Re: [QE-users] Quantum-ESPRESSO test run using GPU

[Pietro Bonfa']

Dear Dr. Cantele,

which of the two GPU enabled versions of QE are you testing?
I'm a bit confused by your error message. A quick google search pointed
me to the old qe-gpu-plugin
(https://github.com/fspiga/qe-gpu-plugin/search?utf8=%E2%9C%93&q=something+went+wrong+inside+query_gpu_specs&type=)
developed by Filippo Spiga, but the script in the benchmark repository
that you are considering targets the new porting developed by NVidia and
Spiga (https://github.com/fspiga/qe-gpu).

If you want to try the new version I suggest to use the openmpi bundled
with the PGI compiler and run with 1 MPI process per GPU.

Kind regards,
Pietro Bonfa'


On 03/12/2018 03:50 PM, Giovanni Cantele wrote:
> Dear all,
> 
> I would like to test Quantum-ESPRESSO using GPU. I think I’m not
> properly executing the running command, because I encounter errors like:
> 
> *** ERROR *** something went wrong inside query_gpu_specs! (rank
> 0)---
> Primary job  terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> ———
> 
> 
> These are my system specifications:
> i) version: qe-gpu-1.0
> ii) compiler: pgf90 17.10-0 64-bit 
> iii) OpenMPI 3.0.0 compiled with options: ./configure FC=pgfortran
> CC=pgcc CXX=pg++ —with-cuda=/opt/pgi/linux86-64/2017/cuda/8.0
> 
> I’m trying to run the AUSURF112 test, downloaded from the
> benchmark https://github.com/romerojosh/qe-gpu-benchmarks using the
> included run.sh.
> Probably I’m misunderstanding the parameters included therein.
> 
> My small system is composed by two CPUS with 16 cores each, and one
> NVIDIA Quadro P4000 GPU.
> 
> Could you please advise me about how to set the parameters within run.sh?
> 
> #!/bin/bash
> export QE_EXE=/home/cantele/CODES/Quantum-ESPRESSO/qe-5.4.0-GPU/bin/pw-gpu.x
> if [ -z "${QE_EXE}" ]; then echo "ERROR: Please export QE_EXE before
> running script." ; exit; fi
> 
> # QE run parameters
> NGPU=1
> NPOOL=2
> 
> # Node-specific parameters
> GPU_PER_SOCKET=2
> CORES_PER_SOCKET=16
> 
> NCORE_PER_RANK=$((${CORES_PER_SOCKET}/${GPU_PER_SOCKET}))
> 
> export OMP_NUM_THREADS=${NCORE_PER_RANK}
> export MKL_NUM_THREADS=${NCORE_PER_RANK}
> 
> /opt/openmpi/Portland/17.10/bin/mpirun -np ${NGPU} --map-by
> ppr:${GPU_PER_SOCKET}:socket ${QE_EXE} -input ../pw.in -npool ${NPOOL}
> | tee output_${NGPU}GPU_${NPOOL}POOL.txt
> 
> 
> 
> I thank you in advance,
> 
>     Giovanni
> 
> -- 
> 
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cant...@spin.cnr.it 
> Phone: +39 081 676910
> Skype contact: giocan74
> 
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.fisica.unina.it/~cantele
> 
> 
> 
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Re: [QE-users] obsolete mailing list on website

[Paolo Giannozzi]

On Mon, Mar 12, 2018 at 6:42 PM, Paolo Giannozzi 
wrote:

(the text in the main body of the page was instead updated no later than a
> few days ago)
>

but of course not on 29 March 2018 as written at the end of the page!

>
> On Mon, Mar 12, 2018 at 6:24 PM, Ye Luo  wrote:
>
>> Hi QE website maintainers,
>>
>> On the left side of http://www.quantum-espresso.org/forum.
>> The three mailing listed are not up-to-date.
>> Please mark them obsolete and add the new ones.
>>
>> Best,
>> Ye
>> ===
>> Ye Luo, Ph.D.
>> Leadership Computing Facility
>> Argonne National Laboratory
>>
>> ___
>> users mailing list
>> users@lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216 <+39%200432%20558216>, fax +39-0432-558222
> <+39%200432%20558222>
>
>


-- 
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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] obsolete mailing list on website

[Paolo Giannozzi]

I am afraid that nobody knows any longer how to do that (the text in the
main body of the page was instead updated no later than a few days ago).
Since the new web site is hopefully going online soon, I think it is wiser
to spend time on it than on the old one. Sorry for the inconvenient.

Paolo

On Mon, Mar 12, 2018 at 6:24 PM, Ye Luo  wrote:

> Hi QE website maintainers,
>
> On the left side of http://www.quantum-espresso.org/forum.
> The three mailing listed are not up-to-date.
> Please mark them obsolete and add the new ones.
>
> Best,
> Ye
> ===
> Ye Luo, Ph.D.
> Leadership Computing Facility
> Argonne National Laboratory
>
> ___
> users mailing list
> users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>



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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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[QE-users] obsolete mailing list on website

[Ye Luo]

Hi QE website maintainers,

On the left side of http://www.quantum-espresso.org/forum.
The three mailing listed are not up-to-date.
Please mark them obsolete and add the new ones.

Best,
Ye
===
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory
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[QE-users] Adding zero weight k-point in hybrid functional calculation

[Ye Luo]

Hi all,

When I used hybrid functional, there were some results I couldn't
understand.
When I added 8 extra k-points with weight 0, the total energy doesn't
change. This is good.
However, the eigenvalues for the zero weight k-points are very different
from the ones having weights, almost by 10 eV. Could somebody explain me
why they are so different?

I'm using 6.2.1 and the input/output files are attached.

Best,
Ye

K-points with non zero weights

  k = 0.0625 0.0625 0.0970 ( 36979 PWs)   bands (ev):

*   -53.0839 -52.9906 -28.0827 -28.0368 -27.9204* -27.8593 -27.8356 -27.7968
   -12.1235 -10.9444 -10.2473 -10.1599   1.3972   1.8189   2.3804   3.1172
 3.1651   4.5989   4.6761   5.0642   6.2827   6.6244   6.7135   7.1938
12.2533

  k = 0.0625 0.0625 0.2911 ( 36988 PWs)   bands (ev):

   *-53.1117 -53.0153 -28.0928 -28.0546 -28.0480* -27.9769 -27.9020 -27.8822
   -11.7609 -10.6965 -10.3172 -10.2280   1.8505   2.1602   2.7827   3.1244
 3.2151   4.2624   5.0855   5.1805   5.3720   6.2135   6.2331   7.1360
12.4254


K-points with zero weights

  k =-0.2500 0.5000-0.1941 ( 37004 PWs)   bands (ev):

*   -42.5037 -42.4122 -19.3809 -19.3714 -19.2420 *-19.2141 -19.1805 -19.1305
-3.4162  -3.3687  -2.3823  -2.3308   7.9738   8.0176   8.9348   8.9699
10.2413  10.2707  11.3846  11.4094  11.5913  11.6235  12.5038  12.5195
15.5560

  k =-0.2500 0.5000 0.5823 ( 36986 PWs)   bands (ev):

 *  -42.4692 -42.3774 -19.5967 -19.5241 -19.2954* -19.2666 -19.1922 -19.1602
-2.9201  -2.8660  -2.4351  -2.3823   7.9845   8.0040   8.8546   8.8783
 9.9004   9.9266  11.0131  11.0685  11.6606  11.6923  12.7962  12.8092
15.2910

===
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory


TiO2-rutile.tgz
Description: application/compressed-tar
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[QE-users] Quantum-ESPRESSO test run using GPU

[Giovanni Cantele]

Dear all,

I would like to test Quantum-ESPRESSO using GPU. I think I’m not properly 
executing the running command, because I encounter errors like:

*** ERROR *** something went wrong inside query_gpu_specs! (rank 
0)---
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
———


These are my system specifications:
i) version: qe-gpu-1.0
ii) compiler: pgf90 17.10-0 64-bit 
iii) OpenMPI 3.0.0 compiled with options: ./configure FC=pgfortran CC=pgcc 
CXX=pg++ —with-cuda=/opt/pgi/linux86-64/2017/cuda/8.0

I’m trying to run the AUSURF112 test, downloaded from the benchmark 
https://github.com/romerojosh/qe-gpu-benchmarks 
 using the included run.sh.
Probably I’m misunderstanding the parameters included therein.

My small system is composed by two CPUS with 16 cores each, and one NVIDIA 
Quadro P4000 GPU.

Could you please advise me about how to set the parameters within run.sh?

#!/bin/bash
export QE_EXE=/home/cantele/CODES/Quantum-ESPRESSO/qe-5.4.0-GPU/bin/pw-gpu.x
if [ -z "${QE_EXE}" ]; then echo "ERROR: Please export QE_EXE before running 
script." ; exit; fi

# QE run parameters
NGPU=1
NPOOL=2

# Node-specific parameters
GPU_PER_SOCKET=2
CORES_PER_SOCKET=16

NCORE_PER_RANK=$((${CORES_PER_SOCKET}/${GPU_PER_SOCKET}))

export OMP_NUM_THREADS=${NCORE_PER_RANK}
export MKL_NUM_THREADS=${NCORE_PER_RANK}

/opt/openmpi/Portland/17.10/bin/mpirun -np ${NGPU} --map-by 
ppr:${GPU_PER_SOCKET}:socket ${QE_EXE} -input ../pw.in -npool ${NPOOL} | tee 
output_${NGPU}GPU_${NPOOL}POOL.txt



I thank you in advance,

Giovanni

-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.fisica.unina.it/~cantele

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[QE-users] Defining a radical

[Laurens Siemons]

Dear all,


I'm not sure about the parameters you have to specify when you want to perform 
a (relax) calculation on a radical. For example, I want to perform a relax 
calculation on an ethyl radical. I don't find a lot of information about it in 
the manual/archives, but from the things I found I guess you have to specify 
'nspin = 2' and 'tot_magnetization = 1'. Is this correct? Or do you have to 
specify starting magnetization as well?


Do you have to specify this as well for an ethyl anion? or is it in this case 
enough to specify the charge like:


&SYSTEM
  ibrav = 0,
  nat   = 7,
  ntyp  = 2,
  ecutwfc   = 60,
  ecutrho   = 480,
  tot_charge = -1


Thanks in advance,

Laurens Siemons
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Re: [QE-users] ERROR(FoX) when executing crossing nodes

[Stefano Baroni]

Sorry. I though I had addressed my post *ONLY* to an Italian colleague … 
Multitasking is killing me … SB


> On 12 Mar 2018, at 10:36, Paolo Giannozzi  wrote:
> 
> For non-italian speakers: "Can't we solve with an initial check and if the 
> filesystem is not shared we read everything from a single node?"
> 
> Maybe: there is a check I wrote some time that should report whether the 
> filesystem is visible to all processors or not. The check is however never 
> used and I am not sure how well it works.
> 
> Paolo
> 
> On Mon, Mar 12, 2018 at 9:01 AM, Stefano Baroni  > wrote:
> non possiamo risolvere con un check all’inizio e se il file sistema non è 
> condiviso facciamo leggere tutto da un nodo? S.
> 
> 
>> On 12 Mar 2018, at 08:55, Pietro Delugas > > wrote:
>> 
>> Dear Duc-Long 
>> You are may be  using a file system which is not shared between all nodes. 
>> There in an issue in current implementation in using such filesystems which 
>> will be hopefully solved in the next future. For the time being you can 
>> compile QE  running the use configure script with the option --enable-xml=no 
>> ./configure --enable-xml=no
>> 
>> and the code should work. 
>> 
>> regard - pietro
>> 
>> 
>> 
>> On 12/03/2018 04:50, Duc-Long Nguyen wrote:
>>> Dear all,
>>> 
>>> Since the release of QE 6.2.1 I encountered the error message as following 
>>> when executing parallel pw.x on multi nodes:
>>> -
>>> ERROR(FoX)
>>> Cannot open file
>>> -
>>> There is no errors when running parallel on single node with the same input 
>>> file. I did not encounter this error using previous version of QE like 6.2, 
>>> 5.4.0 with the same make.inc (or make.sys).
>>> Attached please find the make.inc and the output file.
>>> 
>>> With best regards,
>>> Duc-Long
>>>  -- 
>>> Duc-Long Nguyen
>>> PhD Student, Molecular Science and Technology Program, TIGP
>>> Institute of Atomic and Molecular Sciences,
>>> Academia Sinica, Taipei 106, Taiwan
>>> Phone +886-979279073 
>>> 
>>> ___
>>> users mailing list
>>> users@lists.quantum-espresso.org 
>>> https://lists.quantum-espresso.org/mailman/listinfo/users 
>>> 
>> ___
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>> 
> 
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> 
> 
> 
> -- 
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
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Re: [QE-users] ERROR(FoX) when executing crossing nodes

[Paolo Giannozzi]

For non-italian speakers: "Can't we solve with an initial check and if the
filesystem is not shared we read everything from a single node?"

Maybe: there is a check I wrote some time that should report whether the
filesystem is visible to all processors or not. The check is however never
used and I am not sure how well it works.

Paolo

On Mon, Mar 12, 2018 at 9:01 AM, Stefano Baroni  wrote:

> non possiamo risolvere con un check all’inizio e se il file sistema non è
> condiviso facciamo leggere tutto da un nodo? S.
>
>
> On 12 Mar 2018, at 08:55, Pietro Delugas  wrote:
>
> Dear Duc-Long
>
> You are may be  using a file system which is not shared between all nodes.
> There in an issue in current implementation in using such filesystems which
> will be hopefully solved in the next future. For the time being you can
> compile QE  running the use configure script with the option
> --enable-xml=no
>
> ./configure --enable-xml=no
>
> and the code should work.
>
> regard - pietro
>
>
> On 12/03/2018 04:50, Duc-Long Nguyen wrote:
>
> Dear all,
>
> Since the release of QE 6.2.1 I encountered the error message as following
> when executing parallel pw.x on multi nodes:
> -
> ERROR(FoX)
> Cannot open file
> -
> There is no errors when running parallel on single node with the same
> input file. I did not encounter this error using previous version of QE
> like 6.2, 5.4.0 with the same make.inc (or make.sys).
> Attached please find the make.inc and the output file.
>
> With best regards,
> Duc-Long
>
> --
> Duc-Long Nguyen
> PhD Student, Molecular Science and Technology Program, TIGP
> Institute of Atomic and Molecular Sciences,
> Academia Sinica, Taipei 106, Taiwan
> Phone +886-979279073 <+886%20979%20279%20073>
>
>
>
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-- 
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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] ERROR(FoX) when executing crossing nodes

[Stefano Baroni]

non possiamo risolvere con un check all’inizio e se il file sistema non è 
condiviso facciamo leggere tutto da un nodo? S.


> On 12 Mar 2018, at 08:55, Pietro Delugas  wrote:
> 
> Dear Duc-Long 
> You are may be  using a file system which is not shared between all nodes. 
> There in an issue in current implementation in using such filesystems which 
> will be hopefully solved in the next future. For the time being you can 
> compile QE  running the use configure script with the option --enable-xml=no 
> ./configure --enable-xml=no
> 
> and the code should work. 
> 
> regard - pietro
> 
> 
> 
> On 12/03/2018 04:50, Duc-Long Nguyen wrote:
>> Dear all,
>> 
>> Since the release of QE 6.2.1 I encountered the error message as following 
>> when executing parallel pw.x on multi nodes:
>> -
>> ERROR(FoX)
>> Cannot open file
>> -
>> There is no errors when running parallel on single node with the same input 
>> file. I did not encounter this error using previous version of QE like 6.2, 
>> 5.4.0 with the same make.inc (or make.sys).
>> Attached please find the make.inc and the output file.
>> 
>> With best regards,
>> Duc-Long
>>  -- 
>> Duc-Long Nguyen
>> PhD Student, Molecular Science and Technology Program, TIGP
>> Institute of Atomic and Molecular Sciences,
>> Academia Sinica, Taipei 106, Taiwan
>> Phone +886-979279073
>> 
>> 
>> ___
>> users mailing list
>> users@lists.quantum-espresso.org 
>> https://lists.quantum-espresso.org/mailman/listinfo/users 
>> 
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Re: [QE-users] ERROR(FoX) when executing crossing nodes

[Pietro Delugas]

Dear Duc-Long

You are may be  using a file system which is not shared between all 
nodes. There in an issue in current implementation in using such 
filesystems which will be hopefully solved in the next future. For the 
time being you can compile QE  running the use configure script with the 
option --enable-xml=no


./configure --enable-xml=no

and the code should work.

regard - pietro


On 12/03/2018 04:50, Duc-Long Nguyen wrote:

Dear all,

Since the release of QE 6.2.1 I encountered the error message as 
following when executing parallel pw.x on multi nodes:

-
ERROR(FoX)
Cannot open file
-
There is no errors when running parallel on single node with the same 
input file. I did not encounter this error using previous version of 
QE like 6.2, 5.4.0 with the same make.inc (or make.sys).

Attached please find the make.inc and the output file.

With best regards,
Duc-Long
-- Duc-Long Nguyen PhD Student, Molecular Science and Technology 
Program, TIGP Institute of Atomic and Molecular Sciences, Academia 
Sinica, Taipei 106, Taiwan Phone +886-979279073



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