[FLASH-USERS] [EXT] Library conflict at the end of make and segmentation fault
Reyes, Adam
adam.reyes at rochester.edu
Wed Feb 7 08:13:49 EST 2024
Hi Mattia,
Are you using a version of hyper >= 2.29?
We noticed recently that starting with that version the library depends on some initialize/finalize calls that are not being called from FLASH.
*********************************************
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 Feb 7, 2024, at 2:09 PM, Mattia Cipriani <mattia.cipriani at enea.it> wrote:
>
> Dear Adam,
>
> I solved the issue about the conflicting library, which was cluster-related.
>
> I run a simulation which ended with the segmentation fault error.
> I list the output from the job on the cluster here, maybe it can help in identifying the issue:
>
> 420 1.3202E-10 1.9789E-13 ( 1.377E-02, 2.573E-02, 0.00 ) | 1.979E-13 5.081E+79 8.265E+85 0.4000000
> 421 1.3222E-10 1.9781E-13 ( 1.389E-02, 2.552E-02, 0.00 ) | 1.978E-13 5.043E+79 8.036E+85 0.4000000
> 422 1.3242E-10 1.9765E-13 ( 1.389E-02, 2.552E-02, 0.00 ) | 1.976E-13 5.048E+79 7.501E+85 0.4000000
> 423 1.3262E-10 1.9752E-13 ( 1.389E-02, 2.552E-02, 0.00 ) | 1.975E-13 5.101E+79 7.625E+85 0.4000000
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
>
> Backtrace for this error:
> #0 0x2b8611c3336f in ???
> #1 0x2b8622d73762 in ???
> #2 0x2b86126ea84b in ???
> #3 0x2b8610e31c2c in ???
> #4 0x2b8610e75c6e in ???
> #5 0x6f0270 in ???
> #6 0x701354 in ???
> #7 0x6981e1 in ???
> #8 0x687315 in ???
> #9 0x67597d in ???
> #10 0x678284 in ???
> #11 0x559c43 in gr_hypresolve_
> at /afs/enea.it/project/iner/SIMULAZIONI/FSim/exp_infn-fusion-simsesperimento_SiO2_t1/gr_hypreSolve.F90:181
> #12 0x42c41a in grid_advancediffusion_
> at /afs/enea.it/project/iner/SIMULAZIONI/FSim/exp_infn-fusion-simsesperimento_SiO2_t1/Grid_advanceDiffusion.F90:351
> #13 0x465623 in radtrans_
> at /afs/enea.it/project/iner/SIMULAZIONI/FSim/exp_infn-fusion-simsesperimento_SiO2_t1/RadTrans.F90:419
> #14 0x4120e0 in driver_evolveflash_
> at /afs/enea.it/project/iner/SIMULAZIONI/FSim/exp_infn-fusion-simsesperimento_SiO2_t1/Driver_evolveFlash.F90:306
> #15 0x407fc6 in flash
> at /afs/enea.it/project/iner/SIMULAZIONI/FSim/exp_infn-fusion-simsesperimento_SiO2_t1/Flash.F90:51
> #16 0x407fc6 in main
> at /afs/enea.it/project/iner/SIMULAZIONI/FSim/exp_infn-fusion-simsesperimento_SiO2_t1/Flash.F90:43
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun noticed that process rank 11 with PID 0 on node cresco6x005 exited on signal 11 (Segmentation fault).
> —————————————————————————————————————
>
> Thanks,
> 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!exAwgr543bZGIXI5dU7Etu6rYav_iVMUvLAg5qJuoK10ez1YrtR55Bi8vLhP0kcRUchD4quv1loCimTwEzpWu1gyIn_ejLU$>
> LinkedIn <https://urldefense.com/v3/__https://www.linkedin.com/in/mattia-cipriani-0707bb2a/__;!!CGUSO5OYRnA7CQ!exAwgr543bZGIXI5dU7Etu6rYav_iVMUvLAg5qJuoK10ez1YrtR55Bi8vLhP0kcRUchD4quv1loCimTwEzpWu1gyIM-oODk$>
> ResearcherID AAG-9269-2021 <https://urldefense.com/v3/__https://publons.com/researcher/AAG-9269-2021/__;!!CGUSO5OYRnA7CQ!exAwgr543bZGIXI5dU7Etu6rYav_iVMUvLAg5qJuoK10ez1YrtR55Bi8vLhP0kcRUchD4quv1loCimTwEzpWu1gyq_XHuv8$>
> ORCID 0000-0002-2500-605X <https://urldefense.com/v3/__https://orcid.org/0000-0002-2500-605X__;!!CGUSO5OYRnA7CQ!exAwgr543bZGIXI5dU7Etu6rYav_iVMUvLAg5qJuoK10ez1YrtR55Bi8vLhP0kcRUchD4quv1loCimTwEzpWu1gyf7jAkEA$>
> ---------------------------------------------
>
>
>
>
>> Il giorno 7 feb 2024, alle ore 11:49, Reyes, Adam <adam.reyes at rochester.edu> ha scritto:
>>
>> Hi Mattia,
>>
>> I think openmpi provides a “ompi_info” command that should print out all information on how it was built. Somewhere in there should have the compiler version.
>> *********************************************
>> 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
>> Web https://flash.rochester.edu
>> (he / him / his)
>> <FLASH-pride-sml.png>
>>
>> *********************************************
>>
>>
>>
>>> On Feb 7, 2024, at 11:45 AM, Mattia Cipriani <mattia.cipriani at enea.it> wrote:
>>>
>>> Hi Adam,
>>>
>>> thank you for the reply.
>>> I was aware that this might be the problem, but I don’t know how to check it.
>>> How can I know which is the version of the compiler used for building the mpi library?
>>>
>>> ---------------------------------------------
>>> 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!aazmSSqcrCVxyt9iupeL-dXWjtLDp4mgnGfpdRHPDGN1AXkNZIlpwgoCGjMq3bmNkVsWzm6yxMBbPjxv4Og_PBsmxR3d7uw$>
>>> LinkedIn <https://urldefense.com/v3/__https://www.linkedin.com/in/mattia-cipriani-0707bb2a/__;!!CGUSO5OYRnA7CQ!aazmSSqcrCVxyt9iupeL-dXWjtLDp4mgnGfpdRHPDGN1AXkNZIlpwgoCGjMq3bmNkVsWzm6yxMBbPjxv4Og_PBsmKaabxww$>
>>> ResearcherID AAG-9269-2021 <https://urldefense.com/v3/__https://publons.com/researcher/AAG-9269-2021/__;!!CGUSO5OYRnA7CQ!aazmSSqcrCVxyt9iupeL-dXWjtLDp4mgnGfpdRHPDGN1AXkNZIlpwgoCGjMq3bmNkVsWzm6yxMBbPjxv4Og_PBsmvZhY6Ck$>
>>> ORCID 0000-0002-2500-605X <https://urldefense.com/v3/__https://orcid.org/0000-0002-2500-605X__;!!CGUSO5OYRnA7CQ!aazmSSqcrCVxyt9iupeL-dXWjtLDp4mgnGfpdRHPDGN1AXkNZIlpwgoCGjMq3bmNkVsWzm6yxMBbPjxv4Og_PBsmlFo2Oo8$>
>>> ---------------------------------------------
>>>
>>>
>>>
>>>
>>>> Il giorno 7 feb 2024, alle ore 11:30, Reyes, Adam <adam.reyes at rochester.edu> ha scritto:
>>>>
>>>> Hi Mattia,
>>>>
>>>> The warning suggests that compiler that you’re using for FLASH is different from the one used to compile the openmpi library. You could check that “mpif90 --version” returns the same GCC 7.3.0 version your warning says that openmpi was built with.
>>>>
>>>> It’s difficult to say if this is related to your seg fault or not without more context about where the error is occurring, either from the stdout or the log file.
>>>> *********************************************
>>>> 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
>>>> Web https://flash.rochester.edu
>>>> (he / him / his)
>>>> <FLASH-pride-sml.png>
>>>>
>>>> *********************************************
>>>>
>>>>
>>>>
>>>>> On Feb 7, 2024, at 11:06 AM, Mattia Cipriani <mattia.cipriani at enea.it> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I am recently experiencing some issues with FLASH 4.7.1 simulations, after updating from FLASH 4.5.
>>>>> I am using the same site-specific Makefile.h which was working before, since the configuration of the cluster did not change from the past.
>>>>> Also the compilers are the same as before.
>>>>> I use the setup script to collect all the needed files and objects for compiling the simulation and then I use make to compile it.
>>>>> At the end of the execution of make, I get the following warning
>>>>>
>>>>> /bin/ld: warning: libgfortran.so.4, needed by /usr/mpi/gcc730/openmpi-3.1.2/lib/libmpi_usempif08.so, may conflict with libgfortran.so.3
>>>>>
>>>>> If I run the flash4 executables with mpirun it starts to run ok, but at some apparently random point of the simulation I get a segmentation fault error.
>>>>>
>>>>> I am wondering if the warning from make could be the reason for the segmentation fault error.
>>>>> How can I solve the warning?
>>>>> I know it is a linux-related question rather than a FLASH problem, but I would be glad if you can help or at least give me a feedback if the segmentation fault error might be due to the warning from make.
>>>>>
>>>>> Best regards,
>>>>> Mattia
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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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.
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>>> 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) on ly.
>>>
>>> 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.
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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) on ly.
>
> 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.
>
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