Changeset 977 for codes

Timestamp:

09/26/19 18:49:01 (5 years ago)

Author:

dubos

Message:

devel/Python : now only dynamico.dev modules require link to DYNAMICO/XIOS shared objects

Location:

codes/icosagcm/devel

Files:

• Python/dev (moved) (moved from codes/icosagcm/devel/Python/dynamico/dev)
• Python/dev/cxios.pyx (copied) (copied from codes/icosagcm/devel/Python/src/cxios.pyx)
• Python/dev/functions.h (copied) (copied from codes/icosagcm/devel/Python/src/functions.h)
• Python/dev/setup.py (copied) (copied from codes/icosagcm/devel/Python/src/setup.py)
• Python/dev/unstructured.pyx (copied) (copied from codes/icosagcm/devel/Python/src/unstructured.pyx) (1 diff)
• Python/dynamico/meshes.py (modified) (4 diffs)
• Python/dynamico/partition.h (copied) (copied from codes/icosagcm/devel/Python/src/partition.c) (2 diffs)
• Python/dynamico/partition.pyx (added)
• Python/dynamico/setup.py (added)
• Python/src (deleted)
• Python/test/py/partition.py (modified) (6 diffs)
• make_python (modified) (3 diffs)

codes/icosagcm/devel/Python/dev/unstructured.pyx

@@ -82 +82 @@
                      ['dynamico_scalar_laplacian', c_void_p,2],
                      ['dynamico_curl_laplacian', c_void_p,2],
-                     ['dynamico_partition_graph', c_int,2, c_void_p,3, c_int, c_void_p],
                      ['dynamico_init_transfer', c_int, c_int,2,c_void_p,3, c_int,2,c_void_p,3],
-                     ['dynamico_update_halo', c_int,3,c_void_p],
-                     ['dynamico_morton_encode', c_int,c_void_p,4]
-                     ])
+                     ['dynamico_update_halo', c_int,3,c_void_p] ])
 
 # set/get global variables

codes/icosagcm/devel/Python/dynamico/meshes.py

@@ -1 +1 @@
 from __future__ import absolute_import     
-
-from dynamico.dev import unstructured as unst
 
 import time
@@ -15 +13 @@
 from dynamico.util import list_stencil, BaseClass, inverse_list
 from dynamico import getargs
-# TODO from dynamico.parmetis import partition_mesh
-from dynamico.dev.unstructured import partition_mesh
+from dynamico.partition import partition_mesh
 
 log_master, log_world = getargs.getLogger(__name__)
@@ -419 +416 @@
                     vertex_lat[cell, ivertex] = vlat
             return vertex_lon, vertex_lat
-        mesh.primal_bounds_lon, mesh.primal_bounds_lat = bounds(mesh.primal_deg, mesh.primal_vertex, mesh.lon_v, mesh.lat_v)
+        mesh.primal_bounds_lon, mesh.primal_bounds_lat = bounds(mesh.primal_own_deg, mesh.primal_vertex, mesh.lon_v, mesh.lat_v)
         mesh.dual_bounds_lon, mesh.dual_bounds_lat = bounds(mesh.dual_deg, mesh.dual_vertex, mesh.lon_i, mesh.lat_i)
 
@@ -766 +763 @@
     nn, xx, yy, zz = x.size, toint(x), toint(y), toint(z)
     idx=np.zeros(nn, dtype=np.int64)
-    unst.ker.dynamico_morton_encode(nn, xx,yy,zz, idx)
+    partition.dynamico_morton_encode(nn, xx,yy,zz, idx)
     return idx
 

codes/icosagcm/devel/Python/dynamico/partition.h

@@ -3 +3 @@
 #include <parmetis.h>
 
-void dynamico_partition_graph(int mpi_rank, int mpi_size, 
+static inline void dynamico_partition_graph(int mpi_rank, int mpi_size, 
                      idx_t vtxdist[], idx_t xadj_loc[], idx_t adjncy_loc[],
                      idx_t nparts, idx_t part[])
@@ -49 +49 @@
 }
 
-void dynamico_morton_encode(int n, const int *x, const int *y, const int *z, uint64_t *m)
+static inline void dynamico_morton_encode(int n, const int *x, const int *y, const int *z, uint64_t *m)
 {
   for(int i=0; i<n; i++)

codes/icosagcm/devel/Python/test/py/partition.py

@@ -3 +3 @@
 from dynamico import meshes
 from dynamico import parallel
-from dynamico.dev import unstructured as unst
 from dynamico import maps
-from dynamico.parmetis import partition_graph
+from dynamico import partition
 
 from mpi4py import MPI
@@ -11 +10 @@
 mpi_rank, mpi_size = comm.Get_rank(), comm.Get_size()
 print '%d/%d starting'%(mpi_rank,mpi_size)
-
-#from dynamico import partition
 
 import math as math
@@ -50 +47 @@
     part = 0*xadj_loc[0:-1];
 
-#    unst.ker.dynamico_partition_graph(mpi_rank, mpi_size, vtxdist, xadj_loc, adjncy_loc, 4, part)
-    partition_graph(comm, vtxdist, xadj_loc, adjncy_loc, part, nparts=4)
+    partition.partition_graph(comm, vtxdist, xadj_loc, adjncy_loc, part, nparts=4)
 
     for i in range(len(part)):
@@ -66 +62 @@
     mydegree, mybounds = [get_mycells(x) for x in primal_deg, primal_vertex]
     print '%d : len(mydegree)=%d'%(mpi_rank, len(mydegree))
-    vertex_list = sorted(set(unst.list_stencil(mydegree,mybounds))) 
+    vertex_list = sorted(set(partition.list_stencil(mydegree,mybounds))) 
     print '%d : len(vertex_list))=%d'%(mpi_rank, len(vertex_list))
     get_myvertices = parallel.Get_Indices(dim_vertex, vertex_list)
@@ -116 +112 @@
 plt.xlim(-190.,190.)
 plt.ylim(-90.,90.)
-plt.savefig('fig_partition/A%03d.pdf'%mpi_rank, dpi=1600)
+plt.savefig('fig_partition/A%03d.png'%mpi_rank, dpi=160)
 
 fig, ax = plt.subplots()
@@ -124 +120 @@
 plt.xlim(-190.,190.)
 plt.ylim(-90.,90.)
-plt.savefig('fig_partition/B%03d.pdf'%mpi_rank, dpi=1600)
+plt.savefig('fig_partition/B%03d.png'%mpi_rank, dpi=160)

codes/icosagcm/devel/make_python

@@ -13 +13 @@
     rm -rf *.o *.so build/
 }
-
-#------------------ Default action , invoked by : './make_python' --------------------
 
 function make_so()
@@ -33 +31 @@
 }
 
-
-function cmd_()
+function check_python_modules()
 {
-    echo "XIOS_ROOTDIR : $XIOS_ROOTDIR"
     MISSING=""
-    for module in netCDF4 jinja2 mpi4py; do
+    for module in $*; do
         echo "import $module"
         python -c "import $module" || MISSING="$MISSING $module"
@@ -49 +45 @@
         exit
     fi
+}
 
-    log mpicc -c -std=c99 -fPIC $PARMETIS_CFLAGS Python/src/partition.c -o obj/partition.o
-    make_so $XIOS_ROOTDIR/lib/libxios.a $LIBDIR/libxios.so "$NETCDF_LDFLAGS -lstdc++"
-    make_so $LIBDIR/libicosa.a $LIBDIR/libicosa.so "-L$LIBDIR -lxios $KERNELS_LDFLAGS" "physics_external_mod.o physics_mod.o timeloop_gcm_mod.o icosa_init_mod.o" obj/partition.o
-
-    # Cythonize Python modules
-    cd $DYNAMICO_ROOT/Python/src
-    NUMPY=$(python -c 'import numpy as np ; print np.get_include()')
-    CYTHONFLAGS="$SOFLAGS $LDFLAGS -L$LIBDIR -licosa $KERNELS_LDFLAGS"
-    LDSHARED="$LINK" CFLAGS="-fno-strict-aliasing -O2 -I$NUMPY" LDFLAGS="$CYTHONFLAGS" log python setup.py build_ext --inplace || exit
-
-    cp -fpr $DYNAMICO_ROOT/Python/dynamico $DYNAMICO_ROOT/lib
-    cp -fp *.so $DYNAMICO_ROOT/lib/dynamico/dev/
+function check_dynamico_modules()
+{
     cd $DYNAMICO_ROOT
-
-    for module in dev.cxios dev.unstructured meshes dyn time_step DCMIP; do
+    for module in $*; do
         echo "import dynamico.$module"
         LD_PRELOAD=$PYTHON_PRELOAD python -c "import dynamico.$module"
     done
 }
+
+function cythonize()
+{
+    EXTRA=$1
+    NUMPY=$(python -c 'import numpy as np ; print np.get_include()')
+    CYTHONFLAGS="$SOFLAGS $LDFLAGS -L$LIBDIR $KERNELS_LDFLAGS $EXTRA"
+    CC=mpicc LDSHARED="$LINK" CFLAGS="-fno-strict-aliasing -O2 -I$NUMPY $PARMETIS_CFLAGS" LDFLAGS="$CYTHONFLAGS" log python setup.py build_ext --inplace || exit
+    rm -rf build *.c # temp files
+}
+
+#------------------ Default action , invoked by : './make_python' --------------------
+
+function make_user()
+{
+    check_python_modules netCDF4 mpi4py
+    # Cythonize Python modules
+    cd $DYNAMICO_ROOT/Python/dynamico
+    cythonize
+    rm -rf build *.c # temp files
+    cp -fpr $DYNAMICO_ROOT/Python/dynamico $DYNAMICO_ROOT/lib
+    check_dynamico_modules partition meshes dyn time_step DCMIP
+}
+
+function make_dev()
+{
+    check_python_modules jinja2
+    echo "XIOS_ROOTDIR : $XIOS_ROOTDIR"
+
+    make_so $XIOS_ROOTDIR/lib/libxios.a $LIBDIR/libxios.so "$NETCDF_LDFLAGS -lstdc++"
+    make_so $LIBDIR/libicosa.a $LIBDIR/libicosa.so "-L$LIBDIR -lxios $KERNELS_LDFLAGS" "physics_external_mod.o physics_mod.o timeloop_gcm_mod.o icosa_init_mod.o"
+
+    cd $DYNAMICO_ROOT/Python/dev
+    cythonize "-licosa"
+    cp -fpr $DYNAMICO_ROOT/Python/dev $DYNAMICO_ROOT/lib/dynamico/
+    check_dynamico_modules dev.cxios dev.unstructured
+}
+
+function cmd_()
+{
+    make_user
+}
+
+function cmd_dev()
+{
+    make_user
+    make_dev
+}
+
 
 #------------------------- script starts here ------------------------