Dear Lorenzo Paulatto This is Jay Lee. The affiliate is Cug. I downloaded the tar file which contains the make.sys, however, I cannot succeed compiling it anyway. Then I tried to type ./configure to see what's wrong with my system, as reported the fortran 77 seems to be unavailable. I probably found where the bug is, because I updated the gcc to 4.4.1 version and the glibc to 2.9.3 version. The config.log reported that option '-cxxlib-gcc' not supported with the current installed GCC. I guess this is the problem that caused the error above.
By the way, I want to learn more about how to switch the options in make.sys, but I cannot find any document that can help. Is there some? The system is FC10, the kernel is 2.6.27.35-170.2.94.fc10.x86_64 On Thu, Oct 22, 2009 at 2:13 AM, <pw_forum-request at pwscf.org> wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: Problem on compiling pwscf (Lorenzo Paulatto) > 2. Re: lelfield (Lorenzo Paulatto) > 3. Re: "cannot open xml_recover file for writing" (Lorenzo Paulatto) > 4. Re: "cannot open xml_recover file for writing" (Prasenjit Ghosh) > 5. Re: "cannot open xml_recover file for writing" (Lorenzo Paulatto) > 6. Re: Cr GGA potential is underestimating the cohesive energy. > (udayagiri sai babu) > 7. Re: "cannot open xml_recover file for writing" (Ari P Seitsonen) > 8. Re: "cannot open xml_recover file for writing" > (marsamos at democritos.it) > 9. Left and right going Bloch's states from PWCOND (Manoj Srivastava) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 21 Oct 2009 14:33:23 +0200 > From: "Lorenzo Paulatto" <paulatto at sissa.it> > Subject: Re: [Pw_forum] Problem on compiling pwscf > To: "PWSCF Forum" <pw_forum at pwscf.org> > Message-ID: <op.u15g5xuha8x26q at paulax> > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 21 ottobre 2009 alle ore 13:45:30, JAY <jameslipd at gmail.com> ha > scritto: > > Thank you for the reply. I tried to understand the makefile of pwscf, but > > due to the lack of my knowledge, I am not able to find what should do. I > > typed ./configure in the source directory, it reports that the Fortran 77 > > compiler cannot create executables. I will check what's wrong with the > > Fortran compiler. > > We are not able to understand what you should do either: your are sending > contradicting emails. Let's try to recap what you've tried so far: > > 1. you run ./configure and it said it could not find a working f77 > compiler, which means you could not create a make.sys whatsoever > > 2. you have a make.sys prepared for gfortran (GNU fortran compiler) in > which you have simply replaced gfortran with mpif90, and added the > location of mpich to MPI_LIBS. > This make.sys will never work, as several additional switches are required > to compile the parallel code. > > 3. where was the original make.sys coming from? > > 4. are you sure that mpif90 is actually belonging to the installation of > mpich that is situated in /opt/mpich-1.2.5.2/? System administrators love > to install many different versions of the same or equivalent libraries, > often only one of them is actually working. > > 5. maybe the system you are using is module-based, you should really read > the system documentation. Or, at the *very* least, type the command > "module avail" and report the result... > > > cheers > > > P.S. please provide your full name+surname and affiliation, this is an > informal mailing list, but we like to know who we're talking to. > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > Message: 2 > Date: Wed, 21 Oct 2009 14:39:16 +0200 > From: "Lorenzo Paulatto" <paulatto at sissa.it> > Subject: Re: [Pw_forum] lelfield > To: "PWSCF Forum" <pw_forum at pwscf.org> > Message-ID: <op.u15hfqzfa8x26q at paulax> > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 21 ottobre 2009 alle ore 10:41:33, Jiri Houska > <jhouska at kfy.zcu.cz> ha scritto: > > > Dear Lorenzo, > > thanks for the answer. The relaxation is from scratch (not restarted), > > QE 4.0.3, running on cluster consisting of quadcore Xeon E5472 (3 GHz, > > 12 MB cache), happened for both (1) fixed occupations [used originally > > for material with a band gap] and (2) cold smearing. > > > Dear Jiri, > what happened in both cases? The i/o error or the algebra error? > As far as I know, the Berry-phase method does not work with pools (for > implementation reasons), also I'm not quite sure it works with smearing, > and with metals in general (I think the theory only applies to insulators). > > The davcio error you have experienced may happen if you restart a > calculation with a different number of pools. On the other hand, the zgefa > error may be caused by dipfield+smearing or dipfield+pools. > > You could check if one of the aforementioned conditions is verified in > your setup. > > cheers > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > Message: 3 > Date: Wed, 21 Oct 2009 14:44:43 +0200 > From: "Lorenzo Paulatto" <paulatto at sissa.it> > Subject: Re: [Pw_forum] "cannot open xml_recover file for writing" > To: "Ari Paavo Seitsonen" <Ari.P.Seitsonen at iki.fi>, "PWSCF Forum" > <pw_forum at pwscf.org> > Message-ID: <op.u15hotrta8x26q at paulax> > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 21 ottobre 2009 alle ore 09:31:01, Ari P Seitsonen > <Ari.P.Seitsonen at iki.fi> ha scritto: > > 25 RECL= specifier omitted on an OPEN statement for a direct file. > > > > But I don't see where RECL's would be used for the XML files... > > It would go in iotk/src/iotk_tool.spp. > I'm having tons of i/o errors on sp6 too, I suspect it may have something > to do with the specific filesystem used, but couldn't get reproducible > fails so far. > > cheers > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > Message: 4 > Date: Wed, 21 Oct 2009 16:45:58 +0200 > From: Prasenjit Ghosh <prasenjit.jnc at gmail.com> > Subject: Re: [Pw_forum] "cannot open xml_recover file for writing" > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <627e0ffa0910210745x65b5eb5dq5b85a0236f8d0b14 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > > > > I'm having tons of i/o errors on sp6 too, I suspect it may have something > > to do with the specific filesystem used, but couldn't get reproducible > > fails so far. > > > > > Lorenzo, > > the i/o errors on sp6 is most probably due to the problem in the > $CINECA_SCRATCH area. > In fact I'm also getting input output errors there and I think many other > people are also getting it. > > Prasenjit > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > +39 3807528672 (M) > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20091021/cef54fa9/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Wed, 21 Oct 2009 16:53:53 +0200 > From: "Lorenzo Paulatto" <paulatto at sissa.it> > Subject: Re: [Pw_forum] "cannot open xml_recover file for writing" > To: "PWSCF Forum" <pw_forum at pwscf.org> > Message-ID: <op.u15nn3wda8x26q at paulax> > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 21 ottobre 2009 alle ore 16:45:58, Prasenjit Ghosh > <prasenjit.jnc at gmail.com> ha scritto: > > the i/o errors on sp6 is most probably due to the problem in the > > $CINECA_SCRATCH area. > > In fact I'm also getting input output errors there and I think many other > > people are also getting it. > > Yep, I suspected it. They started after some maintenance last month, so > I'm hoping they will disappear sooner or later. > > We're really going off-topic now, but I wished to post this, to reassure > other users who may be clueless and frustrated. Thank you for confirming. > > cheers > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > Message: 6 > Date: Wed, 21 Oct 2009 20:35:13 +0530 > From: udayagiri sai babu <udayagiri3 at gmail.com> > Subject: Re: [Pw_forum] Cr GGA potential is underestimating the > cohesive energy. > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <d3964cb10910210805p5cb2d1acv1734eee0a135d01b at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Thank you dear Paolo for the reference you provided me. > > On Sat, Oct 17, 2009 at 4:07 PM, Paolo Giannozzi <giannozz at democritos.it > >wrote: > > > > > On Oct 17, 2009, at 11:31 , udayagiri sai babu wrote: > > > > > I am calculated the cohesive energy of Cr using the pseudopotential > > > Cr.pbe-sp-van.UPF. I got is 3.63 ev/atom as the cohesive energy > > > where as the experimental value is 4.1 ev/atom. As i know the GGA > > > pseudopotential should overestimate the cohesive energy value > > > > should it? LDA overestimates, GGA not necessarily so. > > > > The cohesive energy of Cr has been already calculated by many authors, > > for sure. You may want to have a look at what other people have done > > before you. For instance, here: > > http://dare.ubvu.vu.nl/bitstream/1871/9949/1/B4.pdf > > (found in 5' of google search). They get 3.58eV for Becke-Perdew, > > 3.80eV for Perdew-Wang. So 3.63eV for PBE after all is not that bad. > > > > P. > > --- > > Paolo Giannozzi, Dept of Physics, University of Udine > > via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20091021/7dbda4e4/attachment-0001.htm > > ------------------------------ > > Message: 7 > Date: Wed, 21 Oct 2009 17:30:52 +0200 (CEST) > From: Ari P Seitsonen <Ari.P.Seitsonen at iki.fi> > Subject: Re: [Pw_forum] "cannot open xml_recover file for writing" > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <alpine.LNX.2.00.0910211728290.6042 at pcihpc19.uzh.ch> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Dear Lorenzo et al, > > I can confirm that I also manage to run exactly the same system on a > Linux cluster (ifort 10.*, MKL) that caused the problem on the IBM Power6. > Unfortunately the latter is the only machine where I could run the > biiiiiig system... Well, I'll think of something. Thanks to all for the > support!! > > Greetings, > > apsi > > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ > Physikalisch-Chemisches Institut der Universitaet Zuerich > Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 > > On Wed, 21 Oct 2009, Lorenzo Paulatto wrote: > > > In data 21 ottobre 2009 alle ore 16:45:58, Prasenjit Ghosh > > <prasenjit.jnc at gmail.com> ha scritto: > >> the i/o errors on sp6 is most probably due to the problem in the > >> $CINECA_SCRATCH area. > >> In fact I'm also getting input output errors there and I think many > other > >> people are also getting it. > > > > Yep, I suspected it. They started after some maintenance last month, so > > I'm hoping they will disappear sooner or later. > > > > We're really going off-topic now, but I wished to post this, to reassure > > other users who may be clueless and frustrated. Thank you for confirming. > > > > cheers > > > > > > -- > > Lorenzo Paulatto > > SISSA & DEMOCRITOS (Trieste) > > phone: +39 040 3787 511 > > skype: paulatz > > www: http://people.sissa.it/~paulatto/ > > > > *** save italian brains *** > > http://saveitalianbrains.wordpress.com/ > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > ------------------------------ > > Message: 8 > Date: Wed, 21 Oct 2009 17:57:55 +0200 > From: marsamos at democritos.it > Subject: Re: [Pw_forum] "cannot open xml_recover file for writing" > To: pw_forum at pwscf.org > Message-ID: <20091021175755.x7sl43e3kgso8csw at mail.democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format="flowed" > > Dear all, I also find big i-o problems on sp6 (running GW) in > particular when handling big files ... sometimes it works sometimes it > does not work!!!!! HPC ;-) > > Layla > > Quoting Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>: > > > > > Dear Lorenzo et al, > > > > I can confirm that I also manage to run exactly the same system on a > > Linux cluster (ifort 10.*, MKL) that caused the problem on the IBM > Power6. > > Unfortunately the latter is the only machine where I could run the > > biiiiiig system... Well, I'll think of something. Thanks to all for the > > support!! > > > > Greetings, > > > > apsi > > > > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > > Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ > > Physikalisch-Chemisches Institut der Universitaet Zuerich > > Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 > > > > On Wed, 21 Oct 2009, Lorenzo Paulatto wrote: > > > >> In data 21 ottobre 2009 alle ore 16:45:58, Prasenjit Ghosh > >> <prasenjit.jnc at gmail.com> ha scritto: > >>> the i/o errors on sp6 is most probably due to the problem in the > >>> $CINECA_SCRATCH area. > >>> In fact I'm also getting input output errors there and I think many > other > >>> people are also getting it. > >> > >> Yep, I suspected it. They started after some maintenance last month, so > >> I'm hoping they will disappear sooner or later. > >> > >> We're really going off-topic now, but I wished to post this, to reassure > >> other users who may be clueless and frustrated. Thank you for > confirming. > >> > >> cheers > >> > >> > >> -- > >> Lorenzo Paulatto > >> SISSA & DEMOCRITOS (Trieste) > >> phone: +39 040 3787 511 > >> skype: paulatz > >> www: http://people.sissa.it/~paulatto/ > >> > >> *** save italian brains *** > >> http://saveitalianbrains.wordpress.com/ > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > ------------------------------ > > Message: 9 > Date: Wed, 21 Oct 2009 14:13:31 -0400 (EDT) > From: Manoj Srivastava <manoj at phys.ufl.edu> > Subject: [Pw_forum] Left and right going Bloch's states from PWCOND > To: pw_forum at pwscf.org > Message-ID: > <Pine.GSO.4.21.0910211324430.20574-100000 at neptune.phys.ufl.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Dear All, > I am trying to figure out the left and right going Bloch's states in the > lead from PWCOND. For a given (kx,ky)and energy we get kz. The code only > prints out Bloch's state moving in one direction. eg. in one of the > calculation- > k//=(0.375,-0.375) > Nchannels of the left tip = 1 > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > 0.3157801 0.0000000 0.0000000 > > Now if I want Bloch's state moving in right as well as left direction, I > can go to kbloch.f90 subroutine, and print out all the eigen values of > AX=exp(ikd)BX, and out of those the ones with real solution would be our > Bloch's state, so I get for each channel two solutions- > kval (-0.275409421993275,1.823688001395235E-010) > kval (0.315780119742506,-3.611201785292708E-012) > > To figure out the direction, I can calculate current associated with these > Bloch's sate and if the current is +ive it is right moving , and if '-'ive > its left moving Bloch's state. I can print out current from jbloch.f90 > subroutine which are - > current eigenvalue -1.86502143831863 1.59149029314457 > > So, clearly the first state with kval=-0.2754094 is left moving and the > other one right moving. Upto here its clear to me how to identify left and > right moving states. > > I get confused when for a given (kx,ky,E), I have more than one Bloch' > state. In another calculation where i get multiple Bloch's state- > Nchannels of the left tip = 5 > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > -0.0746301 0.0000000 0.0000000 > 0.1205527 0.0000000 0.0000000 > 0.3112908 0.0000000 0.0000000 > 0.4200218 0.0000000 0.0000000 > -0.4935150 0.0000000 0.0000000 > > so i did the same trick i did above to first print out kz and then > current, which gives me - > kval (-0.420023481074359,1.979595081419732E-010) (call it a) > kval (0.420023367986768,2.500979698670295E-011) (b) > kval (-0.306507431678779,-1.236804629184431E-011) (c) > kval (-0.125376071175573,-6.134512510438736E-011) (d) > kval (-7.945001124706894E-002,6.683546930037856E-011)(e) > kval (0.106554601758169,-6.427946951285107E-011) (f) > kval (8.866867725358024E-002,8.342250371574646E-011) (g) > kval (0.325333314672671,1.260810749228185E-011) (h) > kval (-0.488725859521576,1.769197678346003E-010) (i) > kval (0.479509832763231,1.765499400037283E-010) (j) > > current eigenvalue -9.31389492882581 -1.24296522993488 > -1.21324078359658 -1.11950286753963 -1.08166842367443 > 1.08187482164864 1.11973146584263 1.21295295042188 > 1.24280031534940 9.313897787790 > > So, the first 5 are left moving and rest are right moving. But I dont know > the pairs. for example for left moving state a, what is the corresponding > right moving state whether its f or g ... j ? > > Any help would be appreciated. > > Regards, > Manoj Srivastava > University of Florida, Gainesville. > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 28, Issue 54 > **************************************** > -- Sincerely Jay -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091022/b8117b01/attachment-0001.htm