[Pw_forum] Problem on compiling pwscf
JAY
jameslipd at gmail.com
Thu Oct 22 03:07:35 CEST 2009
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:
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> 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)
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> ------------------------------
>
> 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.
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> ------------------------------
>
> 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
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