(fp, x(d));
-            fprint_string(fp, "\n");
-        }
-        fprint_string(fp, "\n");
-    }
-    fprint_string(fp, "SCALARS mass");
-    fprint_line(fp, " double");
-    fprint_line(fp, "LOOKUP_TABLE default");
-    for ic, pl in iterate_over_particle_system(ic_start, ic_end, P) {
-        let p = get_particle_from_cell(*pl);
-        let m = p.getMass();
-        fprint_double(fp, m);
-        fprint_string(fp, "\n");
-    }
-    fprint_string(fp, "\n");
-
-
-    close_file(fp);
-    
-}
-*/
-
-fn print_statistics(P: ParticleSystem, t: real) -> ()
-{
-
-    let sqr = |x : real| {x*x};
-    let e : real = 0.0;
-    /*
-    loop(0 as size_t, P.np(), |i| {
-        let v = P.velocities().get(i).reduce(sqr, |x,y|{x+y}, 0.0);
-        e += 0.5 * P.masses().get(i) * v;
-    });*/
-    print_string("t: ");
-    print_double(t);
-    print_string("\tE: ");
-    print_double(e);
-    print_char('\n');
-}

apps/impala/boundary/rigid_walls.impala

-fn boundary(p: Particle, l: Vector) -> () {
-    let mut x = p.getCoordinates().x();
-    let mut change = false;
-    for d in @loop(0 as size_t, DIM) {
-        if(x(d) < 0.0) {
-            x(d) = 0.0+EPS;
-            change = true;
-        }
-        else if(x(d) > l.x()(d)) {
-            x(d) = l.x()(d)-EPS;
-            change = true;
-        }
-    }
-    if(change == true) {
-        p.setCoordinates(get_vector(x));
-    }
-}   

apps/impala/clean_build

-#!/bin/sh
-rm -rf Makefile CMakeFiles cmake_install.cmake CMakeCache.txt CTestTestfile.cmake *.o *.ll md

apps/impala/clib/allocate.c

-#include <stdlib.h>
-#include <string.h>
-
-static size_t ALIGNMENT = 64ul;
-unsigned char * allocate(size_t size) {
-    return (unsigned char *)aligned_alloc(ALIGNMENT, size);
-}
-
-
-unsigned char * allocate_and_initialize(size_t size, int val) {
-    void *ptr = aligned_alloc(ALIGNMENT, size);
-    memset(ptr, val, size);
-    return (unsigned char *)ptr;
-}
-
-unsigned char * reallocate(unsigned char *ptr, size_t size) {
-    return (unsigned char *)realloc((void *)ptr, size);
-}
-
-void initialize(unsigned char * ptr, size_t size, int val) {
-    memset((void *)ptr, val, size);
-}
-
-void deallocate(unsigned char *ptr) {
-    free(ptr);
-}

apps/impala/clib/allocate.h

-unsigned char * allocate(size_t size);
-unsigned char * allocate_and_initialize(size_t size, int val);
-unsigned char * reallocate(unsigned char *ptr, size_t size);
-void initialize(unsigned char *ptr, size_t size, int val);
-void deallocate(unsigned char *ptr);

apps/impala/clib/fileIO.c

-#include <stdio.h>
-#include <stdint.h>
-
-
-
-void size_t_to_string(size_t i, unsigned char *buf, size_t bufsize) {
-    snprintf(buf, bufsize, "%lu", i);
-}
-
-void generate_filename(size_t i, unsigned char *buf, size_t bufsize) {
-    snprintf(buf, bufsize, "../impala_vtk/particles%lu.vtk", i); 
-}
-
-uintptr_t open_file(unsigned char const *fname) {
-    FILE *fp = fopen(fname, "w");
-    if(fp == NULL) {
-        fprintf(stderr, "open_file: Could not open file %s", fname);
-        perror("");
-        return 0;
-    }
-    else {
-        return (uintptr_t)fp;
-    }
-}
-void close_file(uintptr_t fp) {
-    fclose((FILE *)fp);
-}
-
-void fprint_string(uintptr_t fp, unsigned char const *str) {
-    fputs(str, (FILE *)fp);
-}
-
-void fprint_line(uintptr_t fp, unsigned char const *str) {
-    fprintf((FILE *)fp, "%s\n", str);
-}
-void fprint_double(uintptr_t fp, double d) {
-    fprintf((FILE *)fp, "%f", d);
-}
-
-void fprint_float(uintptr_t fp, float f) {
-    fprintf((FILE *)fp, "%f", f);
-}
-
-void fprint_int(uintptr_t fp, int i) {
-    fprintf((FILE *)fp, "%d", i);
-}
-
-
-void fprint_size_t(uintptr_t fp, size_t i) {
-    fprintf((FILE *)fp, "%lu", i);
-}
-
-void fprint_char(uintptr_t fp, unsigned char c) {
-    fputc((int)c, (FILE *)fp);
-}

apps/impala/clib/fileIO.h

-#include <stdio.h>
-#include <stdint.h>
-
-
-
-void size_t_to_string(size_t i, unsigned char *buf, size_t bufsize); 
-
-void generate_filename(size_t i, unsigned char *buf, size_t bufsize);
-
-uintptr_t open_file(unsigned char const *fname);
-
-void close_file(uintptr_t fp);
-
-void fprint_string(uintptr_t fp, unsigned char const *str);
-
-void fprint_line(uintptr_t fp, unsigned char const *str);
-void fprint_double(uintptr_t fp, double d);
-
-void fprint_float(uintptr_t fp, float f);
-
-void fprint_int(uintptr_t fp, int i);
-
-void fprint_size_t(uintptr_t fp, size_t i);
-
-void fprint_char(uintptr_t fp, unsigned char c);
-

apps/impala/common.impala

-extern "C"
-{
-    fn size_t_to_string(size_t, &mut[u8], size_t) -> ();
-    fn generate_filename(size_t , &mut[u8], size_t) -> ();
-    fn open_file(&[u8]) -> u64;
-    fn close_file(u64) -> ();
-    fn fprint_string(u64, &[u8]) -> ();
-    fn fprint_line(u64, &[u8]) -> ();
-    fn fprint_double(u64, f64) -> ();
-    fn fprint_float(u64, f32) -> ();
-    fn fprint_int(u64, i32) -> ();
-    fn fprint_size_t(u64, size_t) -> ();
-    fn fprint_char(u64, u8) -> ();
-    fn allocate(size_t) -> &u8;
-    fn allocate_and_initialize(size_t, i32) -> &u8;
-    fn initialize(&u8, size_t, i32) -> ();
-    fn deallocate(&u8) -> ();
-}
-
-type size_t = u64;
-type ptr_t = u64;