Compile Yambo-4.4.0 with abinit 8.10.3

Having trouble compiling the Yambo source? Using an unusual architecture? Problems with the "configure" script? This is the place to look.

Moderators: Davide Sangalli, Daniele Varsano, andrea.ferretti, andrea marini, myrta gruning, Conor Hogan

Forum rules
If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message
Post Reply
mutta
Posts: 3
Joined: Wed Apr 11, 2012 6:12 am
Location: Department of Science, Faculty of Science and Technology Prince of Songkla University Pattani Campus

Compile Yambo-4.4.0 with abinit 8.10.3

Post by mutta » Thu Apr 23, 2020 8:13 am

Dear Sir

I try to compile the Yambo-4.4.0 code with Abinit-8.10.4 on Ubuntu 18.10 and 3 days ago is not finish.

For a newbies user, Could you teach me a step by step for comp[ile Yambo-4.4.0 with Abinit-8.10.3 ?

Such as First How? for not an expert user
You do not have the required permissions to view the files attached to this post.
Abdulmutta Thatribud

Department of Science, Faculty of Science and Technology
Prince of Songkla University Pattani Campus, Thailand

User avatar
Daniele Varsano
Posts: 2322
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: Compile Yambo-4.4.0 with abinit 8.10.3

Post by Daniele Varsano » Thu Apr 23, 2020 10:09 am

Dear mutta,
please sign your post with your full name and affiliation, this is a rule of the forum and you can do once for all by filling your signature in the user profile.
First, I strongly suggest you update to the latest source (yambo 4.5) as I'm not totally sure that the 4.4 is compatible with abinit.
Next, there is not specific compilation for yambo to be compatible with abinit, you need to compile yambo and its interfaces and use the a2y executable to generate yambo databases from a previous abinit calculation.
If you have problem in compiling yambo, please post here the problem you are facing with any detail that can be useful to spot the problem.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

mutta
Posts: 3
Joined: Wed Apr 11, 2012 6:12 am
Location: Department of Science, Faculty of Science and Technology Prince of Songkla University Pattani Campus

Re: Compile Yambo-4.4.0 with abinit 8.10.3

Post by mutta » Fri May 08, 2020 8:44 am

Dear Daniele

I try Yambo-4.5.1 a few days and ./configure was fine but to "make all" Yambo build failed



Best Regard
Abdulmutta Thatribud

Department of Science,
Prince of Songkla University Pattani Campus, Thailand
You do not have the required permissions to view the files attached to this post.
Abdulmutta Thatribud

Department of Science, Faculty of Science and Technology
Prince of Songkla University Pattani Campus, Thailand

User avatar
Daniele Varsano
Posts: 2322
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: Compile Yambo-4.4.0 with abinit 8.10.3

Post by Daniele Varsano » Fri May 08, 2020 8:52 am

Dear Abdulmutta,

please post the error message you get, otherwise, it is very hard to understand what is going on.
Furthermore, you are not interested in all the executable of the yambo package so I suggest you to do a
> make yambo interfaces ypp
Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

mutta
Posts: 3
Joined: Wed Apr 11, 2012 6:12 am
Location: Department of Science, Faculty of Science and Technology Prince of Songkla University Pattani Campus

Re: Compile Yambo-4.4.0 with abinit 8.10.3

Post by mutta » Sun May 10, 2020 6:01 am

Dear Daniele

I try with your introducing, and it also got error see below

>>>[Making qe_pseudo]<<<
<command-line>: warning: ISO C99 requires whitespace after the macro name
make[1]: Entering directory '/home/mutta/Downloads/yambo-4.5.1/lib/qe_pseudo'
cd /home/mutta/Downloads/yambo-4.5.1/lib/qe_pseudo; /home/mutta/Downloads/yambo-4.5.1/sbin/moduledep.sh atom.o becmod.o constants.o kind.o parameters.o pseudo_types.o s_psi.o uspp.o qe_auxdata.o invmat.o init_us_1.o init_us_2.o radial_grids.o ylmr2.o us_module.o recvec.o spin_orb.o simpsn.o upf_to_internal.o upf.o read_upf_v1.o read_upf_v2.o read_pseudo.o read_ncpp.o read_uspp.o struct_fact.o sph_ind.o spinor.o sph_bes.o qvan2.o setqf.o matches.o erf.o allocate_nlpot.o init_run.o qe_pseudo_module.o qe_errore.o addusdens.o sum_bec.o d_matrix.o > /home/mutta/Downloads/yambo-4.5.1/lib/qe_pseudo/make.dep
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
kind.f90(46): remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
WRITE( stdout,'(/,T2,A,T78,A,2(/,T2,A,T75,I6),3(/,T2,A,T67,E14.8))') &
--------------------------------------------------------------------^
kind.f90(52): remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
WRITE( stdout,'(/,T2,A,T78,A,2(/,T2,A,T75,I6),3(/,T2,A,T67,E14.8))') &
--------------------------------------------------------------------^
kind.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
constants.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
radial_grids.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
atom.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
parameters.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
qe_auxdata.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
recvec.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
becmod.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
pseudo_types.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
spin_orb.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
invmat.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
uspp.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
s_psi.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
us_module.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
init_us_1.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
init_us_2.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
ylmr2.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
simpsn.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
upf_to_internal.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
read_upf_v1.F f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/mutta/Downloads/yambo-4.5.1/lib/external/gfortran//home/mutta/mpich3-intel/bin/mpifort/v4/parallel/include’ [-Wmissing-include-dirs]
read_upf_v2.f90(20): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_MODULE]
USE iotk_module
------------^
read_upf_v2.f90(54): error #6632: Keyword arguments are invalid without an explicit interface. [ATTR]
CALL iotk_open_read(u, attr=attr, root=root, ierr=ierr_)
--------------------------^
read_upf_v2.f90(54): error #6632: Keyword arguments are invalid without an explicit interface. [ROOT]
CALL iotk_open_read(u, attr=attr, root=root, ierr=ierr_)
-------------------------------------^
read_upf_v2.f90(54): error #6632: Keyword arguments are invalid without an explicit interface. [IERR]
CALL iotk_open_read(u, attr=attr, root=root, ierr=ierr_)
------------------------------------------------^
read_upf_v2.f90(58): error #6632: Keyword arguments are invalid without an explicit interface. [IERR]
CALL iotk_close_read(u,ierr=ierr_)
------------------------------^
read_upf_v2.f90(70): error #6632: Keyword arguments are invalid without an explicit interface. [FOUND]
CALL iotk_scan_begin(u,'PP_INFO',found=found)
------------------------------------^
read_upf_v2.f90(39): error #6279: A specification expression object must be a dummy argument, a COMMON block object, or an object accessible through host or use association. [IOTK_NAMLENX]
CHARACTER(len=iotk_namlenx) :: root
-----------------^
read_upf_v2.f90(40): error #7915: A specification expression object must be a dummy argument, a COMMON block object, or an object accessible through host or use association - may be used in multiple contained procedures. [IOTK_ATTLENX]
CHARACTER(len=iotk_attlenx) :: attr
-----------------^
read_upf_v2.f90(40): error #6404: This name does not have a type, and must have an explicit type. [IOTK_ATTLENX]
CHARACTER(len=iotk_attlenx) :: attr
-----------------^
read_upf_v2.f90(39): error #6404: This name does not have a type, and must have an explicit type. [IOTK_NAMLENX]
CHARACTER(len=iotk_namlenx) :: root
-----------------^
read_upf_v2.f90(146): error #6632: Keyword arguments are invalid without an explicit interface. [ATTR]
CALL iotk_scan_empty(u, 'PP_HEADER', attr=attr)
-------------------------------------------^
read_upf_v2.f90(147): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'generated', upf%generated, default=' ')
--------------------------------------------------------------------^
read_upf_v2.f90(148): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'author', upf%author, default='anonymous')
--------------------------------------------------------------------^
read_upf_v2.f90(149): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'date', upf%date, default=' ')
--------------------------------------------------------------------^
read_upf_v2.f90(150): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'comment', upf%comment, default=' ')
--------------------------------------------------------------------^
read_upf_v2.f90(158): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'is_coulomb', upf%tcoulombp, default=.false.)
--------------------------------------------------------------------^
read_upf_v2.f90(160): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'has_so', upf%has_so, default=.false.)
--------------------------------------------------------------------^
read_upf_v2.f90(161): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'has_wfc', upf%has_wfc, default=upf%tpawp)
--------------------------------------------------------------------^
read_upf_v2.f90(162): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'has_gipaw', upf%has_gipaw, default=.false.)
--------------------------------------------------------------------^
read_upf_v2.f90(175): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'total_psenergy', upf%etotps, default=0._dp)
--------------------------------------------------------------------^
read_upf_v2.f90(176): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'wfc_cutoff', upf%ecutwfc, default=0._dp)
--------------------------------------------------------------------^
read_upf_v2.f90(177): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'rho_cutoff', upf%ecutrho, default=0._dp)
--------------------------------------------------------------------^
read_upf_v2.f90(178): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'l_max', upf%lmax, default=0)
--------------------------------------------------------------------^
read_upf_v2.f90(179): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'l_max_rho', upf%lmax_rho, default=2*upf%lmax)
--------------------------------------------------------------------^
read_upf_v2.f90(180): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'l_local', upf%lloc, default=0)
--------------------------------------------------------------------^
read_upf_v2.f90(202): error #6632: Keyword arguments are invalid without an explicit interface. [ATTR]
CALL iotk_scan_begin(u, 'PP_MESH', attr=attr)
-----------------------------------------^
read_upf_v2.f90(204): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'dx', upf%dx, default=0._dp)
---------------------------------------------------^
read_upf_v2.f90(205): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'mesh', upf%mesh, default=upf%mesh)
---------------------------------------------------^
read_upf_v2.f90(206): error #6632: Keyword arguments are invalid without an explicit interface. [DEFAULT]
CALL iotk_scan_attr(attr, 'xmin', upf%xmin, default=0._dp)
---------------------------------------------------^
read_upf_v2.f90(724): catastrophic error: Too many errors, exiting
compilation aborted for read_upf_v2.f90 (code 1)
make[1]: *** [Makefile:169: read_upf_v2.o] Error 1
make[1]: Leaving directory '/home/mutta/Downloads/yambo-4.5.1/lib/qe_pseudo'
make: *** [Makefile:180: int-libs] Error 2
Abdulmutta Thatribud

Department of Science, Faculty of Science and Technology
Prince of Songkla University Pattani Campus, Thailand

User avatar
Daniele Varsano
Posts: 2322
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: Compile Yambo-4.4.0 with abinit 8.10.3

Post by Daniele Varsano » Sun May 10, 2020 8:13 am

Dear Abdulmutta,
please use attachment instead of copy-paste long part of the files.
There are some inconsistencies in your configuration, it seems you want to use intel compilers but the FC_KIND is set to gfortran.
You have the compilers in your home and you should be sure that the environment is set properly.
My suggestion is:
1) Install properly your compilers and not leave them in your home.
2) When configuring yambo assign also the compiler (ifort or gfortran) to the FC/F77 variables and not only to the MPIFC/MPIF77. I suspect that here there are some inconsistencies. Note that now the FC compiler points to gfortran libraries.
3) It is important you do a

Code: Select all

make distclean
before trying to compile the code again.


Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

Post Reply