[CP2K-user] [CP2K:11011] ASE CP2K interface

[Geng Sun]

Hello,

Finally, I found the possible reasons for this problem:

It seems that MPI will only read parts of the stdin, only part of the data 
in the PIPE is consumed.

THE MPICH2 user guide saied: "the redirection of large amounts of data to 
stdin is discouraged, and may cause unexpected results"

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)

Now everything loosk correct.

Geng
        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






在 2018年12月4日星期二 UTC-8下午12:59:20，Ole Schütt写道：
>
> 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 
> >>> 
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>
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