Yambo 5.1 "build failed"

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

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

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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
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matteo_dalessio
Posts: 5
Joined: Wed Jun 22, 2022 6:23 pm

Yambo 5.1 "build failed"

Post by matteo_dalessio » Wed Jun 22, 2022 7:55 pm

Hello everyone,
I'm new to the forum and I'll try to do my best to explain my problem.

I'm trying to install Yambo 5.1.0 on a linux machine (x86_64) with Intel oneAPI. I looked at recent posts which reported errors similar to the ones I was getting and I tried in different ways, always starting from scratch. The procedure that seems to work best (although it fails during the make all) is the following:

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% wget https://github.com/yambo-code/yambo/archive/refs/tags/5.1.0.tar.gz -O yambo-5.1.0.tar.gz

% tar zxvf  yambo-5.1.0.tar.gz 

% cd yambo-5.1.0

% git clone https://github.com/yambo-code/yambo-libraries.git lib/yambo

% ./configure FC=mpiifort F77=mpiifort --enable-open-mp --enable-par-linalg --enable-hdf5-par-io --with-scalapack-libs=mkl --with-blacs-libs=mkl --enable-slepc-linalg

% make ext-libs

% make core

% make all
At this point I got the error

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	[I][...]
        [driver] yambo_nl (checking work to be done)
	[driver] yambo
	[driver] yambo_nl (link)
	yambo_nl linking failed. Check logs/compile_yambo_nl.log
	make[1]: *** [config/mk/global/actions/compile_yambo.mk:41: yambo_nl] Error 1
	yambo_nl build failed[/i]
and I did (as suggested in another post)

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% rm lib/iotk/package-ready-stamp

% rm lib/iotk/package-installed

% make iotk

% make nl-project
But this gave the same error

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	[I][...]
        [driver] yambo_nl (checking work to be done)
	[driver] yambo_nl (link)
	yambo_nl linking failed. Check logs/compile_yambo_nl.log
	make[1]: *** [config/mk/global/actions/compile_yambo.mk:41: yambo_nl] Error 1
	yambo_nl build failed[/I]
I attach the config report and the compile_yambo_nl.log files.

Thank you for your time and help.
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Matteo D'Alessio
Università degli Studi di Modena e Reggio Emilia
Dipartimento di Scienze Fisiche, Informatiche e Matematiche

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claudio
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Re: Yambo 5.1 "build failed"

Post by claudio » Thu Jun 23, 2022 10:30 am

Dear Matteo

it seems there is a problem with the slepc libraries,
try to remove the flag --enable-slepc-linalg from your configure

do
make distclean

and then reconfigure without that flag.

let me know if it works
best
Claudio
Claudio Attaccalite
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com

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Nicola Spallanzani
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Joined: Thu Nov 21, 2019 10:15 am

Re: Yambo 5.1 "build failed"

Post by Nicola Spallanzani » Thu Jun 23, 2022 11:54 am

I'm not sure, but I think there is a bug that remove all the external libraries before to start the compilation of yambo_nl.
So, for now a workaround could be to not use the "make all" command, and instead use this list of commands:

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make -j4 ext-libs
make -j4 core
make -j4 sc-project
make -j4 ph-project
make -j4 rt-project
make -j4 nl-project
Please, let me know if this workaround works.

Best,
Nicola
Nicola Spallanzani, PhD
S3 Centre, Istituto Nanoscienze CNR and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu

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matteo_dalessio
Posts: 5
Joined: Wed Jun 22, 2022 6:23 pm

Re: Yambo 5.1 "build failed"

Post by matteo_dalessio » Thu Jun 23, 2022 4:33 pm

I tried both methods but I end up with the same error as before. I attach the log file resulting from the procedure that dr. Spallanzani suggested.

I thought the other binaries didn't work if the full compilation was not completed, but on the contrary the look like they do. Since I don't need yambo_nl at the moment, this is not a major concern.So it's not a problem if no solution is found.

Thank you for your help,
Matteo
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Matteo D'Alessio
Università degli Studi di Modena e Reggio Emilia
Dipartimento di Scienze Fisiche, Informatiche e Matematiche

DavidPolito93
Posts: 71
Joined: Sat Jun 06, 2020 10:43 am

Re: Yambo 5.1 "build failed"

Post by DavidPolito93 » Tue Jun 28, 2022 8:34 am

Dear all,

I am facing too a problem in the compilation of Yambo-5.1.0 on the HPC facility.

Here are my libraries:

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Currently Loaded Modulefiles:
  1) intel/intel-cc-18.2/18.2          3) intel/intel-compilers-18.2/18.2   5) intel/intel-mpi/2018.2
  2) intel/intel-fc-18.2/18.2          4) intel/intel-cmkl-18.2/18.2 
I do have acces to internet on the cluster. The configuration command is the following:

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./configure     --enable-open-mp --enable-mpi     --enable-time-profile --enable-memory-profile --enable-msgs-comps     --enable-hdf5-par-io --enable-par-linalg --enable-slepc-linalg 
The error I get is the following:

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/home/romanind/yambo-5.1.0/config/mk/local/rules.mk:9: recipe for target 'mod_xc_functionals.o' failed
make[2]: *** [mod_xc_functionals.o] Error 1
make[2]: *** Waiting for unfinished jobs....
(echo -e "\t[src/modules] mod_timing" )
	[src/modules] mod_timing
(echo -e "\t[src/modules] mod_D_lattice" )
	[src/modules] mod_D_lattice
(echo -e "\t[src/modules] mod_BS" )
	[src/modules] mod_BS
config/mk/global/actions/compile_yambo.mk:32: recipe for target 'yambo' failed
make[1]: *** [yambo] Error 2
yambo build failed
I am attaching the .log file

Best,

Davide Romanin
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Polytech - Paris-Saclay University
C2N, CNRS
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91120 Palaiseau

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Daniele Varsano
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Re: Yambo 5.1 "build failed"

Post by Daniele Varsano » Mon Jul 04, 2022 9:17 am

Dear David,

looking at your config file it seems there are some confusion with compilers. You are loading intel compilers which are recognized as mpiifort and mpiicc, but next FCKIND is set to 'gfortran'.

Can you try to configure assigning explicitly the intel compiler (including the serial one).

./configure FC=ifort, CC=icc etc...

I strongly suggest performing a make distclean before reconfiguring.
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/

sabrine
Posts: 21
Joined: Tue Apr 26, 2022 3:05 pm
Location: Paris , France

Re: Yambo 5.1 "build failed"

Post by sabrine » Thu Jul 27, 2023 4:36 pm

Dear yambo develloper and user:

I wanted to run yambo_nl in a cluster in parallele but i get the folowing error

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<09m-28s> [DIP] Writing dipoles header
[ERROR] STOP signal received while in[04] Dipoles
[ERROR] Writing File ./SAVE//ndb.dipoles; Variable NOT DEFINED; Permission denied
and in the repport file show always 'serial' even though i run it in parallel

Code: Select all

Version 5.1.0 Revision 21422 Hash (prev commit) fde6e2a07
Branch is
Serial+HDF5_IO Build
The support team in the cluster try to install yambo again and they get this error during the compilation of yambo_nl :

In src/interface/INIT_load.f90 ..

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INIT_load.f90(161): error #6285: There is no matching specific subroutine for this generic subroutine call.   [IT]
The compilation stoped after create this :

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a2y  c2y  p2y  yambo  yambo_ph  yambo_rt    yambo_sc  ypp  ypp_ph  ypp_rt  ypp_sc
IS there a way to fix this bag .
Many thanks.
Sabrine.
Dr.Sabrine Ayari
Laboratoire de Physique de lÉcole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France

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claudio
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Re: Yambo 5.1 "build failed"

Post by claudio » Fri Jul 28, 2023 1:04 pm

Dear Sabrine

I advice you to download the last GPL version from github

https://github.com/yambo-code/yambo

just click on "Code->Download ZIP"

many bugs including compilation bugs has been fixed here.

Let me know if it works

best
Claudio
Claudio Attaccalite
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com

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Davide Sangalli
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Re: Yambo 5.1 "build failed"

Post by Davide Sangalli » Fri Jul 28, 2023 2:09 pm

I also suggest to try to compile with parallel IO.

We plan to drop serial IO in the future.
The issue is likely related to that.

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

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