Hdf5 auto open (#330)

* auto-open HDF5 and use REQUIRE more

* Fix some formatting issues in HDF5

* Add vs code to gitignore

* Update HDF5 test

.gitignore

@@ -18,3 +18,4 @@ fort.*
 /.egdist
 /.gitdist
 *.sublime-*
+.vscode

src/MemProf.f90

@@ -74,11 +74,12 @@ CHARACTER(LEN=*),PARAMETER :: modName='MEMORYPROFILER'
 CONTAINS
 !
 !-------------------------------------------------------------------------------
-!> @brief the procudere to
+!> @brief the procedure to intialize a memory profiler object
 !> @param thisMP the memory profiler
-!> @param params
+!> @param pe the parallel environment
+!> @param myLog the log file; optional
+!> @param params the input parameter list; optional
 !>
-!TODO  Need to get control rod movement passed in
 SUBROUTINE init_MemProf(thisMP,pe,mylog,params)
   CLASS(Memory_Profiler),INTENT(INOUT) :: thisMP
   TYPE(ParallelEnvType),TARGET,INTENT(IN) :: pe

unit_tests/testHDF5FileType/testHDF5FileType.f90

@@ -57,7 +57,6 @@ CALL testHDF5FileTypeSetup()
 CALL HDF5Open()
 REGISTER_SUBTEST("Uninit",testHDF5FileTypeUninit)
 REGISTER_SUBTEST("Init",testHDF5FileTypeCreateDelete)
-REGISTER_SUBTEST("Error Checks",testHDF5FileTypeErrorCheck)
 REGISTER_SUBTEST("%fread",testHDF5FileTypeRead)
 IF(utest_nfail == 0) THEN
   REGISTER_SUBTEST("%fwrite",testHDF5FileTypeWrite)
@@ -354,8 +353,6 @@ SUBROUTINE testHDF5FileTypeCreateDelete()
   CALL h5%fopen()
   ASSERT(.NOT.(h5%isWrite()),'HDF object %isWrite() should be .FALSE.')
   CALL h5%e%setStopOnError(.FALSE.)
-  CALL h5%mkdir('testGroup')
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),1,'hdf5_filetype%init ''READ''')
   CALL h5%fdelete()
   ASSERT(h5%isinit,'HDF5 object still initialized after deletion.')
   INQUIRE(FILE='createdeletetest.h5',EXIST=exists)
@@ -373,243 +370,6 @@ SUBROUTINE testHDF5FileTypeCreateDelete()
 ENDSUBROUTINE testHDF5FileTypeCreateDelete
 !
 !-------------------------------------------------------------------------------
-SUBROUTINE testHDF5FileTypeErrorCheck()
-  TYPE(HDF5FileType) :: h5
-  INTEGER(SIK) :: tmpi
-  REAL(SDK),POINTER :: d4ptr(:,:,:,:)
-  d4ptr => NULL()
-
-  CALL h5%e%setQuietMode(.TRUE.)
-  !Adding the *2 for now to get the test passing.  Since the simplification,
-  !the pre and post routines have two %isinit checks.  All these checks are
-  !mostly redundant now though, one check checks the same code as all of them now.
-  CALL h5%fwrite('groupR->memD0',refD0)
-  tmpi=1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_d0 %isinit check')
-  CALL h5%fwrite('groupR->memD1',refD1,SHAPE(refD1))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_d1 %isinit check')
-  CALL h5%fwrite('groupR->memD2',refD2,SHAPE(refD2))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_d2 %isinit check')
-  CALL h5%fwrite('groupR->memD3',refD3,SHAPE(refD3))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_d3 %isinit check')
-  CALL h5%fwrite('groupR->memD4',refD4,SHAPE(refD4))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_d4 %isinit check')
-  CALL h5%fwrite('groupR->memD5',refD5,SHAPE(refD5))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_d5 %isinit check')
-  CALL h5%fwrite('groupR->memD6',refD6,SHAPE(refD6))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_d6 %isinit check')
-  CALL h5%fwrite('groupR->memD7',refD7,SHAPE(refD7))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_d7 %isinit check')
-  CALL h5%fwrite('groupR->memS0',refS0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_s0 %isinit check')
-  CALL h5%fwrite('groupR->memS1',refS1,SHAPE(refS1))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_s1 %isinit check')
-  CALL h5%fwrite('groupR->memS2',refS2,SHAPE(refS2))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_s2 %isinit check')
-  CALL h5%fwrite('groupR->memS3',refS3,SHAPE(refS3))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_s3 %isinit check')
-  CALL h5%fwrite('groupR->memS4',refS4,SHAPE(refS4))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_s4 %isinit check')
-  CALL h5%fwrite('groupR->memS5',refS5,SHAPE(refS5))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_s5 %isinit check')
-  CALL h5%fwrite('groupR->memS6',refS6,SHAPE(refS6))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_s6 %isinit check')
-  CALL h5%fwrite('groupR->memS7',refS7,SHAPE(refS7))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_s7 %isinit check')
-  CALL h5%fwrite('groupI->memL0',refL0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_l0 %isinit check')
-  CALL h5%fwrite('groupI->memL1',refL1,SHAPE(refL1))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_l1 %isinit check')
-  CALL h5%fwrite('groupI->memL2',refL2,SHAPE(refL2))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_l2 %isinit check')
-  CALL h5%fwrite('groupI->memL3',refL3,SHAPE(refL3))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_l3 %isinit check')
-  CALL h5%fwrite('groupI->memL4',refL4,SHAPE(refL4))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_l4 %isinit check')
-  CALL h5%fwrite('groupI->memL5',refL5,SHAPE(refL5))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_l5 %isinit check')
-  CALL h5%fwrite('groupI->memL6',refL6,SHAPE(refL6))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_l6 %isinit check')
-  CALL h5%fwrite('groupI->memL7',refL7,SHAPE(refL7))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_l7 %isinit check')
-  CALL h5%fwrite('groupI->memN0',refN0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_n0 %isinit check')
-  CALL h5%fwrite('groupI->memN1',refN1,SHAPE(refN1))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_n1 %isinit check')
-  CALL h5%fwrite('groupI->memN2',refN2,SHAPE(refN2))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_n2 %isinit check')
-  CALL h5%fwrite('groupI->memN3',refN3,SHAPE(refN3))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_n3 %isinit check')
-  CALL h5%fwrite('groupI->memN4',refN4,SHAPE(refN4))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_n4 %isinit check')
-  CALL h5%fwrite('groupI->memN5',refN5,SHAPE(refN5))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_n5 %isinit check')
-  CALL h5%fwrite('groupI->memN6',refN6,SHAPE(refN6))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_n6 %isinit check')
-  CALL h5%fwrite('groupI->memN7',refN7,SHAPE(refN7))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_n7 %isinit check')
-  CALL h5%fwrite('groupB->memB0',refB0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_b0 %isinit check')
-  CALL h5%fwrite('groupB->memB1',refB1,SHAPE(refB1))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_b1 %isinit check')
-  CALL h5%fwrite('groupB->memB2',refB2,SHAPE(refB2))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_b2 %isinit check')
-  CALL h5%fwrite('groupB->memB3',refB3,SHAPE(refB3))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_b3 %isinit check')
-  CALL h5%fwrite('groupST->CNULLCHAR0',refCNCHAR0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_st0 %isinit check')
-  CALL h5%fwrite('groupST->CNULLCHAR1',refCNCHAR1)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_st1 %isinit check')
-  CALL h5%fwrite('groupST->CNULLCHAR2',refCNCHAR2)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_st2 %isinit check')
-  CALL h5%fwrite('groupST->CNULLCHAR3',refCNCHAR3)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_st3 %isinit check')
-  CALL h5%fwrite('groupST->memST0',refST0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_st0 %isinit check')
-  CALL h5%fwrite('groupST->memST1',refST1,SHAPE(refST1))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_st1 %isinit check')
-  CALL h5%fwrite('groupST->memST2',refST2,SHAPE(refST2))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_st2 %isinit check')
-  CALL h5%fwrite('groupST->memST3',refST3,SHAPE(refST3))
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_st3 %isinit check')
-  CALL h5%fwrite('groupC->memC1',refC1)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%write_c1 %isinit check')
-  CALL h5%mkdir('groupI')
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2-1,'%mkdir %isinit check')
-  CALL h5%ls('groupR',refST1)
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%ls %isinit check')
-
-  CALL h5%fread('groupR->memD0',refD0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_d0 %isinit check')
-  CALL h5%fread('groupR->memD1',refD1)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_d1 %isinit check')
-  CALL h5%fread('groupR->memD2',refD2)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_d2 %isinit check')
-  CALL h5%fread('groupR->memD3',refD3)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_d3 %isinit check')
-  CALL h5%fread('groupR->memD4',refD4)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_d4 %isinit check')
-  CALL h5%freadp('groupR->memD4',d4ptr)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_d4 %isinit check')
-  CALL h5%fread('groupR->memS0',refS0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_s0 %isinit check')
-  CALL h5%fread('groupR->memS1',refS1)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_s1 %isinit check')
-  CALL h5%fread('groupR->memS2',refS2)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_s2 %isinit check')
-  CALL h5%fread('groupR->memS3',refS3)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_s3 %isinit check')
-  CALL h5%fread('groupR->memS4',refS4)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_s4 %isinit check')
-  CALL h5%fread('groupI->memL0',refL0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_l0 %isinit check')
-  CALL h5%fread('groupI->memL1',refL1)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_l1 %isinit check')
-  CALL h5%fread('groupI->memL2',refL2)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_l2 %isinit check')
-  CALL h5%fread('groupI->memL3',refL3)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_l3 %isinit check')
-  CALL h5%fread('groupI->memN0',refN0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_n0 %isinit check')
-  CALL h5%fread('groupI->memN1',refN1)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_n1 %isinit check')
-  CALL h5%fread('groupI->memN2',refN2)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_n2 %isinit check')
-  CALL h5%fread('groupI->memN3',refN3)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_n3 %isinit check')
-  CALL h5%fread('groupB->memB0',refB0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_b0 %isinit check')
-  CALL h5%fread('groupB->memB1',refB1)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_b1 %isinit check')
-  CALL h5%fread('groupB->memB2',refB2)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_b2 %isinit check')
-  CALL h5%fread('groupB->memB3',refB3)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_b3 %isinit check')
-  CALL h5%fread('groupST->memST0',refST0)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_st0 %isinit check')
-  CALL h5%fread('groupST->memST1',refST1)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_st1 %isinit check')
-  CALL h5%fread('groupST->memST2',refST2)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_st2 %isinit check')
-  CALL h5%fread('groupST->memST3',refST3)
-  tmpi=tmpi+1
-  ASSERT_EQ(h5%e%getCounter(EXCEPTION_ERROR),tmpi*2,'%read_st3 %isinit check')
-
-  CALL h5%clear(.TRUE.)
-ENDSUBROUTINE testHDF5FileTypeErrorCheck
-!
-!-------------------------------------------------------------------------------
 SUBROUTINE testHDF5FileTypeWrite()
   TYPE(HDF5FileType) :: h5
   REAL(SDK),ALLOCATABLE :: testD1(:),testD2(:,:),testD3(:,:,:),testD4(:,:,:,:)