Extremely large dumps of information when running LAMMPS

Dear Lammps-users,

I have am having a rather peculiar issue. I have compiled the latest version of LAMMPS without any errors. However, when testing LAMMPS by running a script which worked on previous versions (Feb and Apr 2013), I get extremely large amounts of information being written to files with names like “core.10345”. This might not be a LAMMPS problem, but could anyone kindly point out what the issue might be?

Thank you very much!

Best Regards,
Jingjie Yeo
Ph.D. Student
School of Mechanical and Aerospace Engineering
Nanyang Technological University, Singapore

Dear Lammps-users,

I have am having a rather peculiar issue. I have compiled the latest version
of LAMMPS without any errors. However, when testing LAMMPS by running a
script which worked on previous versions (Feb and Apr 2013), I get extremely
large amounts of information being written to files with names like
"core.10345". This might not be a LAMMPS problem, but could anyone kindly
point out what the issue might be?

those files are core dumps.

the interesting question is now, what exactly triggers this.
so please do

gdb lmp_<whatever your lammps executable has here> core.10345

and then type

where

and send us the result. please also make sure, you do have the very
latest version of lammps.

axel.

Dear Dr. Kohlmeyer,

Thank you very much for the assistance. I have compiled the very latest 14th Aug 2013 version of LAMMPS. I forgot to mention that this was performed on a cluster running CentOS 5.6. The errorlog is as follows:

Reading symbols from /scratch/ihpc/ihpcjyeo/lammps-14Aug13/lmp_linux...(no debugging symbols found)...done.
warning: .dynamic section for "/lib64/libdl.so.2" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
warning: .dynamic section for "/usr/lib64/libjpeg.so.62" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
warning: .dynamic section for "/usr/lib64/libgfortran.so.1" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
warning: .dynamic section for "/usr/lib64/libstdc++.so.6" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
warning: .dynamic section for "/lib64/libpthread.so.0" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
warning: .dynamic section for "/lib64/librt.so.1" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
warning: .dynamic section for "/lib64/libm.so.6" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
warning: .dynamic section for "/lib64/libgcc_s.so.1" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
warning: .dynamic section for "/lib64/libc.so.6" is not at the expected address (wrong library or version mismatch?)
warning: .dynamic section for "/lib64/ld-linux-x86-64.so.2" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
Error while mapping shared library sections:
t: No such file or directory.
Reading symbols from /lib64/libdl.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libdl.so.2
Reading symbols from /usr/lib64/libjpeg.so.62...(no debugging symbols found)...done.
Loaded symbols for /usr/lib64/libjpeg.so.62
Reading symbols from /usr/lib64/libgfortran.so.1...(no debugging symbols found)...done.
Loaded symbols for /usr/lib64/libgfortran.so.1
Reading symbols from /usr/lib64/libstdc++.so.6...(no debugging symbols found)...done.
Loaded symbols for /usr/lib64/libstdc++.so.6
Reading symbols from /opt/intel/impi/4.0.1.007/intel64/lib/libmpi.so.4...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/impi/4.0.1.007/intel64/lib/libmpi.so.4
Reading symbols from /opt/intel/impi/4.0.1.007/intel64/lib/libmpigf.so.4...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/impi/4.0.1.007/intel64/lib/libmpigf.so.4
Reading symbols from /lib64/libpthread.so.0...(no debugging symbols found)...done.
Loaded symbols for /lib64/libpthread.so.0
Reading symbols from /lib64/librt.so.1...(no debugging symbols found)...done.
Loaded symbols for /lib64/librt.so.1
Reading symbols from /lib64/libm.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/libm.so.6
Reading symbols from /lib64/libgcc_s.so.1...(no debugging symbols found)...done.
Loaded symbols for /lib64/libgcc_s.so.1
Reading symbols from /lib64/libc.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/libc.so.6
Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/ld-linux-x86-64.so.2
Symbol file not found for t
warning: no loadable sections found in added symbol-file system-supplied DSO at 0x7fffdb5fc000
Core was generated by `/scratch/ihpc/ihpcjyeo/lammps-14Aug13/lmp_linux'.
Program terminated with signal 11, Segmentation fault.
#0 0x00000031e820a885 in _dl_relocate_object ()
   from /lib64/ld-linux-x86-64.so.2

(gdb) where

#0 0x00000031e820a885 in _dl_relocate_object ()
   from /lib64/ld-linux-x86-64.so.2
#1 0x00000031e8203627 in dl_main () from /lib64/ld-linux-x86-64.so.2
#2 0x00000031e82133bb in _dl_sysdep_start () from /lib64/ld-linux-x86-64.so.2
#3 0x00000031e8201388 in _dl_start () from /lib64/ld-linux-x86-64.so.2
#4 0x00000031e8200a78 in _start () from /lib64/ld-linux-x86-64.so.2
#5 0x0000000000000001 in ?? ()
#6 0x00007fffdb522726 in ?? ()
#7 0x0000000000000000 in ?? ()

Best Regards,
Jingjie Yeo
Ph.D. Student
School of Mechanical and Aerospace Engineering
Nanyang Technological University, Singapore

Talk to your system manager. There seems to be something very bad happening on the machine that you are on. This is a rather low level failure and not lammps related.

Dear Dr. Kohlmeyer,

I have suspected as much, I shall check with the admin, thank you for taking the time to check this for me!

Best Regards,
Jingjie Yeo
Ph.D. Student
School of Mechanical and Aerospace Engineering
Nanyang Technological University, Singapore