Re: [QE-users] users Digest, Vol 204, Issue 18

2024-07-22 Thread Robinson Juma Musembi 
2. Pencil decomposition (Suraj P)
Quantum Espresso automatically chooses Slab decomposition, the error you
are encountering can be avoided by reducing the number of processors you
are requesting in your command: mpirun -np xx pw.x  -i file.in -o|tee
file.out. if in case you feel that you want to use the same number of
processors, then use the command that commands Quantum espresso to use
Pencil decomposition instead of the default Slab decomposition: mpirun -np
xx pw.x -pd .true. -i file.in -o|tee file.out. Take note that the number of
processors the QE picks depends on the MPI software installed, example if
your machine is installed with mpich, the command mpirun -np 8 the machine
will pick 8 logical processors, if your machine is installed with openmpi,
the command mpirun -np 8, the machine will pick 16 logical processors.

*Robinson J.  Musembi (PhD)*
Solid State and Materials Research
Department of Physics, University of Nairobi
P.O. Box 30197 Nairobi

On Mon, Jul 22, 2024 at 1:01 PM 
wrote:

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> Today's Topics:
>
>1. Phonon calculation error. (Gulshan Kumar)
>2. Pencil decomposition (Suraj P)
>3. Re: Pencil decomposition (Ghosh, Prasenjit)
>
>
> --
>
> Message: 1
> Date: Sun, 21 Jul 2024 18:28:39 +0530
> From: Gulshan Kumar 
> To: Quantum ESPRESSO users Forum 
> Subject: [QE-users] Phonon calculation error.
> Message-ID:
>  6cj9-fpzkuj_mnioox...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi everyone,
>
> I am getting the error in phonon calculation:
>
>  kpoint  54 ibnd  81 solve_linter: root not convergedNaN
>
>  Pert. #  1: Fermi energy shift (Ry) =NaNNaN
>
>
>  
> %%
>  Error in routine broyden (1):
>  factorization
>
>  
> %%
>
>  stopping ...
>
> My input file is :
>
>
> 
>   prefix = 'a1'
>   amass(1) = 26.982
>   amass(2) = 9.012
>   amass(3) = 1.008
>   amass(4) = 15.999
>   amass(5) = 28.085
>   outdir = './pwscf_out/'
>   fildyn = 'phonon.dyn'
>   trans = .true.
>   ldisp = .true.
>   nq1 = 6
>   nq2 = 6
>   nq3 = 6
>   start_q = 1
>   last_q = 1
>   tr2_ph = 1.0d-14
>   alpha_mix(1) = 0.7
>   alpha_mix(2) = 0.3
>   diagonalization = 'david'
> /
> 0.0 0.0 0.0
>
> my k points in input file are :
>
> *6 6 6 1 1 1*
> Thank you for the help
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> --
>
> Message: 2
> Date: Mon, 22 Jul 2024 11:09:06 +0530 (IST)
> From: Suraj P 
> To: users 
> Subject: [QE-users] Pencil decomposition
> Message-ID:
> <577399914.4146722.1721626746365.javamail.zim...@iitkgp.ac.in>
> Content-Type: text/plain; charset="utf-8"
>
> Dear QE users,
> Im getting an error when I have done vc-relax calcualtion for Ni2P
> hexagonal lattice asking me to use pencil decomposition. Under which cards
> and what comment should be written to eliminate this error.
> Im  attaching the input and output files of the same. kindly have a look
> into these.
>
> Thanking you,
> Suraj
> Research student,
> IIT Kharagpur
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> --
>
> Message: 3
> Date: Mon, 22 Jul 2024 14:45:56 +0530 (IST)
> From: "Ghosh, Prasenjit" 
> To: users 
> Subject: Re: [QE-users] Pencil decomposition
> Message-ID:
> <953161903.13048274.1721639756396.javamail.zim...@iiserpune.ac.in>
> Content-Type: text/plain; charset=utf-8
>
> In the command line you should add the following:
>
> -pd .true.
>
> For eg.
>
> $/path_to_your_mpirun/mpirun -np 4 /path_to_your_qe/pw.x -pd .true. <
> name_of_input_file > name_of_output_file
>
> With regards,
> Prasenjit
>
> - Original Message -
> From: "Suraj P" 
>

[QE-users] [QE-GPU] Seeking Step-by-Step Installation Guide for GPU Version of Quantum Espresso (Miguel Urbiztondo) (Miguel Urbiztondo)

2023-07-18 Thread Robinson Juma Musembi 
Dear Miguel
the command --with-cuda-cc=xx is machine specific, to get details for your
specific machine run the following command at the terminal
nvaccelinfo
This will produce some useful information for example
$ nvaccelinfo | grep -e 'Target' -e 'Driver'
CUDA Driver Version:   11000
Default Target:cc70
You will input as
./configure --enable-openmp --with-cuda-mpi=yes
--with-cuda-prefix=/usr/local/2023/cuda --with-cuda-cc=70
--with-cuda-runtime=11.0

for openmpi use folder named 2023 instead of 23.3 as for example

 ./configure --with-cuda=/usr/local/Linux_x86_64/2023/cuda/
--prefix=/usr/local/openmpi-4.1.5/
path where hpc_sdk cuda has been installed example
=/usr/local/Linux_x86_64/2023/cuda/
path where you want to install openmpi example = /usr/local/openmpi-4.1.5/
regards

*Robinson J.  Musembi*
Solid State and Materials Research
Department of Physics, University of Nairobi

-- 
-
A KEBS 9001:2015 Certified 
Organization, No. KEBS/QMS/RF:064 Rev. 03



___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
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[QE-users] [QE-GPU] Seeking Step-by-Step Installation Guide for GPU Version of Quantum Espresso (Miguel Urbiztondo)

2023-07-14 Thread Robinson Juma Musembi 
Let me share the steps I followed in installing QE-GPU Quantum Espresso 7.2
on a desktop with an NVidia GTX 970 and Pop_OS_Nvidia 22.04 Linux distro.
The following method installs smoothly without error, but pw.x there is not
much difference in terms of speed, maybe anyone with an idea why
step1
start by installing the nvidia hpc_sdk software bundled with cuda
 start by downloading
 $ wget
https://developer.download.nvidia.com/hpc-sdk/23.3/nvhpc_2023_233_Linux_x86_64_cuda_12.0.tar.gz

 open the tarball
 $ tar xpzf nvhpc_2023_233_Linux_x86_64_cuda_12.0.tar.gz
 install
 $ sudo nvhpc_2023_233_Linux_x86_64_cuda_12.0/install
 the specify path to local as /usr/local
 export all path given after the installation
 gedit ~/.bashrc
 source ~/.bashrc

step 2
 install quantum espresso-built essentials

step 3
 install cuda aware openmpi
 ./configure --with-cuda=/usr/local/Linux_x86_64/2023/cuda/
--prefix=/usr/local/openmpi-4.1.5/
or
if path is as follows
./configure --with-cuda=/usr/local/cuda/ --prefix=/usr/local/openmpi-4.1.5/
then
  sudo make all install

step 4
  sudo apt install git  ==this is required by quantum espresso


step 5
 install quantum espresso
tar -xzvf quantum espresso tar.gz
then
quantum espresso install with cuda libxc and hdf5
./configure --enable-openmp --with-cuda-mpi=yes
--with-cuda-prefix=/usr/local/2023/cuda --with-cuda-cc=50
--with-cuda-runtime=12.0

Note that --with-cuda-cc=50 is machine dependent, some machines cc=70, or
80 etc

All the following files should have been exported to bashrc

export to bashrc
gedit ~/.bashrc
MANPATH=$MANPATH:/usr/local/Linux_x86_64/23.3/compilers/man; export MANPATH
PATH=/usr/local/Linux_x86_64/23.3/compilers/bin:$PATH; export PATH
export PATH=/usr/local/Linux_x86_64/23.3/comm_libs/mpi/bin:$PATH
export MANPATH=$MANPATH:/usr/local/Linux_x86_64/23.3/comm_libs/mpi/man
export PATH=$PATH:/usr/local/openmpi-4.1.5/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/openmpi-4.1.5/lib
export PATH=$PATH:/home/robinsonmusembi/DFT/qe-7.2/bin
source ~/.bashrc

*Robinson J.  Musembi*
Solid State and Materials Research
Department of Physics, University of Nairobi

-- 
-
A KEBS 9001:2015 Certified 
Organization, No. KEBS/QMS/RF:064 Rev. 03



___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

[QE-users] 2. k-point parallelisation using ESM-RISM: seg fault (Tom Demeyere)

2023-06-24 Thread Robinson Juma Musembi 
items in quote marks are interpreted as data type string by the computer,
the error might be triggered by how you have written the prefix

   calculation  = 'relax'
   restart_mode = 'from_scratch'
   nstep= 999
   tstress  = .false.
   tprnfor  = .true.
   outdir   = 'pw.dir'
   prefix   = ?pw'
   etot_conv_thr= 1e-06
   forc_conv_thr= 0.001
   trism= .true.
/

*Robinson J.  Musembi*
Solid State and Materials Research
Department of Physics, University of Nairobi

-- 
-
A KEBS 9001:2015 Certified 
Organization, No. KEBS/QMS/RF:064 Rev. 03



___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users