<div dir="ltr"><div>Hello Ole,</div><div> </div><div>Thank you very much for your reply:</div><div>I changed the code as you suggested (below), but the problem is still present in the test.</div><div> </div><div>Best</div><div> </div><div>Geng </div><div><div style="background-color: rgb(250, 250, 250); border-color: rgb(187, 187, 187); border-style: solid; border-width: 1px; overflow-wrap: break-word;" class="prettyprint"><code class="prettyprint"><div class="subprettyprint"> def send(self, line): """Send a line to the cp2k_shell""" assert self._child.poll() is None # child process still alive? if self._debug: #print('Sending: ' + line) sys.stderr.write("Sending: {}\n".format(line)) sys.stderr.flush() if self.version < 2.1 and len(line) >= 80: raise Exception('Buffer overflow, upgrade CP2K to r16779 or later') assert(len(line) < 800) # new input buffer size self.isready = False self._child.stdin.write(line + '\n') self._child.stdin.flush() </div></code></div></div><div> </div> 在 2018年12月4日星期二 UTC-8上午11:05:43，Ole Schütt写道：<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">Hi Geng, this sounds indeed like a buffering issue. Could you once try to add a flush() on the python side. Basically add the following line after cp2k.py:498. self._child.stdin.write(line + '\n') + self._child.stdin.flush() This is probably quite inefficient. So, if it works I'll add some logic to flush only when recv() follows a send(). -Ole On 2018-12-04 18:08, Geng Sun wrote: > Dear CP2K users, > > In the past several weeks, I frequently faced a problem when I use > the CP2K -ASE interface. > > The calculations frequently got stuck during the calculations. > > 1) Firstly I switched on the debug=True option in the ASE-CP2K > calculator and I found that the calculation always gets stuck at a > line with *END after sending the positions to the subroutine > cp2k_shell.popt (I printed the information to the standard error, so > they are not buffered) > > 2) Then, I modified the cp2k_shell.F to print a lot of "labels". Then > I found that the code may get stuck at the line of "READ > (*,*,iostat=iostat) pos" like below. I can always get "begin to read > pos" in the standard error, but I can not reach "LABEL-1". > > WRITE(0,*) "begin to read pos" > CALL m_flush(0) > READ (*,*,iostat=iostat) pos > WRITE(0,*) "LABEL-1" > CALL m_flush(0) > > I attached the modified cp2k_shell.F and the standard out/error > generated by the slurm batch system with this post. You can see that > the program get stuck at the second optimization step just after > sending the positions. > > I greatly appreciate your suggestions for fixing this confusing bugs. > > Thanks in advance. > > Geng > > -- > You received this message because you are subscribed to the Google > Groups "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send > an email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="qXF3Cbt5AAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp2k+uns...@googlegroups.com</a>. > To post to this group, send email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="qXF3Cbt5AAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a>. > Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/group/cp2k';return true;" onclick="this.href='https://groups.google.com/group/cp2k';return true;">https://groups.google.com/group/cp2k</a>. > For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/d/optout';return true;" onclick="this.href='https://groups.google.com/d/optout';return true;">https://groups.google.com/d/optout</a>. </blockquote></div>