<div dir="ltr"><div dir="ltr">Dr. Vahid Derakhshan Maman</div><div dir="ltr"><br></div><div dir="ltr">use pw.x -ndiag 1 <<a href="http://input.in" target="_blank">input.in</a>> input.out. This will make the diagonalisation process serial, slower but you won't get the error.<br clear="all"><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 5 Apr 2021 at 15:30, <<a href="mailto:users-request@lists.quantum-espresso.org">users-request@lists.quantum-espresso.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send users mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Error in neb.x calculation on Cedar cluster (Rutika Savaliya)<br>
2. Re: Error in neb.x calculation on Cedar cluster (Dr. K. C. Bhamu)<br>
3. problems computing cholesky (Riemann Derakhshan)<br>
4. QE e-School 17-28 May 2021 (Paolo Giannozzi)<br>
5. Re: Error in neb.x calculation on Cedar cluster (Paolo Giannozzi)<br>
6. Re: problems computing cholesky (=?utf-8?B?SmliaWFvIExp?=)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sun, 4 Apr 2021 22:12:50 +0000<br>
From: Rutika Savaliya <<a href="mailto:rutika.savaliya@mail.mcgill.ca" target="_blank">rutika.savaliya@mail.mcgill.ca</a>><br>
To: "<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>"<br>
<<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: [QE-users] Error in neb.x calculation on Cedar cluster<br>
Message-ID:<br>
<<a href="mailto:YQBPR0101MB11401C64951C89DF12C46329D7789@YQBPR0101MB1140.CANPRD01.PROD.OUTLOOK.COM" target="_blank">YQBPR0101MB11401C64951C89DF12C46329D7789@YQBPR0101MB1140.CANPRD01.PROD.OUTLOOK.COM</a>><br>
<br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello<br>
My name is Rutika, user srutika. I run quantum espresso calculation on the Cedar cluster. The Job script is located /scratch/srutika. While neb.x calculation is running into the same issue after starting. It started after recent changes on computecanada. My run.sh file and error appearing is as below:<br>
<br>
#!/bin/sh<br>
#SBATCH --nodes=6<br>
#SBATCH --ntasks-per-node=48<br>
#SBATCH --time=08-00:00<br>
#MPI tasks<br>
#SBATCH --mem=0<br>
#SBATCH --account=def-jkopysci<br>
<br>
module load quantumespresso/6.5<br>
<br>
srun neb.x -i RR8.in > RR8.out<br>
<br>
<br>
My error is as below:<br>
<br>
[cdr2189:54345] *** An error occurred in MPI_Type_free<br>
[cdr2189:54345] *** reported by process [500170752,196]<br>
[cdr2189:54345] *** on communicator MPI_COMM_WORLD<br>
[cdr2189:54345] *** MPI_ERR_TYPE: invalid datatype<br>
[cdr2189:54345] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,<br>
[cdr2189:54345] *** and potentially your MPI job)<br>
In: PMI_Abort(3, N/A)<br>
slurmstepd: error: *** STEP 65543632.0 ON cdr2092 CANCELLED AT 2021-04-04T13:58:54 ***<br>
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.<br>
srun: error: cdr2106: tasks 96-143: Killed<br>
srun: launch/slurm: _step_signal: Terminating StepId=65543632.0<br>
srun: error: cdr2096: tasks 48-95: Killed<br>
srun: error: cdr2159: tasks 144-191: Killed<br>
srun: error: cdr2189: tasks 192-195,197-239: Killed<br>
srun: error: cdr2092: tasks 0-47: Killed<br>
srun: error: cdr2190: tasks 240-287: Killed<br>
srun: error: cdr2189: task 196: Exited with exit code 3<br>
<br>
<br>
I have also attached the slurm file for reference.<br>
<br>
Hope to find the solution for this issue.<br>
<br>
Thank You.<br>
Rutika<br>
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<br>
Message: 2<br>
Date: Mon, 5 Apr 2021 11:32:32 +0900<br>
From: "Dr. K. C. Bhamu" <<a href="mailto:kcbhamu85@gmail.com" target="_blank">kcbhamu85@gmail.com</a>><br>
To: Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] Error in neb.x calculation on Cedar cluster<br>
Message-ID:<br>
<CAJYci+TDwV7+soQEx8eFoPxh=<a href="mailto:ajkNbMU77kcB5NyVhAM6bK53Q@mail.gmail.com" target="_blank">ajkNbMU77kcB5NyVhAM6bK53Q@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Could you please check with<br>
<br>
srun neb.x -inp RR8.in > RR8.out<br>
<br>
Replace -i with -inp<br>
<br>
<br>
Thank you<br>
Bhamu<br>
<br>
On Mon, Apr 5, 2021, 07:29 Rutika Savaliya <<a href="mailto:rutika.savaliya@mail.mcgill.ca" target="_blank">rutika.savaliya@mail.mcgill.ca</a>><br>
wrote:<br>
<br>
> Hello<br>
> My name is Rutika, user srutika. I run quantum espresso calculation on the<br>
> Cedar cluster. The Job script is located /scratch/srutika. While neb.x<br>
> calculation is running into the same issue after starting. It started after<br>
> recent changes on computecanada. My run.sh file and error appearing is as<br>
> below:<br>
><br>
> #!/bin/sh<br>
> #SBATCH --nodes=6<br>
> #SBATCH --ntasks-per-node=48<br>
> #SBATCH --time=08-00:00<br>
> #MPI tasks<br>
> #SBATCH --mem=0<br>
> #SBATCH --account=def-jkopysci<br>
><br>
> module load quantumespresso/6.5<br>
><br>
> srun neb.x -i RR8.in > RR8.out<br>
><br>
><br>
> My error is as below:<br>
><br>
> [cdr2189:54345] *** An error occurred in MPI_Type_free<br>
> [cdr2189:54345] *** reported by process [500170752,196]<br>
> [cdr2189:54345] *** on communicator MPI_COMM_WORLD<br>
> [cdr2189:54345] *** MPI_ERR_TYPE: invalid datatype<br>
> [cdr2189:54345] *** MPI_ERRORS_ARE_FATAL (processes in this communicator<br>
> will now abort,<br>
> [cdr2189:54345] *** and potentially your MPI job)<br>
> In: PMI_Abort(3, N/A)<br>
> slurmstepd: error: *** STEP 65543632.0 ON cdr2092 CANCELLED AT<br>
> 2021-04-04T13:58:54 ***<br>
> srun: Job step aborted: Waiting up to 32 seconds for job step to finish.<br>
> srun: error: cdr2106: tasks 96-143: Killed<br>
> srun: launch/slurm: _step_signal: Terminating StepId=65543632.0<br>
> srun: error: cdr2096: tasks 48-95: Killed<br>
> srun: error: cdr2159: tasks 144-191: Killed<br>
> srun: error: cdr2189: tasks 192-195,197-239: Killed<br>
> srun: error: cdr2092: tasks 0-47: Killed<br>
> srun: error: cdr2190: tasks 240-287: Killed<br>
> srun: error: cdr2189: task 196: Exited with exit code 3<br>
><br>
><br>
> I have also attached the slurm file for reference.<br>
><br>
> Hope to find the solution for this issue.<br>
><br>
> Thank You.<br>
> Rutika<br>
> _______________________________________________<br>
> Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer" target="_blank">www.max-centre.eu</a>)<br>
> users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Mon, 5 Apr 2021 09:57:02 +0200<br>
From: Riemann Derakhshan <<a href="mailto:riemann.derakhshan@gmail.com" target="_blank">riemann.derakhshan@gmail.com</a>><br>
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
Subject: [QE-users] problems computing cholesky<br>
Message-ID:<br>
<CA+YmQbmbGZCf7uxNKLxtkpf=<a href="mailto:wqFL9DFLKm3VQO_r1wfGEzychQ@mail.gmail.com" target="_blank">wqFL9DFLKm3VQO_r1wfGEzychQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear PWSCF Community,<br>
<br>
Hope you are fine.<br>
<br>
Through the vc-relax calculations for the Pb slab, after some iterations<br>
I'm getting the below error:<br>
<br>
Error in routine cdiaghg (95):<br>
problems computing cholesky<br>
<br>
I will highly appreciate it if you share your ideas with me about what<br>
causes this error and how it can be fixed.<br>
<br>
Herewith I've attached my input file and relevant part of the output file<br>
for your consideration.<br>
<br>
Regards,<br>
Vahid<br>
<br>
================ INPUT ==================================================<br>
&CONTROL<br>
calculation = 'vc-relax' ,<br>
restart_mode = 'from_scratch' ,<br>
wf_collect = .true. ,<br>
outdir = './' ,<br>
pseudo_dir = '${HOME}/Pseudo' ,<br>
prefix = 'Pb' ,<br>
disk_io = 'low' ,<br>
verbosity = 'high' ,<br>
/<br>
&SYSTEM<br>
ibrav = 0,<br>
celldm(1) = 9.5770828664d0,<br>
nat = 10,<br>
ntyp = 1,<br>
ecutwfc = 350 ,<br>
occupations = 'smearing' ,<br>
degauss = 0.005d0 ,<br>
smearing = 'marzari-vanderbilt' ,<br>
/<br>
&ELECTRONS<br>
conv_thr = 1d-06 ,<br>
mixing_beta = 0.3d0 ,<br>
/<br>
&IONS<br>
ion_dynamics = 'bfgs' ,<br>
/<br>
&CELL<br>
cell_dynamics = 'bfgs' ,<br>
cell_dofree = 'xyz' ,<br>
/<br>
CELL_PARAMETERS alat<br>
0.707106781 -0.707106781 0.000000000<br>
0.707106781 0.707106781 0.000000000<br>
0.000000000 0.000000000 8.419525238<br>
ATOMIC_SPECIES<br>
Pb 207.20000 Pb_PBE.upf<br>
ATOMIC_POSITIONS crystal<br>
Pb 0.000000000 0.000000000 0.410921343<br>
Pb 0.500000000 0.500000000 0.410921343<br>
Pb 0.500000000 -0.000000000 0.470307114<br>
Pb 1.000000000 0.500000000 0.470307114<br>
Pb 0.000000000 0.000000000 0.529692886<br>
Pb 0.500000000 0.500000000 0.529692886<br>
Pb 0.500000000 0.000000000 0.589078657<br>
Pb 0.000000000 0.500000000 0.589078657<br>
Pb 0.000000000 0.000000000 0.648464428<br>
Pb 0.500000000 0.500000000 0.648464428<br>
K_POINTS automatic<br>
12 12 1 0 0 0<br>
<br>
================ OUTPUT =================================================<br>
<br>
Total force = 0.030286 Total SCF correction = 0.001308<br>
<br>
<br>
Computing stress (Cartesian axis) and pressure<br>
<br>
total stress (Ry/bohr**3) (kbar) P=<br>
-5.93<br>
-0.00004600 0.00000000 0.00000000 -6.77 0.00<br>
0.00<br>
-0.00000000 -0.00004600 0.00000000 -0.00 -6.77<br>
0.00<br>
0.00000000 0.00000000 -0.00002896 0.00 0.00<br>
-4.26<br>
<br>
kinetic stress (kbar) 9163.73 -0.00 0.00<br>
-0.00 9163.73 0.00<br>
0.00 0.00 9164.69<br>
<br>
local stress (kbar)-359922.74 -0.00 -0.00<br>
-0.00-359922.74 0.00<br>
-0.00 0.00 362267.51<br>
<br>
nonloc. stress (kbar) -4413.05 0.00 0.00<br>
0.00 -4413.05 0.00<br>
0.00 0.00 -4416.09<br>
<br>
hartree stress (kbar) 181406.68 0.00 0.00<br>
0.00 181406.68 -0.00<br>
0.00 -0.00-177773.50<br>
<br>
exc-cor stress (kbar) 3339.47 0.00 -0.00<br>
0.00 3339.47 -0.00<br>
-0.00 -0.00 3338.34<br>
<br>
corecor stress (kbar) -4931.22 -0.00 0.00<br>
-0.00 -4931.22 0.00<br>
0.00 0.00 -4931.14<br>
<br>
ewald stress (kbar) 175350.37 -0.00 0.00<br>
-0.00 175350.37 0.00<br>
0.00 0.00-187654.08<br>
<br>
hubbard stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
london stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
DFT-D3 stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
XDM stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
dft-nl stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
TS-vdW stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
<br>
<br>
number of scf cycles = 3<br>
number of bfgs steps = 2<br>
<br>
enthalpy old = -1404.1369323220 Ry<br>
enthalpy new = -1404.1396592796 Ry<br>
<br>
CASE: enthalpy_new < enthalpy_old<br>
<br>
new trust radius = 0.0345760219 bohr<br>
new conv_thr = 0.0000001090 Ry<br>
<br>
new unit-cell volume = 7321.96851 a.u.^3 ( 1085.00378 Ang^3 )<br>
density = 3.17108 g/cm^3<br>
<br>
CELL_PARAMETERS (alat= 9.57708287)<br>
0.702858310 -0.707106781 0.000000000<br>
0.707106781 0.702858310 0.000000000<br>
0.000000000 0.000000000 8.385663933<br>
<br>
ATOMIC_POSITIONS (crystal)<br>
Pb 0.0000000000 0.0000000000 0.4116796836<br>
Pb 0.5000000000 0.5000000000 0.4116796677<br>
Pb 0.5000000000 -0.0000000000 0.4695686463<br>
Pb 1.0000000000 0.5000000000 0.4695686463<br>
Pb 0.0000000000 0.0000000000 0.5296894606<br>
Pb 0.5000000000 0.5000000000 0.5296894615<br>
Pb 0.5000000000 -0.0000000000 0.5898160423<br>
Pb 0.0000000000 0.5000000000 0.5898160423<br>
Pb 0.0000000000 0.0000000000 0.6477105834<br>
Pb 0.5000000000 0.5000000000 0.6477106219<br>
<br>
<br>
<br>
Writing output data file ./Pb.save/<br>
NEW-OLD atomic charge density approx. for the potential<br>
<br>
negative rho (up, down): 4.239E-06 0.000E+00<br>
extrapolated charge 139.33910, renormalised to 140.00000<br>
<br>
total cpu time spent up to now is 5450.5 secs<br>
<br>
Self-consistent Calculation<br>
<br>
iteration # 1 ecut= 350.00 Ry beta= 0.30<br>
Davidson diagonalization with overlap<br>
ethr = 1.00E-06, avg # of iterations = 12.0<br>
<br>
negative rho (up, down): 2.981E-06 0.000E+00<br>
<br>
total cpu time spent up to now is 5718.7 secs<br>
<br>
total energy = -1399.22364359 Ry<br>
Harris-Foulkes estimate = -1491.08426468 Ry<br>
estimated scf accuracy < 8.73203731 Ry<br>
<br>
iteration # 2 ecut= 350.00 Ry beta= 0.30<br>
Davidson diagonalization with overlap<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
Error in routine cdiaghg (95):<br>
problems computing cholesky<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
<br>
stopping ...<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
Error in routine cdiaghg (95):<br>
problems computing cholesky<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
<br>
stopping ...<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
Error in routine cdiaghg (95):<br>
problems computing cholesky<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
<br>
--<br>
<br>
*Dr. Vahid Derakhshan Maman*<br>
<br>
<br>
Postdoctoral Research Associate<br>
Utrecht University, Debye Institute for Nanomaterials Science<br>
Heidelberglaan 83584 CS Utrecht<br>
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------------------------------<br>
<br>
Message: 4<br>
Date: Mon, 5 Apr 2021 10:46:58 +0200<br>
From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>><br>
To: Quantum Espresso users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: [QE-users] QE e-School 17-28 May 2021<br>
Message-ID:<br>
<CAPMgbCsdmnh16NiNSXsP0f0zkGjWCUFjEVccEtEYNhfPa=<a href="mailto:XNbg@mail.gmail.com" target="_blank">XNbg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
The ICTP, in collaboration with the MaX EU Centre for Excellence in<br>
Supercomputing application and the Quantum ESPRESSO Foundation, together<br>
with the support of SISSA, CECAM, Shanghai University, CINECA<br>
and the Jo?ef Stefan Institute, hosts the first "MaX e-School on Advanced<br>
Materials and Molecular Modelling with Quantum ESPRESSO".<br>
<br>
The virtual event is scheduled between 17 and 28 May 2021 (registration<br>
deadline: 30 April 2021)<br>
<br>
The school will introduce students and young researchers to materials and<br>
molecular modelling with Quantum ESPRESSO (QE), covering basic concepts,<br>
recent advances and developments, with emphasis on<br>
density-functional-theory (DFT) based methods and high-performance<br>
computing (HPC). The school aims to train beginners in computational<br>
materials sciences to the efficient use of QE on modern massively parallel<br>
architectures, with special emphasis on the emerging architectures based on<br>
GPGPUs and on the use of advanced tools for generating, managing, storing,<br>
and sharing results.<br>
<br>
Additional detailed information as well as the link to the online form for<br>
application are available at the following link:<br>
<a href="http://indico.ictp.it/event/9616" rel="noreferrer" target="_blank">http://indico.ictp.it/event/9616</a><br>
<br>
Organizers:<br>
Stefano Baroni (SISSA)<br>
Ralph Gebauer (ICTP)<br>
Anton Kokalj (Jo?ef Stefan Institute)<br>
Wei Ren (Shanghai University)<br>
Alessandro Stroppa (CNR-Spin)<br>
<br>
Local Organizer:<br>
Ivan Girotto (ICTP)<br>
-- <br>
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
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<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Mon, 5 Apr 2021 10:52:08 +0200<br>
From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>><br>
To: Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] Error in neb.x calculation on Cedar cluster<br>
Message-ID:<br>
<<a href="mailto:CAPMgbCsL%2BY0iXNd9aaXX3soq29W5d7VkTXR329SXG8dFKiYggg@mail.gmail.com" target="_blank">CAPMgbCsL+Y0iXNd9aaXX3soq29W5d7VkTXR329SXG8dFKiYggg@mail.gmail.com</a>><br>
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On Mon, Apr 5, 2021 at 4:33 AM Dr. K. C. Bhamu <<a href="mailto:kcbhamu85@gmail.com" target="_blank">kcbhamu85@gmail.com</a>> wrote:<br>
<br>
Replace -i with -inp<br>
><br>
<br>
this cannot have any effect: -i, -in, -inp are all accepted.<br>
<br>
It is impossible to say anything without more and better information.<br>
<br>
Paolo<br>
<br>
On Mon, Apr 5, 2021, 07:29 Rutika Savaliya <<a href="mailto:rutika.savaliya@mail.mcgill.ca" target="_blank">rutika.savaliya@mail.mcgill.ca</a>><br>
> wrote:<br>
><br>
>> Hello<br>
>> My name is Rutika, user srutika. I run quantum espresso calculation on<br>
>> the Cedar cluster. The Job script is located /scratch/srutika. While neb.x<br>
>> calculation is running into the same issue after starting. It started after<br>
>> recent changes on computecanada. My run.sh file and error appearing is<br>
>> as below:<br>
>><br>
>> #!/bin/sh<br>
>> #SBATCH --nodes=6<br>
>> #SBATCH --ntasks-per-node=48<br>
>> #SBATCH --time=08-00:00<br>
>> #MPI tasks<br>
>> #SBATCH --mem=0<br>
>> #SBATCH --account=def-jkopysci<br>
>><br>
>> module load quantumespresso/6.5<br>
>><br>
>> srun neb.x -i RR8.in > RR8.out<br>
>><br>
>><br>
>> My error is as below:<br>
>><br>
>> [cdr2189:54345] *** An error occurred in MPI_Type_free<br>
>> [cdr2189:54345] *** reported by process [500170752,196]<br>
>> [cdr2189:54345] *** on communicator MPI_COMM_WORLD<br>
>> [cdr2189:54345] *** MPI_ERR_TYPE: invalid datatype<br>
>> [cdr2189:54345] *** MPI_ERRORS_ARE_FATAL (processes in this communicator<br>
>> will now abort,<br>
>> [cdr2189:54345] *** and potentially your MPI job)<br>
>> In: PMI_Abort(3, N/A)<br>
>> slurmstepd: error: *** STEP 65543632.0 ON cdr2092 CANCELLED AT<br>
>> 2021-04-04T13:58:54 ***<br>
>> srun: Job step aborted: Waiting up to 32 seconds for job step to finish.<br>
>> srun: error: cdr2106: tasks 96-143: Killed<br>
>> srun: launch/slurm: _step_signal: Terminating StepId=65543632.0<br>
>> srun: error: cdr2096: tasks 48-95: Killed<br>
>> srun: error: cdr2159: tasks 144-191: Killed<br>
>> srun: error: cdr2189: tasks 192-195,197-239: Killed<br>
>> srun: error: cdr2092: tasks 0-47: Killed<br>
>> srun: error: cdr2190: tasks 240-287: Killed<br>
>> srun: error: cdr2189: task 196: Exited with exit code 3<br>
>><br>
>><br>
>> I have also attached the slurm file for reference.<br>
>><br>
>> Hope to find the solution for this issue.<br>
>><br>
>> Thank You.<br>
>> Rutika<br>
>> _______________________________________________<br>
>> Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer" target="_blank">www.max-centre.eu</a>)<br>
>> users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
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><br>
> _______________________________________________<br>
> Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer" target="_blank">www.max-centre.eu</a>)<br>
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<br>
<br>
-- <br>
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
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Message: 6<br>
Date: Mon, 5 Apr 2021 16:59:13 +0800<br>
From: "=?utf-8?B?SmliaWFvIExp?=" <<a href="mailto:jibiaoli@foxmail.com" target="_blank">jibiaoli@foxmail.com</a>><br>
To: "=?utf-8?B?UXVhbnR1bSBFU1BSRVNTTyB1c2VycyBGb3J1bQ==?="<br>
<<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] problems computing cholesky<br>
Message-ID: <<a href="mailto:tencent_291ED07FBA91E922071AD9B504F4A7CDCA06@qq.com" target="_blank">tencent_291ED07FBA91E922071AD9B504F4A7CDCA06@qq.com</a>><br>
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<br>
please lower the values of the number of cpu and ecut<br>
<br>
<br>
<br>
---Original---<br>
From: "Riemann Derakhshan"<<a href="mailto:riemann.derakhshan@gmail.com" target="_blank">riemann.derakhshan@gmail.com</a>><br>
Date: Mon, Apr 5, 2021 16:05 PM<br>
To: "users"<<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>>;<br>
Subject: [QE-users] problems computing cholesky<br>
<br>
<br>
Dear PWSCF Community,<br>
<br>
<br>
Hope you are fine.<br>
<br>
<br>
Through the vc-relax calculations for the Pb slab, after some iterations I'm getting the below error: <br>
<br>
<br>
<br>
Error in routine cdiaghg (95):<br>
problems computing cholesky<br>
<br>
<br>
I will highly appreciate it if you share your ideas with me about what causes this error and how it can be fixed. <br>
<br>
<br>
Herewith I've attached my input file and relevant part of the output file for your consideration.<br>
<br>
<br>
Regards,<br>
Vahid<br>
<br>
<br>
================ INPUT ==================================================<br>
&CONTROL<br>
calculation = 'vc-relax' ,<br>
restart_mode = 'from_scratch' ,<br>
wf_collect = .true. ,<br>
outdir = './' ,<br>
pseudo_dir = '${HOME}/Pseudo' ,<br>
prefix = 'Pb' ,<br>
disk_io = 'low' ,<br>
verbosity = 'high' ,<br>
/<br>
&SYSTEM<br>
ibrav = 0,<br>
celldm(1) = 9.5770828664d0,<br>
nat = 10,<br>
ntyp = 1,<br>
ecutwfc = 350 ,<br>
occupations = 'smearing' ,<br>
degauss = 0.005d0 ,<br>
smearing = 'marzari-vanderbilt' ,<br>
/<br>
&ELECTRONS<br>
conv_thr = 1d-06 ,<br>
mixing_beta = 0.3d0 ,<br>
/<br>
&IONS<br>
ion_dynamics = 'bfgs' ,<br>
/<br>
&CELL<br>
cell_dynamics = 'bfgs' ,<br>
cell_dofree = 'xyz' ,<br>
/<br>
CELL_PARAMETERS alat <br>
0.707106781 -0.707106781 0.000000000 <br>
0.707106781 0.707106781 0.000000000 <br>
0.000000000 0.000000000 8.419525238 <br>
ATOMIC_SPECIES<br>
Pb 207.20000 Pb_PBE.upf <br>
ATOMIC_POSITIONS crystal <br>
Pb 0.000000000 0.000000000 0.410921343 <br>
Pb 0.500000000 0.500000000 0.410921343 <br>
Pb 0.500000000 -0.000000000 0.470307114 <br>
Pb 1.000000000 0.500000000 0.470307114 <br>
Pb 0.000000000 0.000000000 0.529692886 <br>
Pb 0.500000000 0.500000000 0.529692886 <br>
Pb 0.500000000 0.000000000 0.589078657 <br>
Pb 0.000000000 0.500000000 0.589078657 <br>
Pb 0.000000000 0.000000000 0.648464428 <br>
Pb 0.500000000 0.500000000 0.648464428 <br>
K_POINTS automatic <br>
12 12 1 0 0 0 <br>
<br>
<br>
<br>
================ OUTPUT =================================================<br>
<br>
<br>
Total force = 0.030286 Total SCF correction = 0.001308<br>
<br>
<br>
Computing stress (Cartesian axis) and pressure<br>
<br>
total stress (Ry/bohr**3) (kbar) P= -5.93<br>
-0.00004600 0.00000000 0.00000000 -6.77 0.00 0.00<br>
-0.00000000 -0.00004600 0.00000000 -0.00 -6.77 0.00<br>
0.00000000 0.00000000 -0.00002896 0.00 0.00 -4.26<br>
<br>
kinetic stress (kbar) 9163.73 -0.00 0.00<br>
-0.00 9163.73 0.00<br>
0.00 0.00 9164.69<br>
<br>
local stress (kbar)-359922.74 -0.00 -0.00<br>
-0.00-359922.74 0.00<br>
-0.00 0.00 362267.51<br>
<br>
nonloc. stress (kbar) -4413.05 0.00 0.00<br>
0.00 -4413.05 0.00<br>
0.00 0.00 -4416.09<br>
<br>
hartree stress (kbar) 181406.68 0.00 0.00<br>
0.00 181406.68 -0.00<br>
0.00 -0.00-177773.50<br>
<br>
exc-cor stress (kbar) 3339.47 0.00 -0.00<br>
0.00 3339.47 -0.00<br>
-0.00 -0.00 3338.34<br>
<br>
corecor stress (kbar) -4931.22 -0.00 0.00<br>
-0.00 -4931.22 0.00<br>
0.00 0.00 -4931.14<br>
<br>
ewald stress (kbar) 175350.37 -0.00 0.00<br>
-0.00 175350.37 0.00<br>
0.00 0.00-187654.08<br>
<br>
hubbard stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
london stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
DFT-D3 stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
XDM stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
dft-nl stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
TS-vdW stress (kbar) 0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
0.00 0.00 0.00<br>
<br>
<br>
<br>
number of scf cycles = 3<br>
number of bfgs steps = 2<br>
<br>
enthalpy old = -1404.1369323220 Ry<br>
enthalpy new = -1404.1396592796 Ry<br>
<br>
CASE: enthalpy_new < enthalpy_old<br>
<br>
new trust radius = 0.0345760219 bohr<br>
new conv_thr = 0.0000001090 Ry<br>
<br>
new unit-cell volume = 7321.96851 a.u.^3 ( 1085.00378 Ang^3 )<br>
density = 3.17108 g/cm^3<br>
<br>
CELL_PARAMETERS (alat= 9.57708287)<br>
0.702858310 -0.707106781 0.000000000<br>
0.707106781 0.702858310 0.000000000<br>
0.000000000 0.000000000 8.385663933<br>
<br>
ATOMIC_POSITIONS (crystal)<br>
Pb 0.0000000000 0.0000000000 0.4116796836<br>
Pb 0.5000000000 0.5000000000 0.4116796677<br>
Pb 0.5000000000 -0.0000000000 0.4695686463<br>
Pb 1.0000000000 0.5000000000 0.4695686463<br>
Pb 0.0000000000 0.0000000000 0.5296894606<br>
Pb 0.5000000000 0.5000000000 0.5296894615<br>
Pb 0.5000000000 -0.0000000000 0.5898160423<br>
Pb 0.0000000000 0.5000000000 0.5898160423<br>
Pb 0.0000000000 0.0000000000 0.6477105834<br>
Pb 0.5000000000 0.5000000000 0.6477106219<br>
<br>
<br>
<br>
Writing output data file ./Pb.save/<br>
NEW-OLD atomic charge density approx. for the potential<br>
<br>
negative rho (up, down): 4.239E-06 0.000E+00<br>
extrapolated charge 139.33910, renormalised to 140.00000<br>
<br>
total cpu time spent up to now is 5450.5 secs<br>
<br>
Self-consistent Calculation<br>
<br>
iteration # 1 ecut= 350.00 Ry beta= 0.30<br>
Davidson diagonalization with overlap<br>
ethr = 1.00E-06, avg # of iterations = 12.0<br>
<br>
negative rho (up, down): 2.981E-06 0.000E+00<br>
<br>
total cpu time spent up to now is 5718.7 secs<br>
<br>
total energy = -1399.22364359 Ry<br>
Harris-Foulkes estimate = -1491.08426468 Ry<br>
estimated scf accuracy < 8.73203731 Ry<br>
<br>
iteration # 2 ecut= 350.00 Ry beta= 0.30<br>
Davidson diagonalization with overlap<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
Error in routine cdiaghg (95):<br>
problems computing cholesky<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
<br>
stopping ...<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
Error in routine cdiaghg (95):<br>
problems computing cholesky<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
<br>
stopping ...<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
Error in routine cdiaghg (95):<br>
problems computing cholesky<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
<br>
<br>
<br>
<br>
--<br>
<br>
Dr. Vahid Derakhshan Maman<br>
<br>
<br>
<br>
<br>
<br>
Postdoctoral Research Associate<br>
<br>
Utrecht University, Debye Institute for Nanomaterials Science <br>
<br>
Heidelberglaan 83584 CS Utrecht<br>
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