Re: [Pw_forum] Compilation error with Environ and TDDFPT

atory of Theory and Simulation of Materials (THEOS) CH-1015 Lausanne, Switzerland +41 21 69 34 881 *From:* pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> on behalf of Rolly Ng <roll...@gmail.com> *Sent:* Tuesday, J

Re: [Pw_forum] QE-GPU 14.10.0 with intel compilers

Dear Filippo, I am able to compile the pw-gpu.x finally and I am able to run all the 8x C2050 GPU cards with the AUSURF112 benchmark. I have just aware that although I have ifort, gfortran is also needed for the MAGMA package. I found the performance enhancement is about 2.7 times comparing to

Re: [Pw_forum] 5.2.1 release building issue

Hi Eric, Please try this, ./configure CC=icc CXX=icpc F90=ifort F77=ifort MPIF90=mpiifort \ BLAS_LIBS="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" \ SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" \ FFT_LIBS="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core"

[Pw_forum] Using solvent on QE-GPU?

Dear QE developers, I am running QE-5.2.0 and I also have the GPU plugin v14.10.0. Therefore, I have pw-gpu.x in the bin directory. Can I add the current Environ-0.1 to the GPU executable? Should I do the following steps for pw-gpu? Any modification needed? For PW and NEB:

Re: [Pw_forum] Using solvent on QE-GPU?

: olivieroandreussi Web: https://sites.google.com/site/olivieroandreussi On 11/29/2015 09:12 AM, Rolly Ng wrote: Dear QE developers, I am running QE-5.2.0 and I also have the GPU plugin v14.10.0. Therefore, I have pw-gpu.x in the bin directory. Can I add the current Environ-0.1 to the GPU

Re: [Pw_forum] Using solvent on QE-GPU?

Dear Filippo, Thanks for your attention. I will report my findings after. Regards, Rolly -Original Message- From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf Of Filippo Spiga Sent: 2015年12月1日 22:22 To: PWSCF Forum Subject: Re: [Pw_forum] Using solvent on

[Pw_forum] Structural optimization of Biotin molecule

Dear QE developers and users, I am trying to run a "relax" structural optimization of the Biotin molecule on QE-5.2.0, the default nstep=50 does complete but I made a few observations on the output file. (1) "Check: negative starting charge= -0.823869" Is this quite large since I have

Re: [Pw_forum] Structural optimization of Biotin molecule

psi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/ Ecole Normale Supérieure (ENS), Département de Chimie, Paris Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935 On Mon, 7 Dec 2015, Rolly Ng wrote: > > Dear QE developers and users, > &

[Pw_forum] QE-GPU with Nvidia K80 failed

Dear QE-GPU developers, I am testing the latest NV K80 for QE-GPU, and the test bed has 4x K80, total of 8 GPU cores. I was successful using QE-GPU on C2050 with sm_20, but the K80 comes with sm_37. I have cuda-6.5 installed and I am using QEv5.2.0 + QE-GPUv14.10.0 complied okay. However,

Re: [Pw_forum] QE-GPU with Nvidia K80 failed

gt; > Cheers > > -- > Mr. Filippo SPIGA, M.Sc. > Quantum ESPRESSO Foundation > http://www.quantum-espresso.org ~ skype: filippo.spiga > > >> On Jan 9, 2016, at 9:28 AM, Rolly Ng <roll...@gmail.com> wrote: >> >> Dear QE-GPU developers, >&g

Re: [Pw_forum] QE-GPU with Nvidia K80 failed

Quantum ESPRESSO Foundation > http://www.quantum-espresso.org ~ skype: filippo.spiga > > >> On Jan 9, 2016, at 9:28 AM, Rolly Ng <roll...@gmail.com> wrote: >> >> Dear QE-GPU developers, >> >> I am testing the latest NV K80 for QE-GPU, and the test bed

[Pw_forum] System memory issue using --with-pinned-mem on QE-GPU

Dear Filippo and GPU developers, I find the new option "--with-pinned-mem" for the v5.3 QE-GPU but I am not sure what effect it has on the system memory. My server has total of 144GB RAM and 8x C2050. These cards have 3GB memory each, so there are 24 GB of video RAM. If I compile px-gpu.x

[Pw_forum] Geometry optimization on QE530-GPU with memory allocation error?

Dear Filippo and QE-GPU users, I am running a geometry optimization and the system contains 128 atoms. It runs fine but until the time spent reaches 590,000 seconds it stops with the error, and the job fails to complete L and I have this error 3 times for 3 different cases. "Error in

Re: [Pw_forum] Geometry optimization on QE530-GPU with memory allocation error?

, valid with or without GPU: unless not possible, _never_ run continuously for so long. It is a bad idea for multiple reasons. Always safely checkpoit/restart your calculation more often. Cheers -- Filippo SPIGA * Sent from my iPhone, sorry for typos * On 16 Feb 2016, at 04:01, Rolly Ng

Re: [Pw_forum] Geometry optimization on QE530-GPU with memory allocation error?

if you restart from a previous run (after a clean stop) Paolo On Tue, Feb 16, 2016 at 6:39 AM, Rolly Ng <roll...@gmail.com> wrote: Dear Filippo, Thanks for the quick tip. I would like to know the correct method of stop-restart a geometry optimization. 1) Initiall

Re: [Pw_forum] [QE-GPU] Maxwell architecture

Hello Gunnar, I would recommend Kepler cards (K80 or K40) or even Fermi cards (m2090 or c2075) for QE. If you are limited by budget, then it would be worth to try the Titan Z and Titan Black which performs decently on QE. I found that 2x Titan Z can double the scf speed comparing to 4x c2075.

Re: [Pw_forum] mpi error using pw.x

Hi Chong Wang, Perhaps it would be better to run ./configure with, ./configure CC=icc CXX=icpc F90=ifort F77=ifort MPIF90=mpiifort --with-scalapack=intel so that QE knows which compiler to use, verified with QE v5.3.0. Rolly On 05/16/2016 05:52 PM, Paolo Giannozzi wrote: On Mon, May 16,

Re: [Pw_forum] HELP: How to submit job on multi-node cluster?

Hi Pratik, May I ask what kind of connection do you have between the two nodes when you run in parallel? Is it Gigabit Ethernet or something else? I would like to do the same thing but now have to pause as your experience. Thanks, Rolly On 05/25/2016 06:50 PM, PRATIK DAS wrote: Dear QE

[Pw_forum] 回复: Nickel doped graphene supercell scf calculation with nspin=2 stopped

Dear QE experts,I can confirm that setting nbnd=400 still receives the stopping error. Can you please hlep? Is nspin=2 the correct way of adding spin polarization to my nickel doped graphene supercell?Thank you,Rolly___ Pw_forum mailing list

Re: [Pw_forum] Nickel doped graphene supercell scf calculation with nspin=2 stopped

y. Setting mixing_mode='TF-local- improves the convergency. Paolo On Sat, Jul 16, 2016 at 6:34 PM, Rolly Ng <roll...@gmail.com> wrote: > Dear QE experts, > > I would like to compute the DOS of Nickel doped graphene supercell > with QE v5.3.0, and our group has already done that

Re: [Pw_forum] Nickel doped graphene supercell scf calculation with nspin=2 stopped

mal version > first. You do not need more than a few bands over the Fermi energy. > Setting mixing_mode='TF-local- improves the convergency. > > Paolo > > On Sat, Jul 16, 2016 at 6:34 PM, Rolly Ng <roll...@gmail.com> wrote: >> Dear QE experts, >> >> I

[Pw_forum] How to improve the DOS plot?

Dear QE experts, I have managed to do spin polarized calculation on gold-doped graphene supercell with total of 72 atoms. There are 71 carbon atoms and 1 gold atom at the center of the supercell. I did scf with 6x6x1 (automatic) k-points, then nscf with 6x6x1 and 12x12x1 (automatic)

Re: [Pw_forum] How to improve the DOS plot?

r /cyr...@nanotech.dtu.dk > Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ > > > > De : pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] de la part de > Rolly Ng [roll...@gmail.com] > Envoyé : vendredi 22 j

[Pw_forum] Graphene kpoint shift for scf and nscf calculation?

result? K_POINTS {automatic} 6 6 1 1 1 0 I have read P. E. Bloechl et al, PRB49, 16223 (1994) but I cannot get a clear picture. Thanks, Rolly Ng PhD, Research Fellow, Department of Physics and Materials Science, City University of Hong Kong Tel: +852 3442 4000 Fax:+852 3442 0538

Re: [Pw_forum] GPU and gamma only routines

Hi, I have test scf on GPU and it runs okay except that nspin=2 failed. If your model is non-magnetic, I believe it works. Regards, Rolly From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf Of Giuseppe Romano Sent: 2016年7月27日 9:20 To: PWSCF Forum Subject:

[Pw_forum] Conceptual question on molecularpdos.x?

ole system (surface + molecule)? or the other way round? Why? Thanks for your patient. Regards, Rolly Ng -- PhD. Research Fellow, Dept. of Physics & Materials Science, City University of Hong Kong Tel: +852 3442 4000 Fax: +852 3442 0538 ___ Pw_foru

[Pw_forum] Using molecularpdos.x for adsorption on metal-doped graphene

Dear QE experts, I am trying to refine computation of 3-NT adsorption on metal doped graphene using QE. This is according to our previous work http://dx.doi.org/10.1016/j.commatsci.2011.07.045 With the help of Dr. Guido Fratesi, I am exploring molecularpdos.x to find the change of HOMO and

[Pw_forum] 回复: Using molecularpdos.x for adsorption on metal-doped graphene

rresponding atomic states in the range for molecularpdos.x.Hope this helps,GuidoOn 09/08/2016 18:46, Rolly Ng wrote:> Dear QE experts,>> I am trying to refine computation of 3-NT adsorption on metal doped > graphene using QE. This is according to our previous work> http://dx.doi.org/10.1016/j.commatsci.2

Re: [Pw_forum] Using molecularpdos.x for adsorption on metal-doped graphene

Dear Guido, Here are my updates. On 08/11/2016 05:57 PM, Guido Fratesi wrote: > Dear Rolly, >> 3) Full-system Up, HOMO -2.1696 eV, LUMO -2.1449 eV, so |delta| >> HOMO-LUMO gap is 0.0247 eV >> 4) Full-system Down, HOMO -2.1935 eV, LUMO -2.1177 eV, so |delta| >> HOMO-LUMO gap is 0.0758 eV > Uhm,

Re: [Pw_forum] Using molecularpdos.x for adsorption on metal-doped graphene

12/2016 08:46 PM, Guido Fratesi wrote: Can you send me the results you get by running /the example/ up to the point where it hangs? Have you tried running on a different PC? Have you tried running it on top of the files I sent you? GF On 12/08/2016 14:42, Rolly Ng wrote: Dear Guido, I am using QE

Re: [Pw_forum] Using molecularpdos.x for adsorption on metal-doped graphene

/the example/ up to the point where it hangs? Have you tried running on a different PC? Have you tried running it on top of the files I sent you? GF On 12/08/2016 14:42, Rolly Ng wrote: Dear Guido, I am using QE ver 5.3.0 and I am running it on an OpenSUSE 13.2 server. I also have Intel

Re: [Pw_forum] Using molecularpdos.x for adsorption on metal-doped graphene

attitude to take anything for granted. Every single line of code requires time and effort. Paolo Il 13/ago/2016 07:14 AM, "Rolly Ng" <roll...@gmail.com <mailto:roll...@gmail.com>> ha scritto: Dear Guido, Oh, I just realize that the option kresolveddos=.false

[Pw_forum] Total energy of adsorbed molecule in a full system

have searched the .out file for "energy" but I cannot find energy of individual atoms in the full system so I cannot do any summation like sumpdos.x? Can anyone help? Thank you, Rolly Ng -- PhD. Research Fellow, Dept. of Physics & Materials Science, City University of Hong Kong

Re: [Pw_forum] Total energy of adsorbed molecule in a full system

energy of adsorbed molecule in a full system On 17 Aug 2016, at 10:40, Rolly Ng <roll...@gmail.com> wrote: Dear QE experts, I read about molecule deformation energy in the following article, I believe it was computed with VASP. DFT studies of the bonding mechanism of 8-hydroxyqui

Re: [Pw_forum] Total energy of adsorbed molecule in a full system

in a full system I don't think so. You just have to compute the energy of an isolated molecule with the geometry of the absorbed molecule. Paolo Il 17/ago/2016 07:45 AM, "Rolly Ng" <roll...@gmail.com> ha scritto: Dear Prof. Stefano, Thank you. So, is this a special

Re: [Pw_forum] Projected Band structure

Hi Riemann, You may try molecularpdos.x where you can project the selected atomic wave functions of the full system (corresponding to your graphene) onto the isolated graphene structure (without substrate). Rolly On 08/17/2016 02:05 PM, Riemann Derakhshan wrote: Dear QE Developer and

Re: [Pw_forum] quantum espresso GPU

Hi Francesco, There are two things for QE-GPU, 1) Hardware, the Maxwell GPU is not recommended for QE since its double precision is very slow. You shall look for Fermi (C207X) or Kepler (Titan Black/Z, K40/80) cards for QE-GPU computation. 2) Software, cuda-6.5 works okay for QE-GPU v.530

Re: [Pw_forum] Tutorial: Install QE-GPU binaries in latest ubuntu systems (v. 16.04), Nvidia Cuda 7.5 , Intel MKL and Intel MPI software with NVIDIA cards hardware

Dear Josué, Very nice and detail steps. Thank you! I would like to add that it also works for QE ver 5.3.0 on OpenSUSE 13.2. Supported GPU including: 1) Tesla C2050 2) Tesla C2070/75 3) Titan Z/Black/Original Regards, Rolly On 08/25/2016 04:21 AM, Josue Itsman Clavijo Penagos wrote:

[Pw_forum] Calculation of Gibbs free energy for NO2 gas

Dear QE experts, I am trying to calculate the Gibbs free energy of a NO2 gas molecule via the following steps, 1) pw.x to "relax" a NO2 gas molecule in a cube box 2) pw.x to calculate the "scf" energy with the relaxed NO2 gas geometry, using only 1 K-point at 0 0 0. (NO2_scf.in) 3) ph.x

Re: [Pw_forum] can not install parallel run of QE

Hi Tao, Your problem seems rather related to the operation system. Are you using Linux or Windows? If you are using Linux and Intel CPUs then you need to install the Intel MPI library and make sure that you load the MPI environmental variable before you run pw.x. Please baidu it. If

[Pw_forum] Running Environ with pw.x

./pw.x --environ -inp h2o.in |tee h2o.out, I can see the output file is being generated but I cannot see any subsection stating Environ in the output file as attached. Did it run with Environ plugin enabled? Is QE v.5.3.0 supported? Thanks for your advise. Regards, Rolly Ng -- PhD. Research

Re: [Pw_forum] Running Environ with pw.x

of Hong Kong Tel: +852 3442 4000 Fax: +852 3442 0538 From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf Of Oliviero Andreussi Sent: Thursday, September 15, 2016 8:40 PM To: PWSCF Forum Subject: Re: [Pw_forum] Running Environ with pw.x Dear Rolly Ng, I am

Re: [Pw_forum] Running Environ with pw.x

Dear Oliviero, Thanks for the very detailed explanation. It works now, and I might have missed some important steps in the previous trial. Besides, I notice that I have to place the environ.in at the same directory as with pw.x. Can I place it elsewhere instead? I am using pw.x --environ -inp

Re: [Pw_forum] Environ failed with graphene

you have any > other question. > > Best regards, > > Oliviero > -- > Senior Postdoctoral Researcher > École Polytechnique Fédérale de Lausanne (EPFL) and > Università della Svizzera Italiana (USI) of Lugano > USI Campus, Via G. Buffi 17, 6904 Lugano, Switzerland > Emai

Re: [Pw_forum] Quantum ESPRESSO @ Exabyte.io

Hi Timur, Very interesting. May I know the cost of using the facility? Best, Rolly On 10/06/2016 02:09 PM, Timur Bazhirov wrote: Fellow Quantum ESPRESSO users, Let me bring to your attention to exabyte.io : a web-based materials simulations platform with full support

[Pw_forum] cp.x output with cppp.x not showing correct atom type?

Dear cp.x users, I have completed my first cp simulation with benzene and its output with cppp.x to produce an axfs file. The geometry at ground state looks okay and the starting atomic position was copied from a previous pw.x run with 'relax'. My question with the cp.x output is that the

Re: [Pw_forum] cp.x output with cppp.x not showing correct atom type?

Hi all, Found my careless mistakes, cppp.x demands atomic_number instead of atomic mass. It works okay! On 10/15/2016 02:28 PM, Rolly Ng wrote: > Dear cp.x users, > > I have completed my first cp simulation with benzene and its output > with cppp.x to produce an axfs file. >

[Pw_forum] cppp.x axsf output range selection

Dear QE experts, I am using cp.x to do molecular dynamics and I divided the computation into parts and my starting structure is obtained from previous pw.x relaxation. 1) electron minimization, file_cp1.in, file_cp1.out, data directory created is file_51.save 2) randomization, file_cp2.in,

[Pw_forum] Adsorption energy calculation with cp.x and pw.x?

Dear Prof. Paolo and Dr. Furlan, I read about your article published in PCCP, DOI:10.1039/c3cp50696g, about NO2 adsorption with graphene-Rh cluster. I understand that molecular dynamic was performed with cp.x and geometrical optimization was performed with pw.x. I known that pw.x can

[Pw_forum] Howto DIY a small cluster with Infiniband for QE simulation?

Dear QE users, I used to run QE on individual server and the computation speed is quite limited. I am planning to build a small cluster with Intel CPUs and Nvidia GPUs dedicated to QE and the cluster will be used by a few people within the research group. The networking hardware that I

Re: [Pw_forum] QE-GPU problems.

Hi Konrad, My experience with QE-GPU is that it works only with double precision supported GPUs but not single precision. I am using TitanZ and Intel compiler, it works fast. Here is my ./configure ./configure CC=icc F90=ifort F77=ifort MPIF90=mpiifort --enable-parallel --disable-openmp

[Pw_forum] cp.x stops exceeding the maximum number of iteration

Dear QE users, I am running MD with cp.x and I am trying to observe the trajectory of a molecule detaching from nickel-doped graphene surface. It started with the molecule attached to the nickel atom in graphene sheet, electron minimization and ionic minimization in cp.x completed

[Pw_forum] Intel Xeon Phi support in QE6.0?

Dear QE developers, I would like to know the latest development in support of the Intel Xeon Phi accelerator in QE6.0. In particular, does it speed up calculation of pw.x with spin polarization, i.e. nspin=2? Thanks, Rolly PhD. Research Fellow, Dept. of Physics & Materials

[Pw_forum] pw.x slurm srun failed with intel mpi?

Dear QE users, I have srun problem on ubuntu 16.04 cluster with intel mpi. Could you please me to check what is going on? Thank you! I am trying to install slurm in a cluster running ubuntu 16.04. I am using intel mpi and the installation directory is located at the head node

Re: [Pw_forum] pw.x slurm srun failed with intel mpi?

lly, > > this mailing-list is about QE, not about fixing people's HPC clusters. I am > sorry but you need to find someone in your IT department that can help you on > this matter > > On Jan 15, 2017, at 7:51 AM, Rolly Ng <roll...@gmail.com> wrote: >> I have srun problem on ub

Re: [Pw_forum] Intel Xeon Phi support in QE6.0?

-for-intel-xeon-phi-coprocessor Thanks, Rolly On 01/15/2017 09:33 PM, Filippo SPIGA wrote: > Dear Rolly, > > On Jan 13, 2017, at 5:23 PM, Rolly Ng <roll...@gmail.com> wrote: >> I would like to know the latest development in support of the Intel Xeon Phi >> accel

[Pw_forum] Should I enable hyper-threading on QE v5.3.0?

Dear All, I think that it is generally recommended to switch off hyper-threading on Intel processors for running QE. My machine has dual E5-2683v3 and 256GB RAM, QE v5.3.0 was compiled with Intel Parallel Studio 2015. The AUSURF112 benchmark output (as attached) shows that enabling

[Pw_forum] Problem while compiling QE v5.3.0 with ELPA

Dear QE users, I am trying to compile QE v5.3.0 with ELPA by following the steps instructed here, https://software.intel.com/en-us/articles/quantum-espresso-for-the-intel-xeon-phi-processor But I am having unexpected error that fft_scalar.f90 complains unable to find fft_def.h? It stops

Re: [Pw_forum] Problem while compiling QE v5.3.0 with ELPA

eitsonen Sent: 2017年3月7日 16:51 To: PWSCF Forum Subject: Re: [Pw_forum] Problem while compiling QE v5.3.0 with ELPA Dear Rolly Ng, First a question: Why do you try to compile v5.3.0, in particular with pre-processor options that are meaningful only in newer versions of QE ("-D__EXX_ACE&q

[Pw_forum] Failed to explicit offload QE on Intel Xeon Phi 7120P (KNC)

Dear QE users, I am referring to the guide on Explicit offload QE to Xeon Phi KNC (7120P) here, https://software.intel.com/en-us/articles/explicit-offload-for-quantum-espresso I tried to follow the above steps but I failed to run pw.x (QE v5.3.0) on 2 Xeon Phi 7120P using the mpirun.sh

Re: [Pw_forum] QE-GPU performance

Dear Phanikumar, Please include your affiliation when posting to the forum. In my experience with QE-GPU v5.3.0 and v5.4.0, the working combination of software is, 1) Intel PSXE 2017 2) CUDA 6.5 or 7.0 3) Centos 7.1 Please try the above combination. Regards, Rolly PhD. Research Fellow,

Re: [Pw_forum] QE-GPU performance

5.68 pw-gpu.x 20064 x 20 0 0.158t 408012 153100 R 100.0 0.3 36:25.54 pw-gpu.x 20098 x 20 0 0.158t 398404 153436 R 100.0 0.3 36:27.92 pw-gpu.x -- Message: 5 Date: Sun, 10 Dec 2017 17:07:59 +0800 From: Rolly Ng <roll...@gmail.com> Subj