[FLASH-USERS] [EXT] Problem with restart: almost empty output files
Reyes, Adam
adam.reyes at rochester.edu
Tue May 14 03:18:58 EDT 2024
Hi Mattia,
I can confirm this bug, it seems to be specific to the "IO/IOMain/hdf5/parallel/NoFbs” implementation and maybe also all of the "IO/IOMain/hdf5/parallel” subunits. You do have two conflicting setup arguments: "+hdf5TypeIO -unit=IO/IOMain/hdf5/parallel/NoFbs” and the latter is winning out. The “+hdf5TypeIO” is preferred and will still work even with the UG grids and doesn’t seem to have the same affliction.
The good news is that all the hdf5 implementations can restart from each other so you should be able to recompile using just the “+hdf5TypeIO” and restart from your previous checkpoint.
*********************************************
Adam Reyes

Code Group Leader, Flash Center for Computational Science
Research Scientist, Dept. of Physics and Astronomy
University of Rochester
River Campus: Bausch and Lomb Hall, 369
500 Wilson Blvd. PO Box 270171, Rochester, NY 14627
Email adam.reyes at rochester.edu
Web https://flash.rochester.edu
(he / him / his)

*********************************************
> On May 14, 2024, at 8:09 AM, Mattia Cipriani <mattia.cipriani at enea.it> wrote:
>
> Hi Adam,
>
> Yes, sorry, version 4.7.1.
>
> Best regards
> Mattia
>
> ---------------------------------------------
> Dr Mattia Cipriani, PhD
> ENEA
> FSN-PLAS-PAX
> 45, Via E. Fermi
> 00044 Frascati (Rome)
> Italy
> Office: Building 12
> Room 12223
> Tel: +39 069400 5145
> Mobile: +39 328 5552077
> Skype: matcipriani
> Researchgate <https://urldefense.com/v3/__https://www.researchgate.net/profile/Mattia-Cipriani-2__;!!CGUSO5OYRnA7CQ!ecROYnbUw5AJW_mYDqLQ9ZLej_GtbDDto6c5xkFcdfknWZOScYGO95cklt42VpBwAFELRhGimfvEFTjInwTm9aZlR0S3WVA$>
> LinkedIn <https://urldefense.com/v3/__https://www.linkedin.com/in/mattia-cipriani-0707bb2a/__;!!CGUSO5OYRnA7CQ!ecROYnbUw5AJW_mYDqLQ9ZLej_GtbDDto6c5xkFcdfknWZOScYGO95cklt42VpBwAFELRhGimfvEFTjInwTm9aZlS_0DDK4$>
> ResearcherID AAG-9269-2021 <https://urldefense.com/v3/__https://publons.com/researcher/AAG-9269-2021/__;!!CGUSO5OYRnA7CQ!ecROYnbUw5AJW_mYDqLQ9ZLej_GtbDDto6c5xkFcdfknWZOScYGO95cklt42VpBwAFELRhGimfvEFTjInwTm9aZl9wmICEQ$>
> ORCID 0000-0002-2500-605X <https://urldefense.com/v3/__https://orcid.org/0000-0002-2500-605X__;!!CGUSO5OYRnA7CQ!ecROYnbUw5AJW_mYDqLQ9ZLej_GtbDDto6c5xkFcdfknWZOScYGO95cklt42VpBwAFELRhGimfvEFTjInwTm9aZl_ebCf-c$>
> ---------------------------------------------
>
>> Il giorno 14 mag 2024, alle ore 08:05, Reyes, Adam <adam.reyes at rochester.edu <mailto:adam.reyes at rochester.edu>> ha scritto:
>>
>> Hi Mattia,
>>
>> Can you confirm which version of FLASH that you’re using?
>> *********************************************
>> Adam Reyes
>>
>> <FLASH.jpg>
>>
>> Code Group Leader, Flash Center for Computational Science
>> Research Scientist, Dept. of Physics and Astronomy
>> University of Rochester
>> River Campus: Bausch and Lomb Hall, 369
>> 500 Wilson Blvd. PO Box 270171, Rochester, NY 14627
>> Email adam.reyes at rochester.edu <mailto:adam.reyes at rochester.edu>
>> Web https://flash.rochester.edu <https://flash.rochester.edu/>
>> (he / him / his)
>> <FLASH-pride-sml.png>
>>
>> *********************************************
>>
>>
>>
>>> On May 14, 2024, at 6:10 AM, Mattia Cipriani <mattia.cipriani at enea.it> wrote:
>>>
>>> Hi all,
>>>
>>> I am running a 3D simulation derived from LaserSlab.
>>> The simulation cannot be run entirely with a single run for the time limit on the queue, then I stop the simulation by setting wall_clock_time_limit appropriately and FLASH outputs a checkpoint file about one hour before the time limit of the queue on the cluster.
>>> When I restart the simulation from this checkpoint file, everything goes fine but the first about 10 output plot files have a size of 110 kB, compared to the size of the files from the first run of 471 MB. As a confirmation of this, from the flash log file (attached) I can see that the plot file stays open for only a couple of seconds in the second run, compared to three minutes of the first.
>>> The size of the checkpoint file used for restart is normal.
>>> I also tried to free up some space on the storage on the cluster, even though I check that I am far from my quota limit. And in fact this did not solve the issue.
>>>
>>> What could be the problem?
>>>
>>> Thank you in advance.
>>> Best regards,
>>> Mattia
>>>
>>>
>>> ---------------------------------------------
>>> Dr Mattia Cipriani, PhD
>>> ENEA
>>> NUC-PLAS-FIPI
>>> 45, Via E. Fermi
>>> 00044 Frascati (Rome)
>>> Italy
>>> Office: Building 12
>>> Room 12223
>>> Tel: +39 069400 5145
>>> Mobile: +39 328 5552077
>>> Skype: matcipriani
>>> Researchgate <https://urldefense.com/v3/__https://www.researchgate.net/profile/Mattia-Cipriani-2__;!!CGUSO5OYRnA7CQ!ecROYnbUw5AJW_mYDqLQ9ZLej_GtbDDto6c5xkFcdfknWZOScYGO95cklt42VpBwAFELRhGimfvEFTjInwTm9aZlR0S3WVA$>
>>> LinkedIn <https://urldefense.com/v3/__https://www.linkedin.com/in/mattia-cipriani-0707bb2a/__;!!CGUSO5OYRnA7CQ!ecROYnbUw5AJW_mYDqLQ9ZLej_GtbDDto6c5xkFcdfknWZOScYGO95cklt42VpBwAFELRhGimfvEFTjInwTm9aZlS_0DDK4$>
>>> ResearcherID AAG-9269-2021 <https://urldefense.com/v3/__https://publons.com/researcher/AAG-9269-2021/__;!!CGUSO5OYRnA7CQ!ecROYnbUw5AJW_mYDqLQ9ZLej_GtbDDto6c5xkFcdfknWZOScYGO95cklt42VpBwAFELRhGimfvEFTjInwTm9aZl9wmICEQ$>
>>> ORCID 0000-0002-2500-605X <https://urldefense.com/v3/__https://orcid.org/0000-0002-2500-605X__;!!CGUSO5OYRnA7CQ!ecROYnbUw5AJW_mYDqLQ9ZLej_GtbDDto6c5xkFcdfknWZOScYGO95cklt42VpBwAFELRhGimfvEFTjInwTm9aZl_ebCf-c$>
>>> ---------------------------------------------
>>>
>>>
>>>
>>>
>>>
>>>
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>
>
>
> Questo messaggio e i suoi allegati sono indirizzati esclusivamente alle persone indicate e la casella di posta elettron ica da cui è stata inviata è da qualificarsi quale strumento aziendale.
>
> La diffusione, copia o qualsiasi altra azione derivante dalla conoscenza di queste informazioni sono rigorosamente viet ate (art. 616 c.p, D.Lgs. n. 196/2003 s.m.i. e GDPR Regolamento - UE 2016/679).
>
> Qualora abbiate ricevuto questo documento per errore siete cortesemente pregati di darne immediata comunicazione al mit tente e di provvedere alla sua distruzione. Grazie.
>
> This e-mail and any attachments is confidential and may contain privileged information intended for the addressee(s) only.
>
> Dissemination, copying, printing or use by anybody else is unauthorised (art. 616 c.p, D.Lgs. n. 196/2003 and subsequen t amendments and GDPR UE 2016/679).
>
> If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e -mail. Thanks.
>
> <FLASH.jpg><FLASH-pride-sml.png>
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