[Pw_forum] Question about slow speed of version 4.1.3
On May 7, 2010, at 19:42 , saqib.javaid at ipcms.u-strasbg.fr wrote: > I have recently complied 4.1.3 (...) but surprised to see that it > is a lot > slower than 4.0.3. Installation has been done in the same envirement. are you sure? make a "diff" of both make.sys and of the output in the two cases 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] Installation Problems: Can not found MKL
Hi, All I am installing espresso-4.1.3 in intel cluster. I have installed the latest intel compiler(v11.069) and MKL(the same as compiler). I compiled with configure like this: ./configure -enable-shared LIBDIRS="/home/software/intel/Compiler/11.1/069/lib/intel64 /home/software/intel/Compiler/11.1/069/mkl/lib/em64t" --prefix=/home/software/espresso F77=ifort CC=icc But shows as follow: checking whether Fortran files must be preprocessed... no checking how to get verbose linking output from ifort... -v checking for Fortran libraries of ifort... -L/home/software/intel/Compiler/11.1/069/lib/intel64 -L/home/software/intel/Compiler/11.1/069/ipp/em64t/lib -L/home/software/intel/Compiler/11.1/069/mkl/lib/em64t -L/home/software/intel/Compiler/11.1/069/tbb/intel64/cc4.1.0_libc2.4_kernel2.6.16.21/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../.. -L/lib64 -L/lib -L/usr/lib64 -L/usr/lib -lifport -lifcore -limf -lsvml -lm -lipgo -lirc -lpthread -lgcc_s -lirc_s -ldl checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking for library containing dgemm... no in /opt/intel/mkl/*/lib/em64t: checking for library containing dgemm... no in /opt/intel/mkl*/lib/em64t: checking for library containing dgemm... no checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no checking for library containing dspev... no in /usr/local/lib: checking for library containing dspev... no setting BLAS_LIBS... ../flib/blas.a setting LAPACK_LIBS... ../flib/lapack.a checking for library containing dfftw_execute_dft... -lfftw3 setting FFT_LIBS... -lfftw3 setting MASS_LIBS... checking for library containing mpi_init... none required setting MPI_LIBS... checking for library containing mpi_init... (cached) none required setting DFLAGS... -D__INTEL -D__FFTW3 -D__MPI -D__PARA setting IFLAGS... -I../include setting FDFLAGS... $(DFLAGS) checking for ranlib... ranlib setting RANLIB... ranlib configure: creating ./config.status config.status: creating include/fft_defs.h config.status: creating make.sys config.status: creating configure.msg config.status: creating include/c_defs.h config.status: include/c_defs.h is unchanged ESPRESSO can take advantage of several optimized numerical libraries (essl, fftw, mkl...). This configure script attempts to find them, but may fail if they have been installed in non-standard locations. If a required library is not found, the local copy will be compiled. The following libraries have been found: BLAS_LIBS=../flib/blas.a LAPACK_LIBS=../flib/lapack.a FFT_LIBS= -lfftw3 Please check if this is what you expect. If any libraries are missing, you may specify a list of directories to search and retry, as follows: ./configure LIBDIRS="list of directories, separated by spaces" Parallel environment detected successfully. Configured for compilation of parallel executables. For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex). configure: success It seems not found the MKL. What's the problem? How to solve it? Thanks Weiguang - * *Chen, Weiguang (PhD Student) * Laboratory of Condensed Matter Theory and Computatational Materials & * School of Physics and Engineering * 75 North University Road, Physics Building Rm#202 * Zhengzhou University, Zhengzhou, 450052 Henan, China * * Tel: 86-13203730117? 86-13783677861; Fax: 86-371-67767758; * Email: chenweiguang82 at gmail.com -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100507/57a50a7a/attachment.htm
[Pw_forum] Question about slow speed of version 4.1.3
Dear PWSCF users, I have a question regarding newer PWSCF version 4.1.3. I have been using 4.0.3 version for a while. I have recently complied 4.1.3 (which is done successfully) but surprised to see that it is a lot slower than 4.0.3. Installation has been done in the same envirement. I have been using Intell-cc-10, intell_fc_10, mkl10 and openmpi Apparently i am stuck somewhere in compatability. I would appreciate if you could help me solve this problem with best regards saqib javaid University of strasbourg This message was sent using IMP, the Internet Messaging Program.
[Pw_forum] Phonon_quarry
partha sarathi ghosh wrote: > How to calculate phonon dispersion curve using ph.x that I know > but I want to displace a particular atom in a particular direction > with adjustable displacement. doesn't make sense to me. There is no "real" dispacement in the phonon code (unlike in "frozen phonon" method): the linear response to a displacement is calculated instead P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] GWW+U
Dear Ali Kazempour, The CVS version of the GWW code is implemented to work also with the LDA or GGA+U w.f. and energies as a starting guess for the G0W0 calculations. The way to use the code is similar than without the U, excepted that in the initial scf input file, you have to add all the "espresso input flags" performing the U calculations. The other files "*.pw4gww.in" and "inputgww" are unchanged (see http://gww.qe-forge.org) ... Good work, Joe On Mon, Apr 26, 2010 at 11:31:55AM +0430, kazempoor at ph.iut.ac.ir wrote: > Dear Gabriele > > I want to investigate the GW sensitivity to range of U. > Moreover there are some publication that GW at GGA+U work well for > (f-electron oxides). > Thanks > > Ali Kazempour > Physics Department, Isfahn University of Technology > > - Original Message - > From: "Gabriele Sclauzero" > To: "PWSCF Forum" > Sent: Monday, April 26, 2010 10:31:41 AM > Subject: Re: [Pw_forum] GWW+U > > > > kazempoor at ph.iut.ac.ir wrote: > > Dear all I want to do GW at GGA+U, But as far as I know the authers said > > that the phonon > > calculation with U has not been implemented yet? is it implemented right > > now or not > > yet? > > DFPT+U is not implemented in QE and I'w not aware of any plan to do it. > Moreover, I think > that the DFT+U theory has not yet been extended to DFPT. > > Anyway, why would you apply GW to DFT+U? People who uses GW corrections > usually believe > that these are more precise than +U corrections. > > GS > > > thanks a lot Ali Kazempour Physics Department, Isfahan University of > Technology > > ___ Pw_forum mailing list > > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > o o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > |via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o o > ___ > 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
[Pw_forum] Installation Problems: Can not found MKL
> Hi, All > I am installing espresso-4.1.3 in intel cluster. I have installed the > latest > intel compiler(v11.069) and MKL(the same as compiler). > I compiled with configure like this: ./configure -enable-shared > LIBDIRS="/home/software/intel/Compiler/11.1/069/lib/intel64 > /home/software/intel/Compiler/11.1/069/mkl/lib/em64t" > --prefix=/home/software/espresso F77=ifort CC=icc > It seems not found the MKL. What's the problem? How to solve it? > Thanks > Weiguang try linking as follows: LDFLAGS="-L$MKL_PATH $MKL_PATH/libmkl_solver_lp64_sequential.a -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" also have a look here: http://www.quantum-espresso.org/user_guide/node13.html#SECTION00036350 Finally, here http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/ you can get hel on the correct way of linking to mkl. Giovanni -- Giovanni Cantele, PhD CNR-SPIN and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 - Fax: +39 081 676346 Skype contact: giocan74 ResearcherID: http://www.researcherid.com/rid/A-1951-2009 Web page: http://people.na.infn.it/~cantele http://www.nanomat.unina.it
[Pw_forum] relax
Dear Gabriele, Thank you for helping over my problem! Best regards, Olga Sedelnikova Nikolaev Institute of Inorganic Chemistry SB RAS Novosibirsk, Russia > Probably you are trying to use at the same time PPs that have been built > for different XC functionals. > > This is a FAQ, so please take some time to search in the forum archives > and in the user guide. For instance you can have a look here: > > http://www.quantum-espresso.org/user_guide/node42.html > > GS > > Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100507/b3cfd9e2/attachment.htm
[Pw_forum] General question about occupations
Dear Paolo You were right, changing the number of processors has worked, no matter the option of occupations I choose and the length of the vacuum. Even more, trying with the same script than before, the same numbers of processors, the same machine, etc. has worked. Thus, I guess there is not any real problem and that the machines where I sent the scripts were having some kind of problem those days and have been fixed, I should ask. Sorry for that and thank you very much for your help Julen University of the Basque Country -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100507/43092fe8/attachment.htm
[Pw_forum] relax
Dear All,
I am trying to optimize NH3 molecul.
The error was:
from readpp : error # 2
inconsistene DFT read
My input file was:
&control
calculation='relax',
restart_mode='from_scratch',
prefix='nh3',
disk_io='low',
wf_collect=.TRUE.,
pseudo_dir='',
outdir=''
/
&system
ibrav = 0,
celldm(1)= 1.0
nat = 4,
ntyp = 2,
ecutwfc = 16.0,
nbnd = 128,
ecutrho=200.0,
occupations='smearing',
degauss=0.02
/
&electrons
mixing_mode='local-TF'
mixing_beta = 0.7,
conv_thr = 1.0d-6
/
&ions
ion_dynamics='bfgs'
ion_positions='default'
/
ATOMIC_SPECIES
H 1.0d0 H.vbc.UPF
N 16.0d0 N.BLYP.UPF
CELL_PARAMETERS {cubic}
30.0 0.00 0.00
0.00 30.00 0.00
0.00 0.00 30.00
ATOMIC_POSITIONS {angstrom}
N-1.1110.001 -1.058
H-0.900 -0.555 -1.882
H-1.939 -0.397 -0.623
H-1.3490.938 -1.372
K_POINTS {automatic}
1 1 1 0 0 0
I did not see this error before.
I great appreciate all your instructions.
Best regards,
Olga Sedelnikova
Nikolaev Institute of Inorganic Chemistry SB RAS
Novosibirsk, Russia
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[Pw_forum] relax
Dear All,
I am trying to optimize NH3 molecul.
The error was:
from readpp : error # 2
inconsistene DFT read
My input file was:
&control
calculation='relax',
restart_mode='from_scratch',
prefix='nh3',
disk_io='low',
wf_collect=.TRUE.,
pseudo_dir='',
outdir=''
/
&system
ibrav = 0,
celldm(1)= 1.0
nat = 4,
ntyp = 2,
ecutwfc = 16.0,
nbnd = 128,
ecutrho=200.0,
occupations='smearing',
degauss=0.02
/
&electrons
mixing_mode='local-TF'
mixing_beta = 0.7,
conv_thr = 1.0d-6
/
&ions
ion_dynamics='bfgs'
ion_positions='default'
/
ATOMIC_SPECIES
H 1.0d0 H.vbc.UPF
N 16.0d0 N.BLYP.UPF
CELL_PARAMETERS {cubic}
30.0 0.00 0.00
0.00 30.00 0.00
0.00 0.00 30.00
ATOMIC_POSITIONS {angstrom}
N-1.1110.001 -1.058
H-0.900 -0.555 -1.882
H-1.939 -0.397 -0.623
H-1.3490.938 -1.372
K_POINTS {automatic}
1 1 1 0 0 0
The error was:
from readpp : error # 2
inconsistene DFT read
I did not see this error before.
I great appreciate all your instructions.
-- next part --
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[Pw_forum] relax
Ngoc Linh Nguyen wrote: > The problem comes from Pseudo Potential files. Their formats are old ones. > You should download the new Pseudo Potential files of N and H from > http://www.quantum-espresso.org/pseudo.php, then rerun your problem. it's not a problem of new or old format. The problem is that one PP is generated with Perdew-Zunger LDA, the other with BLYP P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] relax
The problem comes from Pseudo Potential files. Their formats are old ones.
You should download the new Pseudo Potential files of N and H from
http://www.quantum-espresso.org/pseudo.php, then rerun your problem.
I checked for new ones, and it works well
Good lucks,
Linh
Olga Sedelnikova wrote:
> Dear All,
>
> I am trying to optimize NH3 molecul.
> The error was:
> from readpp : error # 2
> inconsistene DFT read
>
> My input file was:
> &control
> calculation='relax',
> restart_mode='from_scratch',
> prefix='nh3',
> disk_io='low',
> wf_collect=.TRUE.,
> pseudo_dir='',
> outdir=''
> /
> &system
> ibrav = 0,
> celldm(1)= 1.0
> nat = 4,
> ntyp = 2,
> ecutwfc = 16.0,
> nbnd = 128,
> ecutrho=200.0,
> occupations='smearing',
> degauss=0.02
> /
> &electrons
> mixing_mode='local-TF'
> mixing_beta = 0.7,
> conv_thr = 1.0d-6
> /
> &ions
> ion_dynamics='bfgs'
> ion_positions='default'
> /
> ATOMIC_SPECIES
> H 1.0d0 H.vbc.UPF
> N 16.0d0 N.BLYP.UPF
>CELL_PARAMETERS {cubic}
>30.0 0.00 0.00
>0.00 30.00 0.00
>0.00 0.00 30.00
> ATOMIC_POSITIONS {angstrom}
> N-1.1110.001 -1.058
>H-0.900 -0.555 -1.882
>H-1.939 -0.397 -0.623
>H-1.3490.938 -1.372
> K_POINTS {automatic}
> 1 1 1 0 0 0
>
> The error was:
> from readpp : error # 2
> inconsistene DFT read
>
> I did not see this error before.
> I great appreciate all your instructions.
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
-
Nguyen Ngoc Linh, PhD Student
c/o: SISSA & CNR-INFM Democritos,
via Beirut 2-4, 34014 Trieste (Italy)
email: nnlinh at sissa.it
phone: +39 04 03787 319
skype: ngoclinh84phys
-
"The physics is theoretical but the fun is real"
[Pw_forum] relax
Probably you are trying to use at the same time PPs that have been built
for different XC functionals.
This is a FAQ, so please take some time to search in the forum archives
and in the user guide. For instance you can have a look here:
http://www.quantum-espresso.org/user_guide/node42.html
GS
On 05/07/2010 05:28 AM, Olga Sedelnikova wrote:
> Dear All,
>
> I am trying to optimize NH3 molecul.
> The error was:
> from readpp : error # 2
> inconsistene DFT read
>
> My input file was:
> &control
> calculation='relax',
> restart_mode='from_scratch',
> prefix='nh3',
> disk_io='low',
> wf_collect=.TRUE.,
> pseudo_dir='',
> outdir=''
> /
> &system
> ibrav = 0,
> celldm(1)= 1.0
> nat = 4,
> ntyp = 2,
> ecutwfc = 16.0,
> nbnd = 128,
> ecutrho=200.0,
> occupations='smearing',
> degauss=0.02
> /
> &electrons
> mixing_mode='local-TF'
> mixing_beta = 0.7,
> conv_thr = 1.0d-6
> /
> &ions
> ion_dynamics='bfgs'
> ion_positions='default'
> /
> ATOMIC_SPECIES
> H 1.0d0 H.vbc.UPF
> N 16.0d0 N.BLYP.UPF
>CELL_PARAMETERS {cubic}
>30.0 0.00 0.00
>0.00 30.00 0.00
>0.00 0.00 30.00
> ATOMIC_POSITIONS {angstrom}
> N-1.1110.001 -1.058
>H-0.900 -0.555 -1.882
>H-1.939 -0.397 -0.623
>H-1.3490.938 -1.372
> K_POINTS {automatic}
> 1 1 1 0 0 0
>
> The error was:
> from readpp : error # 2
> inconsistene DFT read
>
> I did not see this error before.
> I great appreciate all your instructions.
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne
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