diff --git a/CMakeLists.txt b/CMakeLists.txt
index 47ff4752..fb218fc1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -218,6 +218,12 @@ if(PROGRESS_MPI)
 #  add_definitions(-DDO_MPI_BLOCK)
 endif()
 
+set(SANITY_CHECK FALSE CACHE BOOL "Additional sanity checks")
+if(SANITY_CHECK)
+  message(STATUS "Will add sanity checks")
+  add_definitions(-DSANITY_CHECK)
+endif()
+
 add_subdirectory(src)
 
 find_package(Doxygen)
diff --git a/build.sh b/build.sh
index 00e67ff4..6ea96181 100755
--- a/build.sh
+++ b/build.sh
@@ -40,20 +40,22 @@ EOF
     echo "INSTALL_DIR        Path to install dir      (default is ${INSTALL_DIR})"
     echo "EXTRA_FCFLAGS      Extra fortran flags      (default is ${EXTRA_FCFLAGS})"
     echo "EXTRA_LINK_FLAGS   Any extra link flag      (default is ${EXTRA_LINK_FLAGS})"
+    echo "SANITY_CHECK       Add sanity checks        (default is ${SANITY_CHECK})"
 }
 
 set_defaults() {
-    CMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE:=Release}
-    CC="${CC:=gcc}"
-    CXX="${CXX:=g++}"
-    FC="${FC:=gfortran}"
-    PROGRESS_OPENMP=${PROGRESS_OPENMP:=yes}
-    PROGRESS_MPI=${PROGRESS_MPI:=no}
-    PROGRESS_EXAMPLES=${PROGRESS_EXAMPLES:=no}
-    PROGRESS_GRAPHLIB=${PROGRESS_GRAPHLIB:=no}
-    EXTRA_FCFLAGS="${EXTRA_FCFLAGS:=}"
-    EXTRA_LINK_FLAGS=${EXTRA_LINK_FLAGS:=""}
-    PROGRESS_TESTING=${PROGRESS_TESTING:=no}
+    : ${CMAKE_BUILD_TYPE:=Release}
+    : "${CC:=gcc}"
+    : "${CXX:=g++}"
+    : "${FC:=gfortran}"
+    : ${PROGRESS_OPENMP:=yes}
+    : ${PROGRESS_MPI:=no}
+    : ${PROGRESS_TESTING:=no}
+    : ${PROGRESS_EXAMPLES:=no}
+    : ${PROGRESS_GRAPHLIB:=no}
+    : "${EXTRA_FCFLAGS:=}"
+    : ${EXTRA_LINK_FLAGS:=""}
+    : ${SANITY_CHECK:=no}
 }
 
 die() {
@@ -111,6 +113,7 @@ configure() {
         -DEXTRA_FCFLAGS="${EXTRA_FCFLAGS}" \
         -DEXTRA_LINK_FLAGS="${EXTRA_LINK_FLAGS}" \
         -DCMAKE_VERBOSE_MAKEFILE=${VERBOSE_MAKEFILE} \
+        -DSANITY_CHECK=${SANITY_CHECK} \
         | tee -a "${LOG_FILE}"
     check_pipe_error
     cd "${TOP_DIR}"
diff --git a/examples/gpmdcov/gpmdcov.F90 b/examples/gpmdcov/gpmdcov.F90
index e9f792ac..314d3999 100644
--- a/examples/gpmdcov/gpmdcov.F90
+++ b/examples/gpmdcov/gpmdcov.F90
@@ -291,6 +291,7 @@ subroutine gpmd_Part
     integer, allocatable :: graph_h(:,:)
     integer, allocatable :: graph_p(:,:)
     real(dp)             :: mls_ii
+    integer              :: iptt
 
     if(mdstep < 1)then
       if(lt%verbose >= 1 .and. myRank == 1)call prg_get_mem("gpmdcov", "Before prg_get_covgraph")
@@ -385,6 +386,24 @@ subroutine gpmd_Part
     ! write(*,*)"part by mol"
     ! call prg_molpartition(sy,nparts_cov,nl%nnStructMindist,nl%nnStruct,nl%nrnnstruct,"O ",gpat)
 
+#ifdef SANITY_CHECK
+    write(*, *) "sanity check before bml_matrix2submatrix_index"
+    do ipt = 1,gpat%TotalParts
+      do iptt = ipt+1,gpat%TotalParts
+        do i = 1, gpat%sgraph(ipt)%llsize
+          do j = 1, gpat%sgraph(iptt)%llsize
+            if(gpat%sgraph(ipt)%core_halo_index(i) == gpat%sgraph(iptt)%core_halo_index(j))then
+              write(*,*)"cores are repeated in partitions",mdstep
+              write(*,*)ipt,gpat%sgraph(ipt)%core_halo_index(i),iptt,gpat%sgraph(ipt)%core_halo_index(j)
+              write(*,*)i,j
+              stop
+            endif
+          enddo
+        enddo
+      enddo
+    enddo
+#endif
+
     mls_ii = mls()
     do i=1,gpat%TotalParts
       call bml_matrix2submatrix_index(g_bml,&
@@ -397,9 +416,25 @@ subroutine gpmd_Part
 
     if(lt%verbose >= 1 .and. myRank == 1)write(*,*)"Time for bml_matrix2submatrix_index "//to_string(mls()-mls_ii)//" ms"
 
-
     call gpmd_reshuffle()
 
+#ifdef SANITY_CHECK
+    write(*, *) "sanity check after bml_matrix2submatrix_index"
+    do ipt = 1,gpat%TotalParts
+      do iptt = ipt+1,gpat%TotalParts
+        do i = 1, gpat%sgraph(ipt)%llsize
+          do j = 1, gpat%sgraph(iptt)%llsize
+            if(gpat%sgraph(ipt)%core_halo_index(i) == gpat%sgraph(iptt)%core_halo_index(j))then
+              write(*,*)"cores are repeated in partitions",mdstep
+              write(*,*)ipt,gpat%sgraph(ipt)%core_halo_index(i),iptt,gpat%sgraph(ipt)%core_halo_index(j)
+              write(*,*)i,j
+              stop
+            endif
+          enddo
+        enddo
+      enddo
+    enddo
+#endif
 
     if(allocated(syprt))deallocate(syprt)
     allocate(syprt(gpat%TotalParts))
@@ -434,7 +469,6 @@ subroutine gpmd_Part
 
   end subroutine gpmd_Part
 
-
   !>  Initialize the partition.
   !!
   subroutine gpmd_InitParts