Removal of time interval and closing files within BasisWriter::writeB…

…asis (#261) * BasisWriter::writeBasis create/open a file and closes the file at the end. * stylization. * HDFDatabase::putIntegerArray - overwrites if the dataset exists. * enforce single time interval in Options. * HDFDatabase::putIntegerArray does not allow overwrite. * BasisWriter::writeBasis always create the file, which will overwrite the exisiting file. * add a header and stylization. * remove increase time interval test, as time interval is fixed to 1. * add an error message for a guidance. * remove test_SVD from ci workflow. * SVD::increaseTimeInterval - allow the initial time interval. * minor fix in test_IncrementalSVDBrand. * reflecting the comments. * removed the concept of time interval in BasisReader. time argument remains for backward compatibility. * BasisWriter: removed the concept of time interval. * minor fix in BasisReader. * SVD: removed the concept of time intervals. * BasisGenerator: removed the concept of time interval. * add test_SVD.cpp for resolving conflict. * stylization. * changed function signature of BasisGenerator::takeSample. * rebased to resolve conflict. * changed function signature for BasisReader::getSpatialBasis. * changed function signature for BasisReader::getTemporalBasis. * changed function signature for BasisReader::getSingularValues. * changed function signature for BasisReader::getSnapshotMatrix. * removed Options::max_time_intervals * SVD::isNewSample -> isFirstSample * update comments for StaticSVD::isBasisCurrent * minor comment updates. * stylization. * update dataset names and added python script for dataset name update. * fixed the ci workflow * minor fix in ci workflow. * minor fix * removed BasisReader:isNewBasis * minor doxygen comment update
LLNL · Apr 2, 2024 · fde345c · fde345c
1 parent 9a1e42b
commit fde345c
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diff --git a/.github/workflows/run_tests/action.yml b/.github/workflows/run_tests/action.yml
@@ -4,7 +4,6 @@ runs:
     - name: Run unit tests
       run: |
           cd ${GITHUB_WORKSPACE}/build
-          ./tests/test_SVD
           ./tests/test_Vector
           ./tests/test_Matrix
           mpirun -n 3 --oversubscribe ./tests/test_Matrix
@@ -24,7 +23,15 @@ runs:
           mpirun -n 3 --oversubscribe tests/test_StaticSVD
           ./tests/test_IncrementalSVDBrand
           mpirun -n 3 --oversubscribe tests/test_IncrementalSVDBrand
-          
+      shell: bash
+    - name: Basis dataset update test
+      run: |
+          cd ${GITHUB_WORKSPACE}/build/tests
+          cp ${GITHUB_WORKSPACE}/unit_tests/baselines/basis_conversion/* ./
+          cp ${GITHUB_WORKSPACE}/scripts/data/update_basis_format.py ./
+          python3 update_basis_format.py test_basis.000000
+          python3 update_basis_format.py test_basis_snapshot.000000
+          ./test_basis_conversion
       shell: bash
 
     - name: Run regression tests

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -271,12 +271,12 @@ if(GTEST_FOUND)
     GNAT
     QDEIM
     S_OPT
-    SVD
     StaticSVD
     RandomizedSVD
     IncrementalSVD
     IncrementalSVDBrand
-    GreedyCustomSampler)
+    GreedyCustomSampler
+    basis_conversion)
   foreach(stem IN LISTS unit_test_stems)
     add_executable(test_${stem} unit_tests/test_${stem}.cpp)
     target_link_libraries(test_${stem} PRIVATE ROM

diff --git a/examples/misc/combine_samples.cpp b/examples/misc/combine_samples.cpp
@@ -101,8 +101,8 @@ int main(int argc, char* argv[])
     for (const auto& sample_name: sample_names) {
         CAROM::BasisReader reader(sample_name);
 
-        dim    = reader.getDim(kind, 0);
-        snaps += reader.getNumSamples(kind, 0);
+        dim    = reader.getDim(kind);
+        snaps += reader.getNumSamples(kind);
         if (dimFirst == 0) dimFirst = dim;
 
         CAROM_VERIFY(dim ==
@@ -180,7 +180,7 @@ int main(int argc, char* argv[])
         CAROM::Vector snap_cur(num_rows, true);
         for (int col = 0; col < num_cols; col++) {
             snap_cur = *snapshots->getColumn(col);
-            static_basis_generator2->takeSample(snap_cur.getData(), 0.0, false);
+            static_basis_generator2->takeSample(snap_cur.getData(), false);
         }
 
         /*-- Compute SVD and save file --*/

diff --git a/examples/prom/de_parametric_maxwell_greedy.cpp b/examples/prom/de_parametric_maxwell_greedy.cpp
@@ -221,7 +221,7 @@ double simulation()
     // 12. Set BasisGenerator if offline
     if (offline)
     {
-        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots, 1,
+        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots,
                                      update_right_SV);
         if (myid == 0) cout << "Saving basis to: " << saveBasisName << endl;
         generator = new CAROM::BasisGenerator(*options, isIncremental, saveBasisName);
@@ -316,7 +316,7 @@ double simulation()
         // 19. take and write snapshot for ROM
         if (offline)
         {
-            bool addSample = generator->takeSample(X.GetData(), 0.0, 0.01);
+            bool addSample = generator->takeSample(X.GetData());
             generator->writeSnapshot();
             basisIdentifiers.push_back(saveBasisName);
             delete generator;
@@ -329,7 +329,7 @@ double simulation()
         // 21. read the reduced basis
         assembleTimer.Start();
         CAROM::BasisReader reader(loadBasisName);
-        spatialbasis = reader.getSpatialBasis(0.0);
+        spatialbasis = reader.getSpatialBasis();
         numRowRB = spatialbasis->numRows();
         numColumnRB = spatialbasis->numColumns();
 
@@ -513,7 +513,7 @@ double simulation()
     {
         mergeTimer.Start();
         std::unique_ptr<CAROM::BasisGenerator> basis_generator;
-        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots, 1,
+        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots,
                                      update_right_SV);
         generator = new CAROM::BasisGenerator(*options, isIncremental, loadBasisName);
         for (int i = 0; i < basisIdentifiers.size(); ++i)

diff --git a/examples/prom/dg_advection_global_rom.cpp b/examples/prom/dg_advection_global_rom.cpp
@@ -692,19 +692,19 @@ int main(int argc, char *argv[])
     // 10. Set BasisGenerator if offline
     if (offline)
     {
-        options = new CAROM::Options(U->Size(), max_num_snapshots, 1, update_right_SV);
+        options = new CAROM::Options(U->Size(), max_num_snapshots, update_right_SV);
         generator = new CAROM::BasisGenerator(*options, isIncremental, basisFileName);
         Vector u_curr(*U);
         Vector u_centered(U->Size());
         subtract(u_curr, u_init, u_centered);
-        bool addSample = generator->takeSample(u_centered.GetData(), t, dt);
+        bool addSample = generator->takeSample(u_centered.GetData());
     }
 
     // 11. The merge phase
     if (merge)
     {
         mergeTimer.Start();
-        options = new CAROM::Options(U->Size(), max_num_snapshots, 1, update_right_SV);
+        options = new CAROM::Options(U->Size(), max_num_snapshots, update_right_SV);
         generator = new CAROM::BasisGenerator(*options, isIncremental, basisName);
         for (int paramID=0; paramID<nsets; ++paramID)
         {
@@ -731,11 +731,11 @@ int main(int argc, char *argv[])
         CAROM::BasisReader reader(basisName);
         if (rdim != -1)
         {
-            spatialbasis = reader.getSpatialBasis(0.0, rdim);
+            spatialbasis = reader.getSpatialBasis(rdim);
         }
         else
         {
-            spatialbasis = reader.getSpatialBasis(0.0, ef);
+            spatialbasis = reader.getSpatialBasis(ef);
         }
         numRowRB = spatialbasis->numRows();
         numColumnRB = spatialbasis->numColumns();
@@ -831,7 +831,7 @@ int main(int argc, char *argv[])
             Vector u_curr(*U);
             Vector u_centered(U->Size());
             subtract(u_curr, u_init, u_centered);
-            bool addSample = generator->takeSample(u_centered.GetData(), t, dt);
+            bool addSample = generator->takeSample(u_centered.GetData());
         }
 
         if (done || ti % vis_steps == 0)

diff --git a/examples/prom/dg_advection_local_rom_matrix_interp.cpp b/examples/prom/dg_advection_local_rom_matrix_interp.cpp
@@ -706,12 +706,12 @@ int main(int argc, char *argv[])
     // 10. Set BasisGenerator if offline
     if (offline)
     {
-        options = new CAROM::Options(U->Size(), max_num_snapshots, 1, update_right_SV);
+        options = new CAROM::Options(U->Size(), max_num_snapshots, update_right_SV);
         generator = new CAROM::BasisGenerator(*options, isIncremental, basisName);
         Vector u_curr(*U);
         Vector u_centered(U->Size());
         subtract(u_curr, u_init, u_centered);
-        bool addSample = generator->takeSample(u_centered.GetData(), t, dt);
+        bool addSample = generator->takeSample(u_centered.GetData());
     }
 
     if (online)
@@ -723,11 +723,11 @@ int main(int argc, char *argv[])
             CAROM::BasisReader reader(basisName);
             if (rdim != -1)
             {
-                spatialbasis = reader.getSpatialBasis(0.0, rdim);
+                spatialbasis = reader.getSpatialBasis(rdim);
             }
             else
             {
-                spatialbasis = reader.getSpatialBasis(0.0, ef);
+                spatialbasis = reader.getSpatialBasis(ef);
             }
             numRowRB = spatialbasis->numRows();
             numColumnRB = spatialbasis->numColumns();
@@ -819,7 +819,7 @@ int main(int argc, char *argv[])
                 CAROM::BasisReader reader(parametricBasisName);
 
                 MFEM_VERIFY(rdim != -1, "rdim must be used for interpolation.");
-                CAROM::Matrix* parametricSpatialBasis = reader.getSpatialBasis(0.0, rdim);
+                CAROM::Matrix* parametricSpatialBasis = reader.getSpatialBasis(rdim);
                 numRowRB = parametricSpatialBasis->numRows();
                 numColumnRB = parametricSpatialBasis->numColumns();
                 bases.push_back(parametricSpatialBasis);
@@ -932,7 +932,7 @@ int main(int argc, char *argv[])
             Vector u_curr(*U);
             Vector u_centered(U->Size());
             subtract(u_curr, u_init, u_centered);
-            bool addSample = generator->takeSample(u_centered.GetData(), t, dt);
+            bool addSample = generator->takeSample(u_centered.GetData());
         }
 
         if (done || ti % vis_steps == 0)

diff --git a/examples/prom/grad_div_global_rom.cpp b/examples/prom/grad_div_global_rom.cpp
@@ -225,7 +225,7 @@ int main(int argc, char *argv[])
     // 10. Set BasisGenerator if offline
     if (offline)
     {
-        options = new CAROM::Options(fespace.GetTrueVSize(), max_num_snapshots, 1,
+        options = new CAROM::Options(fespace.GetTrueVSize(), max_num_snapshots,
                                      update_right_SV);
         generator = new CAROM::BasisGenerator(*options, isIncremental, basisFileName);
     }
@@ -234,7 +234,7 @@ int main(int argc, char *argv[])
     if (merge)
     {
         mergeTimer.Start();
-        options = new CAROM::Options(fespace.GetTrueVSize(), max_num_snapshots, 1,
+        options = new CAROM::Options(fespace.GetTrueVSize(), max_num_snapshots,
                                      update_right_SV);
         generator = new CAROM::BasisGenerator(*options, isIncremental, basisName);
         for (int paramID=0; paramID<nsets; ++paramID)
@@ -358,7 +358,7 @@ int main(int argc, char *argv[])
         // 18. take and write snapshot for ROM
         if (offline)
         {
-            generator->takeSample(X.GetData(), 0.0, 0.01);
+            generator->takeSample(X.GetData());
             generator->writeSnapshot();
             delete generator;
             delete options;
@@ -370,7 +370,7 @@ int main(int argc, char *argv[])
         // 20. read the reduced basis
         assembleTimer.Start();
         CAROM::BasisReader reader(basisName);
-        const CAROM::Matrix* spatialbasis = reader.getSpatialBasis(0.0);
+        const CAROM::Matrix* spatialbasis = reader.getSpatialBasis();
         const int numRowRB = spatialbasis->numRows();
         const int numColumnRB = spatialbasis->numColumns();
         if (myid == 0) printf("spatial basis dimension is %d x %d\n", numRowRB,

diff --git a/examples/prom/linear_elasticity_global_rom.cpp b/examples/prom/linear_elasticity_global_rom.cpp
@@ -235,7 +235,7 @@ int main(int argc, char* argv[])
     // 10. Set BasisGenerator if offline
     if (offline)
     {
-        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots, 1,
+        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots,
                                      update_right_SV);
         generator = new CAROM::BasisGenerator(*options, isIncremental, basisFileName);
     }
@@ -244,7 +244,7 @@ int main(int argc, char* argv[])
     if (merge)
     {
         mergeTimer.Start();
-        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots, 1,
+        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots,
                                      update_right_SV);
         generator = new CAROM::BasisGenerator(*options, isIncremental, basisName);
         for (int paramID = 0; paramID < nsets; ++paramID)
@@ -367,7 +367,7 @@ int main(int argc, char* argv[])
         // 18. take and write snapshot for ROM
         if (offline)
         {
-            bool addSample = generator->takeSample(X.GetData(), 0.0, 0.01);
+            bool addSample = generator->takeSample(X.GetData());
             generator->writeSnapshot();
             delete generator;
             delete options;
@@ -379,7 +379,7 @@ int main(int argc, char* argv[])
         // 20. read the reduced basis
         assembleTimer.Start();
         CAROM::BasisReader reader(basisName);
-        const CAROM::Matrix* spatialbasis = reader.getSpatialBasis(0.0);
+        const CAROM::Matrix* spatialbasis = reader.getSpatialBasis();
         numRowRB = spatialbasis->numRows();
         numColumnRB = spatialbasis->numColumns();
         printf("On rank %d, spatial basis dimension is %d x %d\n", myid,

diff --git a/examples/prom/maxwell_global_rom.cpp b/examples/prom/maxwell_global_rom.cpp
@@ -229,7 +229,7 @@ int main(int argc, char *argv[])
     // 10. Set BasisGenerator if offline
     if (offline)
     {
-        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots, 1,
+        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots,
                                      update_right_SV);
         generator = new CAROM::BasisGenerator(*options, isIncremental, basisFileName);
     }
@@ -238,7 +238,7 @@ int main(int argc, char *argv[])
     if (merge)
     {
         mergeTimer.Start();
-        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots, 1,
+        options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots,
                                      update_right_SV);
         generator = new CAROM::BasisGenerator(*options, isIncremental, basisName);
         for (int paramID=0; paramID<nsets; ++paramID)
@@ -348,7 +348,7 @@ int main(int argc, char *argv[])
         // 18. take and write snapshot for ROM
         if (offline)
         {
-            bool addSample = generator->takeSample(X.GetData(), 0.0, 0.01);
+            bool addSample = generator->takeSample(X.GetData());
             generator->writeSnapshot();
             delete generator;
             delete options;
@@ -360,7 +360,7 @@ int main(int argc, char *argv[])
         // 20. read the reduced basis
         assembleTimer.Start();
         CAROM::BasisReader reader(basisName);
-        spatialbasis = reader.getSpatialBasis(0.0);
+        spatialbasis = reader.getSpatialBasis();
         numRowRB = spatialbasis->numRows();
         numColumnRB = spatialbasis->numColumns();
         if (myid == 0) printf("spatial basis dimension is %d x %d\n", numRowRB,

diff --git a/examples/prom/maxwell_local_rom_greedy.cpp b/examples/prom/maxwell_local_rom_greedy.cpp
@@ -374,7 +374,7 @@ int main(int argc, char *argv[])
         // 12. Set BasisGenerator if offline
         if (offline)
         {
-            options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots, 1,
+            options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots,
                                          update_right_SV);
             if (myid == 0) cout << "Saving basis to: " << saveBasisName << endl;
             generator = new CAROM::BasisGenerator(*options, isIncremental, saveBasisName);
@@ -469,7 +469,7 @@ int main(int argc, char *argv[])
             // 19. take and write snapshot for ROM
             if (offline)
             {
-                bool addSample = generator->takeSample(X.GetData(), 0.0, 0.01);
+                bool addSample = generator->takeSample(X.GetData());
                 generator->writeSnapshot();
                 basisIdentifiers.push_back(saveBasisName);
                 delete generator;
@@ -482,7 +482,7 @@ int main(int argc, char *argv[])
             // 21. read the reduced basis
             assembleTimer.Start();
             CAROM::BasisReader reader(loadBasisName);
-            spatialbasis = reader.getSpatialBasis(0.0);
+            spatialbasis = reader.getSpatialBasis();
             numRowRB = spatialbasis->numRows();
             numColumnRB = spatialbasis->numColumns();
             if (myid == 0) printf("spatial basis dimension is %d x %d\n", numRowRB,
@@ -635,7 +635,7 @@ int main(int argc, char *argv[])
         {
             mergeTimer.Start();
             std::unique_ptr<CAROM::BasisGenerator> basis_generator;
-            options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots, 1,
+            options = new CAROM::Options(fespace->GetTrueVSize(), max_num_snapshots,
                                          update_right_SV);
             generator = new CAROM::BasisGenerator(*options, isIncremental, loadBasisName);
             for (int i = 0; i < basisIdentifiers.size(); ++i)