[FLASH-USERS] Runtime error when adding 3rd species to LaserSlab
Marissa Adams
madams at pas.rochester.edu
Mon Apr 6 16:20:51 EDT 2020
Hi Kelin,
Instead of calling the third species, TARG2, try calling it another name,
like WIND for "window" for instance. Species can only have names that are
four letters long. Try that and see if the bug persists.
Best,
Marissa
On Mon, Apr 6, 2020 at 4:13 PM Kelin KO <kkurzero at gmail.com> wrote:
> Hi all,
>
> I am a novice FLASH user and am trying to construct a composite target
> from the default LaserSlab problem. My configuration is a thin aluminum
> layer sandwiched between two polystyrene layers. Initially, I modified the
> if statements in initblock to define 4 regions (chamber, 1st/2nd/3rd target
> layer) and modified the other init files as well as Config and .par to
> reflect this. I only used the two species defined in the default LaserSlab
> problem, using CHAM_SPEC (helium) for the middle target layer, just to
> establish that I changed the geometry correctly). This compiles and runs as
> expected.
>
> However, when I tried to define a third species, it compiled but gave a
> strange error at runtime that I'm struggling to find the cause of (see
> attached .Log file):
>
> HDF5-DIAG: Error detected in HDF5 (1.8.17) MPI-process 0:
> #000: H5Ddeprec.c line 193 in H5Dcreate1(): unable to create dataset
> major: Dataset
> minor: Unable to initialize object
> #001: H5Dint.c line 455 in H5D__create_named(): unable to create and
> link to dataset
> major: Dataset
> minor: Unable to initialize object
> #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to
> object
> major: Links
> minor: Unable to initialize object
> #003: H5L.c line 1882 in H5L_create_real(): can't insert link
> major: Symbol table
> minor: Unable to insert object
> #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal
> failed
> major: Symbol table
> minor: Object not found
> #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator
> failed
> major: Symbol table
> minor: Callback failed
> #006: H5L.c line 1674 in H5L_link_cb(): name already exists
> major: Symbol table
> minor: Object already exists
> flash4: io_h5create_dataset.c:61: io_h5create_dataset: Assertion `dataset
> >= 0' failed.
> forrtl: error (76): Abort trap signal
> Image PC Routine Line Source
>
> flash4 0000000000B50CC1 tbk_trace_stack_i Unknown Unknown
> flash4 0000000000B4EDFB tbk_string_stack_ Unknown Unknown
> flash4 0000000000AFE444 Unknown Unknown Unknown
> flash4 0000000000AFE256 Unknown Unknown Unknown
> flash4 0000000000AA7569 Unknown Unknown Unknown
> flash4 0000000000AAB374 Unknown Unknown Unknown
> libpthread-2.17.s 00002B9C6787E5D0 Unknown Unknown Unknown
> libc-2.17.so
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__libc-2D2.17.so&d=DwMFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=g6majbT8WMLt7mVKPDafFL0xsMf-8SY6y2gfx4NveiE&s=TxgKhO5lmnLQWGLmi0hnzN2MnvSitj0lFQPwQG38GpU&e=>
> 00002B9C67DC3207 gsignal Unknown Unknown
> libc-2.17.so
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__libc-2D2.17.so&d=DwMFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=g6majbT8WMLt7mVKPDafFL0xsMf-8SY6y2gfx4NveiE&s=TxgKhO5lmnLQWGLmi0hnzN2MnvSitj0lFQPwQG38GpU&e=>
> 00002B9C67DC48F8 abort Unknown Unknown
> libc-2.17.so
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__libc-2D2.17.so&d=DwMFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=g6majbT8WMLt7mVKPDafFL0xsMf-8SY6y2gfx4NveiE&s=TxgKhO5lmnLQWGLmi0hnzN2MnvSitj0lFQPwQG38GpU&e=>
> 00002B9C67DBC026 Unknown Unknown Unknown
> libc-2.17.so
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__libc-2D2.17.so&d=DwMFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=g6majbT8WMLt7mVKPDafFL0xsMf-8SY6y2gfx4NveiE&s=TxgKhO5lmnLQWGLmi0hnzN2MnvSitj0lFQPwQG38GpU&e=>
> 00002B9C67DBC0D2 Unknown Unknown Unknown
> flash4 0000000000671D09 Unknown Unknown Unknown
> flash4 000000000066A53A Unknown Unknown Unknown
> flash4 000000000066A995 Unknown Unknown Unknown
> flash4 000000000067A45C Unknown Unknown Unknown
> flash4 000000000047F1D8 Unknown Unknown Unknown
> flash4 000000000047EAA1 Unknown Unknown Unknown
> flash4 0000000000416A21 Unknown Unknown Unknown
> flash4 000000000043CD5E Unknown Unknown Unknown
> flash4 000000000040839E Unknown Unknown Unknown
> libc-2.17.so
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__libc-2D2.17.so&d=DwMFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=g6majbT8WMLt7mVKPDafFL0xsMf-8SY6y2gfx4NveiE&s=TxgKhO5lmnLQWGLmi0hnzN2MnvSitj0lFQPwQG38GpU&e=>
> 00002B9C67DAF3D5 __libc_start_main Unknown Unknown
> flash4 00000000004082A9 Unknown Unknown Unknown
> /var/spool/slurm/job13017474/slurm_script: line 22: 23813 Aborted
> ./flash4
>
>
> All I have changed from the last working configuration is that I added a
> TARG2_SPEC to the initblock file (and used it in the if statement), defined
> all the necessary variables for "targ2" in the init/Config/par files by
> copying those for the "targ" species and renaming, and changed my ./setup
> line to reflect the new species (changed -species=targ,cham to
> -species=cham,targ,targ2). The log file created by flash.par does not
> mention any errors, it just ends after the creation of the first checkpoint.
>
> Does anyone have some insight as to where I can begin looking to debug
> this? I have gone through all the files I changed using the compare plugin
> in notepad++ and verified that the only changes are the addition of the new
> variables and that they are syntactically correct, and as I said the
> executable compiles without issue, so I don't think that's where the
> problem is.
>
> Thanks so much for any guidance you can provide and for your time.
>
> Best,
> Kelin Kurzer-Ogul
>
> ---------------------------
>
> Kelin Kurzer-Ogul
>
> Graduate Student
>
> Department of Mechanical Engineering
>
> University of Rochester
>
>
--
%---------------------------------------------%
Marissa B. P. Adams
(she/her/hers)
Phd Candidate, University of Rochester
*E-mail:* madams at pas.rochester.edu
*Website:* https://www.pas.rochester.edu/~madams
<http://www.pas.rochester.edu/~madams>
*Twitter:* https://twitter.com/mbpadams
*Current Location:*
371 Bausch and Lomb Hall
University of Rochester
Rochester, NY 14627
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