Open
Description
Hi, I noticed that when I would run a ts.iterate over many output iterations on OLCF's Jupyter Service and afterwards I would try to simply create a directory with a magic command from a Jupyter cell (! mkdir <path/to/dir>) the directory would get created but I would receive an error that reads:
ValueError: filedescriptor out of range in select()
openpmd-viewer version: 1.6.0
To reproduce:
- run WarpX sim and write openPMD output
- read in large time series (e.g. 500 iterations)
- execute in separate cells:
ts = LpaDiagnostics('diags/diag_btd/') ex, ey = ts.iterate( ts.get_emittance ) # Emittance as a function of time g, _ = ts.iterate( ts.get_energy_spread, property='gamma' ) # Mean energy as a function of time ! mkdir -p "analysis"
full error message
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[6], line 1
----> 1 get_ipython().system(' mkdir -p "analysis"')
File /gpfs/alpine/proj-shared/aph114/mgarten/environments/conda-warpx/lib/python3.10/site-packages/ipykernel/zmqshell.py:649, in ZMQInteractiveShell.system_piped(self, cmd)
647 self.user_ns["_exit_code"] = system(cmd)
648 else:
--> 649 self.user_ns["_exit_code"] = system(self.var_expand(cmd, depth=1))
File /gpfs/alpine/proj-shared/aph114/mgarten/environments/conda-warpx/lib/python3.10/site-packages/IPython/utils/_process_posix.py:153, in ProcessHandler.system(self, cmd)
149 flush = sys.stdout.flush
150 while True:
151 # res is the index of the pattern that caused the match, so we
152 # know whether we've finished (if we matched EOF) or not
--> 153 res_idx = child.expect_list(patterns, self.read_timeout)
154 print(child.before[out_size:].decode(enc, 'replace'), end='')
155 flush()
File /gpfs/alpine/proj-shared/aph114/mgarten/environments/conda-warpx/lib/python3.10/site-packages/pexpect/spawnbase.py:372, in SpawnBase.expect_list(self, pattern_list, timeout, searchwindowsize, async_, **kw)
370 return expect_async(exp, timeout)
371 else:
--> 372 return exp.expect_loop(timeout)
File /gpfs/alpine/proj-shared/aph114/mgarten/environments/conda-warpx/lib/python3.10/site-packages/pexpect/expect.py:169, in Expecter.expect_loop(self, timeout)
167 return self.timeout()
168 # Still have time left, so read more data
--> 169 incoming = spawn.read_nonblocking(spawn.maxread, timeout)
170 if self.spawn.delayafterread is not None:
171 time.sleep(self.spawn.delayafterread)
File /gpfs/alpine/proj-shared/aph114/mgarten/environments/conda-warpx/lib/python3.10/site-packages/pexpect/pty_spawn.py:458, in spawn.read_nonblocking(self, size, timeout)
450 return select_ignore_interrupts([self.child_fd], [], [], timeout)[0]
452 # If there is data available to read right now, read as much as
453 # we can. We do this to increase performance if there are a lot
454 # of bytes to be read. This also avoids calling isalive() too
455 # often. See also:
456 # * https://github.com/pexpect/pexpect/pull/304
457 # * http://trac.sagemath.org/ticket/10295
--> 458 if select(0):
459 try:
460 incoming = super(spawn, self).read_nonblocking(size)
File /gpfs/alpine/proj-shared/aph114/mgarten/environments/conda-warpx/lib/python3.10/site-packages/pexpect/pty_spawn.py:450, in spawn.read_nonblocking.<locals>.select(timeout)
449 def select(timeout):
--> 450 return select_ignore_interrupts([self.child_fd], [], [], timeout)[0]
File /gpfs/alpine/proj-shared/aph114/mgarten/environments/conda-warpx/lib/python3.10/site-packages/pexpect/utils.py:143, in select_ignore_interrupts(iwtd, owtd, ewtd, timeout)
141 while True:
142 try:
--> 143 return select.select(iwtd, owtd, ewtd, timeout)
144 except InterruptedError:
145 err = sys.exc_info()[1]
ValueError: filedescriptor out of range in select()