Attached below is a small piece of code I wrote in fortran. It reads files of specially formatted filename and yields information about aminoacids. If i compile it with compiler flag -O0, it all works fine. But with flag O1, it gives weired output, and gives segmentation fault with -O2 onwards.
Even strange is the fact that on line #127, if i uncomment a blank print statement, it works fine with all optimizations. I understand that optimizations can result in such faults, but I was curious to know
1) Why? whats going on here and how to prevent it
2) How to analyze such errors, I tried getting assembly output and diffing it, but it is quite overwhelming to pinpoint the error. Any simpler method?
!< this module contains basic arrays of length 45, which contains the information about
!! forst 3 characters of 45 aminoacids, and their chiralities, each amino acid has been assigned a number in range 1-45
!! and position of amide nitrogen in that aminoacid. Two functions getAminoNumberFromString getAminoStringFromNumber
!! can be used to get information about the serial number from the amino acid string and vice versa. and position of amide bond
!! can be retrived using getAmidePosition
module aminoacid_symbol_table
implicit none
character(len=9), dimension(45), parameter :: aminoSymbol = &
&(/ 'Ala_2S ', 'Cys_2R ', 'Asp_2S ', 'Glu_2S ', 'Phe_2S ',&
& 'Gly ', 'His_2S ', 'Ile_2S_3S', 'Lys_2S ', 'Leu_2S ',&
& 'Met_2S ', 'Asn_2S ', 'Pro_2S ', 'Gln_2S ', 'Arg_2S ',&
& 'Ser_2S ', 'Thr_2S_3R', 'Sec_2R ', 'Val_2S ', 'Trp_2S ',&
& 'Tyr_2S ', 'Ala_2R ', 'Cys_2S ', 'Asp_2R ', 'Glu_2R ',&
& 'Phe_2R ', 'His_2R ', 'Ile_2R_3S', 'Lys_2R ', 'Leu_2R ',&
& 'Met_2R ', 'Asn_2R ', 'Pro_2R ', 'Gln_2R ', 'Arg_2R ',&
& 'Ser_2R ', 'Thr_2R_3R', 'Sec_2S ', 'Val_2R ', 'Trp_2R ',&
& 'Tyr_2R ', 'Ile_2R_3R', 'Ile_2S_3R', 'Thr_2R_3S', 'Thr_2S_3S' /)
integer(kind=8), dimension(45), parameter :: aminoNumber = &
&(/ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 ,&
& 10, 11, 12, 13, 14, 15, 16, 17, 18,&
& 19, 20, 21, 22, 23, 24, 25, 26, 27,&
& 28, 29, 30, 31, 32, 33, 34, 35, 36,&
& 37, 38, 39, 40, 41, 42, 43, 44, 45/)
integer(kind=8), dimension(45), parameter :: amidePosition = &
&(/ 7, 8, 10, 11, 13, 5, 12, 11, 11,&
& 10, 10, 10, 9, 11, 14, 8, 10, 9,&
& 9, 16, 14, 7, 8, 10, 11, 13, 12,&
& 11, 11, 10, 10, 10, 9, 11, 14, 8,&
& 10, 9, 9, 16, 14, 11, 11, 10, 10 /)
integer(kind=8), dimension(45), parameter :: aminoSize = &
&(/13, 14, 16, 19, 23, 10, 20, 22, 24,&
& 22, 20, 17, 17, 20, 26, 14, 17, 14,&
& 19, 27, 24, 13, 14, 16, 19, 23, 20,&
& 22, 24, 22, 20, 17, 17, 20, 26, 14,&
& 17, 14, 19, 27, 24, 22, 22, 17, 17/)
contains
function getAminoNumberFromString(aminoStringCode) result(aminoNumericCode)
implicit none
character(len=9), intent(in) :: aminoStringCode
integer(kind=8) :: aminoNumericCode
integer(kind=4) :: i
! print *, aminoStringCode
string_match: do i = 1,45
if(aminoStringCode .eq. aminoSymbol(i)) then
aminoNumericCode = i
end if
end do string_match
end function getAminoNumberFromString
function getAminoStringFromNumber(aminoNumericCode) result(aminoStringCode)
implicit none
integer(kind=8), intent(in) :: aminoNumericCode
character(len=9) :: aminoStringCode
integer(kind=4) :: i
string_match: do i = 1,45
if(aminoNumericCode .eq. aminoNumber(i)) then
aminoStringCode = aminoSymbol(i)
end if
end do string_match
end function getAminoStringFromNumber
function getAmidePosition(aminoNumericCode) result(amideBondPosition)
implicit none
integer(kind=8), intent(in) :: aminoNumericCode
integer(kind=8) :: amideBondPosition
amideBondPosition = amidePosition(aminoNumericCode)
end function getAmidePosition
function getAminoSize(aminoNumericCode) result(aminoTotalSize)
implicit none
integer(kind=8), intent(in) :: aminoNumericCode
integer(kind=8) :: aminoTotalSize
aminoTotalSize = aminoSize(aminoNumericCode)
end function getAminoSize
function get3AminoFromFilename(fileName) result(aminoList)
implicit none
character(len=80), intent(in) :: fileName
! character, dimension(9) :: firstAmino
character(len=9) :: firstAmino, aminoList(3)
integer(kind=4) :: i, aminoCounter, scnt
! Thr_2S_3S__Leu_2S__Ile_2S_3R.smi
firstAmino = ' '
aminoCounter = 1
scnt = 1
i=1
do while (i<35)
if((fileName(i:i+1)/='__') .and. (fileName(i:i+1)/='.x')) then
! print *,fileName(i:i)
firstAmino(scnt:scnt) = fileName(i:i)
scnt=scnt+1
i=i+1
else if(aminoCounter<=3) then
! print *,firstAmino
aminoList(aminoCounter) = firstAmino
firstAmino =''
aminoCounter=aminoCounter+1
scnt=1
i=i+2
else
return
end if
end do
end function get3AminoFromFilename
subroutine getSelected6(fileName, neighboursList)
implicit none
character(len=80), intent(in) :: fileName
character(len=9) :: aminoList(3)
integer(kind=8) :: sizeAmino1, sizeAmino2, sizeAmino3
integer(kind=8) :: amidePosition1, amidePosition2, amidePosition3
integer(kind=8) :: aminoNumber1, aminoNumber2, aminoNumber3
integer(kind=8), intent(out) :: neighboursList(2,6)
aminoList = get3AminoFromFilename(fileName)
! print *,""
aminoNumber1 = getAminoNumberFromString(aminoList(1))
aminoNumber2 = getAminoNumberFromString(aminoList(2))
aminoNumber3 = getAminoNumberFromString(aminoList(3))
sizeAmino1 = getAminoSize(aminoNumber1)
sizeAmino2 = getAminoSize(aminoNumber2)
sizeAmino3 = getAminoSize(aminoNumber3)
amidePosition1 = getAmidePosition(aminoNumber1)
amidePosition2 = getAmidePosition(aminoNumber2)
amidePosition3 = getAmidePosition(aminoNumber3)
! for R1CR2NH2COCR3R4, list is organized as [N, H_N/C_N, C1, C, O, C_C]
neighboursList(1,1) = amidePosition1
neighboursList(1,3) = 4
neighboursList(1,4) = amidePosition1+1
neighboursList(1,5) = amidePosition1+1+1
neighboursList(1,6) = amidePosition1+1+2
if ((aminoNumber1 .eq. 13) .or. (aminoNumber1 .eq. 33)) then
neighboursList(1,2) = amidePosition1 - 1
else
neighboursList(1,2) = sizeAmino1 - 1 + amidePosition2 + amidePosition3 - 2
endif
neighboursList(2,1) = amidePosition2+amidePosition1-1
neighboursList(2,3) = amidePosition1+3
neighboursList(2,4) = amidePosition2+amidePosition1
neighboursList(2,5) = amidePosition2+amidePosition1+1
neighboursList(2,6) = amidePosition2+amidePosition1+2
if ((aminoNumber2 .eq. 13) .or. (aminoNumber2 .eq. 33)) then
neighboursList(2,2) = amidePosition1+amidePosition2 - 2
else
neighboursList(2,2) = sizeAmino1 -1 + sizeAmino2 -3 + amidePosition3 - 1
endif
end subroutine getSelected6
end module aminoacid_symbol_table
program main
use aminoacid_symbol_table
implicit none
character(len=80) :: fileName
integer(kind=8) :: neighboursList(2,6)
fileName = 'Gly__Gly__Gly.xyz'
call getSelected6(fileName,neighboursList)
print *, neighboursList
end program main
compiled using GNU Fortran (Ubuntu 7.3.0-27ubuntu1~18.04) 7.3.0
Output expected (O0 flag):
$ ./a.out
5 9 17 20 4 8 6 10 7 11 8 12
I think its related to this question: Execution of printf() and Segmentation Fault
Edit: output with O1 and O2 flag
$ gfortran -O1 -g -C aminotrial.f90
$ ./a.out
0 268435456 0 0 0 0 0 0 0 0 0 0
$ gfortran -O2 -g -C aminotrial.f90
$ ./a.out
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7f68a90812da in ???
#1 0x7f68a9080503 in ???
#2 0x7f68a8cb3f1f in ???
#3 0x561db7603a62 in __aminoacid_symbol_table_MOD_getaminosize
at /aminotrial.f90:82
#4 0x561db7603a62 in __aminoacid_symbol_table_MOD_getselected6
at /aminotrial.f90:131
#5 0x561db7603b91 in MAIN__
at /aminotrial.f90:169
#6 0x561db760374e in main
at /aminotrial.f90:164
Segmentation fault (core dumped)
O3 is exactly same as O2
I am not sure how it is duplicate of generic question regarding flags of gfortran
