[FLASH-USERS] Runtime error when adding 3rd species to LaserSlab

Kelin KO kkurzero at gmail.com
Mon Apr 6 16:45:24 EDT 2020 

Hi Marissa,

Thanks so much for the quick reply. I suspected it might have had
something to do with using "2" in the species name, but I didn't
consider the length. I will check that now.

Best,
Kelin
________________________________________
From: Marissa Adams <madams at pas.rochester.edu>
Sent: Monday, April 6, 2020 1:20:51 PM
To: Kelin KO
Cc: flash-users
Subject: Re: [FLASH-USERS] Runtime error when adding 3rd species to LaserSlab

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<mailto: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<mailto: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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