Lammps does not run properly after I installed Anaconda on system

LAMMPS LAMMPS Installation
1

I had lammps installed properly on my linux system (lammps-2Aug2023). and it was working fine until Today that I installed anaconda. when I run lammps on my system:

it prints out the following lines 64 times: Ignoring PCI device with non-16bit domain.

It looks like it prints the regular lammps’s output on screen 64 times (including this statement "OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (…/comm.cpp:98)
") and the file is not running parallel (it runs very slow). those two lines also show up if I run lammps in series without mpirun.

I tried to reinstall lammps but it is still not working. I use the following lines to install lammps:
tar -xvf hwloc-1.11.13.tar.gz
cd hwloc-1.11.13/
./configure
make
sudo make install
sudo apt-get install libhwloc5
sudo apt-get install openmpi-bin
sudo apt-get install openmpi-common

sudo apt-get install g++
sudo apt-get install openmpi-
sudo apt-get install kissplice
sudo apt-get install openmpi-bin
sudo apt-get install kissplice
sudo apt-get install fftw
sudo apt-get install fftw-dev
sudo apt-get install mpi-default-dev
sudo apt-get install mpi-default-bin
cd …/lammps-2Aug2023/src
make clean-all
make purge
make no-all
make yes-manybody
make yes-mc
make yes-meam
make yes-misc
make yes-opt
make yes-replica
make yes-rigid
make yes-snap
make yes-user-diffraction
make yes-user-misc
make yes-user-omp
make ubuntu_simple

sudo mv lmp_ubuntu_simple /usr/local/bin/lmp
cd …/…
sudo cp -r lammps-2Aug2023/ /usr/local

Would you please help me solve this issue?
Best,
Sepideh

2

Well, then this is the cause. Just uninstall anaconda and it should be back to normal.

This would happen if you are using an mpirun command that is not the one from the MPI library you have compiled LAMMPS with.

These two messages are OK. The OMP_NUM_THREADS one can be silenced by setting the OMP_NUM_THREADS environment variable to the desired value (typically that would be 1 unless you explicitly want to use OpenMP threads in LAMMPS and have selected the corresponding accelerated styles). The PCI device message is printed by OpenMPI and harmless.

3

You can also deactivate the Conda base environment for the remainder of the shell session by running

conda deactivate

in the base environment (that is, when the prompt is prefixed with (base)).

If your previous LAMMPS install starts working again, that will suggest that the Conda installation has disrupted environment variables needed to run LAMMPS (primarily the mpirun used for LAMMPS). As most websites will suggest, you can set Conda to not auto-activate on a new shell with the command:

conda config --set auto_activate_base false

If you must use Conda in a HPC environment (and I can understand why some might do so) this is the recommended setting.

4

Thanks . The problem is solved!