[FLASH-USERS] [EXT] Library conflict at the end of make and segmentation fault

Wed Feb 7 05:49:38 EST 2024

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

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 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
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> ---------------------------------------------
> 
> 
> 
> 
>> 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.
> 
> 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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