[Pw_forum] make[2]: warning: Clock skew detected. Your build may be incomplete.
Dear, sir: When I make the Quantum-Espresso, a problem always appeared in the last ,so I want to know a way to solve. The problem list as fllows: make[2]: warning: Clock skew detected. Your build may be incomplete. make[2]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/src' make[2]: Entering directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/tools' make[2]: Warning: File `../../make.sys' has modification time 1.3e+04 s in the future test -n "" && ( cd ../.. ; make -w || exit 1) || : gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../../include -I../../iotk/src -I../../Modules -I. -c tddfpt_calculate_spectrum.f90 gfortran -g -o turbo_spectrum.x \ tddfpt_calculate_spectrum.o ../../Modules/libqemod.a ../../PW/libpw.a ../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a ../../iotk/src/libiotk.a /export/home1/yqsu/espresso-4.3.2/lapack-3.2/lapack.a /export/home1/yqsu/espresso-4.3.2/BLAS/blas.a ( cd ../../bin ; ln -fs ../TDDFPT/tools/turbo_spectrum.x . ) if [ -d ../bin ] ; then ( cd ../bin ; ln -fs ../tools/turbo_spectrum.x . ); fi make[2]: warning: Clock skew detected. Your build may be incomplete. make[2]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/tools' make[1]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT' make: warning: Clock skew detected. Your build may be incomplete. Thank you for your suggestion ! Best wishes ! Su Yaqiong -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120719/3a846913/attachment-0001.htm
[Pw_forum] Input error?
The possibilities I guessed: 1, Do you have authority to access that directory? 2, Do you have enough HDD space for the wavefunction file? 3, How about cleaning the directory /home/.../exec/ and re-running the task? -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-07-19 05:05:13,"Pedro Augusto F. P. Moreira" wrote: > Dear all, > > I am trying to pw.x, but the following error happens: > > > %% > task # 0 > from diropn : error #10 > error opening /home/pedro/Documentos/espresso-5.0/exec/h2o.wfc1 > > %% > > I imagine that the pw.x should open the wcf1 file. Am I rigth? Can >anyone say why this error is happening? I managed to run the same >simulation, but with an isolated molecule. My input follows below. > > Thanks, > > Pedro > >-- >Pedro Moreira > >IFGW - Unicamp - Brazil > ># >&control >calculation='relax', >restart_mode='from_scratch', >pseudo_dir='/home/pedro/Documentos/espresso-5.0/pseudo', >outdir='/home/pedro/Documentos/espresso-5.0/exec', >prefix='h2o', >tprnfor = .true., >nstep = 1, >/ >&system >ibrav = 0, >nat = 1080, ntyp = 2, >ecutwfc = 70.0, ecutrho = 850.0, >/ >&electrons >electron_maxstep = 500, >/ >&ions >/ >ATOMIC_SPECIES >H 1.00790 H.blyp-van_ak.UPF >O 15.9994 O.blyp-van_ak.UPF >CELL_PARAMETERS angstrom >22.15 0.000 0.000 >0.000 23.02 0.000 >0.000 0.000 21.55 >K_POINTS crystal >1 >0. 0. 0. 1.00e+00 >ATOMIC_POSITIONS angstrom > >1080 atoms >## >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120719/965a40e2/attachment.htm
[Pw_forum] Band Structure and nscf calculation
Dear
I ran scf for MoS2 in K_Points Automatic 4X4x4 mesh with 20 nband and followed
calculation for band Structure
but i observed that sufficient no. of bands are not there;;
then i perform nscf calculation for DOS which seems to be alright
So i did scf calculation again in K-Points Automatic 12x12x12 with a little
increase in nband (keeping it in mind nband = # of VE/2 +20% more in metal)
Now i have few questions
1-- While performing band calculation, how should i take K-points
K-POINTS AUTOMATIC
12x12x12 1 1 1
??? or the one which i generated manually (150 Points)
150
1
2
like that,which one is a better option?
2. While performing nscf calculation, should i write it or no
??? restart_mode = 'from_scratch',
??? i believe no as it may take longer time and some convergence conflict
??? but i need confirmation
??
??? Its mentioned in the user guide, that occupations = tetrahedra for DOS
??? Is it required in every case irrespective of magnetic or non magnetic? ???
3? i think nscf is required only for DOS, So can i perform nscf calculation
befor the post ? ? ? ?? processing calculation of band calculation? ?
? ? This question i am asking because i am using computational facility of some
other??? place which is available to me for short time only and i am running
short of time
Sohail
KKU
SAUDI
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[Pw_forum] make[2]: warning: Clock skew detected. Your build may be incomplete.
On Thu, Jul 19, 2012 at 3:21 AM, yqsu wrote: > Dear, sir: > > When I make the Quantum-Espresso, a problem always appeared in the last ,so > I want to know a way to solve. The problem list as fllows: > > make[2]: warning: Clock skew detected. Your build may be incomplete. this warning indicates that the time stamps on the created files are newer than your current time. this can happen, if you are compiling on a NFS file system where the clock of the file server and the compilation host are not synchronized and the clock on the file server is ahead of the compilation host. you should talk to you system administrator and suggest to install/configure NTP software to synchronize the clocks across the cluster. cheers, axel. > > make[2]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/src' > > make[2]: Entering directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/tools' > > make[2]: Warning: File `../../make.sys' has modification time 1.3e+04 s in > the future > > test -n "" && ( cd ../.. ; make -w || exit 1) || : > > gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW > -I../../include -I../../iotk/src -I../../Modules -I. -c > tddfpt_calculate_spectrum.f90 > > gfortran -g -o turbo_spectrum.x \ > > tddfpt_calculate_spectrum.o ../../Modules/libqemod.a ../../PW/libpw.a > ../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a > ../../iotk/src/libiotk.a > /export/home1/yqsu/espresso-4.3.2/lapack-3.2/lapack.a > /export/home1/yqsu/espresso-4.3.2/BLAS/blas.a > > ( cd ../../bin ; ln -fs ../TDDFPT/tools/turbo_spectrum.x . ) > > if [ -d ../bin ] ; then ( cd ../bin ; ln -fs ../tools/turbo_spectrum.x . ); > fi > > make[2]: warning: Clock skew detected. Your build may be incomplete. > > make[2]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT/tools' > > make[1]: Leaving directory `/export/home1/yqsu/espresso-4.3.2/TDDFPT' > > make: warning: Clock skew detected. Your build may be incomplete. > > Thank you for your suggestion ! > > Best wishes ! > > Su Yaqiong > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] Band Structure and nscf calculation
Hi Sohail ,
Please see carefully the example01 of any versins of the QE.
This example tells you how to set K-points for band structure
as well as the structure of nscf file. Be sure for band calculation
one has to look for the high symmetric K-points.
Best, Kaloni
http://cpms.kaust.edu.sa/Pages/People.aspx?t=Current
Message: 2
Date: Thu, 19 Jul 2012 13:33:18 +0800 (SGT)
From: Sohail Ahmad
Subject: [Pw_forum] Band Structure and nscf calculation
To: Plane Wave
Message-ID:
<1342675998.31647.YahooMailClassic at web192202.mail.sg3.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear
I ran scf for MoS2 in K_Points Automatic 4X4x4 mesh with 20 nband and
followed calculation for band Structure
but i observed that sufficient no. of bands are not there;;
then i perform nscf calculation for DOS which seems to be alright
So i did scf calculation again in K-Points Automatic 12x12x12 with a little
increase in nband (keeping it in mind nband = # of VE/2 +20% more in metal)
Now i have few questions
1-- While performing band calculation, how should i take K-points
K-POINTS AUTOMATIC
12x12x12 1 1 1
??? or the one which i generated manually (150 Points)
150
1
2
like that,which one is a better option?
2. While performing nscf calculation, should i write it or no
??? restart_mode = 'from_scratch',
??? i believe no as it may take longer time and some convergence conflict
??? but i need confirmation
??
??? Its mentioned in the user guide, that occupations = tetrahedra for DOS
??? Is it required in every case irrespective of magnetic or non magnetic?
???
3? i think nscf is required only for DOS, So can i perform nscf calculation
befor the post ? ? ? ?? processing calculation of band calculation? ?
? ? This question i am asking because i am using computational facility of
some other??? place which is available to me for short time only and i am
running short of time
Sohail
KKU
SAUDI
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[Pw_forum] Band structure of Diamagnetic system
On Wed, 2012-07-18 at 16:41 +0100, Abolore Musari wrote: > shld l also include starting_magnetization in it for fe atom > in the system namelist for fes2 diamagnetic semiconductor. for diamagnnetic semiconductors, it is sufficient to perform a calculation without spin polarization P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] TDDFT with turbo_lanczos.x
Hello users, ? I am calculating the absorption spetrum. If?I run the code turbo_lanczos.x after performing the ground state scf, the calculation stops and I get the error message bellow: ? * from orthogonalize: error? #?? 1 degauss with gamma point algorithm * ? Could any one help. ? Thank you. ? Henry Otunga Dept. of Physics Maseno University Kenya -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120719/5ede62f0/attachment.htm
[Pw_forum] TDDFT with turbo_lanczos.x
Hello users, ? I am calculating the absorption spetrum. If?I run the code turbo_lanczos.x after performing the ground state scf, the calculation stops and I get the error message bellow: ? * from orthogonalize: error? #?? 1 degauss with gamma point algorithm * ? Could any one help. ? Thank you. ? Henry Otunga Dept. of Physics Maseno University Kenya -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120719/a2d28030/attachment.htm
[Pw_forum] TDDFT with turbo_lanczos.x
Hi there, You are trying to use some form of smearing for the occupation numbers when you calculate the ground state wavefunctions. This currently isn't supported with turboTDDFT. Brgrds, Simon On Thu, 19 Jul 2012 14:37:42 +0200, henry odhiambo wrote: > Hello users, > I am calculating the absorption spetrum. If I run the code > turbo_lanczos.x after performing the ground state scf, the calculation > stops and I get the error message bellow: > > * > from orthogonalize: error # 1 > degauss with gamma point algorithm > * > Could any one help. > Thank you. > Henry Otunga > Dept. of Physics > Maseno University > Kenya -- Simon Binnie | Post Doc, Condensed Matter Sector Scuola Internazionale di Studi Avanzati (SISSA) Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it
