[TerminalIPythonApp] ERROR | Failed to open SQLite history

Here’s how the error occurs ; I’m working on a slurm-managed shared cluster:

$ module load anaconda/3
$ source $CONDA_ACTIVATE
$ conda create --name 'clouds' python=3.6.4
[...]
$ conda install ipython
[... no error]
$ which ipython
/network/home/schmidtv/.conda/envs/clouds/bin/ipython # as expected
$ ipython
[TerminalIPythonApp] ERROR | Failed to open SQLite history /network/home/schmidtv/.ipython/profile_default/history.sqlite (disk I/O error).
[TerminalIPythonApp] ERROR | History file was moved to /network/home/schmidtv/.ipython/profile_default/history-corrupt.sqlite and a new file created.
[TerminalIPythonApp] ERROR | Failed to open SQLite history /network/home/schmidtv/.ipython/profile_default/history.sqlite (disk I/O error).
[TerminalIPythonApp] ERROR | History file was moved to /network/home/schmidtv/.ipython/profile_default/history-corrupt.sqlite and a new file created.
[TerminalIPythonApp] ERROR | Failed to open SQLite history /network/home/schmidtv/.ipython/profile_default/history.sqlite (disk I/O error).
[TerminalIPythonApp] ERROR | Failed to load history too many times, history will not be saved.
Python 3.6.4 |Anaconda, Inc.| (default, Mar 13 2018, 01:15:57)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.8.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import sqlite3

In [2]: sqlite3.sqlite_version
Out[2]: '3.29.0'

In [3]: sqlite3.version
Out[3]: '2.6.0'

In [4]: import IPython

In [5]: print(IPython.sys_info())
{'commit_hash': 'c233c25ab',
 'commit_source': 'installation',
 'default_encoding': 'UTF-8',
 'ipython_path': '/network/home/schmidtv/.conda/envs/clouds/lib/python3.6/site-packages/IPython',
 'ipython_version': '7.8.0',
 'os_name': 'posix',
 'platform': 'Linux-4.15.0-54-generic-x86_64-with-debian-buster-sid',
 'sys_executable': '/network/home/schmidtv/.conda/envs/clouds/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.6.4 |Anaconda, Inc.| (default, Mar 13 2018, 01:15:57) \n'
                '[GCC 7.2.0]'}

I’m aware of #9909 and #11407 but none help as it seems my sqlite dist is up to date

[ashkan-leo]

I also face this issue. I’m opening an ipython repl through Emacs. I get the following exceptiosn:

[TerminalIPythonApp] ERROR | Failed to create history session in /Users/ashkanaleali/.ipython/profile_default/history.sqlite. History will not be saved.
Traceback (most recent call last):
  File "/Users/ashkanaleali/w/fantasysports/.direnv/python-venv-3.7.3/lib/python3.7/site-packages/IPython/core/history.py", line 543, in __init__
    self.new_session()
  File "</Users/ashkanaleali/w/fantasysports/.direnv/python-venv-3.7.3/lib/python3.7/site-packages/decorator.py:decorator-gen-22>", line 2, in new_session
  File "/Users/ashkanaleali/w/fantasysports/.direnv/python-venv-3.7.3/lib/python3.7/site-packages/IPython/core/history.py", line 58, in needs_sqlite
    return f(self, *a, **kw)
  File "/Users/ashkanaleali/w/fantasysports/.direnv/python-venv-3.7.3/lib/python3.7/site-packages/IPython/core/history.py", line 570, in new_session
    self.session_number = cur.lastrowid
sqlite3.OperationalError: database is locked
Python 3.7.3 (default, Sep  5 2019, 17:14:41) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.11.1 -- An enhanced Interactive Python. Type '?' for help.

[liwt31]

This seems to be an issue with the network file system. You can try the following C code to test if the flock system call works normally:

#include <stdio.h>
#include <sys/file.h>

int main(){
    int fd = open("test.db", O_RDWR | O_CREAT);
    fprintf(stderr, "Prepare Locking File: %d\n", fd);
    int res = flock(fd, LOCK_SH);
    fprintf(stderr, "Result: %d\n", res);
}

For me, the system call hangs forever, although it works perfectly fine for local disks.

My solution to the problem is reporting the issue to the cluster manager, who restarted the NFS, and then the problem is solved.