When I tried to run a huge Fortran code (the code is compiled using Intel compiler version 13.1.3.192), it gave me error message like this:
...
Info[FDFI_Setup]: HPDF code version number is 1.00246
forrtl: severe (153): allocatable array or pointer is not allocated
Image PC Routine Line Source
arts 0000000002AD96BE Unknown Unknown Unknown
arts 0000000002AD8156 Unknown Unknown Unknown
arts 0000000002A87532 Unknown Unknown Unknown
...
Nonetheless, if I insert a small write statement (which is just to check the code, not to disturb the original purpose of the code) in one of the subroutines as the following (I couldn't put all the codes since they are too huge):
...
endif
call GetInputLine(Unit,line,eof,err)
enddo
if(err) return
! - [elfsummer] 20140815 Checkpoint 23
open(unit = 1, file = '/bin/monitor/log_checkpoint',status='old',position='append')
write(1,*) "BEFORE checking required keys: so far so good!"
close(1)
! check required keys
! for modes = 2,3, P and T are the required keys
if(StrmDat%ModeCI==2.or.StrmDat%ModeCI==3) then
...
then suddenly, the error message shown above disappears and the code can run correctly! I also tried to insert such write statements in other locations in the source code but the above error message still exists.
According to Intel's documentation:
severe (153): Allocatable array or pointer is not allocated
FOR$IOS_INVDEALLOC. A Fortran 90 allocatable array or pointer must already be allocated when you attempt to deallocate it. You must allocate the array or pointer before it can again be deallocated.
Note: This error can be returned by STAT in a DEALLOCATE statement.
However, I couldn't see any relations between the error and the "write statements" I added to the code. There is no such "allocate" command in the location I add the write statements.
So I am quite confused. Does anybody know the reasons? Any help is greatly appreciated!!
With traceback option, I could locate the error source directly:
subroutine StringRead(Str,delimiter,StrArray,ns) ! [private] read strings separated by delimiter
implicit none
character*(*),intent(in) :: Str
character*(*),intent(in) :: delimiter
character*(*),pointer :: StrArray(:)
integer,intent(out) :: ns
! - local variables
character(len=len(Str)) :: tline
integer :: nvalue,nvalue_max
character(len=len(StrArray)),pointer:: sarray(:),sarray_bak(:)
integer :: len_a,len_d,i
! deallocate StrArray
if(associated(StrArray)) deallocate(StrArray)
The error, according to the information the traceback gave me, lies in the last statement shown above. If I comment out this statement, then the "forrtl: severe (153)" error would disappear while new errors being generated... But still, I don't think this statement itself could go wrong...It acts as if it just ignores the if... condition and directly reads the deallocate commend, which seems weird to me.
You could have a bug in which you are illegally writing to memory and damaging the structure that stores the allocation information. Changing the code might cause the memory damage to occur elsewhere and that specific error to disappear. Generally, illegal memory accesses typically occur two ways in Fortran. 1) illegal subscripts, 2) mismatch between actual and dummy arguments, i.e., between variables in call and variables as declared in procedures. You can search for the first type of error by using your compiler's option for run-time subscript checking. You can guard against the second by placing all of your procedures in modules and useing those modules so that the compiler can check for argument consistency.
Sounds like some of the earlier comments give the general explanation. However,
1) Is StrArray(:) an Intent(out)? That is, are you reading the file's lines into StrArray() in the s/r, with the hope of returning that as the file's content? If so, declare it as an (Out), or whatever it should be.
2) Why is StrArray() a Pointer? Does it need to be a Pointer? If all you want is file content, you may be better off using a non-Pointer.
You may still need an Allocatable, or Automatic or something, but non-Pointers are easier in many cases.
3) If you must have StrArray(:) as a Pointer, then its size/shape etc must be created prior to use. If the calling sequence ACTUAL Arg is correctly defined (and if StrArray() is Intent(In) or Intent(InOUT), then that might do it.
By contrast, if it is an (Out), then, as with all Pointer arrays, it must be FIRST Allcoated() in the s/r.
If it is not Allocated somewhere early on, then it is undefined, and so the DeAllocate() fails, since it has nothing to DeAlloc, hence Stat = 153.
4) It is possible that you may wish to use this to read files without first knowing the number of lines to read. In that case, you cannot (at least not easily), Allocate StrArray() in advance, since you don't know the Size. In this case, alternate strategies are required.
One possible solution is a loop that simple reads the first char, or advances somehow, for each line in the file. Have the loop track the "sum" of each line read, until EOF. Then, you will know the size of the file (in terms of num lines), and you then allocate StrArray(SumLines) or something. Something like
SumLines = 0
Do i=1, ?? (or use a While)
... test to see if "line i" exists, or EOF, if so, Exit
SumLines = SumLines + 1
End Do
It may be best to do this in a separate s/r, so that the Size etc are known prior to calling the FileRead bits (i.e. that the file size is set prior to the FileRead s/r call).
However, that still leaves you with the problem of what Character(Len) to use. There are many possible solutions to this. Three of which are:
a) Use max length, like Character(Len = 2048), Intent(Out), or better yet, some compile time constant Parameter, call it MaxLineWidth
This has the obvious limitation to lines that <= MaxLineWidth, and that the memory usage may be excessively large when there many "short lines", etc.
b) Use a single char array, like Character(Len = 1), Intent(Out) :: StrArrayChar(:,:)
This is 2-D, since you need 1 D for the chars in each line, and the 2nd D for the lines.
This is a bit better compared to a) since it gives control over line width.
c) A more general approach might rely on a User Defined Type such as:
Type MyFileType
Character(Len=1), Allocatable :: FileLine(:) ! this give variable length lines, but each "line" must be allocated to the length of the line
End Type MyFileType
Then, create an array of this Type, such as:
Type(MyFileType), Allocatable :: MyFile(:) ! or, instead of Allocatable, can use Automatic etc etc
Then, Allocate MyFile to Size = num lines
... anyway, there are various choices, each with its own suitability for varying circumstances (and I have omitted much "housekeeping" re DeAllocs etc, which you will need to implement).
Incidentally, c) is also one possible prototype for "variable length strings" for many Fortran compilers that don't support such explicitly.
I'm having a problem of variables getting over-written for I don't know what reason. I've posted a chunk of the code below so you can see how things are declared. The variables strain,Qi,Qf,Qd,tel and Gc are passed into the subroutine and used to calculate ssgrad,strn0,strss0.
My problem is that tel and Gc are passed into the subroutine OK but are for some reason change value during this chunk of code.
Using print statements I've found that the problem first occurs during the 2nd do loop. When I set strss0 to 0, Gc and tel change value from both being equal to 1, to seemingly random numbers: tel=11.52822 Gc=-8.789086 (Just shown for the sake of example)
Each time I run the code they are set to the same values though.
Just to let you know, this subroutine interfaces with a commercial finite element package.
Many thanks in advance for any help with this
subroutine initcalcs(strain,Qi,Qf,Qd,tel,Gc,ssgrad,strn0,strss0)
implicit none
integer :: i,j
real*8:: nstrn0,nstrs0,strn0,strnf,varsq,normvar,lmbda0,lmbdaf,
# ssgrad,t0,tt,tel,nstrnf,nstrsf,Gc
real*8, dimension(3) :: strain,stran0,stranf,strss0,strssf,var
real*8, dimension(3,3) :: Qd,Qi,Qf
lmbda0=1.0d0
nstrn0=0.0d0
do i=1,3
stran0(i)=0.0d0
stran0(i)=strain(i)*lmbda0
nstrn0=nstrn0+stran0(i)**2
end do
nstrn0=dsqrt(nstrn0)
do i=1,3
strss0(i)=0.0d0
end do
In Fortran, there are two common causes of the corruption of memory values. One is a subscript error, where you assign to an array element using an incorrect subscript value. This writes to a memory location outside of the array. The other is a disagreement between the arguments in the call to a procedure (subroutine or function) and the dummy arguments of the procedure. Either can cause problems to appear at source code locations different from the actual cause. Suggestions: inspect your code for these problems. Turn on stringent warning and error checking options of your compiler. The use of Fortran >=90 and modules gives Fortran much better ability to automatically find argument consistency problems. You could monitor the memory locations with a debugger and see what it modifying it.
I concur with M. S. B.: turn on stringent warnings and error checking and verify the subroutine calls are passing arguments that have the same type and shape (array dimensions) as the subroutine expects.
The colons in the variable declaration syntax imply this is Fortran90 or later. If that's the case, I strongly suggest using the INTENT modifier to specify whether arguments are intended to be read-only.
For example, let's assume that of the arguments passed to this routine, strain, Qi, Qf, Qd, tel, and Gc are read-only input and the arguments are ssgrad, strn0, and strss0 are returned as output; that is, whatever value they have is overwritten by this routine.
The variable declarations for the arguments would change to:
real*8, dimension(3), intent(in) :: strain
real*8, dimension(3,3), intent(in) :: Qi, Qf, Qd
real*8, intent(in) :: tel, Gc
real*8, intent(out) :: strn0, ssgrad
real*8, dimension(3), intent(out) :: strss0
The INTENT keyword is an addition to Fortran 90 which allows the user to specify which arguments are read-only (INTENT(IN)), initialized but which may be modified within the routine (INTENT(INOUT)) and which are treated as uninitialized and will be set within the routine (INTENT(OUT)).
If INTENT is not specified, it is defaults to INOUT which is consistent with FORTRAN 77 (Note that there are minor differences between INTENT(INOUT) and INTENT not being specified but they aren't relevant in this example).
A good compiler will throw an error if a routine tries to assign a value to a variable declared INTENT(IN) and will at least throw a warning if a variable declared INTENT(OUT) doesn't get assigned a value.
If possible, set INTENT(IN) on all the variables which are supposed to be read-only. This may not be possible, depending on how those variables are passed to other routines. If INTENT isn't specified on arguments to routines called within this routine, it will default to INOUT. If you pass an INTENT(IN) variable as an INTENT(INOUT) argument, the compiler will throw an error. If this is happening in code you control, you have have to specify INTENT in a number of routines. This may or may not be desirable depending on whether you want to generally improve your code or just fix this one problem really quickly.
I'm assuming some of these variables are passed to external routines in the finite element package which I 'm guessing is linked to your code rather than compiled; I'm not sure how compile-time intent checking is handled in that case.
I have written a fairly large program in Fortran 90. It has been working beautifully for quite a while, but today I tried to step it up a notch and increase the problem size (it is a research non-standard FE-solver, if that helps anyone...) Now I get the "stack overflow" error message and naturally the program terminates without giving me anything useful to work with.
The program starts with setting up all relevant arrays and matrices, and after that is done it prints a few lines of stats regarding this to a log-file. Even with my new, larger problem, this works fine (albeit a little slow), but then it fails as the "number crunching" gets going.
What confuses me is that everything at that point is already allocated (and that worked without errors). I'm not entirely sure what the stack is (Wikipedia and several treads here didn't do much since I have only a quite basic knowledge of the "behind the scenes" workings of a computer).
Assume that I for instance have some arrays initialized as:
INTEGER,DIMENSION(64) :: IA
REAL(8),DIMENSION(:,:),ALLOCATABLE :: AA, BB
which after some initialization routines (i.e. read input from file and such) are allocated as (I store some size-integers for easier passing to subroutines in IA of fixed size):
ALLOCATE( AA(N1,N2) , BB(N1,N2) )
IA(1) = N1
IA(2) = N2
This is basically what happens in the initial portion, and so far so good. But when I then call a subroutine
CALL ROUTINE_ONE(AA,BB,IA)
And the routine looks like (nothing fancy):
SUBROUTINE ROUTINE_ONE(AA,BB,IA)
IMPLICIT NONE
INTEGER,DIMENSION(64) :: IA
REAL(8),DIMENSION(IA(1),IA(2)) :: AA, BB
...
do lots of other stuff
...
END SUBROUTINE ROUTINE_ONE
Now I get an error! The output to the screen says:
forrtl: severe (170): Program Exception - stack overflow
However, when I run the program with the debugger it breaks at line 419 in a file called winsig.c (not my file, but probably part of the compiler?). It seems to be part of a routine called sigreterror: and it is the default case that has been invoked, returning the text Invalid signal or error. There is a comment line attached to this which strangely says /* should never happen, but compiler can't tell */ ...?
So I guess my question is, why does this happen and what is actually happening? I thought that as long as I can allocate all the relevant memory I should be fine? Does the call to the subroutine make copies of the arguments, or just pointers to them? If the answer is copies then I can see where the problem might be, and if so: any ideas on how to get around it?
The problem I try to solve is big, but not insane in any way. Standard FE-solvers can handle bigger problems than my current one. I run the program on a Dell PowerEdge 1850 and the OS is Microsoft Server 2008 R2 Enterprise. According to systeminfo at the cmd prompt I have 8GB of physical memory and almost 16GB virtual. As far as I understand the total of all my arrays and matrices should not add up to more than maybe 100MB - about 5.5M integer(4) and 2.5M real(8) (which according to me should be only about 44MB, but let's be fair and add another 50MB for overhead).
I use the Intel Fortran compiler integrated with Microsoft Visual Studio 2008.
Adding some actual source code to clarify a bit
! Update continuum state
CALL UpdateContinuumState(iTask,iArray,posc,dof,dof_k,nodedof,elm,&
bmtrx,detjac,w,mtrlprops,demtrx,dt,stress,strain,effstrain,&
effstress,aa,fi,errmsg)
is the actual call to the routine. Big arrays are posc, bmtrx and aa - all other are at least an order of magnitude smaller (if not more). posc is INTEGER(4) and bmtrx and aa is REAL(8)
SUBROUTINE UpdateContinuumState(iTask,iArray,posc,dof,dof_k,nodedof,elm,bmtrx,&
detjac,w,mtrlprops,demtrx,dt,stress,strain,effstrain,&
effstress,aa,fi,errmsg)
IMPLICIT NONE
!I/O
INTEGER(4) :: iTask, errmsg
INTEGER(4) :: iArray(64)
INTEGER(4),DIMENSION(iArray(15),iArray(15),iArray(5)) :: posc
INTEGER(4),DIMENSION(iArray(22),iArray(21)+1) :: nodedof
INTEGER(4),DIMENSION(iArray(29),iArray(3)+2) :: elm
REAL(8),DIMENSION(iArray(14)) :: dof, dof_k
REAL(8),DIMENSION(iArray(12)*iArray(17),iArray(15)*iArray(5)) :: bmtrx
REAL(8),DIMENSION(iArray(5)*iArray(17)) :: detjac
REAL(8),DIMENSION(iArray(17)) :: w
REAL(8),DIMENSION(iArray(23),iArray(19)) :: mtrlprops
REAL(8),DIMENSION(iArray(8),iArray(8),iArray(23)) :: demtrx
REAL(8) :: dt
REAL(8),DIMENSION(2,iArray(12)*iArray(17)*iArray(5)) :: stress
REAL(8),DIMENSION(iArray(12)*iArray(17)*iArray(5)) :: strain
REAL(8),DIMENSION(2,iArray(17)*iArray(5)) :: effstrain, effstress
REAL(8),DIMENSION(iArray(25)) :: aa
REAL(8),DIMENSION(iArray(14)) :: fi
!Locals
INTEGER(4) :: i, e, mtrl, i1, i2, j1, j2, k1, k2, dim, planetype, elmnodes, &
Nec, elmpnodes, Ndisp, Nstr, Ncomp, Ngpt, Ndofelm
INTEGER(4),DIMENSION(iArray(15)) :: doflist
REAL(8),DIMENSION(iArray(12)*iArray(17),iArray(15)) :: belm
REAL(8),DIMENSION(iArray(17)) :: jelm
REAL(8),DIMENSION(iArray(12)*iArray(17)*iArray(5)) :: dstrain
REAL(8),DIMENSION(iArray(12)*iArray(17)) :: s
REAL(8),DIMENSION(iArray(17)) :: ep, es, dep
REAL(8),DIMENSION(iArray(15),iArray(15)) :: kelm
REAL(8),DIMENSION(iArray(15)) :: felm
dim = iArray(1)
...
And it fails before the last line above.
As per steabert's request, I'll just summarize the conversation in the comments here where it's a bit more visible, even though M.S.B.'s answer already gets right to the nub of the problem.
In technical programming, where procedures often have large local arrays for intermediate computation, this happens a lot. Local variables are generally stored on the stack, which typically (and quite reasonably) a small fraction of overall system memory -- usually of order 10MB or so. When the local variable sizes exceed the stack size, you see exactly the symptoms described here -- a stack overflow occuring after a call to the relevant subroutine but before its first executable statement.
So when this problem happens, the best thing to do is to find the relevant large local variables, and decide what to do. In this case, at least the variables belm and dstrain were getting quite sizable.
Once the variables are located, and you've confirmed that's the problem, there's a few options. As MSB points out, if you can make your arrays smaller, that's one option. Alternatively, you can make the stack size larger; under linux, that's done with ulimit -s [newsize]. That really just postpones the problem, though, and you have to do something different on windows machines.
The other class of ways to avoid this problem is not to put the large data on the stack, but in the rest of memory (the "heap"). You can do that by giving the arrays the save attribute (in C, static); this puts the variable on the heap and thus makes the values persistent between calls. The downside there is that this potentially changes the behavior of the subroutine, and means the subroutine can't be used recursively, and similarly is non-threadsafe (if you're ever in a position where multiple threads will enter the routine simulatneously, they'll each see the same copy of the local varaiable and potentially overwrite each other's results). The upside is that it's easy and very portable -- it should work everywhere. However, this will only work with fixed-size local variables; if the temporary arrays have sizes that depend on the inputs, you can't do this (since there'd no longer be a single variable to save; it could be different size every time the procedure is called).
There are compiler-specific options which put all arrays (or all arrays of larger than some given size) on the heap rather than on the stack; every Fortran compiler I know has an option for this. For ifort, used in the OPs post, it's -heap-arrays in linux, or /heap-arrays for windows. For gfortran, this may actually be the default. This is good for making sure you know what's going on, but it means you have to have different incantations for every compiler to make sure your code works.
Finally, you can make the offending arrays allocatable. Allocated memory goes on the heap; but the variable which points to them is on the stack, so you get the benefits of both approaches. Also, this is completely standard fortran and so totally portable. The downside is that it requires code changes. Also, the allocation process can take nontrivial amounts of time; so if you're going to be calling the routine zillions of times, you may notice this slows things down slightly. (This possible performance regression is easy to fix, though; if you'll be calling it zillions of times with the same size arrays, you can have an optional argument to pass in a pre-allocated local array and use that instead, so that you only allocate/deallocate once).
Allocating/deallocating each time would look like:
SUBROUTINE UpdateContinuumState(iTask,iArray,posc,dof,dof_k,nodedof,elm,bmtrx,&
detjac,w,mtrlprops,demtrx,dt,stress,strain,effstrain,&
effstress,aa,fi,errmsg)
IMPLICIT NONE
!...arguments....
!Locals
!...
REAL(8),DIMENSION(:,:), allocatable :: belm
REAL(8),DIMENSION(:), allocatable :: dstrain
allocate(belm(iArray(12)*iArray(17),iArray(15))
allocate(dstrain(iArray(12)*iArray(17)*iArray(5))
!... work
deallocate(belm)
deallocate(dstrain)
Note that if the subroutine does a lot of work (eg, takes seconds to execute), the overhead from a couple allocate/deallocates should be negligable. If not, and you want to avoid the overhead, using the optional arguments for preallocated worskpace would look something like:
SUBROUTINE UpdateContinuumState(iTask,iArray,posc,dof,dof_k,nodedof,elm,bmtrx,&
detjac,w,mtrlprops,demtrx,dt,stress,strain,effstrain,&
effstress,aa,fi,errmsg,workbelm,workdstrain)
IMPLICIT NONE
!...arguments....
real(8),dimension(:,:), optional, target :: workbelm
real(8),dimension(:), optional, target :: workdstrain
!Locals
!...
REAL(8),DIMENSION(:,:), pointer :: belm
REAL(8),DIMENSION(:), pointer :: dstrain
if (present(workbelm)) then
belm => workbelm
else
allocate(belm(iArray(12)*iArray(17),iArray(15))
endif
if (present(workdstrain)) then
dstrain => workdstrain
else
allocate(dstrain(iArray(12)*iArray(17)*iArray(5))
endif
!... work
if (.not.(present(workbelm))) deallocate(belm)
if (.not.(present(workdstrain))) deallocate(dstrain)
Not all of the memory is created when the program starts. When you call the subroutine the executable is creating the memory that the subroutine needs for local variables. Typically arrays with simple declarations that are local to that subroutine -- neither allocatable, nor pointer -- are allocated on the stack. You could have simply run of of stack space when you reached these declarations. You might have reached a 2GB limit on a 32-bit OS with some array. Sometimes executable statements implicitly create a temporary array on the stack.
Possible solutions: 1) make your arrays smaller (not attractive), 2) make the stack larger), 3) some compilers have options to switch from placing arrays on the stack to dynamically allocating them, similar to the method used for "allocate", 4) identify large arrays and make them allocatable.
The stack is the memory area where the information needed to return from a function, and the information locally defined in a function is stored. So a stack overflow may indicate you have a function that calls another function which in its turn calls another function, etc.
I am not familiar with Fortran (anymore) but another cause might be that those functions declare tons of local variables, or at least variables that need a lot of place.
A last one: the stack is typically rather small, so it's not a priori relevant how much memory the machine has. It should be quite simple to instruct the linker to increase the stack size, at least if you are certain it's just a lack of space, and not a bug in your application.
Edit: do you use recursion in your program? Recursive calls can eat through the stack very quickly.
Edit: have a look at this: (emphasis mine)
On Windows, the stack space to
reserved for the program is set using
the /Fn compiler option, where n is
the number of bytes. Additionally,
the stack reserve size can be
specified through the Visual Studio
IDE which adds the Microsoft Linker
option /STACK: to the linker command
line. To set this, go to Property
Pages>Configuration
Properties>Linker>System>Stack Reserve
Size. There you can specify the stack
size in bytes in either decimal or
C-language notation. If not specified,
the default stack size is 1MB.
The only problem I ran into with a similar test code, is the 2Gb allocation limit for 32-bit compilation. When I exceed it I get an error message on line 419 in winsig.c
Here is the test code
program FortranCon
implicit none
! Variables
INTEGER :: IA(64), S1
REAL(8), DIMENSION(:,:), ALLOCATABLE :: AA, BB
REAL(4) :: S2
INTEGER, PARAMETER :: N = 10960
IA(1)=N
IA(2)=N
ALLOCATE( AA(N,N), BB(N,N) )
AA(1:N,1:N) = 1D0
BB(1:N,1:N) = 2D0
CALL TEST(AA,BB,IA)
S1 = SIZEOF(AA) !Size of each array
S2 = 2*DBLE(S1)/1024/1024 !Total size for 2 arrays in Mb
WRITE (*,100) S2, ' Mb' ! When allocation reached 2Gb then
100 FORMAT (F8.1,A) ! exception occurs in Win32
DEALLOCATE( AA, BB )
end program FortranCon
SUBROUTINE TEST(AA,BB,IA)
IMPLICIT NONE
INTEGER, DIMENSION(64),INTENT(IN) :: IA
REAL(8), DIMENSION(IA(1),IA(2)),INTENT(INOUT) :: AA,BB
... !Do stuff with AA,BB
END SUBROUTINE
When N=10960 it runs ok showing 1832.9 Mb. With N=11960 it crashes. Of course when I compile with x64 it works ok. Each array has 8*N^2 bytes storage. I don't know if it helps but I recommend using the INTENT() keywords for the dummy variables.
Are you using some parallelization? This can be a problem with statically declared arrays. Try all bigger arrays make ALLOCATABLE, otherwise, they will be placed on the stack in autoparallel or OpenMP threads.
For me the issue was the stack reserve size. I went and changed the stack reserved size from 0 to 100000000 and recompiled the code. The code now runs smoothly.