<div dir="ltr"><div>Hello Ole,</div><div> </div><div>I made another change to the cp2k_shell.F: If the code reads individual positions rather than read them as a whole (like the code below), the program will hang at a point where only part of the positions are read in. (I have about 331 atoms, where normally about 250~270 atoms are read) </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"> !READ (*,*,iostat=iostat) pos !READ (*,*,iostat=iostat) ((pos(i,j),j=1,3),i=1,n_atom) !READ (*,*,iostat=iostat) (pos(i),i=1,n_atom2) DO i=1,n_atom m=(i-1)*3+1 n=(i-1)*3+3 READ(*,*) (pos(j),j=m,n) WRITE(0,*) "atom=", i, pos(m),pos(m+1),pos(n) CALL m_flush(0) END DO WRITE(0,*) "LABEL-1" CALL m_flush(0) </div></code></div></div><div> </div><div>This is the tail of the standard error output. Where, only 252 atoms are printed. <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">Sending: 1.576752302496963409e+01 5.503432604574527431e+00 5.202333832524260515e+00 atom= 243 16.662443015797379 1.3742961283890502 3.8763624242357171 Sending: 1.517292733648857705e+01 4.201499193055327375e+00 7.381004145064225419e+00 atom= 244 16.662391280884478 1.3742459215953395 0.65239139651875000 Sending: 1.347251652964376234e+01 6.982201222299000420e+00 7.885207051660287902e-01 Sending: 1.270684522088338753e+01 5.387934046501004381e+00 7.380386770425433340e+00 atom= 245 16.705918168029598 1.3963594659850651 6.5096981880927025 Sending: 1.121215876405216250e+01 5.455761976608218156e+00 7.885247030917259536e-01 Sending: 1.264981900140291593e+01 5.588193026760487570e+00 2.971586044180265063e+00 atom= 246 14.298521645540390 2.7461084273618193 7.4746197668438166 Sending: 1.340077937297150790e+01 4.053634960891928429e+00 7.885301196183434058e-01 Sending: 1.020485628515282706e+01 6.913382900918708884e+00 7.383907976352638514e+00 atom= 247 14.282063640676757 2.7485874649238795 1.6804517810327422 Sending: 1.041632697503036731e+01 6.865228814815203862e+00 2.971592361475913435e+00 atom= 248 14.282106984202624 2.7485910114075263 4.2975637697642934 Sending: 9.521439090500260605e+00 8.245776638331120623e+00 6.218688347483974255e+00 Sending: 9.521360909499742675e+00 8.245771920855188952e+00 1.955237846516025613e+00 atom= 249 15.019369986694146 4.0380913886689607 2.9715839946517644 Sending: 1.190174301579737914e+01 9.620070407982204586e+00 3.876362424235717086e+00 Sending: 1.190169128088448147e+01 9.620020201188493658e+00 6.523913965187499997e-01 atom= 250 15.914380998597084 2.6575812528326686 5.2023401498199107 Sending: 1.189999109458993409e+01 9.622398083668830537e+00 6.496868766581632926e+00 atom= 251 15.925180013305853 8.4795751127617489E-002 5.2023421993484060 Sending: 9.516001797608472756e+00 1.099443356384864323e+01 7.482068722341200129e+00 atom= 252 18.147873024969634 1.3805454647779496 5.2023338325242605 Sending: 9.521363640676758777e+00 1.099436174451703430e+01 1.680451781032742176e+00 Sending: 9.521406984202624102e+00 1.099436529100068149e+01 4.297563769764293440e+00 Sending: 1.025866998669414798e+01 1.228386566826211634e+01 2.971583994651764371e+00 Sending: 1.115368099859708551e+01 1.090335553242582378e+01 5.202340149819910664e+00 Sending: 1.116448001330585527e+01 8.330570030720771513e+00 5.202342199348406027e+00 Sending: 1.338717302496963768e+01 9.626319744371103937e+00 5.202333832524260515e+00 Sending: 1.278402737896498920e+01 8.314253003861532321e+00 7.379054099830940849e+00 Sending: 1.109216652964376415e+01 1.110508836209557870e+01 7.885207051660287902e-01 Sending: 1.032654594512574420e+01 9.507815609387757050e+00 7.379945316851912018e+00 Sending: 8.831808764052164307e+00 9.578649116404795549e+00 7.885247030917259536e-01 Sending: 1.026946900140291774e+01 9.711080166557064075e+00 2.971586044180265063e+00 Sending: 1.102042937297150971e+01 8.176522100688506711e+00 7.885301196183434058e-01 Sending: 7.823467798454666777e+00 1.103241626738852688e+01 7.382163504927960140e+00 Sending: 8.035976975030369118e+00 1.098811595461178214e+01 2.971592361475913435e+00 Sending: 7.141089090500260639e+00 1.236866377812769713e+01 6.218688347483974255e+00 Sending: 7.141010909499744486e+00 1.236865906065176546e+01 1.955237846516025613e+00 Sending: 9.521393015797379178e+00 1.374295754777878109e+01 3.876362424235717086e+00 Sending: 9.521341280884481506e+00 1.374290734098507016e+01 6.523913965187499997e-01 Sending: 9.520851532832354636e+00 1.374528395598669661e+01 6.498168429193992068e+00 Sending: 7.135752205372321910e+00 1.512061403636860391e+01 7.467937815653423961e+00 Sending: 7.141013640676759699e+00 1.511724888431361080e+01 1.680451781032742176e+00 Sending: 7.141056984202625912e+00 1.511725243079725800e+01 4.297563769764293440e+00 Sending: 7.878319986694148902e+00 1.640675280805869107e+01 2.971583994651764371e+00 Sending: 8.773330998597087316e+00 1.502624267222240029e+01 5.202340149819910664e+00 Sending: 8.784130013305857076e+00 1.245345717051734802e+01 5.202342199348406027e+00 Sending: 1.100682302496963771e+01 1.374920688416768044e+01 5.202333832524260515e+00 Sending: 1.040246635779289264e+01 1.243375815304947274e+01 7.378511014138936730e+00 Sending: 8.711816529643764184e+00 1.522797550189215521e+01 7.885207051660287902e-01 Sending: 7.944196067620286072e+00 1.363073238988811653e+01 7.376840927591756802e+00 Sending: 6.451458764052164341e+00 1.370153625620137205e+01 7.885247030917259536e-01 Sending: 7.889119001402919551e+00 1.383396730635364058e+01 2.971586044180265063e+00 Sending: 8.640079372971511518e+00 1.229940924048508322e+01 7.885301196183434058e-01 Sending: 5.442845882770557253e+00 1.515594640055591036e+01 7.382285524632366425e+00 Sending: 5.655626975030369152e+00 1.511100309440835865e+01 2.971592361475913435e+00 Sending: 2.438731539757682254e-01 5.399653964569083087e+00 9.216051601394250170e+00 Sending: 4.943799047278442771e+00 6.359320929803981670e+00 1.078113524315581451e+01 Sending: 3.138843358305583919e+00 3.495089033159221259e+00 9.827428649731281496e+00 Sending: 5.783276526942270124e+00 4.240744460487060330e+00 9.597502013642966290e+00 Sending: 3.616494458058998607e+00 8.325856048791498765e+00 9.585425118565524372e+00 Sending: 3.357219536482951128e+00 7.904624946018040887e+00 1.205591374980337882e+01 Sending: 6.323261420949900513e-01 3.175684482035930234e+00 1.034222361512076382e+01 Sending: 2.466428571964844885e+00 5.952425260037331967e+00 1.043216353271719576e+01 Sending: -2.305837893097886504e-01 6.188097724220211759e+00 1.046543155157912608e+01 Sending: 3.399261249766690085e+00 3.516835622123011262e+00 1.133940075852044416e+01 Sending: 5.923947421334220920e+00 4.113983946240092671e+00 1.115507609006755807e+01 Sending: *END </div></code></div></div><div> </div><div>Geng </div> 在 2018年12月4日星期二 UTC-8下午1:20:19，Geng Sun写道：<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"><div>Hello Ole,</div><div> </div><div>Yes, I am using MPI. I am running CP2K on cori, which is a Cray system.</div><div>I am not very sure, but it seems that the MPI is mpich, because the cray-mpich module is loaded when I run CP2K.</div><div> </div><div>I have 331 atoms in the calculations. I tried to reduce the position string</div><div>self._shell.send('%.18e %.18e %.18e' % tuple(pos))</div><div>to </div><div>self._shell.send('%.8e %.8e %.8e' % tuple(pos))</div><div> </div><div>I assumed this may avoid possible deadlock of the PIPE, but it does not work in the end.</div><div> </div><div>Best</div><div> </div><div>Geng </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" rel="nofollow" target="_blank" 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" rel="nofollow" target="_blank" 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 rel="nofollow">cp2k+...@googlegroups.com</a>. > To post to this group, send email to <a rel="nofollow">cp...@googlegroups.com</a>. > Visit this group at <a href="https://groups.google.com/group/cp2k" rel="nofollow" target="_blank" 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" rel="nofollow" target="_blank" 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" rel="nofollow" target="_blank" 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" rel="nofollow" target="_blank" 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></blockquote></div>