[FLASH-USERS] Segmentation fault - invalid memory reference.

[amar at aries.res.in]

Dear Prof. Reyes, 

Thank you very much for the suggestion. I followed your suggestion and put the patch in the FLASH directory. Thereafter, I ran the following command in the terminal: 

patch -p1 < 0001-MPI_TYPE_GET_EXTENT-in-timers.patch 

The "make" command compiled successfully. Thereafter, I ran FLASH using the "mpirun -np 8 flash4 -par_file flash.par"; then, at the end of the run, It showed the following issue now: 

*** Wrote checkpoint file to sedov_hdf5_chk_0005 **** 
exiting: reached max SimTime 
*** Wrote plotfile to sedov_forced_hdf5_plt_cnt_0000 **** 
[aries:85322] *** An error occurred in MPI_Bcast 
[aries:85322] *** reported by process [2482438145,0] 
[aries:85322] *** on communicator MPI_COMM_WORLD 
[aries:85322] *** MPI_ERR_TYPE: invalid datatype 
[aries:85322] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, 
[aries:85322] *** and potentially your MPI job) 

I can not figure out the possible cause and am looking for your further suggestions. 

With best regards, 
Amar 


From: "adam reyes" <adam.reyes at rochester.edu> 
To: amar at aries.res.in 
Cc: flash-users at flash.rochester.edu 
Sent: Tuesday, December 5, 2023 11:27:01 PM 
Subject: Re: [FLASH-USERS] Segmentation fault - invalid memory reference. 

Hi Amar, 
How exactly did you change those lines? MPI_Type_get_extent has a different interface and so a line like 

call MPI_Type_extent(FLASH_REAL, realExtent, ierr) 

Should be transformed to 

call MPI_Type_extent(FLASH_REAL, realLb,realExtent, ierr) 

Or something similar to maintain the same behavior in FLASH. 

I’m attaching a patch that can be applied to the unmodified source, just put it in the root FLASH directory and run 

patch -p1 < 0001-MPI_TYPE_GET_EXTENT-in-timers.patch 

Or you can look at the diff and see how it should work. 

********************************************* 
Adam Reyes 



[image/jpeg: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) 


[image/png:FLASH-pride-sml.png] 


********************************************* 






On Dec 5, 2023, at 6:34 PM, amar at aries.res.in wrote: 




Dear FLASH users, 

I installed FLASH4.7.1 on two of my systems (both with Ubuntu 20.04). In one of the systems, FLASH is running fine, while the other system shows the following Segmentation fault error at the end of the simulation: 


Program received signal SIGSEGV: Segmentation fault - invalid memory reference. 

Backtrace for this error: 
#0 0x7f5668eaa08f in ??? 
at /build/glibc-BHL3KM/glibc-2.31/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0 
#1 0x7f5669d71737 in ??? 
#2 0x442348 in tmr_broadcastroottimers_ 
at /home/brics/Downloads/FLASH4.7.1/object/Timers_getSummary.F90:382 
#3 0x442553 in tmr_allprocssametimers_ 
at /home/brics/Downloads/FLASH4.7.1/object/Timers_getSummary.F90:258 
#4 0x4430cd in timers_getsummary_ 
at /home/brics/Downloads/FLASH4.7.1/object/Timers_getSummary.F90:179 
#5 0x409b86 in driver_evolveflash_ 
at /home/brics/Downloads/FLASH4.7.1/object/Driver_evolveFlash.F90:497 
#6 0x404ab6 in flash 
at /home/brics/Downloads/FLASH4.7.1/object/Flash.F90:51 
#7 0x404ab6 in main 
at /home/brics/Downloads/FLASH4.7.1/object/Flash.F90:43 

=================================================================================== 
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES 
= PID 77619 RUNNING AT aries 
= EXIT CODE: 139 
= CLEANING UP REMAINING PROCESSES 
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES 
=================================================================================== 
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) 
This typically refers to a problem with your application. 
Please see the FAQ page for debugging suggestions 



While installing FLASH on the system showing the Segmentation fault error, I was required to change "MPI_Type_extent" to "MPI_Type_get_extent" in the Timers_getSummary.F90 file. Without this modification, the "make" command would not proceed successfully. 

Please provide your valuable suggestions regarding this error. Also please let me know if I need to provide more information. 

With best regards, 
Amar 



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