Yambo Community Forum

Posted: **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.

Posted: **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

Posted: **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

Posted: **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

Posted: **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

Posted: **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

Posted: **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

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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.

Posted: **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

Posted: **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.

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