Merge branch 'jose/sync-petsc-mathash' into 'main'

Sync with PETSc after changing Mat to use hash allocation

See merge request slepc/slepc!492

.gitlab-ci.yml

@@ -17,7 +17,6 @@ variables:
   GIT_STRATEGY: fetch
   GIT_CLEAN_FLAGS: -ffdxq
   TIMEOUT: 600
-  PETSC_OPTIONS: -checkfunctionlist
 
 #
 # The most basic template that most tests will expand upon. In particular merge requests and branch pushes DO NOT trigger testing

config/packages/slepc4py.py

@@ -105,8 +105,8 @@ def Process(self,slepcconf,slepcvars,slepcrules,slepc,petsc,archdir=''):
       slepcrules.write('slepc4py-install:\n')
 
     rule =  'slepc4pytest:\n'
-    rule += '\t@echo "*** Testing slepc4py ***"\n'
-    rule += '\t@PYTHONPATH=%s:%s ${PYTHON} %s --verbose\n' % (destdir,pythonpath,os.path.join('src','binding','slepc4py','test','runtests.py'))
+    rule += '\t@echo "*** Testing slepc4py on ${PETSC4PY_NP} processes ***"\n'
+    rule += '\t@PYTHONPATH=%s:%s PETSC_OPTIONS="{PETSC_OPTIONS} -check_pointer_intensity 0 -error_output_stdout -malloc_dump ${PETSC_TEST_OPTIONS}" ${MPIEXEC} -n ${PETSC4PY_NP} ${PYTHON} %s --verbose\n' % (destdir,pythonpath,os.path.join('src','binding','slepc4py','test','runtests.py'))
     rule += '\t@echo "====================================="\n\n'
     slepcrules.write(rule)
 

gmakefile.test

@@ -111,7 +111,7 @@ endif
 $(generatedtest) : $(slepcconf) $(slepcvariables) $(PETSCCONFIGDIR)/gmakegentest.py $(TESTDIR)/.DIR | $$(@D)/.DIR
 	$(PYTHON) $(PETSCCONFIGDIR)/gmakegentest.py --petsc-dir=$(PETSC_DIR) --petsc-arch=$(PETSC_ARCH_DIR) --testdir=$(TESTDIR) --srcdir=$(TESTSRCDIR) --pkg-name=slepc --pkg-pkgs=$(spkgs) --pkg-arch=$(PETSC_ARCH) --pkg-dir=$(SLEPC_DIR)
 
-ifneq ($(filter-out clean check info slepc_libs all checkbadSource checkbadFileChange allfortranstubs alletags get%,$(MAKECMDGOALS:clean%=clean)),)
+ifneq ($(filter-out help clean check info slepc_libs all checkbadSource checkbadFileChange allfortranstubs alletags get%,$(MAKECMDGOALS:clean%=clean)),)
 include $(generatedtest)
 endif
 
@@ -413,7 +413,7 @@ help: help-make ${helpdeps}
 
 help-make:
 	-@echo
-	-@echo "Basic usage:"
+	-@echo "SLEPc makefile basic usage:"
 	-@echo "   make  rule <V=1 for verbose output> <other options>"
 	-@echo
 
@@ -429,6 +429,7 @@ help-nontest:
 	-@echo "   getcxxflags - print the C++ compiler flags PETSc is using"
 	-@echo "   getfortranflags - print the Fortran compiler flags PETSc is using"
 	-@echo "   "
+	-@echo "   slepc4pytest - run the entire slepc4py test suite"
 	-@echo "   alltests - run the entire SLEPc test suite"
 	-@echo "   test - use \"make -f gmakefile.test help\" for help on running the extensive tests"
 	-@echo

src/eps/tests/output/test35_1.out

@@ -39,7 +39,7 @@ ST Object: 1 MPI process
     Mat Object: (st_) 1 MPI process
       type: seqaij
       rows=1225, cols=1225
-      total: nonzeros=5985, allocated nonzeros=6125
+      total: nonzeros=5985, allocated nonzeros=5985
       total number of mallocs used during MatSetValues calls =0
         not using I-node routines
  BLOPEX: using block size 4

src/eps/tests/output/test38_1.out

@@ -57,7 +57,7 @@ ST Object: 1 MPI process
     Mat Object: (st_) 1 MPI process
       type: seqaij
       rows=100, cols=100
-      total: nonzeros=460, allocated nonzeros=500
+      total: nonzeros=460, allocated nonzeros=460
       total number of mallocs used during MatSetValues calls=0
         not using I-node routines
  EPSLYAPII ranks: for Lyapunov solver=30, after compression=10

src/eps/tests/test43.c

@@ -49,7 +49,6 @@ int main(int argc,char **args)
   PetscCall(ISRestoreIndices(sizes,&idx));
   PetscCall(ISDestroy(&sizes));
   PetscCall(PetscViewerDestroy(&viewer));
-  PetscCall(MatSetUp(A));
   PetscCall(PetscSNPrintf(name,sizeof(name),"%s/A.dat",dir));
   PetscCall(PetscViewerBinaryOpen(PETSC_COMM_WORLD,name,FILE_MODE_READ,&viewer));
   PetscCall(MatLoad(A,viewer));

src/lme/tests/output/test1_3.out

@@ -2,13 +2,12 @@
 
 Lyapunov equation, N=100 (10x10 grid)
 
-[0] <mat> MatSetUp(): Warning not preallocating matrix storage
-[0] <mat> MatAssemblyEnd_SeqAIJ(): Matrix size: 100 X 100; storage space: 40 unneeded,460 used
+[0] <mat> MatSetUp_Seq_Hash(): Using hash-based MatSetValues() for MATSEQAIJ because no preallocation provided
+[0] <mat> MatAssemblyEnd_SeqAIJ(): Matrix size: 100 X 100; storage space: 0 unneeded,460 used
 [0] <mat> MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
 [0] <mat> MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 5
 [0] <mat> MatCheckCompressedRow(): Found the ratio (num_zerorows 0)/(num_localrows 100) < 0.6. Do not use CompressedRow routines.
 [0] <mat> MatSeqAIJCheckInode(): Found 100 nodes out of 100 rows. Not using Inode routines
-[0] <mat> MatSetUp(): Warning not preallocating matrix storage
  Equation type set to 1
  Equation type changed to 0
  Solver being used: krylov

src/pep/tests/output/test5_1.out

@@ -61,7 +61,7 @@ ST Object: 1 MPI process
     Mat Object: (st_) 1 MPI process
       type: seqaij
       rows=6, cols=6
-      total: nonzeros=6, allocated nonzeros=30
+      total: nonzeros=6, allocated nonzeros=6
       total number of mallocs used during MatSetValues calls =0
         not using I-node routines
  Polynomial eigensolve converged (12 eigenpairs) due to CONVERGED_TOL; iterations 1

src/pep/tests/output/test5_4.out

@@ -54,7 +54,7 @@ ST Object: 1 MPI process
     Mat Object: (st_) 1 MPI process
       type: seqaij
       rows=6, cols=6
-      total: nonzeros=6, allocated nonzeros=30
+      total: nonzeros=6, allocated nonzeros=6
       total number of mallocs used during MatSetValues calls=0
         not using I-node routines
  ---------------------- --------------------