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 > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > You can reach the person managing the list at > pw_forum-owner at pwscf.org > When replying, please edit your Subject line so it is more specific than "Re: Contents of Pw_forum digest..." > 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) > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110505/d6fa2904/attachment-0001.htm ------------------------------ > 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
