Merge remote-tracking branch 'origin/main' into rygx/20240113_workflow

ANL-CEEESA · Jan 24, 2024 · 9d6ede0 · 9d6ede0
2 parents 24a6b80 + 8af9faf
commit 9d6ede0
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diff --git a/.envrc.local b/.envrc.local
@@ -0,0 +1 @@
+#!/bin/zsh
diff --git a/BUILD.bazel b/BUILD.bazel
@@ -59,29 +59,17 @@ cmake(
 cmake(
     name = "armadillo_lib",
     cache_entries = {
-        # "CMAKE_INSTALL_PREFIX": ".",
-        # "CMAKE_INSTALL_INCLUDEDIR": "include",
-        # deps ":openblas_lib_bazel" will be copied to "$EXT_BUILD_DEPS"
-        # The directory structure of ":openblas_lib_bazel" are retained,
-        # usually libraries are under /lib and headers are under /include
-        # "TPL_BLAS_LIBRARIES": "$EXT_BUILD_DEPS/lib/libopenblas.a"
         "BUILD_SHARED_LIBS": "OFF",
     },
     lib_source = "@armadillo//:all_srcs",
     out_static_libs = ["libarmadillo.a"],
-    # out_include_dir = "include",
     deps = [
-        # cannot directly use ":openblas_lib",
-        # need bridged through a `cc_library` containing ":openblas_lib"
-        # i.e. ":openblas_lib_bazel"
         ":openblas_lib_bazel"
     ],
     copts =[
         "-DARMA_DONT_USE_WRAPPER"
     ],
     linkopts = [
-        # "-lpthread",
-        # "-L$EXT_BUILD_DEPS/lib", "-lopenblas",
         "-lgfortran",
         ],
 )
@@ -94,100 +82,46 @@ cc_library(
     ],
 )
 
-cmake(
+# 
+configure_make(
     name = "hdf5_lib",
-    cache_entries = {
-        # "CMAKE_INSTALL_PREFIX": ".",
-        # "CMAKE_INSTALL_INCLUDEDIR": "include",
-        # deps ":openblas_lib_bazel" will be copied to "$EXT_BUILD_DEPS"
-        # The directory structure of ":openblas_lib_bazel" are retained,
-        # usually libraries are under /lib and headers are under /include
-        # "TPL_BLAS_LIBRARIES": "$EXT_BUILD_DEPS/lib/libopenblas.a"
-        "BUILD_SHARED_LIBS": "OFF",
-        "CMAKE_BUILD_TYPE": "Release",
-        "HDF5_BUILD_TOOLS": "ON",
-        "BUILD_TESTING": "ON",
-        "SZIP_USE_EXTERNAL": "ON",
-        "ZLIB_USE_EXTERNAL": "ON",
-        "USE_LIBAEC_STATIC": "ON",
-        "SZIP_INCLUDE_DIR": "$EXT_BUILD_DEPS/include",
-        "ZLIB_INCLUDE_DIR": "$EXT_BUILD_DEPS/include",
-        "SZIP_LIBRARY": "$EXT_BUILD_DEPS/lib/libsz.a",
-        "ZLIB_LIBRARY": "$EXT_BUILD_DEPS/lib/libz.a",
-    },
+    configure_in_place = True,
+    configure_options = [
+        "--with-szlib=libaec/include,$EXT_BUILD_DEPS/libaec/lib",
+        "--with-zlib=z_lib/include,$EXT_BUILD_DEPS/z_lib/lib",
+    ],
     lib_source = "@hdf5//:all_srcs",
-    out_static_libs = ["libhdf5.a"],
-    # out_include_dir = "include",
     deps = [
-        # cannot directly use ":openblas_lib",
-        # need bridged through a `cc_library` containing ":openblas_lib"
-        # i.e. ":openblas_lib_bazel"
-        # ":openblas_lib_bazel"
         ":hdf5_deps_lib",
     ],
-    linkopts = [
-        # "-lpthread",
-        # "-L$EXT_BUILD_DEPS/lib", "-lopenblas",
-        # "-lgfortran",
-        # "-lsz", "-lz",
-        ],
+    out_static_libs = ["libhdf5.a"],
+    linkopts = ["-lpthread"],
+    includes = [
+        "z_lib/include",
+        "libaec/include",
+    ]
 )
 
 cmake(
     name = "z_lib",
     cache_entries = {
-        # "CMAKE_INSTALL_PREFIX": ".",
-        # "CMAKE_INSTALL_INCLUDEDIR": "include",
-        # deps ":openblas_lib_bazel" will be copied to "$EXT_BUILD_DEPS"
-        # The directory structure of ":openblas_lib_bazel" are retained,
-        # usually libraries are under /lib and headers are under /include
-        # "TPL_BLAS_LIBRARIES": "$EXT_BUILD_DEPS/lib/libopenblas.a"
         "BUILD_SHARED_LIBS": "OFF",
     },
     lib_source = "@zlib//:all_srcs",
     out_static_libs = ["libz.a"],
-    # out_include_dir = "include",
-    deps = [
-        # cannot directly use ":openblas_lib",
-        # need bridged through a `cc_library` containing ":openblas_lib"
-        # i.e. ":openblas_lib_bazel"
-        # ":openblas_lib_bazel"
-    ],
-    linkopts = [
-        # "-lpthread",
-        # "-L$EXT_BUILD_DEPS/lib", "-lopenblas",
-        # "-lgfortran",
-        ],
+    copts = ["-fPIC"] # this is necessary otherwise will cause hdf5 build to complain
 )
 
 cmake(
     name = "libaec",
     cache_entries = {
-        # "CMAKE_INSTALL_PREFIX": ".",
-        # "CMAKE_INSTALL_INCLUDEDIR": "include",
-        # deps ":openblas_lib_bazel" will be copied to "$EXT_BUILD_DEPS"
-        # The directory structure of ":openblas_lib_bazel" are retained,
-        # usually libraries are under /lib and headers are under /include
-        # "TPL_BLAS_LIBRARIES": "$EXT_BUILD_DEPS/lib/libopenblas.a"
         "BUILD_SHARED_LIBS": "OFF",
     },
     lib_source = "@libaec//:all_srcs",
     out_static_libs = [
         "libaec.a",
         "libsz.a",
         ],
-    # out_include_dir = "include",
-    deps = [
-        # cannot directly use ":openblas_lib",
-        # need bridged through a `cc_library` containing ":openblas_lib"
-        # i.e. ":openblas_lib_bazel"
-        # ":openblas_lib_bazel"
-    ],
-    linkopts = [
-        # "-lpthread",
-        # "-L$EXT_BUILD_DEPS/lib", "-lopenblas",
-        # "-lgfortran",
-        ],
 )
 
 # 
@@ -197,15 +131,12 @@ configure_make(
     configure_options = [
         "--enable-mat73=yes",
         "--enable-extended-sparse=yes",
-        "--with-zlib=\"$EXT_BUILD_DEPS/hdf5_lib/lib\"",
-        "--with-hdf5=\"$EXT_BUILD_DEPS/z_lib/lib\"",
+        "--with-hdf5=\"$EXT_BUILD_DEPS/hdf5_lib/lib\"",
+        "--with-zlib=\"$EXT_BUILD_DEPS/z_lib/lib\"",
         "--with-default-file-ver=7.3",
     ],
     lib_source = "@libmatio//:all_srcs",
     deps = [
-        # cannot directly use ":openblas_lib",
-        # need bridged through a `cc_library` containing ":openblas_lib"
-        # i.e. ":openblas_lib_bazel"
         ":hdf5_lib",
         ":z_lib",
     ],
@@ -216,28 +147,10 @@ configure_make(
 cmake(
     name = "libjsoncpp",
     cache_entries = {
-        # "CMAKE_INSTALL_PREFIX": ".",
-        # "CMAKE_INSTALL_INCLUDEDIR": "include",
-        # deps ":openblas_lib_bazel" will be copied to "$EXT_BUILD_DEPS"
-        # The directory structure of ":openblas_lib_bazel" are retained,
-        # usually libraries are under /lib and headers are under /include
-        # "TPL_BLAS_LIBRARIES": "$EXT_BUILD_DEPS/lib/libopenblas.a"
         "BUILD_SHARED_LIBS": "OFF",
     },
     lib_source = "@jsoncpp//:all_srcs",
     out_static_libs = [
         "libjsoncpp.a",
         ],
-    # out_include_dir = "include",
-    deps = [
-        # cannot directly use ":openblas_lib",
-        # need bridged through a `cc_library` containing ":openblas_lib"
-        # i.e. ":openblas_lib_bazel"
-        # ":openblas_lib_bazel"
-    ],
-    linkopts = [
-        # "-lpthread",
-        # "-L$EXT_BUILD_DEPS/lib", "-lopenblas",
-        # "-lgfortran",
-        ],
 )
diff --git a/app/BUILD.bazel b/app/BUILD.bazel
@@ -13,5 +13,8 @@ cc_binary(
         "//sas:sas_expr_parser_lib",
         "//sas:sas_model_parser_lib",
         "@nvwa//:nvwa_pctimer_headers",
-    ]
+    ],
+    env = {
+
+    }
 )
diff --git a/app/main.cpp b/app/main.cpp
@@ -400,7 +400,7 @@ int main(int argc, char **argv)
 		double alphaTol = 1e-4;
 		double diffTol = 1e-6;
 		double diffTolMax = 1e-2;
-		int repeat = 10;
+		int repeat = 1;
 		for (int iArg = 2; iArg < argc; iArg++)
 		{
 			string arg = argv[iArg];

diff --git a/pf/ChePFCalculator.cpp b/pf/ChePFCalculator.cpp
@@ -1232,7 +1232,8 @@ namespace che {
 					if(this->perm_c==NULL){
 						options.ColPerm=arma::superlu::COLAMD;
 					}else{
-						options.ColPerm=arma::superlu::MY_PERMC;
+						// TODO - rygx: work with arma team to fix the enum slip issue
+						options.ColPerm=static_cast<arma::superlu::colperm_t>(8); // This represents the MY_PERMC in SuperLu 6.0
 						arrayops::copy(perm_c,this->perm_c,A.n_cols + 1);
 					}
 					options.Fact=arma::superlu::DOFACT;
@@ -1243,37 +1244,8 @@ namespace che {
 						arrayops::copy(perm_r,this->perm_r,A.n_rows + 1);
 						arrayops::copy(etree,this->etree,A.n_cols + 1);
 					}
-					if (use_iter_solver){
-						// arma_wrapper(dgssvx)(&options, &superA, perm_c, perm_r, etree, equed, R, C, &superL, &superU, &work[0], lwork, &superB, &superX, &rpg, &rcond, ferr, berr, &glu, &mu, &stat, &superInfo);
-						arma_wrapper(ilu_set_default_options)(&options);
-						options.Equil=arma::superlu::NO;
-						lwork=0;
-						char equedx[1]={'N'};
-						arma_wrapper(dgsisx)(&options, &superA, perm_c, perm_r, etree, equedx, R, C, &superL, &superU, NULL, 0, &superB, &superX, &rpg, &rcond, &glu, &mu, &stat, &superInfo);
-						// arma_wrapper(dgsitrf)(&options, &superA, 2, 10, etree, &work[0], lwork, perm_c, perm_r, &superL, &superU, &glu, &stat, &superInfo);
-						// arma_wrapper(dgstrs)(options.Trans, &superL, &superU, perm_c, perm_r, &superX, &stat, &superInfo);
-
-						vec xx=RHS;
-						arma::superlu::SuperMatrix superX2;  arrayops::inplace_set(reinterpret_cast<char*>(&superX2), char(0), sizeof(arma::superlu::SuperMatrix));
-
-						const bool status_x2 = sp_auxlib::wrap_to_supermatrix(superX2, xx);
-						arma_wrapper(dgstrs)(options.Trans, &superL, &superU, perm_c, perm_r, &superX2, &stat, &superInfo);
-						x=xx;
-						sp_auxlib::destroy_supermatrix(superX2);
-
-						int max_it=5000;
-						double tol=1.0e-10;
-						double err=0.0;
-						int iter=0;
-						int flag=0;
-						// x.fill(0.0);
-						// LHS_mat.print("A");
-						vec cbx=RHS;
-						bicgstab(LHS_mat, x, cbx, options.Trans, &superL, &superU, perm_c, perm_r, &stat, &superInfo, max_it, tol, &err, &iter, &flag);
-					}else{						
-						arma_wrapper(dgssvx)(&options, &superA, perm_c, perm_r, etree, equed, R, C, &superL, &superU, &work[0], lwork, &superB, &superX, &rpg, &rcond, ferr, berr, &glu, &mu, &stat, &superInfo);
-					}
-					// arma_wrapper(dgssvx)(&options, &superA, perm_c, perm_r, etree, equed, R, C, &superL, &superU, &work[0], lwork, &superB, &superX, &rpg, &rcond, ferr, berr, &glu, &mu, &stat, &superInfo);
+
+					arma_wrapper(dgssvx)(&options, &superA, perm_c, perm_r, etree, equed, R, C, &superL, &superU, &work[0], lwork, &superB, &superX, &rpg, &rcond, ferr, berr, &glu, &mu, &stat, &superInfo);
 
 					if(this->perm_c==NULL){
 						this->perm_c=new int[A.n_cols + 1];
@@ -1288,39 +1260,8 @@ namespace che {
 					arrayops::copy(this->perm_r,perm_r,A.n_rows + 1);
 					arrayops::copy(this->etree,etree,A.n_cols + 1);
 				}
-				else {
-					if (use_iter_solver){
-						// x.print("xx");
-						// arma_wrapper(dgstrs)(options.Trans, &superL, &superU, perm_c, perm_r, &superX, &stat, &superInfo);
-						// x.print("xx");
-						arma_wrapper(ilu_set_default_options)(&options);
-						options.Equil=arma::superlu::NO;
-						// lwork=0;
-						// char equedx[1]={'B'};
-						// arma_wrapper(dgsisx)(&options, &superA, perm_c, perm_r, etree, equedx, R, C, &superL, &superU, NULL, 0, &superB, &superX, &rpg, &rcond, &glu, &mu, &stat, &superInfo);
-
-						int max_it=5000;
-						double tol=1.0e-10;
-						double err=0.0;
-						int iter=0;
-						int flag=0;
-
-						vec xx=RHS;
-						arma::superlu::SuperMatrix superX2;  arrayops::inplace_set(reinterpret_cast<char*>(&superX2), char(0), sizeof(arma::superlu::SuperMatrix));
-
-						const bool status_x2 = sp_auxlib::wrap_to_supermatrix(superX2, xx);
-						arma_wrapper(dgstrs)(options.Trans, &superL, &superU, perm_c, perm_r, &superX2, &stat, &superInfo);
-						x=xx;
-						sp_auxlib::destroy_supermatrix(superX2);
-
-						// x.print("x");
-						vec cbx=RHS;
-						bicgstab(LHS_mat, x, cbx, options.Trans, &superL, &superU, perm_c, perm_r, &stat, &superInfo, max_it, tol, &err, &iter, &flag);
-						// x.print("x");
-					}else{						
-						arma_wrapper(dgstrs)(options.Trans, &superL, &superU, perm_c, perm_r, &superX, &stat, &superInfo);
-					}
-
+				else {									
+					arma_wrapper(dgstrs)(options.Trans, &superL, &superU, perm_c, perm_r, &superX, &stat, &superInfo);					
 				}
 
 				// x.print("x");	

diff --git a/pf/ChePFCalculator.h b/pf/ChePFCalculator.h
@@ -83,6 +83,7 @@ namespace che {
 
 			virtual CheSolution* getCheSolution();
 		};
+
 	}
 }
 

diff --git a/sas/BUILD.bazel b/sas/BUILD.bazel
@@ -94,7 +94,7 @@ cc_library(
         "ModelParser.cpp",
     ],
     deps = [
-        ":sas_expr_lib",
+        ":sas_expr_parser_lib",
     ]
 )
 

diff --git a/util/SafeArmadillo.h b/util/SafeArmadillo.h
@@ -28,6 +28,7 @@
 #define _Che_SafeArmadillo_H
 
 #define ARMA_USE_SUPERLU
+#define ARMA_USE_LAPACK
 #define ARMA_DONT_USE_WRAPPER
 #include <armadillo>
-Original file line number
+Diff line change
@@ Expand Up / @@ -83,6 +83,7 @@ namespace che { @@
     			virtual CheSolution* getCheSolution();
     		};
     	}
     }
@@ Expand Down @@