[Pw_forum] Segmentation Fault using pw.exe with 'relax' (Windows 10, 64 bit)
Hello, I am trying to use pw.exe to perform a relaxation calculation on a single monomer chain containing 40 atoms of C,H,O, and N. I manually placed the atoms in roughly the correct locations according to the arrangement of the molecule as approximately a chain of benzene rings. I want to use 'relax' to find the true equilibrium positions of the atoms in the chain. However, I get a segmentation fault error when I try to run the command 'pw -in kapton.in' However, the backtrace for this error is strange in that it all eighteen traces list the same memory location: ''. Furthermore, none of the traces actually list where the error took place. I had previously gotten seg-faults when my fftw3 libraries were not compiled properly, and the traces would properly reflect that error. Here there is no information given regarding the nature or source of the overflow. My 64 bit Windows 10 desktop has 32 GB of RAM and a Core i7 6700K among other new, relatively high end components. My coworker was able to run my exact code on his Linux machine (I believe he uses Debian) which has only 16 GB of RAM, so I can't imagine that I am actually running into a hardware limitation on my desktop. At the same time, the auto-configured nature of the .exe installer on Windows coupled with the lack of backtrace information is leaving me a complete loss for possible solutions. I can post my input file if it might help, but this message is already running a bit long. Any help would be greatly appreciated. Thank you! -Matt ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] PWneb reads coordinates of images incorrectly
Dear Paolo Giannozzi Thanks for your help. *Here is the example, where the program reads input for first and last image correctly,* *while for intermediate images the program reads the atomic coordinates incorrectly.* *In this example I have the input files for 4 images and their outputs.* *Thank you so much * *Naseem * Naseem Ud Din Graduate Student University of Central Florida Orlando USA Cell # +1-407-683-3016 On Tue, Jun 28, 2016 at 2:19 PM, naseem wrote: > Dear Paolo Giannozzi > > The input file, I have shown here only last few coordinates for comparison. > > &CONTROL > ! .control.settings. > prefix= 'pwneb', > pseudo_dir= '/home/ndin/PP', > > ! .control.io. > verbosity = 'low', > disk_io = 'low', > wf_collect= .false., > outdir= './tmp/', > > ! .control.ion_relax. > etot_conv_thr = 0.0001, > forc_conv_thr = 0.001, > nstep = 200, > tprnfor = .true., > tstress = .false., > / > > &SYSTEM > ! .system.structure. > a = 1.0, > ibrav = 0, > nat = 56, > ntyp = 5, > > ! .system.ecut. > ecutwfc = 50, > ecutrho = 300, > > ! .system.occupations. > degauss = 0.007, > smearing = 'fd', > occupations = 'smearing', > > ! .system.spin_pol. > nspin = 2, > ! .system.starting_magnetization. > starting_magnetization(1) = 0.0 , > starting_magnetization(2) = 0.0 , > starting_magnetization(3) = 0.0 , > starting_magnetization(4) = 0.5 , > starting_magnetization(5) = 0.0 , > / > > &ELECTRONS > ! .electrons. > diagonalization = 'david', > mixing_mode = 'plain', > electron_maxstep = 300, > mixing_beta = 0.7, > conv_thr = 1e-06, > / > > &IONS > ! .ions. > pot_extrapolation = 'atomic', > wfc_extrapolation = 'none', > ion_dynamics = 'bfgs', > / > > ATOMIC_SPECIES > C 12.0110 C.pbe-n-kjpaw_psl.1.0.0.UPF > H 1.0079 H.pbe-kjpaw_psl.1.0.0.UPF > N 14.0070 N.pbe-n-kjpaw_psl.1.0.0.UPF >Mo 95.9500 Mo.pbe-spn-rrkjus_psl.1.0.0.UPF > O 15.9990 O.pbe-n-kjpaw_psl.1.0.0.UPF > > ATOMIC_POSITIONS crystal > N 0.9548502075 0.5635784967 0.4962439034 1 1 > 1 > N 0.20503544416667 0.6063052660 0.5061812013 1 1 > 1 > N 0.79510299916667 0.3932039887 0.4945467630 1 1 > 1 > N 0.9005930546 0.5040479798 0.4954070975 1 1 > 1 > Mo 0.2500019781 0.528125 0.5038506950 1 1 > 1 > Mo 0.759711 0.496645 0.4949650590 1 1 > 1 > O 0.2785712690 0.5237995800 0.7873582690 1 1 > 1 > O 0.2191770950 0.4751825040 0.7883099620 1 1 > 1 > CELL_PARAMETERS >13.967476 0.00 0.00 > 0.0019.29957382133830 0.00 > 0.00 0.0015.00 > > K_POINTS automatic >311 0 0 0 > > > The out put reads like this > > > coordinates at iteration 0 > > > ATOMIC_POSITIONS (crystal) > N0.957544089 0.564108314 0.491040077 > N0.206819548 0.605649544 0.515574286 > N0.796628928 0.393825710 0.491616776 > N0.902045066 0.504897968 0.488557042 > Mo 0.24821 0.50792 0.503850698 > Mo 0.749998615 0.48178 0.494965059 > O0.278571269 0.523799580 0.690302740 > O0.219177095 0.475182504 0.690540490 > > > >Info: using nr1, nr2, nr3 values from input > >Info: using nr1s, nr2s, nr3s values from input > > Parallelization info > > sticks: dense smooth PW G-vecs:dense smooth PW > Min 89 59 15 9347 5072 655 > Max 90 60 16 9360 5110 662 > Sum 22973 15343 3923 2394473 1303361 168491 > > > Thank you in advance for your help. > > Naseem > > Naseem Ud Din > Graduate Student > University of Central Florida > Orlando USA > Cell # +1-407-683-3016 > > On Mon, Jun 27, 2016 at 1:34 PM, Paolo Giannozzi > wrote: > >> Please support your claim with some data, such as e.g. input and output >> files >> >> Paolo >> >> On Mon, Jun 27, 2016 at 6:32 PM, naseem wrote: >> > Dear All >> > >> > I am trying to calculate reaction barrier using neb. The program doesn't >> > read the coordinates correctly for intermediate image. It reads >> correctly >> > the coordinates of initial and final image. >> > >> > Any help is really appreciated. >> > >> > thanks >> > >> >
Re: [Pw_forum] PWneb reads coordinates of images incorrectly
Please provide an input that can be run and an output that contains some information on what you did. On Wed, Jun 29, 2016 at 6:22 PM, naseem wrote: > Dear All > > I am trying to calculate reaction barrier using neb. The program doesn't > read the coordinates correctly for intermediate image. It reads correctly > the coordinates of initial and final image. > > Any help is really appreciated. > > thanks. > > Here I put the input and output coordinates. > > > Input coordinates Program NEB v.5.2.0 > > > ATOMIC_POSITIONS crystal > N 0.0458087269 0.4357101372 0.5012321465 1 1 > 1 > N 0.0995362024 0.4949877337 0.5040735278 1 1 > 1 > N 0.9544776551 0.5634852461 0.4969233258 1 1 > 1 > N 0.20455961416665 0.6065336165 0.50715900716668 1 1 > 1 > N 0.7948911295 0.3934361415 0.4963889690 1 1 > 1 > N 0.9002404209 0.50402929283332 0.4965848249 1 1 > 1 > Mo0.24999891816665 0.4971083334 0.5173825696 1 1 > 1 > Mo0.75000210116668 0.517712 0.4956577359 1 1 > 1 > O 0.24998766383334 0.4970916667 0.7455726474 1 1 > 1 > C 0.24998865416667 0.501217 0.6672466500 1 1 > 1 > > OUTPUT > > coordinates at iteration 0 > > ATOMIC_POSITIONS crystal > N0.045791964 0.435746632 0.501695225 > N0.099568664 0.495144336 0.503660926 > N0.954391613 0.563630181 0.497000916 > N0.204742419 0.606524793 0.505858492 > N0.794822904 0.393434607 0.497139846 > N0.900260428 0.504122574 0.497178183 > Mo 0.25072 0.50453 0.508613877 > Mo 0.750001857 0.51752 0.497483220 > O0.249987954 0.49100 0.778497829 > C0.249980974 0.49925 0.701865784 > > > Naseem Ud Din > Graduate Student > University of Central Florida > Orlando USA > Cell # +1-407-683-3016 > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] PWneb reads coordinates of images incorrectly
Dear All I am trying to calculate reaction barrier using neb. The program doesn't read the coordinates correctly for intermediate image. It reads correctly the coordinates of initial and final image. Any help is really appreciated. thanks. Here I put the input and output coordinates. Input coordinates Program NEB v.5.2.0 ATOMIC_POSITIONS crystal N 0.0458087269 0.4357101372 0.5012321465 1 1 1 N 0.0995362024 0.4949877337 0.5040735278 1 1 1 N 0.9544776551 0.5634852461 0.4969233258 1 1 1 N 0.20455961416665 0.6065336165 0.50715900716668 1 1 1 N 0.7948911295 0.3934361415 0.4963889690 1 1 1 N 0.9002404209 0.50402929283332 0.4965848249 1 1 1 Mo0.24999891816665 0.4971083334 0.5173825696 1 1 1 Mo0.75000210116668 0.517712 0.4956577359 1 1 1 O 0.24998766383334 0.4970916667 0.7455726474 1 1 1 C 0.24998865416667 0.501217 0.6672466500 1 1 1 OUTPUT coordinates at iteration 0 ATOMIC_POSITIONS crystal N0.045791964 0.435746632 0.501695225 N0.099568664 0.495144336 0.503660926 N0.954391613 0.563630181 0.497000916 N0.204742419 0.606524793 0.505858492 N0.794822904 0.393434607 0.497139846 N0.900260428 0.504122574 0.497178183 Mo 0.25072 0.50453 0.508613877 Mo 0.750001857 0.51752 0.497483220 O0.249987954 0.49100 0.778497829 C0.249980974 0.49925 0.701865784 Naseem Ud Din Graduate Student University of Central Florida Orlando USA Cell # +1-407-683-3016 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] yambo installation
> > Dear Bahara, > Here is my environment_variable > more correctly the output of $ env is what was needed, ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] H-bonding in DFT
Dear user Please remember always to sign your post to this forum with name and scientific affiliation. Your question is very general and very difficult, so that a general answer is impossible, and a detailed answer depends strongly on your system features and on your purposes. I can therefore only suggest you that unless you are interested in very fine details a standard GGA functional should behave decently in describing H-bonds, provided that you combine the electrostatic interactions inscribed in the GGA description with one of the (semiempirical or ab initio) models that add long-range dispersion forces. HTH Giuseppe Quoting ZARA NBSH : > Dear all > > I would like to study the interaction between two organic molecules > (contains C, H and O atoms). > It seems that hydrogen-bonding between H and O atoms of different molecules > play an important role. > > My question is that what is the best method to study this system? > Could usual DFT (GGA for example blyp PP) have a correct prediction of this > system? > > I really appreciate your help in advance. > > WBR > -NN -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] yambo installation
Dear Mansoureh,
This env which you have given is mainly use for running the example
provided in qe.
At the time of compilation, make.sys file tells everything after sucessful
configuration. If you wish more discussion you can contact on my personal
mail id because this conversation may not much useful to others users .
Bdw you can try to compile yambo by uncommenting the F90 flag in make.sys
file.
On Jun 29, 2016 4:13 PM, "Mansoureh Pashangpour"
wrote:
> Dear Bahara,
> Here is my environment_variables
>
>
>
> # environment_variables -- settings for running Quantum ESPRESSO examples
>
> LC_ALL=C
> export LC_ALL
>
> YOU MAY NEED TO EDIT THIS FILE TO MATCH YOUR CONFIGURATION
>
>
> # BIN_DIR = path of compiled executables
> # Usually this is $PREFIX/bin, where $PREFIX is the root of the
> # Quantum ESPRESSO source tree.
> # PSEUDO_DIR = path of pseudopotentials required by the examples
> # if required pseudopotentials are not found in $PSEUDO_DIR,
> # example scripts will try to download them from NETWORK_PSEUDO
> # TMP_DIR = temporary directory to be used by the examples
> # Make sure that it is writable by you and that it doesn't contain
> # any valuable data (EVERYTHING THERE WILL BE DESTROYED)
>
> # The following should be good for most cases
>
> PREFIX=`cd ../../.. ; pwd`
> BIN_DIR=$PREFIX/bin
> PSEUDO_DIR=$PREFIX/pseudo
> # Beware: everything in $TMP_DIR will be destroyed !
> TMP_DIR=$PREFIX/tempdir
>
> # There should be no need to change anything below this line
>
> NETWORK_PSEUDO=
> http://www.quantum-espresso.org/wp-content/uploads/upf_files/
>
>
> # wget or curl needed if some PP has to be downloaded from web site
> # script wizard will surely find a better way to find what is available
> if test "`which curl`" = "" ; then
>if test "`which wget`" = "" ; then
> echo "wget or curl not found: will not be able to download missing
> PP"
>else
> WGET="wget -O"
> # echo "wget found"
>fi
> else
>WGET="curl -o"
># echo "curl found"
> fi
>
> # To run the ESPRESSO programs on a parallel machine, you may have to
> # add the appropriate commands (poe, mpirun, mpprun...) and/or options
> # (specifying number of processors, pools...) before and after the
> # executable's name. That depends on how your machine is configured.
> # For example on an IBM SP4:
> #
> # poe pw.x -procs 4 < file.in > file.out
> # ^^^ PARA_PREFIX PARA_POSTFIX
> #
> # To run on a single processor, you can usually leave them empty.
> # BEWARE: most tests and examples are devised to be run serially or on
> # a small number of processors; do not use tests and examples to benchmark
> # parallelism, do not run on too many processors
>
> PARA_PREFIX="mpirun -np 2"
> PARA_PREFIX=" "
> #
> # available flags:
> # -ni nnumber of images(or -nimage)
> # (only for NEB; for PHonon, see below)
> # -nk nnumber of pools (or -npool,
> -npools)
> # -nb nnumber of band groups (or
> -nbgrp,-nband_group)
> # -nt nnumber of task groups (or -ntg,
> -ntask_groups)
> # -nd nnumber of processors for linear algebra
> #(or -ndiag, -northo)
> #
> PARA_POSTFIX=" -nk 1 -nd 1 -nb 1 -nt 1 "
> #
> # The following variables are used for image parallelization of PHonon
> # (see example in PHonon/examples/Image_example)
> # NB: the number of processors in PARA_IMAGE_PREFIX is the product of the
> # number of processors in PARA_PREFIX and the number of images in
> # PARA_IMAGE_POSTFIX
> #
> PARA_IMAGE_POSTFIX="-ni 2 $PARA_POSTFIX"
> PARA_IMAGE_PREFIX="mpirun -np 4"
>
> # function to test the exit status of a job
> check_failure () {
> # usage: check_failure $?
> if test $1 != 0
> then
> $ECHO "Error condition encountered during test: exit status = $1"
> $ECHO "Aborting"
> exit 1
> fi
> }
>
>
> Now I should change my make.sys or not?
> M. Pashangpour
>
>
>
>
> On Wed, Jun 29, 2016 at 3:03 PM, Bramha Pandey
> wrote:
>
>> Yes. You can try with make yambo.
>> Just one observation it seems you are not using parallel environment. I
>> guess it will also not effect to compile yambo.
>> On Jun 29, 2016 3:55 PM, "Mansoureh Pashangpour"
>> wrote:
>>
>>> Dear Bramha,
>>>
>>> Do you mean in make.sys, I change
>>> MPIF90 = gfortran
>>> #F90 = gfortran
>>> CC = cc
>>> F77= gfortran
>>>
>>> to
>>>
>>> MPIF90 = gfortran
>>> F90 = gfortran
>>> CC = cc
>>> F77= gfortran
>>> Thanks
>>> M. pashangpour
>>>
>>>
>>>
>>> On Wed, Jun 29, 2016 at 2:29 PM, Mike Atambo
>>> wrote:
>>>
Mansoureh:
I can not see anything unexpected in your config.log,
so would you mind providing the output of your `env` command?
possibly
Re: [Pw_forum] yambo installation
Dear Bahara,
Here is my environment_variables
# environment_variables -- settings for running Quantum ESPRESSO examples
LC_ALL=C
export LC_ALL
YOU MAY NEED TO EDIT THIS FILE TO MATCH YOUR CONFIGURATION
# BIN_DIR = path of compiled executables
# Usually this is $PREFIX/bin, where $PREFIX is the root of the
# Quantum ESPRESSO source tree.
# PSEUDO_DIR = path of pseudopotentials required by the examples
# if required pseudopotentials are not found in $PSEUDO_DIR,
# example scripts will try to download them from NETWORK_PSEUDO
# TMP_DIR = temporary directory to be used by the examples
# Make sure that it is writable by you and that it doesn't contain
# any valuable data (EVERYTHING THERE WILL BE DESTROYED)
# The following should be good for most cases
PREFIX=`cd ../../.. ; pwd`
BIN_DIR=$PREFIX/bin
PSEUDO_DIR=$PREFIX/pseudo
# Beware: everything in $TMP_DIR will be destroyed !
TMP_DIR=$PREFIX/tempdir
# There should be no need to change anything below this line
NETWORK_PSEUDO=http://www.quantum-espresso.org/wp-content/uploads/upf_files/
# wget or curl needed if some PP has to be downloaded from web site
# script wizard will surely find a better way to find what is available
if test "`which curl`" = "" ; then
if test "`which wget`" = "" ; then
echo "wget or curl not found: will not be able to download missing PP"
else
WGET="wget -O"
# echo "wget found"
fi
else
WGET="curl -o"
# echo "curl found"
fi
# To run the ESPRESSO programs on a parallel machine, you may have to
# add the appropriate commands (poe, mpirun, mpprun...) and/or options
# (specifying number of processors, pools...) before and after the
# executable's name. That depends on how your machine is configured.
# For example on an IBM SP4:
#
# poe pw.x -procs 4 < file.in > file.out
# ^^^ PARA_PREFIX PARA_POSTFIX
#
# To run on a single processor, you can usually leave them empty.
# BEWARE: most tests and examples are devised to be run serially or on
# a small number of processors; do not use tests and examples to benchmark
# parallelism, do not run on too many processors
PARA_PREFIX="mpirun -np 2"
PARA_PREFIX=" "
#
# available flags:
# -ni nnumber of images(or -nimage)
# (only for NEB; for PHonon, see below)
# -nk nnumber of pools (or -npool, -npools)
# -nb nnumber of band groups (or
-nbgrp,-nband_group)
# -nt nnumber of task groups (or -ntg,
-ntask_groups)
# -nd nnumber of processors for linear algebra
#(or -ndiag, -northo)
#
PARA_POSTFIX=" -nk 1 -nd 1 -nb 1 -nt 1 "
#
# The following variables are used for image parallelization of PHonon
# (see example in PHonon/examples/Image_example)
# NB: the number of processors in PARA_IMAGE_PREFIX is the product of the
# number of processors in PARA_PREFIX and the number of images in
# PARA_IMAGE_POSTFIX
#
PARA_IMAGE_POSTFIX="-ni 2 $PARA_POSTFIX"
PARA_IMAGE_PREFIX="mpirun -np 4"
# function to test the exit status of a job
check_failure () {
# usage: check_failure $?
if test $1 != 0
then
$ECHO "Error condition encountered during test: exit status = $1"
$ECHO "Aborting"
exit 1
fi
}
Now I should change my make.sys or not?
M. Pashangpour
On Wed, Jun 29, 2016 at 3:03 PM, Bramha Pandey
wrote:
> Yes. You can try with make yambo.
> Just one observation it seems you are not using parallel environment. I
> guess it will also not effect to compile yambo.
> On Jun 29, 2016 3:55 PM, "Mansoureh Pashangpour"
> wrote:
>
>> Dear Bramha,
>>
>> Do you mean in make.sys, I change
>> MPIF90 = gfortran
>> #F90 = gfortran
>> CC = cc
>> F77= gfortran
>>
>> to
>>
>> MPIF90 = gfortran
>> F90 = gfortran
>> CC = cc
>> F77= gfortran
>> Thanks
>> M. pashangpour
>>
>>
>>
>> On Wed, Jun 29, 2016 at 2:29 PM, Mike Atambo
>> wrote:
>>
>>> Mansoureh:
>>> I can not see anything unexpected in your config.log,
>>> so would you mind providing the output of your `env` command?
>>> possibly your environment may not be setup properly.
>>> I have got yambo to compile using quantum-espresso 3.4.0
>>> and `make yambo`, and prior to that i could compile yambo on the same
>>> machine. Please do try the latest version of QE as this 5.0.2 you quote
>>> is several
>>> releases behind, and its best practice to work with the most recent
>>> whenever there's
>>> a problem,
>>>
Dear all,
I would like to install yambo package (yambo-3.2.1-r.448.tar.gz). I
have installed espresso-5.0.2. after
./configure --with-iotk='/root/espresso-5.0.2/iotk' --with-p2y=5.0
>>>
>>> Mike.
>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> P
Re: [Pw_forum] yambo installation
Yes. You can try with make yambo. Just one observation it seems you are not using parallel environment. I guess it will also not effect to compile yambo. On Jun 29, 2016 3:55 PM, "Mansoureh Pashangpour" wrote: > Dear Bramha, > > Do you mean in make.sys, I change > MPIF90 = gfortran > #F90 = gfortran > CC = cc > F77= gfortran > > to > > MPIF90 = gfortran > F90 = gfortran > CC = cc > F77= gfortran > Thanks > M. pashangpour > > > > On Wed, Jun 29, 2016 at 2:29 PM, Mike Atambo wrote: > >> Mansoureh: >> I can not see anything unexpected in your config.log, >> so would you mind providing the output of your `env` command? >> possibly your environment may not be setup properly. >> I have got yambo to compile using quantum-espresso 3.4.0 >> and `make yambo`, and prior to that i could compile yambo on the same >> machine. Please do try the latest version of QE as this 5.0.2 you quote >> is several >> releases behind, and its best practice to work with the most recent >> whenever there's >> a problem, >> >>> Dear all, >>> I would like to install yambo package (yambo-3.2.1-r.448.tar.gz). I have >>> installed espresso-5.0.2. after >>> ./configure --with-iotk='/root/espresso-5.0.2/iotk' --with-p2y=5.0 >>> >> >> Mike. >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] H-bonding in DFT
Dear all I would like to study the interaction between two organic molecules (contains C, H and O atoms). It seems that hydrogen-bonding between H and O atoms of different molecules play an important role. My question is that what is the best method to study this system? Could usual DFT (GGA for example blyp PP) have a correct prediction of this system? I really appreciate your help in advance. WBR -NN ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] yambo installation
Dear Bramha, Do you mean in make.sys, I change MPIF90 = gfortran #F90 = gfortran CC = cc F77= gfortran to MPIF90 = gfortran F90 = gfortran CC = cc F77= gfortran Thanks M. pashangpour On Wed, Jun 29, 2016 at 2:29 PM, Mike Atambo wrote: > Mansoureh: > I can not see anything unexpected in your config.log, > so would you mind providing the output of your `env` command? > possibly your environment may not be setup properly. > I have got yambo to compile using quantum-espresso 3.4.0 > and `make yambo`, and prior to that i could compile yambo on the same > machine. Please do try the latest version of QE as this 5.0.2 you quote > is several > releases behind, and its best practice to work with the most recent > whenever there's > a problem, > >> Dear all, >> I would like to install yambo package (yambo-3.2.1-r.448.tar.gz). I have >> installed espresso-5.0.2. after >> ./configure --with-iotk='/root/espresso-5.0.2/iotk' --with-p2y=5.0 >> > > Mike. > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] yambo installation
Mansoureh: I can not see anything unexpected in your config.log, so would you mind providing the output of your `env` command? possibly your environment may not be setup properly. I have got yambo to compile using quantum-espresso 3.4.0 and `make yambo`, and prior to that i could compile yambo on the same machine. Please do try the latest version of QE as this 5.0.2 you quote is several releases behind, and its best practice to work with the most recent whenever there's a problem, > Dear all, > I would like to install yambo package (yambo-3.2.1-r.448.tar.gz). I have > installed espresso-5.0.2. after > ./configure --with-iotk='/root/espresso-5.0.2/iotk' --with-p2y=5.0 > Mike. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] yambo installation
Dear Mansoureh, the below line shows the solution to you. touch uncompress-yambo *** F90 is not defined; please define F90 or edit make.sys Go to your make.sys file in espresso dir and define F90. If it is commented then make it uncomment. It may be help you. On Jun 29, 2016 2:08 PM, "Mansoureh Pashangpour" wrote: > Dear Andrea, > I use espresso-5.2.1. As you said I try 'make yambo'. yambo-3.4.1-rev61 is > downloaded but it dosen't compile. i have this > > touch uncompress-yambo > *** F90 is not defined; please define F90 or edit make.sys > plugins_makefile:286: recipe for target 'configure-yambo' failed > make[1]: *** [configure-yambo] Error 1 > make[1]: Leaving directory '/root/espresso-5.2.1/install' > Makefile:155: recipe for target 'yambo' failed > make: *** [yambo] Error 1 > > Regards, > M. Pashangpour > IAU, Tehran, Iran > > > > On Wed, Jun 29, 2016 at 12:09 PM, Andrea Ferretti < > andrea.ferre...@unimore.it> wrote: > >> >> Dear Mansoureh, >> >> as a follow up on this thread, if you are working with one of the latest >> releases of QE you can also compile yambo directly from QE makefile >> (type "make yambo"): this will download the lastest (stable) release of >> yambo (3.4.2, as Federico pointed out) and compile it... most of the time >> it works out of the box >> >> take care >> Andrea >> >> >> >> Dear all, >>> I would like to install yambo package (yambo-3.2.1-r.448.tar.gz). I have >>> installed espresso-5.0.2. after >>> ./configure --with-iotk='/root/espresso-5.0.2/iotk' --with-p2y=5.0 >>> >>> and make interfaces I have recived following error: >>> >>> >>>[Making slatec]<<< >>> make[1]: Entering directory '/root/yambo/yambo-3.2.1-r.448/lib/slatec' >>> Makefile:68: *** missing separator. Stop. >>> make[1]: Leaving directory '/root/yambo/yambo-3.2.1-r.448/lib/slatec' >>> Makefile:79: recipe for target 'libs' failed >>> make: *** [libs] Error 2 >>> >>> I am sending config.log file as attached file too. >>> what's the problem and how can I solve it? >>> I have linux/ fedora 20 on my PC. >>> >>> Mansoureh Pashangpour, PhD. of Physics >>> IAU, Tehran, Iran >>> >>> >>> >> -- >> Andrea Ferretti, PhD >> S3 Center, Istituto Nanoscienze, CNR >> via Campi 213/A, 41125, Modena, Italy >> Tel: +39 059 2055322; Skype: andrea_ferretti >> URL: http://www.nano.cnr.it >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] yambo installation
Dear Andrea, I use espresso-5.2.1. As you said I try 'make yambo'. yambo-3.4.1-rev61 is downloaded but it dosen't compile. i have this touch uncompress-yambo *** F90 is not defined; please define F90 or edit make.sys plugins_makefile:286: recipe for target 'configure-yambo' failed make[1]: *** [configure-yambo] Error 1 make[1]: Leaving directory '/root/espresso-5.2.1/install' Makefile:155: recipe for target 'yambo' failed make: *** [yambo] Error 1 Regards, M. Pashangpour IAU, Tehran, Iran On Wed, Jun 29, 2016 at 12:09 PM, Andrea Ferretti < andrea.ferre...@unimore.it> wrote: > > Dear Mansoureh, > > as a follow up on this thread, if you are working with one of the latest > releases of QE you can also compile yambo directly from QE makefile > (type "make yambo"): this will download the lastest (stable) release of > yambo (3.4.2, as Federico pointed out) and compile it... most of the time > it works out of the box > > take care > Andrea > > > > Dear all, >> I would like to install yambo package (yambo-3.2.1-r.448.tar.gz). I have >> installed espresso-5.0.2. after >> ./configure --with-iotk='/root/espresso-5.0.2/iotk' --with-p2y=5.0 >> >> and make interfaces I have recived following error: >> >> >>>[Making slatec]<<< >> make[1]: Entering directory '/root/yambo/yambo-3.2.1-r.448/lib/slatec' >> Makefile:68: *** missing separator. Stop. >> make[1]: Leaving directory '/root/yambo/yambo-3.2.1-r.448/lib/slatec' >> Makefile:79: recipe for target 'libs' failed >> make: *** [libs] Error 2 >> >> I am sending config.log file as attached file too. >> what's the problem and how can I solve it? >> I have linux/ fedora 20 on my PC. >> >> Mansoureh Pashangpour, PhD. of Physics >> IAU, Tehran, Iran >> >> >> > -- > Andrea Ferretti, PhD > S3 Center, Istituto Nanoscienze, CNR > via Campi 213/A, 41125, Modena, Italy > Tel: +39 059 2055322; Skype: andrea_ferretti > URL: http://www.nano.cnr.it > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] yambo installation
Dear Mansoureh, as a follow up on this thread, if you are working with one of the latest releases of QE you can also compile yambo directly from QE makefile (type "make yambo"): this will download the lastest (stable) release of yambo (3.4.2, as Federico pointed out) and compile it... most of the time it works out of the box take care Andrea Dear all, I would like to install yambo package (yambo-3.2.1-r.448.tar.gz). I have installed espresso-5.0.2. after ./configure --with-iotk='/root/espresso-5.0.2/iotk' --with-p2y=5.0 and make interfaces I have recived following error: >>>[Making slatec]<<< make[1]: Entering directory '/root/yambo/yambo-3.2.1-r.448/lib/slatec' Makefile:68: *** missing separator. Stop. make[1]: Leaving directory '/root/yambo/yambo-3.2.1-r.448/lib/slatec' Makefile:79: recipe for target 'libs' failed make: *** [libs] Error 2 I am sending config.log file as attached file too. what's the problem and how can I solve it? I have linux/ fedora 20 on my PC. Mansoureh Pashangpour, PhD. of Physics IAU, Tehran, Iran -- Andrea Ferretti, PhD S3 Center, Istituto Nanoscienze, CNR via Campi 213/A, 41125, Modena, Italy Tel: +39 059 2055322; Skype: andrea_ferretti URL: http://www.nano.cnr.it___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
