Do not run this as root. Create a dedicated user (e.g., gaussian ).
ulimit -s unlimited ulimit -n 65536 ulimit -u unlimited Add these to your g16.sub script. If you are using ssh , you may need to edit /etc/security/limits.conf :
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If you are a computational chemist, the phrase "segmentation fault" triggers a specific kind of PTSD. For years, running Gaussian on Windows was the default for many students, but ask any high-throughput researcher: Linux is the native habitat of Gaussian 16.
# Extract to /opt or /home tar -xjvf G16_AVX2.tbz -C /opt/ chmod -R 750 /opt/g16 The critical part: Environment Variables echo 'export g16root=/opt' >> ~/.bashrc echo 'export GAUSS_SCRDIR=/scratch/$USER' >> ~/.bashrc echo 'source /opt/g16/bsd/g16.profile' >> ~/.bashrc Gaussian 16 Linux
cd /opt/g16 ln -sf g16_avx2 g16 Linux handles I/O differently than Windows. Gaussian’s algorithm relies heavily on reading/writing to disk. If you use a standard SATA SSD, your expensive CPU will spend 80% of its time waiting.
This usually means your shell limits are too low. Linux has a hard limit on "Max user processes." Do not run this as root
Whether you are setting up a local workstation (like an AMD Threadripper + 4090 build) or logging into a university HPC cluster, running G16 on Linux isn't just faster—it unlocks the full potential of the software.