<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: style=" font-size:="" 12pt;="" color:="" #000000"=""><div data-marker="__QUOTED_TEXT__"><div style="font-family:'arial' , 'helvetica' , sans-serif"><div>Dear Prof. Reyes,</div><br><div>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:</div><br><div><span class="Apple-tab-span" style="color:#000000;font-family:'arial' , 'helvetica' , sans-serif;font-size:16px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;word-spacing:0px;background-color:#ffffff;white-space:pre"> </span><span style="color:#000000;font-family:'arial' , 'helvetica' , sans-serif;font-size:16px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;word-spacing:0px;white-space:normal;background-color:#ffffff;display:inline !important;float:none">patch -p1 < 0001-MPI_TYPE_GET_EXTENT-in-timers.patch </span></div><div><span style="color:#000000;font-family:'arial' , 'helvetica' , sans-serif;font-size:16px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;word-spacing:0px;white-space:normal;background-color:#ffffff;display:inline !important;float:none"><br data-mce-bogus="1"></span></div></div><div style="font-family:'arial' , 'helvetica' , sans-serif">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:</div><div style="font-family:'arial' , 'helvetica' , sans-serif"><br><div><div> *** Wrote checkpoint file to sedov_hdf5_chk_0005 ****</div><div> exiting: reached max SimTime</div><div> *** Wrote plotfile to sedov_forced_hdf5_plt_cnt_0000 ****</div><div>[aries:85322] *** An error occurred in MPI_Bcast</div><div>[aries:85322] *** reported by process [2482438145,0]</div><div>[aries:85322] *** on communicator MPI_COMM_WORLD</div><div>[aries:85322] *** MPI_ERR_TYPE: invalid datatype</div><div>[aries:85322] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,</div><div>[aries:85322] *** and potentially your MPI job)</div></div></div><div style="font-family:'arial' , 'helvetica' , sans-serif"><br data-mce-bogus="1"></div><div style="font-family:'arial' , 'helvetica' , sans-serif">I can not figure out the possible cause and am looking for your further suggestions.</div><div style="font-family:'arial' , 'helvetica' , sans-serif"><br data-mce-bogus="1"></div><div style="font-family:'arial' , 'helvetica' , sans-serif">With best regards,</div><div style="font-family:'arial' , 'helvetica' , sans-serif">Amar<br><br><hr id="zwchr"><div><b>From: </b>"adam reyes" <adam.reyes@rochester.edu><br><b>To: </b>amar@aries.res.in<br><b>Cc: </b>flash-users@flash.rochester.edu<br><b>Sent: </b>Tuesday, December 5, 2023 11:27:01 PM<br><b>Subject: </b>Re: [FLASH-USERS] Segmentation fault - invalid memory reference.<br></div><br><div>Hi Amar,<br><div>How exactly did you change those lines? MPI_Type_get_extent has a different interface and so a line like</div><br><div><div> call MPI_Type_extent(FLASH_REAL, realExtent, ierr)</div><br><div>Should be transformed to</div><br><div><div> call MPI_Type_extent(FLASH_REAL, realLb,realExtent, ierr)</div></div><br><div>Or something similar to maintain the same behavior in FLASH.</div><br><div>I’m attaching a patch that can be applied to the unmodified source, just put it in the root FLASH directory and run</div><br><div><span class="Apple-tab-span" style="white-space:pre"> </span>patch -p1 < 0001-MPI_TYPE_GET_EXTENT-in-timers.patch </div><br><div>Or you can look at the diff and see how it should work.</div></div><br><div><div>
<div style="color:rgb( 0 , 0 , 0 );font-family:'helvetica';font-size:12px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">*********************************************<br>Adam Reyes</div><br class="Apple-interchange-newline"></div></div><br><br>[image/jpeg:FLASH.jpg]<br><br><br style="color:rgb( 0 , 0 , 0 );font-family:'helvetica';font-size:12px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="color:rgb( 0 , 0 , 0 );font-family:'helvetica';font-size:12px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;display:inline !important;float:none">Code Group Leader, Flash Center for </span><span style="color:rgb( 0 , 0 , 0 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);font-family:'helvetica';font-size:12px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;display:inline !important;float:none">https://flash.rochester.edu</span><br style="color:rgb( 0 , 0 , 0 );font-family:'helvetica';font-size:12px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="color:rgb( 0 , 0 , 0 );font-family:'helvetica';font-size:12px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;display:inline !important;float:none"> </span><span style="color:rgb( 0 , 0 , 0 );font-family:'helvetica';font-size:12px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;display:inline !important;float:none">(he / him / his)</span><br style="color:rgb( 0 , 0 , 0 );font-family:'helvetica';font-size:12px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br><br>[image/png:FLASH-pride-sml.png]<br><br><div><div><div style="color:rgb( 0 , 0 , 0 );font-family:'helvetica';font-size:12px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br>*********************************************</div><div style="color:rgb( 0 , 0 , 0 );font-family:'helvetica';font-size:12px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><br class="Apple-interchange-newline">
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<div><br><blockquote><div>On Dec 5, 2023, at 6:34 PM, amar@aries.res.in wrote:</div><br class="Apple-interchange-newline"><div>
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<div><div style="font-family:'arial' , 'helvetica' , sans-serif"><div><div style="font-family:'arial' , 'helvetica' , sans-serif"><div><div>Dear FLASH users,</div><br><div>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:</div><br><br><div>Program received signal SIGSEGV: Segmentation fault - invalid memory reference.</div><br><div>Backtrace for this error:</div><div>#0 0x7f5668eaa08f in ???</div><div><span style="white-space:normal"><span style="white-space:pre"> </span>at /build/glibc-BHL3KM/glibc-2.31/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0</span></div><div>#1 0x7f5669d71737 in ???</div><div>#2 0x442348 in tmr_broadcastroottimers_</div><div><span style="white-space:normal"><span style="white-space:pre"> </span>at /home/brics/Downloads/FLASH4.7.1/object/Timers_getSummary.F90:382</span></div><div>#3 0x442553 in tmr_allprocssametimers_</div><div><span style="white-space:normal"><span style="white-space:pre"> </span>at /home/brics/Downloads/FLASH4.7.1/object/Timers_getSummary.F90:258</span></div><div>#4 0x4430cd in timers_getsummary_</div><div><span style="white-space:normal"><span style="white-space:pre"> </span>at /home/brics/Downloads/FLASH4.7.1/object/Timers_getSummary.F90:179</span></div><div>#5 0x409b86 in driver_evolveflash_</div><div><span style="white-space:normal"><span style="white-space:pre"> </span>at /home/brics/Downloads/FLASH4.7.1/object/Driver_evolveFlash.F90:497</span></div><div>#6 0x404ab6 in flash</div><div><span style="white-space:normal"><span style="white-space:pre"> </span>at /home/brics/Downloads/FLASH4.7.1/object/Flash.F90:51</span></div><div>#7 0x404ab6 in main</div><div><span style="white-space:normal"><span style="white-space:pre"> </span>at /home/brics/Downloads/FLASH4.7.1/object/Flash.F90:43</span></div><br><div>===================================================================================</div><div>= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES</div><div>= PID 77619 RUNNING AT aries</div><div>= EXIT CODE: 139</div><div>= CLEANING UP REMAINING PROCESSES</div><div>= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES</div><div>===================================================================================</div><div>YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)</div><div>This typically refers to a problem with your application.</div><div>Please see the FAQ page for debugging suggestions</div></div></div><div style="font-family:'arial' , 'helvetica' , sans-serif"><br></div><div style="font-family:'arial' , 'helvetica' , sans-serif"><br></div><div style="font-family:'arial' , 'helvetica' , sans-serif"><br><div>While installing FLASH on the system showing the <span style="font-family:'arial' , 'helvetica' , sans-serif;font-size:16px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;word-spacing:0px;white-space:normal;background-color:rgb( 255 , 255 , 255 );float:none;display:inline !important">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.</span><br></div><div><span style="font-family:'arial' , 'helvetica' , sans-serif;font-size:16px;font-style:normal;font-weight:400;letter-spacing:normal;text-indent:0px;text-transform:none;word-spacing:0px;white-space:normal;background-color:rgb( 255 , 255 , 255 );float:none;display:inline !important"><br></span></div><div>Please provide your valuable suggestions regarding this error. Also please let me know if I need to provide more information.</div><br><div>With best regards,</div><div>Amar</div></div><br></div></div>
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