Module -S does not process data if simulation was terminated due to optional input in non-final step #263

ctriant1 · 2021-07-09T14:57:07Z

ctriant1
Jul 9, 2021

When setting up simulations with the intention to terminate at a set max (engineering) strain and this occurs in the non-final load step, no data is processed by module -S. Using FEPX 1.2.1, Neper 4.2.0, gfortran 9.3.0, OpenMPI 4.0.3, Ubuntu 20.04 in TriaxCSR.

Depending on the texture, the strain target might be reached in a different step. In the example attached, it is reached in step 4 of 6 and FEPX terminates soon after a max engineering strain value of is exceeded. However, when running

neper -S .

The task aborts and shows

neper: malloc.c:4036: _int_malloc: Assertion `(unsigned long) (size) >= (unsigned long) (nb)' failed.
Aborted (core dumped)

Instead of printing 4 steps, the whole processing routine is interrupted (not even the inputs folder is populated properly). Minimal example (10 grains) attached. This is not an issue when the strain target is removed and the simulation completes all steps.

example.zip

Answered by rquey

Jul 9, 2021

What if you run neper -S from outside of the result directory? It works for me:

$ cd example
$ fepx
[...]
$ cd ..
$ neper -S example
                                                                                                         
========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.     
Info   : Version 4.2.0                                                                                   
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full) 
Info   : Running on 8 threads.                                                                           
Info   : <https://neper.inf…

View full answer

rquey · 2021-07-09T15:19:15Z

rquey
Jul 9, 2021
Maintainer

What if you run neper -S from outside of the result directory? It works for me:

$ cd example
$ fepx
[...]
$ cd ..
$ neper -S example
                                                                                                         
========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.     
Info   : Version 4.2.0                                                                                   
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full) 
Info   : Running on 8 threads.                                                                           
Info   : <https://neper.info>                  
Info   : Copyright (C) 2003-2021, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/rquey/.neperrc'...          
Info   : ---------------------------------------------------------------
Info   : MODULE  -S loaded with arguments:
Info   : [ini file] (none) 
Info   : [com line] example
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   :   - Reading arguments...
Info   : Writing simulation directory from FEPX raw result directory...
Info   :     [o] Writing directory `example.sim'...
Info   :   - Parsing FEPX results...
Info   :     > Node number      : 1703
Info   :     > Element number   : 972
Info   :     > Elset number     : 0
Info   :     > Partition number : 6
Info   :     > Step number      : 4
Info   :     > Node results     : coo vel
Info   :     > Element results  : ori crss elt-vol strain-el stress
                                  sliprate stress-eq defrate-eq strain-eq
                                  defrate-pl-eq strain-pl-eq velgrad
                                  defrate-pl spinrate slip work work-pl
                                  defrate
Info   :     > Elset results    :
Info   :   - Writing inputs...
Info   :     [o] Writing directory `example.sim/inputs'...
Info   :       . simulation.tess...
Info   :       . simulation.msh...
Info   :       . simulation.config...
Info   :       . *.sh...
Info   :       . simulation.ori...
Info   :     [o] Wrote directory `example.sim/inputs'.
Info   :     [i] Parsing file `example.sim/inputs/simulation.msh'...
Info   :     [i] Parsed file `example.sim/inputs/simulation.msh'.
Info   :   - Writing results...
Info   :     [o] Writing directory `example.sim/results'...
Info   :     [o] Writing directory `example.sim/results/nodes'...
Info   :       . coo .............................................. 100%
Info   :       . vel .............................................. 100%
Info   :     [o] Wrote directory `example.sim/results/nodes'.
Info   :     [o] Writing directory `example.sim/results/elements'...
Info   :       . ori .............................................. 100%
Info   :       . crss ............................................. 100%
Info   :       . elt-vol .......................................... 100%
Info   :       . strain-el ........................................ 100%
Info   :       . stress ........................................... 100%
Info   :       . sliprate ......................................... 100%
Info   :       . stress-eq ........................................ 100%
Info   :       . defrate-eq ....................................... 100%
Info   :       . strain-eq ........................................ 100%
Info   :       . defrate-pl-eq .................................... 100%
Info   :       . strain-pl-eq ..................................... 100%
Info   :       . velgrad .......................................... 100%
Info   :       . defrate-pl ....................................... 100%
Info   :       . spinrate ......................................... 100%
Info   :       . slip ............................................. 100%
Info   :       . work ............................................. 100%
Info   :       . work-pl .......................................... 100%
Info   :       . defrate .......................................... 100%
Info   :     [o] Wrote directory `example.sim/results/elements'.
Info   :     [o] Wrote directory `example.sim'.
Info   : Elapsed time: 0.073 secs.
========================================================================

7 replies

ctriant1 Jul 9, 2021
Author

I have followed your instructions and data has now been exported for the 4 load steps. What do you make of the errors/warning here? The output is

==346113== Memcheck, a memory error detector
==346113== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==346113== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
==346113== Command: neper -S a235tnep
==346113== 

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.2.0
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 32 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2021, and GNU GPL'd, by Romain Quey.
Info   : No initialization file found (`/home/aura/.neperrc').
Info   : ---------------------------------------------------------------
Info   : MODULE  -S loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] a235tnep
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   :   - Reading arguments...
Info   : Writing simulation directory from FEPX raw result directory...
Info   :     [o] Writing directory `a235tnep.sim'...
Info   :   - Parsing FEPX results...
==346113== Invalid write of size 4
==346113==    at 0x32F5C4: neut_sim_fscanf (neut_sim_gen1.c:140)
==346113==    by 0x25DA08: nes_sim_fepxparse (nes_sim_fepxparse1.c:14)
==346113==    by 0x25D711: nes_sim (nes_sim1.c:12)
==346113==    by 0x25BEF9: neper_s (neper_s.c:34)
==346113==    by 0x186846: main (neper.c:115)
==346113==  Address 0x528e594 is 0 bytes after a block of size 20 alloc'd
==346113==    at 0x483DD99: calloc (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==346113==    by 0x186C1D: ut_alloc_1d_int (ut_alloc.c:37)
==346113==    by 0x32F522: neut_sim_fscanf (neut_sim_gen1.c:127)
==346113==    by 0x25DA08: nes_sim_fepxparse (nes_sim_fepxparse1.c:14)
==346113==    by 0x25D711: nes_sim (nes_sim1.c:12)
==346113==    by 0x25BEF9: neper_s (neper_s.c:34)
==346113==    by 0x186846: main (neper.c:115)
==346113== 
Info   :     > Node number      : 1703
Info   :     > Element number   : 972
Info   :     > Elset number     : 0
Info   :     > Partition number : 31
Info   :     > Step number      : 4
Info   :     > Node results     : coo vel
Info   :     > Element results  : ori crss elt-vol strain-el stress
                                  sliprate stress-eq defrate-eq strain-eq
                                  defrate-pl-eq strain-pl-eq velgrad
                                  defrate-pl spinrate slip work work-pl
                                  defrate
Info   :     > Elset results    :
Info   :   - Writing inputs...
Info   :     [o] Writing directory `a235tnep.sim/inputs'...
Info   :       . simulation.tess...
Info   :       . simulation.msh...
Info   :       . simulation.config...
Info   :       . *.sh...
Info   :       . simulation.ori...
Info   :     [o] Wrote directory `a235tnep.sim/inputs'.
Info   :     [i] Parsing file `a235tnep.sim/inputs/simulation.msh'...
Info   :     [i] Parsed file `a235tnep.sim/inputs/simulation.msh'.
Info   :   - Writing results...
Info   :     [o] Writing directory `a235tnep.sim/results'...
Info   :     [o] Writing directory `a235tnep.sim/results/nodes'...
Info   :       . coo .............................................. 100%
Info   :       . vel .............................................. 100%
Info   :     [o] Wrote directory `a235tnep.sim/results/nodes'.
Info   :     [o] Writing directory `a235tnep.sim/results/elements'...
Info   :       . ori .............................................. 100%
Info   :       . crss ............................................. 100%
Info   :       . elt-vol .......................................... 100%
Info   :       . strain-el ........................................ 100%
Info   :       . stress ........................................... 100%
Info   :       . sliprate ......................................... 100%
Info   :       . stress-eq ........................................ 100%
Info   :       . defrate-eq ....................................... 100%
Info   :       . strain-eq ........................................ 100%
Info   :       . defrate-pl-eq .................................... 100%
Info   :       . strain-pl-eq ..................................... 100%
Info   :       . velgrad .......................................... 100%
Info   :       . defrate-pl ....................................... 100%
Info   :       . spinrate ......................................... 100%
Info   :       . slip ............................................. 100%
Info   :       . work ............................................. 100%
Info   :       . work-pl .......................................... 100%
Info   :       . defrate .......................................... 100%
Info   :     [o] Wrote directory `a235tnep.sim/results/elements'.
Info   :     [o] Wrote directory `a235tnep.sim'.
Info   : Elapsed time: 6.456 secs.
========================================================================

==346113== 
==346113== HEAP SUMMARY:
==346113==     in use at exit: 43,897 bytes in 89 blocks
==346113==   total heap usage: 40,818 allocs, 40,729 frees, 20,035,916 bytes allocated
==346113== 
==346113== LEAK SUMMARY:
==346113==    definitely lost: 21,147 bytes in 33 blocks
==346113==    indirectly lost: 3,990 bytes in 21 blocks
==346113==      possibly lost: 9,920 bytes in 31 blocks
==346113==    still reachable: 8,840 bytes in 4 blocks
==346113==         suppressed: 0 bytes in 0 blocks
==346113== Rerun with --leak-check=full to see details of leaked memory
==346113== 
==346113== For lists of detected and suppressed errors, rerun with: -s
==346113== ERROR SUMMARY: 2 errors from 1 contexts (suppressed: 0 from 0)

rquey Jul 9, 2021
Maintainer

@mkasemer, this is what I get (in post.report) for this simulation:

number_of_steps 4
printed_steps 1 2 3 4 5 6

More printed steps than steps. This is what is causing the issue. It must be a problem in FEPX then?

mkasemer Jul 9, 2021
Maintainer

Hmm, yes, it is. The issue (I think) is in subroutine WRITE_REPORT_FILE_COMPLETE_STEPS of write_output_mod.f90 (see below). FINAL_STEP can be tripped before the planned final step. We can check to see what FINAL_STEP is, and not print any values in PRINT_ARRAY greater than FINAL_STEP (I think this would work...).

EDIT: Actually, if we just change SIZE(PRINT_ARRAY,1) to FINAL_STEP, this might work. @ctriant1, would you mind making this edit and running a quick test? the output in post.report should then look like:

number_of_steps 4
printed_steps 1 2 3 4

    IF (MYID .EQ. 0) THEN
        !
        ! Print the completed number of steps
        !
        WRITE(OUNITS(REPORT_U), '(A,I0)') 'number_of_steps ', &
            & FINAL_STEP
        !
        ! Print the IDs of the steps that were requested to be printed
        !
        WRITE(OUNITS(REPORT_U), '(A)', ADVANCE='NO') 'printed_steps '
        !
        DO I = 1, SIZE(PRINT_ARRAY,1)
            !
            IF (PRINT_ARRAY(I) .EQ. 0) WRITE(OUNITS(REPORT_U), &
                & '(I0, A)', ADVANCE='NO') I, ' '
            !
        END DO
        !
        ! Close the report file before ending the process
        !
        CLOSE(OUNITS(REPORT_U))
        !
    END IF

ctriant1 Jul 22, 2021
Author

Thank you both for your input and apologies for the delay while I've been away. @mkasemer I've replaced SIZE(PRINT_ARRAY,1) to FINAL_STEP in write_output_mod.f90 as suggested and I can confirm that the issue has been resolved when checking using the quick test simulation. Neper was re-installed to the default version and the expected results were printed. Testing with a full scale job at the moment, but I'd expect the outcome to be the same.

mkasemer Aug 2, 2021
Maintainer

Note that this is fixed as of FEPX 1.2.2-1.

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Module -S does not process data if simulation was terminated due to optional input in non-final step #263

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