Error due to libtbbmalloc.so.2

LAMMPS LAMMPS Installation
1

Hi while trying to run the lammps I get the following error, I also tried to add path to libtbbmalloc.so.2 but still the error appears. Thank you in advance.

OSError: libtbbmalloc.so.2: cannot open shared object file: No such file or directory
lmp= lammps.lammps()
File “/globalhome/bwa467/HPC/.local/lib/python3.10/site-packages/lammps/core.py”, line 150, in init
lmp= lammps.lammps()
File “/globalhome/bwa467/HPC/.local/lib/python3.10/site-packages/lammps/core.py”, line 150, in init
self.lib = CDLL(libpath,RTLD_GLOBAL)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx/Core/python/3.10.2/lib/python3.10/ctypes/init.py”, line 374, in init
Traceback (most recent call last):
File “/globalhome/bwa467/HPC/dataraw/MLP_lmp/lmp-64/Min/min.py”, line 6, in
self.lib = CDLL(libpath,RTLD_GLOBAL)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx/Core/python/3.10.2/lib/python3.10/ctypes/init.py”, line 374, in init
self.lib = CDLL(libpath,RTLD_GLOBAL)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx/Core/python/3.10.2/lib/python3.10/ctypes/init.py”, line 374, in init
self.lib = CDLL(libpath,RTLD_GLOBAL)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx/Core/python/3.10.2/lib/python3.10/ctypes/init.py”, line 374, in init
self._handle = _dlopen(self._name, mode)
OSError: libtbbmalloc.so.2: cannot open shared object file: No such file or directory
self._handle = _dlopen(self._name, mode)
OSError: libtbbmalloc.so.2: cannot open shared object file: No such file or directory
self._handle = _dlopen(self._name, mode)
OSError: libtbbmalloc.so.2: cannot open shared object file: No such file or directory
self.lib = CDLL(libpath,RTLD_GLOBAL)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx/Core/python/3.10.2/lib/python3.10/ctypes/init.py”, line 374, in init
self._handle = _dlopen(self._name, mode)
OSError: libtbbmalloc.so.2: cannot open shared object file: No such file or directory
lmp= lammps.lammps()
File “/globalhome/bwa467/HPC/.local/lib/python3.10/site-packages/lammps/core.py”, line 150, in init
self._handle = _dlopen(self._name, mode)
OSError: libtbbmalloc.so.2: cannot open shared object file: No such file or directory
self.lib = CDLL(libpath,RTLD_GLOBAL)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx/Core/python/3.10.2/lib/python3.10/ctypes/init.py”, line 374, in init
self._handle = _dlopen(self._name, mode)
OSError: libtbbmalloc.so.2: cannot open shared object file: No such file or directory
self.lib = CDLL(libpath,RTLD_GLOBAL)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx/Core/python/3.10.2/lib/python3.10/ctypes/init.py”, line 374, in init
self._handle = _dlopen(self._name, mode)
OSError: libtbbmalloc.so.2: cannot open shared object file: No such file or directory

Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.

mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[11528,1],36]
Exit code: 1

2

This is all too vague and unspecific so it is not possible to provide meaningful advice. Please provide more details and specific information. For example, the error you report is an error of the LAMMPS Python module, not of LAMMPS. In particular:

  • which LAMMPS version do you have?
  • what platform is this on?
  • which compilers did you use?
  • how did you compile and install LAMMPS and specifically the LAMMPS python module?
  • which packages are included into your LAMMPS compilation?
  • how exactly do you run your python script?
  • which “path” did you try to add and how to resolve the “cannot open shared object” error?
4

Sorry, but parts of what you wrote is garbled and other parts are missing the exact commands and many details.

A few more issues:

The command to install the LAMMPS python module is: make install-python
When you use pip install lammps it will download an unofficial, separately compiled LAMMPS package from PyPi.org: lammps · PyPI

However, the error message is inconsistent with that.

I don’t see how this would even create a dependency on libtbbmalloc.so.2

What is the output of?

ldd /globalhome/bwa467/HPC/soft/lammps/lammps-install/bin/lmp

What you write here makes no sense. Also it is missing the commands you entered, which is crucial information.

This all so confused and mixed up. I suggest you find somebody local with more experience in compiling software (need not be with LAMMPS) that will help you. From remote this seems very difficult because of the information that is (still) missing and the information that you provide being inconsistent and in part even contradictory.

7

That is useless. I am asking for the exact commands that you used to make liblammps.so find those files.

This is neither compiled with shared libraries enabled, nor does it seem to use the intel compiler somehow and there is no dependency on libtbbmalloc.so.2.

So neither this compilation/installation of LAMMPS can have led to the error, nor the python package that you installed via pip. This all doesn’t make much sense outside of that you are way in over your head, have a mess of settings in your ~/.bashrc, and are withholding crucial information. The liblammps.so must be somehow been left over from some other installation attempt. Also, I didn’t see any mention of the LD_LIBRARY_PATH environment variable and no indication that you understand what it does.

As I wrote before, you need help far beyond what can be through an internet forum. You need to find somebody local that can sort out the mess you have at your hand and educate you better about the various steps needed.