Please find the attached python file where the issue is seen.
The cli to create an executable was:
$pyinstaller run_server_min.spec

Here are the contents of the file (this doesn't support multiple file uploads):
================
# -*- mode: python ; coding: utf-8 -*-

block_cipher = None


a = Analysis(['run_server_min.py'],
             pathex=['<PUT ABSOLUTE PATH OF ABOVE FILE HERE>'],
             binaries=[],
             datas=[],
             hiddenimports=['sklearn.neighbors.typedefs', 'sklearn.neighbors.quad_tree', 'sklearn.tree._utils', 'xgboost', 'xgboost.libpath'],
             hookspath=['pyhooks'],
             runtime_hooks=[],
             excludes=[],
             win_no_prefer_redirects=False,
             win_private_assemblies=False,
             cipher=block_cipher,
             noarchive=False)
pyz = PYZ(a.pure, a.zipped_data,
             cipher=block_cipher)
exe = EXE(pyz,
          a.scripts,
          a.binaries,
          a.zipfiles,
          a.datas,
          [],
          name='run_server_min',
          debug=False,
          bootloader_ignore_signals=False,
          strip=False,
          upx=False,
          runtime_tmpdir=None,
          console=True )
=========

$ pyinstaller run_server_min.spec
69 INFO: PyInstaller: 3.5.dev0+cb8d10af6
69 INFO: Python: 3.6.7
70 INFO: Platform: Linux-3.16.0-77-generic-x86_64-with-debian-jessie-sid
...

When your run ./dist/run_server_min that is generated, it'll spawn the process multiple times. The issue goes away when you add freeze_support on the top.