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Ensure the buffer provided to MPAS_io_get_var_generic is large enough. #1367

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Ensure the buffer provided to MPAS_io_get_var_generic is large enough. #1367

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3 changes: 2 additions & 1 deletion src/core_test/Makefile
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Expand Up @@ -12,7 +12,8 @@ OBJS = mpas_test_core.o \
mpas_test_core_dmpar.o \
mpas_test_core_stream_inquiry.o \
mpas_test_openacc.o \
mpas_test_core_stream_list.o
mpas_test_core_stream_list.o \
mpas_test_core_io.o \

all: core_test

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12 changes: 12 additions & 0 deletions src/core_test/mpas_test_core.F
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Expand Up @@ -97,6 +97,7 @@ function test_core_run(domain) result(iErr)!{{{
use test_core_string_utils, only : mpas_test_string_utils
use mpas_test_core_dmpar, only : mpas_test_dmpar
use mpas_test_core_stream_inquiry, only : mpas_test_stream_inquiry
use test_core_io, only : test_core_io_test
use mpas_test_core_openacc, only : mpas_test_openacc

implicit none
Expand Down Expand Up @@ -224,6 +225,17 @@ function test_core_run(domain) result(iErr)!{{{

call mpas_stream_mgr_write(domain % streamManager, forceWriteNow=.true.)

!
! Run io tests
!
call mpas_log_write('')
call test_core_io_test(domain, threadErrs, iErr)
if (iErr == 0) then
call mpas_log_write('All tests PASSED')
else
call mpas_log_write('$i tests FAILED', intArgs=[iErr])
end if
call mpas_log_write('')
!
! Run mpas_test_openacc
!
Expand Down
208 changes: 208 additions & 0 deletions src/core_test/mpas_test_core_io.F
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@@ -0,0 +1,208 @@
! Copyright (c) 2013, Los Alamos National Security, LLC (LANS)
! and the University Corporation for Atmospheric Research (UCAR).
!
! Unless noted otherwise source code is licensed under the BSD license.
! Additional copyright and license information can be found in the LICENSE file
! distributed with this code, or at http://mpas-dev.github.com/license.html
!
module test_core_io

#define ERROR_WRITE(M) call mpas_log_write( M , messageType=MPAS_LOG_ERR)
#define ERROR_WRITE_ARGS(M, ARGS) call mpas_log_write( M , ARGS, messageType=MPAS_LOG_ERR)
use mpas_log
use mpas_io

implicit none
private
public :: test_core_io_test

contains

!***********************************************************************
!
! routine close_file_with_message
!
!> \brief closes the provided file handle and writes an error message.
!-----------------------------------------------------------------------
subroutine close_file_with_message(fileHandle, message, args)
type(MPAS_IO_Handle_type), intent(inout) :: fileHandle
character (len=*), intent(in), optional :: message
integer, dimension(:), intent(in), optional :: args

integer :: local_ierr

! log an error message
if (present(message)) then
if (present(args)) then
ERROR_WRITE_ARGS(message, intArgs=args)
else
ERROR_WRITE(message)
end if
end if

! close the provided file
call MPAS_io_close(fileHandle, local_ierr)
if (local_ierr /= MPAS_IO_NOERR) then
ERROR_WRITE_ARGS('MPAS_io_close failed with error code:$i', intArgs=(/local_ierr/))
return
endif

end subroutine close_file_with_message

!***********************************************************************
!
! routine test_read_string_buffer_check
!
!> \brief verifies attempts to read strings into buffers which are too small
!> to hold the value fails safely.
!> \details
!> Run these tests with valgrind to ensure there are no buffer overflows when
!> attempting to read strings into undersized buffers.
!-----------------------------------------------------------------------
subroutine test_read_string_buffer_check(domain, threadErrs, ierr)

type (domain_type), intent(inout) :: domain
integer, dimension(:), intent(out) :: threadErrs
integer, intent(out) :: ierr

integer :: local_ierr, i
type(MPAS_IO_Handle_type) :: fileHandle
character (len=StrKIND), dimension(1), parameter :: dimNamesString = ['StrLen']
character (len=StrKIND), dimension(2), parameter :: dimNamesStringTime = ['StrLen', 'Time ']
character (len=32), parameter :: varName1 = 'stringVar'
character (len=32), parameter :: varName2 = 'stringTimeVar'
character (len=*), parameter :: varValue1 = 'This is a string'
character (len=32), dimension(2), parameter :: varNames = [varName1, varName2]
integer, parameter :: bufferSize=128
integer, parameter :: smallBufferSize=bufferSize/2
character (len=bufferSize) :: buffer
character (len=smallBufferSize) :: smallBuffer
character (len=*), parameter :: filename = 'char_data.nc'

ierr = 0

! open a file to write char variables to
fileHandle = MPAS_io_open(filename, MPAS_IO_WRITE, MPAS_IO_NETCDF4, domain % ioContext, &
clobber_file=.true., truncate_file=.true., ierr=local_ierr)
if (local_ierr /= MPAS_IO_NOERR) then
ierr = 1
ERROR_WRITE('Error opening file ' // trim(filename))
return
end if

! define dimensions and char variables
call MPAS_io_def_dim(fileHandle, dimNamesStringTime(1), bufferSize, local_ierr)
if (local_ierr /= MPAS_IO_NOERR) then
ierr = 1
call close_file_with_message(fileHandle, 'Error defining '//trim(dimNamesStringTime(1))//', error=$i', (/local_ierr/))
return
end if
call MPAS_io_def_dim(fileHandle, dimNamesStringTime(2), MPAS_IO_UNLIMITED_DIM, local_ierr)
if (local_ierr /= MPAS_IO_NOERR) then
ierr = 1
call close_file_with_message(fileHandle, 'Error defining '//trim(dimNamesStringTime(2))//', error=$i', (/local_ierr/))
return
end if
call MPAS_io_def_var(fileHandle, varNames(1), MPAS_IO_CHAR, dimNamesString, ierr=local_ierr)
if (local_ierr /= MPAS_IO_NOERR) then
ierr = 1
call close_file_with_message(fileHandle, 'Error defining var "'//trim(varNames(1))//'" error=$i', (/local_ierr/))
return
end if
call MPAS_io_def_var(fileHandle, varNames(2), MPAS_IO_CHAR, dimNamesStringTime, ierr=local_ierr)
if (local_ierr /= MPAS_IO_NOERR) then
ierr = 1
call close_file_with_message(fileHandle, 'Error defining var "'//trim(varNames(2))//'" error=$i', (/local_ierr/))
return
end if

! write the string values
do i=1,2
call MPAS_io_put_var_char0d(fileHandle, varNames(i), varValue1, local_ierr)
if (local_ierr /= MPAS_IO_NOERR) then
ierr = 1
call close_file_with_message(fileHandle, 'Error writing "'//trim(varNames(i))// &
'", error=$i', (/local_ierr/))
return
end if

! verify the strings are read into buffers which are large enough for the strin values
call MPAS_io_get_var_char0d(fileHandle, varNames(i), buffer, local_ierr)
if (local_ierr /= MPAS_IO_NOERR) then
ierr = 1
call close_file_with_message(fileHandle, 'Error reading "'//trim(varNames(i))// &
'", error=$i', (/local_ierr/))
return
end if
end do

! verify attempts to read strings into buffers which are too small generates an error
call mpas_log_write(' ')
call mpas_log_write('Expect to see the following error:')
call MPAS_io_err_mesg(domain % ioContext, MPAS_IO_ERR_INSUFFICIENT_ARG, .false.)
call mpas_log_write(' ')
do i=1,2
! this should return an error
call MPAS_io_get_var_char0d(fileHandle, varNames(i), smallBuffer, local_ierr)
call mpas_log_write(' ')

if (local_ierr /= MPAS_IO_ERR_INSUFFICIENT_ARG) then
ierr = 1
if (local_ierr == MPAS_IO_NOERR) then
call close_file_with_message(fileHandle, 'Expected MPAS_IO_ERR_INSUFFICIENT_ARG ($i)'&
//' but recieved no error reading "'//trim(varName1), (/local_ierr/))
else
call close_file_with_message(fileHandle, 'Expected MPAS_IO_ERR_INSUFFICIENT_ARG ($i)'&
//' but recieved error $i reading "'//trim(varName1)//'"', &
(/MPAS_IO_ERR_INSUFFICIENT_ARG, local_ierr/))
end if
return
end if
end do
call close_file_with_message(fileHandle)

end subroutine test_read_string_buffer_check


!***********************************************************************
! Subroutine test_core_io_test
!
!> \brief Core test suite for I/O
!>
!> \details This subroutine tests mpas_io features.
!> It calls individual tests for I/O operations.
!> See the subroutine body for details.
!> The results of each test are logged with a success or failure message.
!>
!> \param domain The domain object that contains the I/O context
!> \param threadErrs An array to store any errors encountered during
!> the test.
!> \param ierr The error code that indicates the result of the test.
!
!-----------------------------------------------------------------------
subroutine test_core_io_test(domain, threadErrs, ierr)

use mpas_log

type (domain_type), intent(inout) :: domain
integer, dimension(:), intent(out) :: threadErrs
integer, intent(out) :: ierr

integer :: test_status

ierr = 0
test_status = 0

call mpas_log_write('Testing char-0 buffer reads')
call test_read_string_buffer_check(domain, threadErrs, test_status)
if (test_status == 0) then
call mpas_log_write('char-0 buffer tests: SUCCESS')
else
call mpas_log_write('char-0 buffer tests: FAILURE', MPAS_LOG_ERR)
ierr = ierr + abs(test_status)
end if


end subroutine test_core_io_test

end module test_core_io
91 changes: 64 additions & 27 deletions src/framework/mpas_io.F
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Expand Up @@ -7,6 +7,8 @@
!
module mpas_io

#define IO_DEBUG_WRITE(M, ARGS) !call mpas_log_write(M, ARGS)
#define IO_ERROR_WRITE(M, ARGS) call mpas_log_write( M, ARGS, messageType=MPAS_LOG_ERR)
use mpas_derived_types
use mpas_attlist
use mpas_dmpar
Expand Down Expand Up @@ -1847,6 +1849,13 @@ subroutine MPAS_io_get_var_generic(handle, fieldname, intVal, intArray1d, intArr
character (len=:), pointer :: charVal_p
character (len=:), dimension(:), pointer :: charArray1d_p

! local variables returned from MPAS_io_inq_var
integer :: fieldtype
integer :: ndims
integer, dimension(:), pointer :: dimsizes
character (len=StrKIND), dimension(:), pointer :: dimnames
character (len=StrKind) :: message

#ifdef MPAS_SMIOL_SUPPORT
type (SMIOLf_decomp), pointer :: null_decomp

Expand Down Expand Up @@ -1984,22 +1993,40 @@ subroutine MPAS_io_get_var_generic(handle, fieldname, intVal, intArray1d, intArr
! call mpas_log_write(' value is char')

charVal_p => charVal

! get the dimension of the char variable to ensure the provided output buffer is large enough
call MPAS_io_inq_var(handle, fieldname, fieldtype, ndims, dimnames, dimsizes, local_ierr)
do i = 1, ndims
message = ' MPAS_io_get_var_generic len(charVal):$i var "'//trim(fieldname)// &
'" type is $i dim $i is '// trim(dimnames(i))//' size is $i'
IO_DEBUG_WRITE(message , intArgs=(/len(charVal), fieldtype, i, dimsizes(i)/))
end do
! because charVal is provided, assume dimension 1 is the string length
if (dimsizes(1) > len(charVal)) then
local_ierr = MPAS_IO_ERR_INSUFFICIENT_ARG
message = ' MPAS_io_get_var_generic var "'//trim(fieldname)// &
'" len too big, len=$i buflen=$i'
IO_ERROR_WRITE(message, intArgs=(/dimsizes(1), len(charVal)/))
else
#ifdef MPAS_SMIOL_SUPPORT
local_ierr = SMIOLf_get_var(handle % smiol_file, trim(fieldname), null_decomp, charVal_p)
local_ierr = SMIOLf_get_var(handle % smiol_file, trim(fieldname), null_decomp, charVal_p)
#endif

#ifdef MPAS_PIO_SUPPORT
if (field_cursor % fieldhandle % has_unlimited_dim) then
count2(1) = field_cursor % fieldhandle % dims(1) % dimsize
pio_ierr = PIO_get_var(handle % pio_file, field_cursor % fieldhandle % fieldid, start2, count2, tempchar)
charVal(1:count2(1)) = tempchar(1)(1:count2(1))
else
start1(1) = 1
count1(1) = field_cursor % fieldhandle % dims(1) % dimsize
pio_ierr = PIO_get_var(handle % pio_file, field_cursor % fieldhandle % fieldid, start1, count1, tempchar)
charVal(1:count1(1)) = tempchar(1)(1:count1(1))
end if
if (field_cursor % fieldhandle % has_unlimited_dim) then
count2(1) = field_cursor % fieldhandle % dims(1) % dimsize
pio_ierr = PIO_get_var(handle % pio_file, field_cursor % fieldhandle % fieldid, start2, count2, tempchar)
charVal(1:count2(1)) = tempchar(1)(1:count2(1))
else
start1(1) = 1
count1(1) = field_cursor % fieldhandle % dims(1) % dimsize
pio_ierr = PIO_get_var(handle % pio_file, field_cursor % fieldhandle % fieldid, start1, count1, tempchar)
charVal(1:count1(1)) = tempchar(1)(1:count1(1))
end if
#endif
end if
deallocate(dimsizes)
deallocate(dimnames)
else if (present(charArray1d)) then
! call mpas_log_write(' value is char1')
#ifdef MPAS_PIO_SUPPORT
Expand Down Expand Up @@ -2765,28 +2792,34 @@ subroutine MPAS_io_get_var_generic(handle, fieldname, intVal, intArray1d, intArr
end if

! call mpas_log_write('Checking for error')
if (local_ierr == MPAS_IO_ERR_INSUFFICIENT_ARG) then
call MPAS_io_err_mesg(handle % ioContext, local_ierr, .false.)
io_global_err = local_ierr
if (present(ierr)) ierr = local_ierr
else
#ifdef MPAS_PIO_SUPPORT
if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
if (present(ierr)) ierr = MPAS_IO_ERR_BACKEND
return
end if
if (pio_ierr /= PIO_noerr) then
io_global_err = pio_ierr
if (present(ierr)) ierr = MPAS_IO_ERR_BACKEND
return
end if
#endif

#ifdef MPAS_SMIOL_SUPPORT
if (local_ierr /= SMIOL_SUCCESS) then
call mpas_log_write('SMIOLf_get_var failed with error $i', intArgs=[local_ierr], messageType=MPAS_LOG_ERR)
if (local_ierr == SMIOL_LIBRARY_ERROR) then
call mpas_log_write(trim(SMIOLf_lib_error_string(handle % ioContext % smiol_context)), messageType=MPAS_LOG_ERR)
else
call mpas_log_write(trim(SMIOLf_error_string(local_ierr)), messageType=MPAS_LOG_ERR)
end if
if (local_ierr /= SMIOL_SUCCESS) then
call mpas_log_write('SMIOLf_get_var failed with error $i', intArgs=[local_ierr], messageType=MPAS_LOG_ERR)
if (local_ierr == SMIOL_LIBRARY_ERROR) then
call mpas_log_write(trim(SMIOLf_lib_error_string(handle % ioContext % smiol_context)), messageType=MPAS_LOG_ERR)
else
call mpas_log_write(trim(SMIOLf_error_string(local_ierr)), messageType=MPAS_LOG_ERR)
end if

io_global_err = local_ierr
if (present(ierr)) ierr = MPAS_IO_ERR_BACKEND
return
end if
io_global_err = local_ierr
if (present(ierr)) ierr = MPAS_IO_ERR_BACKEND
return
end if
#endif
end if

end subroutine MPAS_io_get_var_generic

Expand Down Expand Up @@ -6498,6 +6531,10 @@ subroutine MPAS_io_err_mesg(ioContext, ierr, fatal)
call mpas_log_write('MPAS IO Error: Would clobber existing file', MPAS_LOG_ERR)
case (MPAS_IO_ERR_NOEXIST_READ)
call mpas_log_write('MPAS IO Error: Attempting to read a file which does not exist.', MPAS_LOG_ERR)
case (MPAS_IO_ERR_MISSING_DIM)
call mpas_log_write('MPAS IO Error: Attempting to read a dimension which does not exist.', MPAS_LOG_ERR)
case (MPAS_IO_ERR_INSUFFICIENT_ARG)
call mpas_log_write('MPAS IO Error: Attempting to read a string into a buffer which is too small.', MPAS_LOG_ERR)
case default
call mpas_log_write('MPAS IO Error: Unrecognized error code...', MPAS_LOG_ERR)
end select
Expand Down
3 changes: 2 additions & 1 deletion src/framework/mpas_io_types.inc
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Expand Up @@ -65,7 +65,8 @@
MPAS_IO_ERR_UNIMPLEMENTED = -18, &
MPAS_IO_ERR_WOULD_CLOBBER = -19, &
MPAS_IO_ERR_NOEXIST_READ = -20, &
MPAS_IO_ERR_MISSING_DIM = -21
MPAS_IO_ERR_MISSING_DIM = -21, &
MPAS_IO_ERR_INSUFFICIENT_ARG = -22

type MPAS_IO_Handle_type
logical :: initialized = .false.
Expand Down