[Pw_forum] Pw_forum Digest, Vol 47, Issue 22

Fri May 6 04:37:17 CEST 2011

Dear Victor,
Thanks. When i type the command ./configure after i move to folder where
quantum espresso is installed, i get the following message:

/home/mahmud/Documents/quanesp/espresso-4.3a
mahmud at mahmud-ubuntu:~/Documents/quanesp/espresso-4.3a$ ./configure
bash: ./configure: Permission denied
mahmud at mahmud-ubuntu:~/Documents/quanesp/espresso-4.3a$ sudo ./configure
sudo: ./configure: command not found

Need help!
Mahmud

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> Today's Topics:
>    1. Re: First PWscf GPU-enabled beta-release (Vit)
>    2. Re: Need help to install quantum espresso (Vit)
>    3. Re: First PWscf GPU-enabled beta-release (Ivan Girotto)
>    4. Re: electron-phonon interaction in QE 4.3 (Paolo Giannozzi) 5. Re:
electron-phonon interaction in QE 4.3 (Nandan Tandon)
>    6. Re: using wf_collect only for a few bands (Paolo Giannozzi)
> ----------------------------------------------------------------------
Message: 1
> Date: Thu, 5 May 2011 23:24:53 +0700
> From: Vit <vitruss at gmail.com>
> Subject: Re: [Pw_forum] First PWscf GPU-enabled beta-release
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <201105052324.54165.vitruss at gmail.com>
> Content-Type: Text/Plain;  charset="utf-8"
> Dear Ivan,
> Can you please proveide any benchmarks and comparison of Hybrid CPU/GPU
vs
> pure CPU computation?
> With best regards,
> Victor.
> Ivan Girotto <ivan.girotto at ichec.ie>
> Thursday 05 May 2011
>> Dear QE users & developers,
>> We are happy to announce that the first beta GPU-enabled release of
Quantum ESPRESSO (QE) has been committed today in the official
>> repository.
>> You can download the new version of the code using the following command:
>> $ svn checkout
>> svn://scm.qe-forge.org/scmrepos/svn/q-e/branches/espresso-PRACE The
Irish Centre for High-End Computing (ICHEC, www.ichec.ie
>> <http://www.ichec.ie>) has been mainly responsible for extending the QE
suite to enhance calculations on NVIDIA GPUs. The porting activity has
been supported within the PRACE 1st Implementation Phase project. It is
currently carried out through the Sub-task "Accelerator", led by ICHEC,
within the Work-Package "Programming Techniques for High-Performance
Applications" in collaboration with CINECA.
>> The porting activity is concerned mainly with the PWscf package. But
ICHEC and the Irish QE user community are interested in exploring any
other initiatives which come forward from QE users or developers
interested in porting on GPGPU architecture any of the QE suite related
codes.
>> We have successfully accelerated the linear algebra part of the QE
suite
>> using a library called phiGEMM, some explicit computational kernels
(newd, addusdense, vloc_psi) and the 3D FFT for the single CPU/GPU
version. Both linear algebra (matrix multiplication) and the FFT
accelerated version make use of CUDA libraries. The porting is mainly
based on wrappers that permit the use of libraries for accelerators.
The
>> distributed 3D FFT version is still in progress, since this porting
requires important changes of the current structure of the code and
data
>> distribution. While running the parallel and distributed multi-GPUs
version it still uses the original 3D FFT implementations.
>> The phiGEMM library is distributed as an independent open-source
external package together with the Quantum ESPRESSO suite. It aims to
perform matrix multiplication ([SDZ]GEMM) taking advantage of the
underlying BLAS kernel functions on both CPU and NVIDIA CUDA-based GPU,
mixing and overlapping computation between the host (CPU) and the
accelerator (GPU). Whatever code makes intensive use of GEMM it can
derive a significant advantage linking this library when running on a
CPU/GPU hybrid system.
>> Even if the 3D FFT is accelerated only for a single CPU process (not
when using MPI), other parts are already enabled to take advantage of a
distributed parallel hybrid system. All of this allows PWscf to
potentially use distributed message-passing parallelization (MPI) plus
multi-threading (OpenMP) plus accelerators (NVIDIA GPUs) all together
and produce good performance enhancement using the latest version of
NVIDIA GPUs (high performance double precision is needed). This porting
activity is still in progress, especially the parallel 3D FFT component
that represents a bottleneck for large calculations. We have been
testing this beta release using some small/medium benchmarks used in
the
>> DEISA official bench-suite and several GPU hardware (Tesla and Fermi
architectures). Special thanks goes to both E4 Computer Engineering and
CEA for providing access to hybrid GPU systems with differing
>> configurations to those available at ICHEC.
>> We look forward with interest to receiving any suggestions for
>> improvement, feedback or request for collaboration by anyone who is
interested to try and validate PWscf CUDA version on different
platforms
>> using different scientific cases.For additional information please
contact qe-gpu at ichec.ie or replay at this mail. We'll be shortly
available a dedicated forum q-e-gpgpu at qe-forge.org
>> <http://qe-forge.org/mail/?group_id=10>. Please use this list for bug
report and any other issue related to the use of the PWscf GPU version.
Although compilation of the GPU implementation is fairly
>> straight-forward, we kindly suggest that users carefully read the
README.GPU that is included. The intrinsic characteristics of hybrid
multi- and many-core systems require careful consideration to best
exploit the available computing power.
>> Any and all suggestions are welcome and will be very much appreciated.
Ivan Girotto & Filippo Spiga
>> ---
>> ICHEC GPU developer team
>> The Tower - 7th floor
>> Trinity Technology&  Enterprise Campus
>> Grand Canal Quay - Dublin 2 - Ireland
>> +353-1-5241608 (ph) / +353-1-7645845 (fax)
> ------------------------------
> Message: 2
> Date: Thu, 5 May 2011 23:26:59 +0700
> From: Vit <vitruss at gmail.com>
> Subject: Re: [Pw_forum] Need help to install quantum espresso
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <201105052326.59676.vitruss at gmail.com>
> Content-Type: Text/Plain;  charset="utf-8"
> Dear Dr. Rahmar!
> I can help. If you can provide me with ssh access to your Ubuntu
installation.
> Or you can specify the problem here (or in private email) to solve it.
With best regards,
> Koroteev Victor
> "Dr. Mahmudur Rahman" <mahmud at science.upm.edu.my>
> Thursday 05 May 2011
>> Dear Users,
>> I have installed Ubuntu linux and would like to install quantum espresso.
>> I followed the user guide but could not succeed. Anybody can help me?
Regards,
>> Mahmud
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> ------------------------------
> Message: 3
> Date: Thu, 05 May 2011 18:01:39 +0100
> From: Ivan Girotto <ivan.girotto at ichec.ie>
> Subject: Re: [Pw_forum] First PWscf GPU-enabled beta-release
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4DC2D7F3.9010903 at ichec.ie>
> Content-Type: text/plain; charset="iso-8859-1"
> Hi Victor,
> benchmark and results will be presented at next ISC2011
> <http://www.supercomp.de/isc11/>.
> We have an agreement with NVIDIA as they want show our work on PWscf
code through a poster at their booth.
> Benchmarks need to be put together and analyzed before to be presented.
Then with the close deadline we'll bring number of upgrade in these
days.
> You can however download the code and test it your own updating
> frequently your source directory keeping it aligned with the SVN
repository.
> I will personally send you some number on your personal address mail
early next week in excel format since you looked particularly
interested.
> Please, let's move the discussion about PWscf GPU version on the
dedicated lists. We don't want spam pw_forum's member that are not
interested at this topic.
> Best regards,
> Ivan Girotto
> On 05/05/2011 17:24, Vit wrote:
>> Dear Ivan,
>> Can you please proveide any benchmarks and comparison of Hybrid CPU/GPU vs
>> pure CPU computation?
>> With best regards,
>> Victor.
>> Ivan Girotto<ivan.girotto at ichec.ie>
>> Thursday 05 May 2011
>>> Dear QE users&  developers,
>>> We are happy to announce that the first beta GPU-enabled release of
Quantum ESPRESSO (QE) has been committed today in the official
repository.
>>> You can download the new version of the code using the following command:
>>> $ svn checkout
>>> svn://scm.qe-forge.org/scmrepos/svn/q-e/branches/espresso-PRACE The
Irish Centre for High-End Computing (ICHEC, www.ichec.ie
>>> <http://www.ichec.ie>) has been mainly responsible for extending the
QE
>>> suite to enhance calculations on NVIDIA GPUs. The porting activity has
been supported within the PRACE 1st Implementation Phase project. It
is
>>> currently carried out through the Sub-task "Accelerator", led by
ICHEC,
>>> within the Work-Package "Programming Techniques for High-Performance
Applications" in collaboration with CINECA.
>>> The porting activity is concerned mainly with the PWscf package. But
ICHEC and the Irish QE user community are interested in exploring any
other initiatives which come forward from QE users or developers
interested in porting on GPGPU architecture any of the QE suite
related
>>> codes.
>>> We have successfully accelerated the linear algebra part of the QE suite
>>> using a library called phiGEMM, some explicit computational kernels
(newd, addusdense, vloc_psi) and the 3D FFT for the single CPU/GPU
version. Both linear algebra (matrix multiplication) and the FFT
accelerated version make use of CUDA libraries. The porting is mainly
based on wrappers that permit the use of libraries for accelerators.
The
>>> distributed 3D FFT version is still in progress, since this porting
requires important changes of the current structure of the code and
data
>>> distribution. While running the parallel and distributed multi-GPUs
version it still uses the original 3D FFT implementations.
>>> The phiGEMM library is distributed as an independent open-source
external package together with the Quantum ESPRESSO suite. It aims to
perform matrix multiplication ([SDZ]GEMM) taking advantage of the
underlying BLAS kernel functions on both CPU and NVIDIA CUDA-based
GPU,
>>> mixing and overlapping computation between the host (CPU) and the
accelerator (GPU). Whatever code makes intensive use of GEMM it can
derive a significant advantage linking this library when running on a
CPU/GPU hybrid system.
>>> Even if the 3D FFT is accelerated only for a single CPU process (not
when using MPI), other parts are already enabled to take advantage of
a
>>> distributed parallel hybrid system. All of this allows PWscf to
potentially use distributed message-passing parallelization (MPI) plus
multi-threading (OpenMP) plus accelerators (NVIDIA GPUs) all together
and produce good performance enhancement using the latest version of
NVIDIA GPUs (high performance double precision is needed). This
porting
>>> activity is still in progress, especially the parallel 3D FFT
component
>>> that represents a bottleneck for large calculations. We have been
testing this beta release using some small/medium benchmarks used in
the
>>> DEISA official bench-suite and several GPU hardware (Tesla and Fermi
architectures). Special thanks goes to both E4 Computer Engineering
and
>>> CEA for providing access to hybrid GPU systems with differing
>>> configurations to those available at ICHEC.
>>> We look forward with interest to receiving any suggestions for
improvement, feedback or request for collaboration by anyone who is
interested to try and validate PWscf CUDA version on different
platforms
>>> using different scientific cases.For additional information please
contact qe-gpu at ichec.ie or replay at this mail. We'll be shortly
available a dedicated forum q-e-gpgpu at qe-forge.org
>>> <http://qe-forge.org/mail/?group_id=10>. Please use this list for bug
report and any other issue related to the use of the PWscf GPU
version.
>>> Although compilation of the GPU implementation is fairly
>>> straight-forward, we kindly suggest that users carefully read the
README.GPU that is included. The intrinsic characteristics of hybrid
multi- and many-core systems require careful consideration to best
exploit the available computing power.
>>> Any and all suggestions are welcome and will be very much appreciated.
Ivan Girotto&  Filippo Spiga
>>> ---
>>> ICHEC GPU developer team
>>> The Tower - 7th floor
>>> Trinity Technology&   Enterprise Campus
>>> Grand Canal Quay - Dublin 2 - Ireland
>>> +353-1-5241608 (ph) / +353-1-7645845 (fax)
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> --
> Girotto Ivan  - ivan.girotto at ichec.ie
> ICHEC - Computational Group - http://www.ichec.ie
> The Tower - 7th floor
> Trinity Technology&  Enterprise Campus
> Grand Canal Quay - Dublin 2 - Ireland
> +353-1-5241608 ex. 32 (ph) / +353-1-7645845 (fax)
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------------------------------
> Message: 4
> Date: Thu, 5 May 2011 19:55:18 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] electron-phonon interaction in QE 4.3
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <29F7F223-578A-4C50-8EB7-AD3D9784B7A0 at democritos.it>
Content-Type: text/plain; charset=US-ASCII; format=flowed
> On May 5, 2011, at 16:49 , Nandan Tandon wrote:
>> Could you please elaborate on the "better alternatives".
> see http://epw.org.uk/, and an alternative implementation:
> http://prb.aps.org/abstract/PRB/v82/i16/e165111
>> I want to calculate electron phonon coupling in semiconductors.
> QE calculates electron-phonon coupling in metals only
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> ------------------------------
> Message: 5
> Date: Thu, 5 May 2011 14:02:41 -0400
> From: Nandan Tandon <nandan.tandon at gmail.com>
> Subject: Re: [Pw_forum] electron-phonon interaction in QE 4.3
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <BANLkTimP=-PHVcQUPhZBcGJsN4N4B_8kSw at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
> Thank you. I will look at these.
> Nandan.
> On Thu, May 5, 2011 at 1:55 PM, Paolo Giannozzi <giannozz at democritos.it>
wrote:
>> On May 5, 2011, at 16:49 , Nandan Tandon wrote:
>>> Could you please elaborate on the "better alternatives".
>> see http://epw.org.uk/, and an alternative implementation:
>> http://prb.aps.org/abstract/PRB/v82/i16/e165111
>>> I want to calculate electron phonon coupling in semiconductors.
>> QE calculates electron-phonon coupling in metals only
>> P.
>> ---
>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> --
> ***********************************************************************************************
Nandan Tandon
> Department of Physics,
> Worcester Polytechnic Institute,
> 100 Institute Road,
> Worcester, MA
> *************************************************************************************************
------------------------------
> Message: 6
> Date: Thu, 5 May 2011 20:48:41 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] using wf_collect only for a few bands
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <5B6DB19F-B0BE-4EAA-96A3-324E3CD5C042 at democritos.it>
Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes;
> 	format=flowed
> On May 3, 2011, at 17:36 , J. D. Burton wrote:
>> Is there a way to use the ?wf_collect? to save wavefunctions ONLY for a
few bands at each k-point, say +/- 1eV around the Fermi energy?
> nothing ready to use, I think
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> ------------------------------
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> End of Pw_forum Digest, Vol 47, Issue 22
> ****************************************

-- 
Dr. Mahmudur Rahman
Senior Lecturer
Department of Physics
Faculty of Science
University Putra Malaysia
43400 UPM Serdang
Selangor
MALAYSIA
Tel:+60-3-8946-6683
Mobile Phone:+60-173369047
Fax:+60-3-8945-4454
Email:mahmud at science.upm.edu.my