forrtl: severe (174): SIGSEGV, segmentation fault occurred

[Hongyu002]

Hello,

I am trying to run a simulation and I receive the error message "forrtl: severe (174): SIGSEGV, segmentation fault occurred" as soon as the simulation starts.

Hope anyone can give me some advise. THANKS

My input file is:

&HEAD CHID='0_02jetfire', TLTLE='jet fire test/ &TIME T_END=20.0/ &DUMP RENDER_FILE='0_02jetfire.ge1', DT_RESTART=300.0/ &MISC TMPA=30.0/

&MESH ID='MESH', IJK=35,220,230, XB=3.0,10.0,2.0,8.0,0.0,7.0/ &TRNY CC=2.27273, PC=3.0, MESH_NUMBER=1/ MESH &TRNY CC=7.72727, PC=7.0, MESH_NUMBER=1/ MESH &TRNZ CC=0.304348, PC=1.0, MESH_NUMBER=1/ MESH &TRNZ CC=6.3913, PC=5.0, MESH_NUMBER=1/ MESH

&PART ID='Fuel', SPEC_ID='PROPANE' DIAMETER=500/

&REAC ID='getfire', FUEL='PROPANE'/

&SURF ID='supply', RGB=26,204,26, VEL=-101, PART_ID='Fuel', NPPC=10000, PARTICLE_MASS_FLUX=275.0/

&SURF ID='burner', COLOR='RED', HRRPUA=1000.0/

&VENT SURF_ID='OPEN', XB=3.0,3.0,2.0,8.0,0.0,7.0/ Mesh Vent: MESH [XMIN] &VENT SURF_ID='OPEN', XB=3.0,10.0,8.0,8.0,0.0,7.0/ Mesh Vent: MESH [YMAX] &VENT SURF_ID='OPEN', XB=3.0,10.0,2.0,2.0,0.0,7.0/ Mesh Vent: MESH [YMIN] &VENT SURF_ID='OPEN', XB=3.0,10.0,2.0,8.0,7.0,7.0/ Mesh Vent: MESH [ZMAX] &VENT SURF_ID='supply', XB=9.99,9.99,5.0,5.02,1.3,1.32/ fule &VENT SURF_ID='burner', XB=9.99,9.99,5.0,5.02,1.26,1.28/ burner

&ISOF QUANTITY='HRRPUV', VALUE=6.5/ &ISOF QUANTITY='TEMPERATURE', VALUE=537.0/

&SLCF QUANTITY='TEMPERATURE', PBZ=1.3/ &SLCF QUANTITY='TEMPERATURE', PBY=5.0/

&TAIL /

[sbenkorichi]

This is know issue. Do this on same terminal before you run the job.$ulimit -s unlimited Then run the job. If it works, then add that line in your .bashrc file, you find it in your home directory (i.e. /home/username/.bashrc )

[Hongyu002]

I tried this but it didnt work. It returned -bash:unlimit: stack size: cannot modify limit:operation not permitted

[sbenkorichi]

You seems to be having a Mac, it might be slightly different than unix. @marcosvanella or @rmcdermo can give more feedback on this. try the following to know the sys limits first:$ ulimit -a , post what it says, your startup file should be bashrc_profile instead of bashrc, I just recall your previous post here https://github.com/firemodels/fds/issues/6219. So, just put it in that file. Try this as well

$ ulimit -Hs unlimited
$ ulimit -Ss unlimited

If it doesn't work, then we need to change the default ulimits on the system, that might involve changes in the lanuchd.conf -- @gforney will have a better suggestion on this as I'm not Mac user.

[rmcdermo]

I added the startup line here:

https://github.com/firemodels/fds/wiki/Installing-and-Running-FDS-under-Mac-OS-X

Glenn, can you see that the bundle script for OSX adds this unlimit command to the "lines to add to startup". Thanks.

[Hongyu002]

when I use ulimit -a，it says ：

core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited file size (blocks, -f) unlimited max locked memory (kbytes, -l) unlimited max memory size (kbytes, -m) unlimited open files (-n) 256 pipe size (512 bytes, -p) 1 stack size (kbytes, -s) 8192 cpu time (seconds, -t) unlimited max user processes (-u) 709 virtual memory (kbytes, -v) unlimited

[Hongyu002]

hi it works with $ ulimit -Ss unlimited :)thank you so much

[yauz3]

Hi, I have the same problem. I am trying to use GalaxyDock3 program. It works sometimes, however, it gives the same error. I have already tried: ulimit -s unlimited ulimit -d unlimited ulimit -f unlimited ulimit -m unlimited ulimit -n 7168 ulimit -Hs unlimited ulimit -Ss unlimited in order to solve problem. Unfortunately, I am taking same error. I am using ubuntu side by windows. Is it the reason? thanks.

[rmcdermo]

On macOS, I have to increase both stack and maxfiles like this:

# unlimit stack and increase maxfiles for OSX
ulimit -s 65532 -n 2048

[sbenkorichi]

Sorry, I'm not following here; are you trying to use FDS or a different program?

[yauz3]

Galaxydock3 is a molecular docking program. Sometimes it works, but sometimes gives forrtl: severe(174) error. my options are: core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 63430 max locked memory (kbytes, -l) 65536 max memory size (kbytes, -m) unlimited open files (-n) 7168 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) unlimited cpu time (seconds, -t) unlimited max user processes (-u) 63430 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited

I have already ready all over the Internet. Everyone says about stack size. Even if I changed it, the same error appears.

[sbenkorichi]

I can't tell much without knowing exactly how you're running it and how your machine is set. The only thing that pops up is that you might be running the application with scheduler which is different, although it shows its unlimited in the terminal but when it runs with scripts it's not. You need to provide more details so someone can help.

[yauz3]

this is the program link: http://galaxy.seoklab.org/softwares/galaxydock.html

It allows us to use in terminal: python GalaxyDock3/script/run_GalaxyDock3.py -d /home/yavuz/yavuz_proje/docking/proteins/GalaxyDock3/ -p 2gl0_receptor.pdb -l 2gl0_ligand.mol2 -x 14 -y 20 -z 11 -size_x 5 -size_y 5 -size_z 5

The code is perfectly working. When I changed 2gl0_ligand.mol2 to Erythromycin.mol2, which is a big drug and have some wrong values, it gives the error. Even if I prepared file manually, it did not work.

Thank you for your help. I am really new starter; therefore, I cannot explain very well sorry.

[JinwenDong]

Hi, I having the same problem. I run the FDS file through a script that puts it on the server node. Here is the return codes:

Starting FDS ...

MPI Process 0 started on node2b07.ecdf.ed.ac.uk MPI Process 2 started on node2b07.ecdf.ed.ac.uk MPI Process 1 started on node2b07.ecdf.ed.ac.uk MPI Process 16 started on node2b07.ecdf.ed.ac.uk MPI Process 25 started on node2b07.ecdf.ed.ac.uk MPI Process 7 started on node2b07.ecdf.ed.ac.uk MPI Process 10 started on node2b07.ecdf.ed.ac.uk MPI Process 13 started on node2b07.ecdf.ed.ac.uk MPI Process 20 started on node2b07.ecdf.ed.ac.uk MPI Process 5 started on node2b07.ecdf.ed.ac.uk MPI Process 6 started on node2b07.ecdf.ed.ac.uk MPI Process 22 started on node2b07.ecdf.ed.ac.uk MPI Process 23 started on node2b07.ecdf.ed.ac.uk MPI Process 3 started on node2b07.ecdf.ed.ac.uk MPI Process 9 started on node2b07.ecdf.ed.ac.uk MPI Process 21 started on node2b07.ecdf.ed.ac.uk MPI Process 29 started on node2b07.ecdf.ed.ac.uk MPI Process 15 started on node2b07.ecdf.ed.ac.uk MPI Process 28 started on node2b07.ecdf.ed.ac.uk MPI Process 8 started on node2b07.ecdf.ed.ac.uk MPI Process 27 started on node2b07.ecdf.ed.ac.uk MPI Process 17 started on node2b07.ecdf.ed.ac.uk MPI Process 30 started on node2b07.ecdf.ed.ac.uk MPI Process 34 started on node2b07.ecdf.ed.ac.uk MPI Process 11 started on node2b07.ecdf.ed.ac.uk MPI Process 12 started on node2b07.ecdf.ed.ac.uk MPI Process 14 started on node2b07.ecdf.ed.ac.uk MPI Process 19 started on node2b07.ecdf.ed.ac.uk MPI Process 24 started on node2b07.ecdf.ed.ac.uk MPI Process 26 started on node2b07.ecdf.ed.ac.uk MPI Process 18 started on node2b07.ecdf.ed.ac.uk MPI Process 4 started on node2b07.ecdf.ed.ac.uk MPI Process 31 started on node2b07.ecdf.ed.ac.uk MPI Process 32 started on node2b07.ecdf.ed.ac.uk MPI Process 33 started on node2b07.ecdf.ed.ac.uk

Reading FDS input file ...

WARNING: SPEC wood is not in the table of pre-defined species. Any unassigned SPEC variables in the input were assigned the properties of nitrogen.

Fire Dynamics Simulator

Current Date : July 6, 2024 23:54:18 Revision : FDS-6.9.1-0-g889da6a-release Revision Date : Sun Apr 7 17:05:06 2024 -0400 Compiler : Intel(R) Fortran Intel(R) 64 Compiler Classic for applications running on Intel(R) 64, Version 2021.7.1 Build 20221019_000000 Compilation Date : Apr 09, 2024 13:24:51

Number of MPI Processes: 35

MPI version: 3.1 MPI library version: Intel(R) MPI Library 2021.6 for Linux* OS

Job TITLE : CaseB1 Job ID string : CaseB1

Time Step: 1, Simulation Time: 0.04 s forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source
libc.so.6 0000150D32C54DB0 Unknown Unknown Unknown fds 0000000006B256E4 Unknown Unknown Unknown fds 0000000006B121A0 Unknown Unknown Unknown fds 0000000006AB8148 Unknown Unknown Unknown fds 000000000040A71D Unknown Unknown Unknown libc.so.6 0000150D32C3FEB0 Unknown Unknown Unknown libc.so.6 0000150D32C3FF60 __libc_start_main Unknown Unknown fds 000000000040A636 Unknown Unknown Unknown

[marcosvanella]

Hi @JinwenDong, segfaults can be due to many things. Please open a new issue and attach your input file. Change the file extension to .txt instead of .fds.