<div dir="ltr"><div>Hello,</div><div> Finally, I found the possible reasons for this problem:</div><div> </div><div>It seems that MPI will only read parts of the stdin, only part of the data in the PIPE is consumed.</div><div> </div><div>THE MPICH2 user guide saied: "the redirection of large amounts of data to stdin is discouraged, and may cause unexpected results" </div><div> </div><div>So I have to write the coordiates to a file in cp2k.py and read the positions from cp2k_shell.F instead of the stdin (codes are shown below) </div><div> </div><div>Now everything loosk correct.</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"> IF (para_env%mepos==para_env%source) THEN !READ (*,*,iostat=iostat) n_atom2 !IF (iostat/=0) CPABORT('setpos read n_atom') !IF (n_atom2/=SIZE(pos)) THEN ! CALL my_assert(.FALSE.,'setpos invalid number of atoms',failure) ! DO i=1,n_atom ! READ(*,'(a)',iostat=iostat) cmdStr ! CALL compress(cmdStr,full=.TRUE.) ! CALL uppercase(cmdStr) ! IF (cmdStr=='*END') EXIT ! END DO ! GOTO 10 !END IF !READ (*,*,iostat=iostat) pos !IF (iostat/=0) CPABORT('setpos read coord') inquire(unit=201,opened=unitalive) if (unitalive) CPABORT('UNIT 201 is being used') inquire(file="CP2K_POSITIONS",exist=filepresence) if (.not. filepresence) CPABORT('FILE CP2K_POSITIONS NOT EXIST') open(201,action='READ',file="CP2K_POSITIONS",iostat=iostat,status='OLD',form='FORMATTED',ACCESS='SEQUENTIAL') if (iostat/=0) CPABORT('read CP2K_POSITIONS') READ(201,*,iostat=iostat) n_atom2 IF (iostat/=0) CPABORT('setpos read n_atom2') IF (n_atom2/=SIZE(pos)) THEN CALL my_assert(.FALSE.,'setpos invalid number of atoms',failure) DO i=1,n_atom READ(201,'(a)',iostat=iostat) cmdStr CALL compress(cmdStr,full=.TRUE.) CALL uppercase(cmdStr) IF (cmdStr=='*END') EXIT END DO GOTO 10 END IF READ (201,*,iostat=iostat) pos CLOSE(201) IF (iostat/=0) CPABORT('setpos read coord') pos(:) = pos(:)/pos_fact READ(*,'(a)',iostat=iostat) cmdStr CALL compress(cmdStr,full=.TRUE.) CALL uppercase(cmdStr) CALL my_assert(cmdStr=='*END',' missing *END',failure) END IF </div></code></div> </div><div> </div><div> </div> 在 2018年12月4日星期二 UTC-8下午12:59:20，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, are you using MPI? Then this is probably where the buffering happens. Depending on which MPI implementation you are using there might be a way to tweak its stdin/out forwarding. Out of curiosity, how many atoms does your system have? Maybe the Fortran side simple tries to read too many values? -Ole On 2018-12-04 21:27, Geng Sun wrote: > Hello Ole, > > Thank you very much for your reply: > I changed the code as you suggested (below), but the problem is still > present in the test. > > Best > > Geng > > 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() > > 在 2018年12月4日星期二 UTC-8上午11:05:43，Ole > Schütt写道： > >> 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>cp2k+...@googlegroups.com</a>. >>> To post to this group, send email to <a>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> [1]. >>> 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> [2]. > > -- > 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="giDjM-5_AAAJ" 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="giDjM-5_AAAJ" 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>. > > > Links: > ------ > [1] <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> > [2] <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>