Yambo Community Forum

Dear colleagues,

I was using our high performance computing to run one of the examples that comes with the Yambo code.i.e, the hBN. I use the quantum espresso code, version 6.6.
I ran the scf and nscf calculations without problems. I then entered the "hBN.save" directory and invoked:

$exe/p2y

in order to generate the "SAVE" directory. However, i got the error below, without the SAVE file being generated.

Kindly advice.
--------------
WARNING: release_mt library was used but no multi-ep feature was enabled. Please use release library instead.

<---> DBs path set to .
<---> detected QE data format: qexsd
<---> == PWscf v.6.x generated data (QEXSD fmt) ==
<---> Header/K-points/Energies...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine qexsd_read_symmetry (2):
fmt problem
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

stopping ...
Abort(2) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 2) - process 0

----------------------------------------


Abdulrafiu.T Raji, PhD (Physics)
Department of Physics,
College of Science, Engineering & Technology (CSET),
University of South Africa (UNISA),
Pretoria, South Africa.
Tel (office): +27-12-429-4201
Skype: abdulrafiuraji

Dear Abdulrafiu.T,
can you please post the nscf qe input file and report which version of yambo code are you using?
Best,
Daniele

Thanks,

Please find the attached 'nscf' input file. I am using this version: "GPL Version 4.5.2".

Thank you.

Dear Abdulrafiu.T,

I wasn't able to reproduce your problem.
I have run a scf+nscf calculation using your input file, and then both yambo 4.5.2 and 4.5.3 work in my case, in serial and in parallel
(I have been using gnu 7.3.1 + opnempi 3.0.1). Which compiler / architecture were you using ?

Andrea

Hi Andrea,

Thanks. i have been in communication with our HPC administrator. He offered the following explanation for the problem and your query concerning the platform/architecture:

".....As far as the compiler that was used for the YAMBO that is on the CHPC I made use of intel parallel studio 2020u1 for the compile...."

"...Seems like the QE 6.6 that is on the machine is the development version and has a number of issues, but does have changes required by other users. I have installed another QE 6.6 on the machine which is the stable release...."

Now I can confirm that the code now works, as I was able to go beyond the 'p2y' executable step. I was able to produce the 'SAVE' directory and go beyond that. However, after executing the ~/p2y , i always get the following:

"WARNING: release_mt library was used but no multi-ep feature was enabled. Please use release library instead."

Although, as I said above, I am able to produce the 'SAVE" file and go beyond. Should I be worried about the warning message?

Thank you.

Dear Abdulrafiu.T,

this warning is not issued by yambo and comes probably from the compiler/runtime used to build the code
(or from some other piece in the machine software stack). Double check with the sys admin/support, though I think this kind of messages are usually harmless for what concerns the code run and results.

take care
Andrea

Hello,

I am also facing this issue. I used qe 7.3 with yambo 4.5.2, openmpi 2021.8, gcc version 11.4.0

How to fix this issue ? I am trying to reproduce the results of on of hBN. I have attached the scf.in ,nscf.in here.

&control
calculation='scf',
prefix='hBN',
restart_mode='from_scratch'
pseudo_dir = '../Pseudos'
wf_collect=.true.
nstep = 200
verbosity = 'high'
/
&system
ibrav = 4,
celldm(1) = 4.716
celldm(3) = 2.582
nat= 4,
ntyp= 2,
force_symmorphic=.true.
ecutwfc = 40,
/
&electrons
electron_maxstep = 100
conv_thr = 1.0e-8
/&control
calculation='nscf',
prefix='hBN',
pseudo_dir = '../Pseudos'
nstep = 200
verbosity = 'high'
wf_collect=.true.
/
&system
ibrav = 4,
celldm(1) = 4.716
celldm(3) = 2.582
nat= 4,
ntyp= 2,
force_symmorphic=.true.
ecutwfc = 40,nbnd = 100
/
&electrons
diago_thr_init=5.0e-6,
diago_full_acc=.true.
electron_maxstep = 100,
diagonalization='david'
mixing_mode = 'plain'
mixing_beta = 0.6
conv_thr = 1.0e-8
/
ATOMIC_SPECIES
B 10 B.pz-vbc.UPF
N 14 N.pz-vbc.UPF
ATOMIC_POSITIONS {crystal}
B 0.6666667 0.3333333 0.0000000
N -0.6666667 -0.3333333 0.0000000
B -0.6666667 -0.3333333 0.5000000
N 0.6666667 0.3333333 0.5000000
K_POINTS {automatic}
6 6 2 0 0 0
ATOMIC_SPECIES
B 10 B.pz-vbc.UPF
N 14 N.pz-vbc.UPF
ATOMIC_POSITIONS {crystal}
B 0.6666667 0.3333333 0.0000000
N -0.6666667 -0.3333333 0.0000000
B -0.6666667 -0.3333333 0.5000000
N 0.6666667 0.3333333 0.5000000
K_POINTS {automatic}
6 6 2 1 1 1

Dear Tasnim,

please add your signature in your post containing your full name and affiliation, this is a rule of the forum. You can do once for all adding the signature in your user profile. I assume the input file you posted is meant for two separate calculations (scf.in and nscf.in).

I suggest you to not shift the k point grid i.e. perform the nscf calculation using:
K_POINTS {automatic}
6 6 2 0 0 0

and see if this solve your problem.

Best,

Daniele

Hello Daniele,

Thank you for your reply. I tried using
K_POINTS {automatic}
6 6 2 0 0 0

It did not solve the issue and got the same error.

__ __ ____ ___ ___ ____ ___
| | |/ | | | \ / \
| | | o | _ _ | o ) |
| ~ | | \_/ | | O |
|___, | _ | | | O | |
| | | | | | | |
|____/|__|__|___|___|_____|\___/


<---> DBs path set to .
<---> detected QE data format: qexsd
<---> == PWscf v.6.x generated data (QEXSD fmt) ==
<---> Header/K-points/Energies...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine qexsd_read_symmetry (2):
fmt problem
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

stopping ...
Abort(2) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 2) - process 0

what should I do?

Dear Farhat,

I was not able to reproduce your problem using your inputs.
I used QE/7.5 and yambo/5.4.

The problem hopefully can be solved by using a more recent release of Yambo. Actually 4.5.2 is rather old and could be incompatible with recente QE version.

Best,

Daniele