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Every time, I run LAMMPS for 4-5 days, the disk space (3TB) would be used up. I tried to find possible temporary files using commands like:

1.du -d 5

2.du -h --max-depth=1

3.du . | sort -nr | head -n50

However, I cannot find these files. du command shows that the diskspace is used by some files in my working directory. There don't seem to be any files that are over large. If I reboot the server, the space is released. How can I find these temporary files and delete them safely? Or any other solution will be highly appreciated.

Output of df -h after running LAMMPS around 24 hours:

Filesystem               Size  Used Avail Use% Mounted on
rootfs                   3.5T  1.2T 2.2T  35%  /
udev                     10M   0    10M   0%   /dev 
tmpfs                    6.4G  2.0M 6.3G  1%   /run 
/dev/mapper/cosmos-root  3.5T  1.2T 2.2T  35%  / 
tmpfs                    5.0M  0    5.0M  0%   /run/lock 
tmpfs                    13G   315M 13G   3%   /run/shm 
/dev/sda2                229M  18M  199M  9%   /boot

Please do not arbitrarily mark my question as duplicated one!

  • This Q should specify where the working directory is mounted. Please also include the output of df -h. – agc Nov 11 '16 at 4:23
  • Thanks for your response. Below is the output. after running LAMMPS around 24hrs. Filesystem Size Used Avail Use% Mounted on rootfs 3.5T 1.2T 2.2T 35% / udev 10M 0 10M 0% /dev tmpfs 6.4G 2.0M 6.3G 1% /run /dev/mapper/cosmos-root 3.5T 1.2T 2.2T 35% / tmpfs 5.0M 0 5.0M 0% /run/lock tmpfs 13G 315M 13G 3% /run/shm /dev/sda2 229M 18M 199M 9% /boot – Leon Nov 11 '16 at 22:44
  • What makes you think the files are in your working directory? – icarus Nov 12 '16 at 0:57
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Since everything seems to be mounted on one big root partition, the du commands clearly aren't being aimed where they should be. Maybe you're running du in some subdirectory of /home, but LAMMPS is filling up log files in /var or /var/log.

Run this in a background terminal during the fillup, it'll show the ten largest files opened by any processes named "lammps*" or "lmp*", and also highlight any changes as those largest files grow:

watch -d "lsof -c lammps -c lmp | tr -s ' ' | cut -d' ' -f8,9 | sort -urn | head"

Note: the above code assumes that disk space is consumed by a few large and growing files. It's possible the disk space might also be consumed by millions of small files.

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