Download the CUDA On Thu, Aug 25, 2016 at 11:00 AM, <[email protected]> wrote:
> Send Pw_forum mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://pwscf.org/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. controlling output (Murray Daw) > 2. Re: error messege igcx (Paolo Giannozzi) > 3. Re: controlling output (Paolo Giannozzi) > 4. 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 (Josue Itsman Clavijo Penagos) > 5. Re: 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 (Rolly Ng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 24 Aug 2016 13:39:18 +0000 > From: Murray Daw <[email protected]> > Subject: [Pw_forum] controlling output > To: "[email protected]" <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8" > > I am writing a driver that will call the PWSCF functions numerous times > (~10,000). > It is producing more output than I need. > Is there any way to reduce the amount of output? > I have verbosity set to ?low? already. > I don?t want to turn it off completely, just lower it. > > Thanks. > > Best, > Murray Daw > > ____________________________________________________ > MURRAY S. DAW > R. A. Bowen Professor of Physics > Dept of Physics & Astronomy > Clemson University > 202A Kinard Labs > Clemson, SC 29634-0978 > Phone: (864)656-6702 > FAX: (864)656-0805 > e-mail: [email protected] > website http://myweb.clemson.edu/~daw > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 24 Aug 2016 15:44:37 +0200 > From: Paolo Giannozzi <[email protected]> > Subject: Re: [Pw_forum] error messege igcx > To: PWSCF Forum <[email protected]> > Message-ID: > <CAPMgbCsSaA5yFZVKeJ7yZRh+m6kGV6UXS3AFMKn=1Pcw4jHkBw@ > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > If you are using option "input_dft", check that he value you provided is > correct. If not: check the DFT label in the header of pseudopotential files > (for UPF files, search for 'Exchange_Correlation') > > Paolo > > On Wed, Aug 24, 2016 at 11:49 AM, mohammadreza hosseini < > [email protected]> wrote: > > > Dear all > > > > I am studding electronic and magnetic properties of SnO2 clusters. I have > > performed relax calculations and now i am doing SCF job using espresso > > v.5.1. In the scf calculations i get this error : > > > > > > Error in routine set_dft_from_name (1): > > conflicting values for igcx > > > > I have searched different webs in particular espresso forum. > > Is it possible for you to help me what i should do? > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > [email protected] > > http://pwscf.org/mailman/listinfo/pw_forum > > > > > > -- > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://pwscf.org/pipermail/pw_forum/attachments/20160824/ > da3d53f9/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Wed, 24 Aug 2016 15:45:39 +0200 > From: Paolo Giannozzi <[email protected]> > Subject: Re: [Pw_forum] controlling output > To: PWSCF Forum <[email protected]> > Message-ID: > <CAPMgbCuBQ9w=ZKCE3WauypSQ2bAXcjy91q-umVGBRxyfkVFXgA@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > See variable "printout" in electrons.f90. Paolo > > On Wed, Aug 24, 2016 at 3:39 PM, Murray Daw <[email protected]> wrote: > > > I am writing a driver that will call the PWSCF functions numerous times > > (~10,000). > > It is producing more output than I need. > > Is there any way to reduce the amount of output? > > I have verbosity set to ?low? already. > > I don?t want to turn it off completely, just lower it. > > > > Thanks. > > > > Best, > > Murray Daw > > > > ____________________________________________________ > > MURRAY S. DAW > > R. A. Bowen Professor of Physics > > Dept of Physics & Astronomy > > Clemson University > > 202A Kinard Labs > > Clemson, SC 29634-0978 > > Phone: (864)656-6702 > > FAX: (864)656-0805 > > e-mail: [email protected] > > website http://myweb.clemson.edu/~daw > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > [email protected] > > http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://pwscf.org/pipermail/pw_forum/attachments/20160824/ > 6ed27313/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Wed, 24 Aug 2016 15:21:10 -0500 > From: Josue Itsman Clavijo Penagos <[email protected]> > Subject: [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 > To: PWSCF Forum <[email protected]> > Message-ID: > <CAJgMqa+H+09SSrJcHU1wTcQWzn_Sk0Jj9Mm+pGR-+ZOYUqk+ww@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I?m posting the following rather introductory, not professional-level > tutorial for Installing QE-GPU binaries In recent ubuntu systems using > Nvidia Cuda, Intel MKL, Intel MPI software and NVIDIA GPU kepler-model > cards hardware, since i think this might be useful for any of you fellow > scientists struggling to get working their quantum espresso GPU-enabled > installations. > > I, by no means, do pretend to offer an in-depth description of every and > all given steps, since i?m no a technology expert; in fact, much of this > are referred to mail discussions, Urls and documentation readings found out > inside the same used installation packages. > > *The only purpose of this post* is to give some useful advice and, mainly, > to unify and share to whom may be interested all the available information > I?ve found in order to get, to the present extent of my technology skills, > a more-or-less complete and comprehensive tutorial containing all what it?s > needed to get success about QE-GPU installation and usage. > > A big *thank you* to the following scholars for all of your highly valuable > advice and key assistance to get this done: > > > *Ari Paavo Seitsonen* > *Claudio Quarti* > and all of you > *PW_FORUM FELLOWS* > > > All trademarks, copyrights and author ownerships over texts, codes and > original information links *are respected and are the exclusive property of > their rightfully legitimate owners*. > > I apologize for any typos or vocabulary/redaction errors; I?m not a native > english speaker. > > > All said above, in the attached file I share what I did to get a flawless > compilation. > > *Best regards, * > > Josu? Clavijo, Dr. Sc. in Chemistry > Assistant Professor > Universidad Nacional de Colombia > Science College > Chemistry Department > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://pwscf.org/pipermail/pw_forum/attachments/20160824/ > e461b163/attachment-0001.html > -------------- next part -------------- > > I?m posting the following rather introductory, not professional-level > tutorial for Installing QE-GPU binaries In ubuntu systems using Nvidia > Cuda, Intel MKL, Intel MPI software and NVIDIA cards hardware since i think > this would be useful for any of you fellow scientists struggling to get > working their quantum espresso GPU-enabled installations. > > I, by no means, do pretend to offer an in-depth description of every and > all given steps, since i?m no a technology expert; in fact, much of this > are referred to Urls and documentation found out inside the same used > installation packages. > > The only purpose of this post is to give some useful advice and, mainly, > to unite all the available information I?ve found in order to get, to the > present extent of my technology skills, a more-or-less complete and > comprehensive tutorial containing all what it?s needed to get success about > QE-GPU installation and usage. > > A BIG THANK YOU to the following scholars for all you you advice and key > assistance to get this done: > > PW_FORUM FELLOWS > Ari Paavo Seitsonen > Claudio Quarti > > All trademarks, copyrights, author ownerships over texts, codes and > original information links are respected and are the exclusive property of > their rightfully legitimate owners. > > I apologize for any typos/missing vocabulary/redaction errors; I?m not a > native english speaker. > > > ALL SAID ABOVE , HERE?S WHAT I DID TO GET A FLAWLESS COMPILATION FOR > QE-GPU BINARIES > > > BASIC HARDWARE/SOFTWARE SYSTEM SETUP EXAMPLE: > > -> UBUNTU MATE 16.04 LTS (MANY People posting in the Web recommends MATE > or another Ubuntu ?Flavor? instead original ubuntu distribution, due to the > Unity graphic desktop interface suffers of crash issues using Nvidia Cards > very often) > > (NOTE: Why using a graphic interface? Mainly due to get able to use PW-Gui > for QE binary executables, Virtual NanoLab Interface, XCrysden and another > auxiliary and useful crystallography tools such as Vesta, and also to be > able to use remote manager solutions such as Teamviewer.) > > -> GPU Card 1: NVIDIA QUADRO K620 > -> GPU Card 2: NVIDIA TESLA K20C > -> CUDA 7.5 > -> NVIDIA DRIVER 364 > -> QUANTUM ESPRESSO 5.4.0 > -> QE-GPU 5.4.0 > > > TESTED pw-gpu.x and ph-gpu.x performance using Barium Titanate and Methyl > Ammonium Lead Iodide perovskite unit cells (from *.cif crystallographic > files, exported to QE format using the free Virtual Nanolab GUI and edited > with the right path for PPs? and outdir folders, and some chosen prefix .) > - not so very extensive benchmarks, only proof-of-working tests -: > > pw-gpu.x works in SCF with full-relativistic PPs and non collinear > spin-orbit settings, Relax and VC-Relax modes including force and stress > minimization in vc-relax and relax modes. The nscf mode was not tested, but > I see no reason this mode would crash) > > ph-gpu.x calculates Raman and IR spectra using a fully relaxed cell in > gamma-only mode, following tutorial examples in the quantum espresso > packages; > > Various automatic k-points grids and e_cutoffs used. Also, the > ./pw_cutoff.sh tests for optimal e_cutoff for PPS used also works: > directions posted in http://larrucea.eu/checking-optimum-cutoff-qe/ . > > Finally, the nvidia-smi test shows the usage of the Tesla GPU for > calculations. > > > I?m open to every comments, suggestions and corrections and they all are > already welcome. > > > ************************************************************ > ************************************************************ > *********************************** > > > > ********* ---- MAJOR TUTORIAL UPDATE : AUG 24th, 2016 ---- ********** > > ############ PRELIMINARY REMARKS: ################# > > 1 - IF YOU?RE BEHIND A PROXY, after a fresh ubuntu installation, do this > to get internet connection (for apt-get), setting the following apt config > via terminal: > > $ sudo pluma /etc/apt/apt.conf > > Paste into that file, and save-and-close after: > > Acquire::http::proxy "http://username:password@proxy-name:8080/";; > Acquire::https::proxy "http://username:password@proxy-name:8080/";; > > 2 - Setup Internet browser proxy config, to download QE and QE-GPU > packages: > > Set automatic proxy settings with something like the URL: > http://proxy-name:8080/proxy.pac (consult your web proxy administrator, > if needed) > > 3 - Install COMPILERS AND Libraries > > GCC > G++ > GFORTRAN > Intel MKL > Intel MPI > > -> FFTW?s are read from MKL libraries. > > OPEN MPI (Follow instructions in the *.tar.gz package downloaded from > https://www.open-mpi.org) (It?s entirely OPTIONAL if you?re gonna use > INTEL MPI) > > ############ END OF PRELIMINARY REMARKS: ################# > > > ############ INSTALLING NVIDIA DRIVER AND CUDA 7.5 SECTION: > ################# > > LATEST WORKING CONFIGURATION FOR FUTURE QE-GPU ./configure step: > > INSTALL THE NVIDIA DRIVER 364 > (As stated at http://askubuntu.com/questions/760934/graphics- > issues-after-installing-ubuntu-16-04-with-nvidia-graphics) > > You need the PPA APT link for Nvidia-364 driver. First, include the > graphics-drivers debian repositories in Ubuntu software origins. Go to > > https://launchpad.net/~graphics-drivers/+archive/ubuntu/ppa > > > And copy the PPA link according to your ubuntu distribution. > > Adde this link in software origins repositories listing, either by > terminal , running > > $ sudo add-apt-repository ppa:graphics-drivers/ppa and then sudo apt-get > update > > or by the same software origins tab via the software updates window. > > > Then install the driver typing in terminal > > $ sudo apt-get install nvidia-364 > > or by choosing the Nvidia-364 driver in additional drivers tab in the the > software updates window. > > It may happen that, when using a former Nvidia driver, you already are > experiencing too many graphic glitches, freezing, blinking, or even you are > not able to log in anymore. To fix this, follow the directions below: > > Log into your account in the TTY. > Run $ sudo apt-get purge nvidia-* > Run $ sudo add-apt-repository ppa:graphics-drivers/ppa and then > sudo apt-get update. > Run $ sudo apt-get install nvidia-364. > Reboot and your graphics issue should be fixed. > > If you are unable to enter a TTY (just a black screen and a blinking > cursor): > Reboot into GRUB. > Highlight the Ubuntu option and press e. > Add nouveau.modeset=0 to the end of the line beginning with the > word ?linux?. > Press F10 to boot. > Follow the instructions above to install the install nvidia-364 > driver. > > INSTALL CUDA-7.5: > > Type the code given below, as suggested in https://www.pugetsystems.com/ > labs/hpc/NVIDIA-CUDA-with-Ubuntu-16-04-beta-on-a-laptop- > if-you-just-cannot-wait-775/ : > > sudo apt-get install ca-certificates-java default-jre default-jre-headless > fonts-dejavu-extra freeglut3 freeglut3-dev java-common libatk-wrapper-java > libatk-wrapper-java-jni libdrm-dev libgl1-mesa-dev libglu1-mesa-dev > libgnomevfs2-0 libgnomevfs2-common libice-dev libpthread-stubs0-dev > libsctp1 libsm-dev libx11-dev libx11-doc libx11-xcb-dev libxau-dev > libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-present-dev > libxcb-randr0-dev libxcb-render0-dev libxcb-shape0-dev libxcb-sync-dev > libxcb-xfixes0-dev libxcb1-dev libxdamage-dev libxdmcp-dev libxext-dev > libxfixes-dev libxi-dev libxmu-dev libxmu-headers libxshmfence-dev > libxt-dev libxxf86vm-dev lksctp-tools mesa-common-dev x11proto-core-dev > x11proto-damage-de x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev > x11proto-input-dev x11proto-kb-dev x11proto-xext-dev > x11proto-xf86vidmode-dev xorg-sgml-doctools xtrans-dev libgles2-mesa-dev > nvidia-modprobe build-essential > > (FORM THE LINK: You can "sudo apt-get install" the above list and that > should get most or all of the dependencies. There is a possibility that > there will still be missing debs. For example I added the last three > entries to the list when I discovered that they were missing on my new > 16.04 install after the others were installed. That's is probably because > they were already installed on the 15.04 system it ran "apt-get -s install > cuda" on i.e. they didn't come up as needed dependencies because they were > already installed.) > > USING CUDA runtime Installer (That?s better than the *.deb file > option, since you are able to NOT install the packed NVIDIA driver (That > WUold overwrite the 364 driver) and just install the Cuda Toolkit and > Samples. > > Download the CUDA .run file from the NVIDIA download site. I used this, > http://developer.download.nvidia.com/compute/cuda/7.5/ > Prod/local_installers/cuda_7.5.18_linux.run > > $ chmod 755 cuda_7.5.18_linux.run > > $ sudo ./cuda_7.5.18_linux.run --override > > NOTICE: The "--override" is needed so you don't get the fatal error > saying: Toolkit: Installation Failed. Using unsupported Compiler, that > prompts the installer when finds that GCC is a >4.9 version, and coda seems > to be incompatible with that. > > Be sure to NOT install the NVIDIA driver that is in the .run file since > you already have a more up to date version installed, as said before. > > YOU SHOULD GET FINALLY: > > Driver: Not Selected > Toolkit: Installed in /usr/local/cuda-7.5 > Samples: Installed in /usr/local/cuda-7.5 > > 3 - To check if CUDA are working and calling to the Tesla card properly, > open a terminal window and go to /deviceQuery folder: > > $ cd /home/quantum/NVIDIA_CUDA-7.5_Samples/1_Utilities/ > deviceQuery > > # AND compile deviceQuery executable: > > $ make > > # Then type > > $ ./deviceQuery > > > # If CUDA was properly installed and Tesla card are recognized, > you should get something like: > > > $ ./deviceQuery Starting... > > CUDA Device Query (Runtime API) version (CUDART static linking) > > Detected 2 CUDA Capable device(s) > > Device 0: "Tesla K20c" > CUDA Driver Version / Runtime Version 6.0 / 6.0 > CUDA Capability Major/Minor version number: 3.5 > Total amount of global memory: 4800 MBytes (5032706048 > bytes) > (13) Multiprocessors, (192) CUDA Cores/MP: 2496 CUDA Cores > GPU Clock rate: 706 MHz (0.71 GHz) > Memory Clock rate: 2600 Mhz > Memory Bus Width: 320-bit > L2 Cache Size: 1310720 bytes > Maximum Texture Dimension Size (x,y,z) 1D=(65536), 2D=(65536, > 65536), 3D=(4096, 4096, 4096) > Maximum Layered 1D Texture Size, (num) layers 1D=(16384), 2048 layers > Maximum Layered 2D Texture Size, (num) layers 2D=(16384, 16384), 2048 > layers > Total amount of constant memory: 65536 bytes > Total amount of shared memory per block: 49152 bytes > Total number of registers available per block: 65536 > Warp size: 32 > Maximum number of threads per multiprocessor: 2048 > Maximum number of threads per block: 1024 > Max dimension size of a thread block (x,y,z): (1024, 1024, 64) > Max dimension size of a grid size (x,y,z): (2147483647, 65535, 65535) > Maximum memory pitch: 2147483647 bytes > Texture alignment: 512 bytes > Concurrent copy and kernel execution: Yes with 2 copy engine(s) > Run time limit on kernels: No > Integrated GPU sharing Host Memory: No > Support host page-locked memory mapping: Yes > Alignment requirement for Surfaces: Yes > Device has ECC support: Enabled > Device supports Unified Addressing (UVA): Yes > Device PCI Bus ID / PCI location ID: 4 / 0 > Compute Mode: > < Default (multiple host threads can use ::cudaSetDevice() with > device simultaneously) > > > Device 1: "Quadro K620" > CUDA Driver Version / Runtime Version 6.0 / 6.0 > CUDA Capability Major/Minor version number: 5.0 > Total amount of global memory: 2048 MBytes (2147155968 > bytes) > ( 3) Multiprocessors, (128) CUDA Cores/MP: 384 CUDA Cores > GPU Clock rate: 1124 MHz (1.12 GHz) > Memory Clock rate: 900 Mhz > Memory Bus Width: 128-bit > L2 Cache Size: 2097152 bytes > Maximum Texture Dimension Size (x,y,z) 1D=(65536), 2D=(65536, > 65536), 3D=(4096, 4096, 4096) > Maximum Layered 1D Texture Size, (num) layers 1D=(16384), 2048 layers > Maximum Layered 2D Texture Size, (num) layers 2D=(16384, 16384), 2048 > layers > Total amount of constant memory: 65536 bytes > Total amount of shared memory per block: 49152 bytes > Total number of registers available per block: 65536 > Warp size: 32 > Maximum number of threads per multiprocessor: 2048 > Maximum number of threads per block: 1024 > Max dimension size of a thread block (x,y,z): (1024, 1024, 64) > Max dimension size of a grid size (x,y,z): (2147483647, 65535, 65535) > Maximum memory pitch: 2147483647 bytes > Texture alignment: 512 bytes > Concurrent copy and kernel execution: Yes with 1 copy engine(s) > Run time limit on kernels: Yes > Integrated GPU sharing Host Memory: No > Support host page-locked memory mapping: Yes > Alignment requirement for Surfaces: Yes > Device has ECC support: Disabled > Device supports Unified Addressing (UVA): Yes > Device PCI Bus ID / PCI location ID: 3 / 0 > Compute Mode: > < Default (multiple host threads can use ::cudaSetDevice() with > device simultaneously) > > > Peer access from Tesla K20c (GPU0) -> Quadro K620 (GPU1) : No > > Peer access from Quadro K620 (GPU1) -> Tesla K20c (GPU0) : No > > deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 6.0, CUDA Runtime > Version = 6.0, NumDevs = 2, Device0 = Tesla K20c, Device1 = Quadro K620 > Result = PASS > ------------------------------------------------------------ > ------------------------------------------------------------ > ------------------------- > > 4 - It seems not necessary to install the basic versions fftw3, mpi > (message passing interface standards) and MPICH libraries, however. In > Software Center, search for each one, but install the -dev options, because > quantum espresso and QE-GPU compilers make calls to *.dev libraries and NOT > to normal libraries (e. g., call to libfftw3-mpi-dev and NOT to > libfftw3-mpi3 !!!) > > 5 - The phiGEMM package comes bundled with the QE-GPU package, then IT is > NOT necessary to download the phigemm package separately. > > 6 - in ./configure, it seems that the openmp option blocks usage of > lapack and fftw3 libraries. Need some research switching ./configure > parameters and flags in order to get optimal configuration and best make > final builds. ?> ANSWER: USE openmp with intel MKL and MPI libraries. > > > ############ END OF INSTALLING NVIDIA DRIVER AND CUDA 7.5 SECTION > ################# > > > POST-INSTALLATION CHECKS for CUDA and Tesla card proper operation: > > ( Remember that ?caja? replaces nautilus and ?pluma? replaces gedit IN > UBUNTU MATE ) > > PLEASE take in account the following, AFTER INSTALLING CUDA-7.5 > > edit /usr/local/cuda/include/host_config.h and comment out line 115: > > $ sudo pluma /usr/local/cuda/include/host_config.h > > line: 115 comment out error > //#error -- unsupported GNU version! gcc versions later than 4.9 are not > supported! > > THAT PREVENTS FATAL ERRORS for the QE-GPU compilation steps, since Cuda > 7.5 and gcc > 5+ are INCOMPATIBLE. > > > **** PRE-QE-GPU CONFIGURATION Requirements: ********** > > > 1. MAKE SURE YOU HAVE INSTALLED ALL THE REQUIRED LIBRARIES > > 2. DECLARE some Environment variables (by pasting as bottom lines in > .bashrc): (examples given, replace with the actual paths for your system) > > $ export PATH=/home/quantum/Descargas/QE-5.4/espresso-5.4.0:$PATH > $ export PATH=/home/quantum/Descargas/QE-5.4/PWgui-5.4.0:$PATH > $ export PHI_DGEMM_SPLIT=0.950 > $ export PHI_ZGEMM_SPLIT=0.950 > $ export PATH=/usr/local/cuda-7.5/bin:$PATH > $ export LD_LIBRARY_PATH=/usr/local/cuda-7.5/lib64:$LD_LIBRARY_PATH > $ source /opt/intel/bin/compilervars.sh intel64 > $ export PATH=/opt/intel/bin:$PATH > $ export LD_LIBRARY_PATH=/opt/intel/lib/intel64:$LD_LIBRARY_PATH > $ export LD_LIBRARY_PATH=/opt/intel/compilers_and_libraries_2016. > 2.181/linux/mpi/intel64/lib:$PATH > > 3. Rebuild library configuration (examples given, replace with the actual > paths): > > Open a nautilus (MATE: caja) windows AS ROOT (nautilus: graphical > file explorer for debian-based linux distros with Unity desktop; Caja= > Nautilus equivalent in MATE desktops flavor) > > Note: You may need to install gksu previously : sudo apt-get > install gksu > > $ sudo gksu nautilus (sudo gksu caja) > > Go to the file /etc/ld.so.conf.d/x86_64-linux-gnu.conf > > put the necessary links one per line at the end of other existing > lines (example): > > Multiarch support > /lib/x86_64-linux-gnu > /usr/lib/x86_64-linux-gnu > /usr/local/cuda-7.5/lib64 > /opt/intel/composer_xe_2015.3.187/mkl/lib/intel64 > /opt/intel/compilers_and_libraries_2016.3.223/linux/ > mkl/lib/intel64_lin > /opt/intel/compilers_and_libraries/linux/mkl/lib/ > intel64_lin > /opt/intel/compilers_and_libraries_2016.3.223/linux/ > mpi/intel64/lib > /opt/intel/compilers_and_libraries_2016.3.223/linux/ > mpi/intel64/lib > /opt/intel/compilers_and_libraries_2016.3.223/linux/ > mkl/interfaces/fftw3xc > /opt/intel/compilers_and_libraries_2016.3.223/linux/ > mkl/interfaces/fftw3x_cdft > /opt/intel/compilers_and_libraries_2016.3.223/linux/ > mkl/interfaces/fftw3x_cdft/obj_intel64_lp64 > /opt/intel/compilers_and_libraries_2016.3.223/linux/ > mkl/interfaces/fftw3xf > > save file and exit the nautilus window. > > Ready to Rebuild library configuration.... > > In terminal: > > $ sudo ldconfig > > Check if libraries are properly installed and listed: > > $ ldconfig -p |less #Scroll lines with the mouse wheel, > when "END" appears, press q > > MAKE SURE YOU SEE MKL, OPENMP, CUDA AND INTEL MPI libraries > (libmkl?) and exit terminal. > > **** END OF PRE-QE-GPU CONFIGURATION Requirements ********** > > > **** AND AT LEAST, QE-GPU CONFIGURATION **** > > > DOWNLOAD THE QUANTUM ESPRESSO AND QE-GPU PACKAGES FROM THEIR RESPECTIVE > URLs. > > ** NOTE: AN ERROR ABOUT TOO MANY DIRECTORY LEVELS COMPLAINS OFTEN. INSTALL > ESPRESSO IN A ROOT DIRECTORY TO AVOID IT. (/home ) ** > > 0.1 Unpack the espresso-5.4.0 tar.gz package in /home/your-username or > just in /home . > > 0.2 Move the packages > > atomic-5.4.0.tar.gz > GWW-5.4.0.tar.gz > neb-5.4.0.tar.gz > PHonon-5.4.0.tar.gz > pwcond-5.4.0.tar.gz > tddfpt-5.4.0.tar.gz > xspectra-5.4.0.tar.gz > > to the ?Archives? Folder in the espresso root directory. > > 1. Copy QE-GPU in espresso directory > > Move to the espresso root directory, uncompress the archive > $ tar zxvf QE-GPU-<TAG-NAME>.tar.gz > > create a symbolic link with the name GPU > $ ln -s QE-GPU-<TAG-NAME> GPU > > Replace <TAG-GPU> with the ACTUAL TAG name/id (example: 5.4.0 ) > > 2. Run QE-GPU configure (in terminal, from GPU dir): > > NOTICE: I did no use the ?with-scalapack option because this is no > a cluster installation. > > $ cd /opt/intel/compilers_and_libraries_2016.2.181/linux/mkl/bin > > $ source mklvars.sh intel64 lp64 > > check that INTEL MPI is running the mpirun protocol, typing in the > same terminal: > > $ cd /opt/intel/compilers_and_libraries_2016.3.223/linux/mpi/intel64/bin > > quantum@quantum-Precision-Tower-7810:/opt/intel/ > compilers_and_libraries_2016.3.223/linux/mpi/intel64/bin$ source > mpivars.sh release > > quantum@quantum-Precision-Tower-7810:/opt/intel/ > compilers_and_libraries_2016.3.223/linux/mpi/intel64/bin$mpirun > > The mpirun command above gives a lot of lines that should end in > something kinda: > > Intel(R) MPI Library for Linux* OS, Version 5.1.3 Build 20160601 (build > id: 15562) > Copyright (C) 2003-2016, Intel Corporation. All rights reserved. > > > NOW GO BACK TO THE GPU FOLDER INSIDE espresso-x.x.x folder: > > $ cd /home/quantum/Descargas/QE-5.4/espresso-5.4.0/GPU > > ./configure --enable-parallel --enable-openmp --enable-cuda > ?-without-scalapack with-gpu-arch=sm_35 > --with-cuda-dir=/usr/local/cuda-7.5/bin > --without-magma --with-phigemm > > > 3. The ./configure command should create new files in the espresso root > folder: > > Make.sys > > makefile.gpu > > # Since your are in terminal inside > /home/quantum/Descargas/QE-5.4/espresso-5.4.0/GPU > folder , type > > cd .. > > # To come back to cd /home/quantum/Descargas/QE-5.4/espresso-5.4.0 > (in terminal). > > 4. ALERT: Before doing Make, edit the Make.sys: > > - if you are using Intel MPI, please add to DFLAGS > "-DMPICH_SKIP_MPICXX" to make.sys DFLAGS > ignore MPI C++ bindings. > > ADD to THE make.sys FILE THE FOLLOWING LD_LIBS flags: > > -L/usr/lib64 -lstdc++ > > ??> THE ABOVE LINE IS CRUCIAL TO AVOID ERRORS during doing make > compilation, errors such as > > ?> ERROR: Too many symbolic link levels > ?> stdc++ errors > ?> A too buggy compilation > ?> Compilation finishes, but the pw-gpu.x or ph-gpu.x executables > does not work properly > > ...AND DON?T FORGET to add to the NVCC line the flag > -D_FORCE_INLINES in make.sys: > > ... > NVCCFLAGS = -O3 -gencode arch=compute_35,code=sm_35 > -D_FORCE_INLINES > > > to make.sys for ph-gpu.x compilation! > > > -> NOTICE: May be too naive or not worthy to comment about, but DO NOT > attempt to compile ph-gpu.x BEFORE to compile pw-gpu.x. If you do so, > you?ll SURELY get a bunch of fatal errors saying something like > > error: modules not found. > > If you do not use the all-gpu option by any reason, use THE VERY SAME > logical compilation order > > make -f Makefile.gpu pw-gpu.x > make -f Makefile.gpu ph-gpu.x > make -f Makefile.gpu neb-gpu.x (if needed) > > > 5. FINAL: To build pw-gpu.x, ph-gpu.x and neb-gpu.x executables: > > make -f Makefile.gpu all-gpu > > > > > **** sMISSION COMPLETE. **** > > > > *** RAMAN: POST-PROCESSING THE *.DMAT FILES THAT ph.x / ph-gpu.x CREATES : > *** (always remember to type the actual paths) > > create a <custom-name>.dm.in file containing (examples given): > > &input fildyn='/home/quantum/PWgui-5.4.0/dmat.Mapbi3pospress', > asr='simple' / > > then, in a terminal, go to dynmat.x location: > > $ cd /home/quantum/Descargas/QE-5.4-NO-GPU/espresso-5.4.0/bin > > and type > > $ ./dynmat.x < /home/quantum/PWgui-5.4.0/mapbi3pospress.dm.in > > /home/quantum/PWgui-5.4.0/mapbi3pospress-asr-simple.dm.out > > note that in the output file, "asr-simple" points out the acoustic sum > rule used; > there are three basic options available: > > simple > crystal > zero-dim > > You should known which is best for each material you study (ask your > tutor/supervisor). > > The resulting file, as in the example, mapbi3pospress-asr-simple.dm.out, > contains the frequencies and intensities for both IR an Raman spectra, > ready to plot. > > > **** ---- END OF TUTORIAL - MAJOR UPDATE : AUG 24TH, 2016 ---- **** > > > THAT?S ALL , THANKS FOR READING AND COMMENTING. > > > KIND REGARDS, > > Josu? Clavijo > Universidad Nacional de Colombia > Science College > Chemistry Department > > ************************************************************ > ************************************************************ > *********************************** > > LINKS: > > http://askubuntu.com/questions/760934/graphics-issues-after-installing- > ubuntu-16-04-with-nvidia-graphics > > https://blog.levilentz.com/?p=312 > > https://www.pugetsystems.com/labs/hpc/NVIDIA-CUDA-with- > Ubuntu-16-04-beta-on-a-laptop-if-you-just-cannot-wait-775/ > > ?> PPA APT link for the Nvidia-364 driver repository: > > https://launchpad.net/~graphics-drivers/+archive/ubuntu/ppa > > > ------------------------------ > > Message: 5 > Date: Thu, 25 Aug 2016 08:07:45 +0800 > From: Rolly Ng <[email protected]> > Subject: 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 > To: PWSCF Forum <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="windows-1252" > > Dear Josu?, > > 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: > > Dear all, > > > > I?m posting the following rather introductory, not professional-level > > tutorial for Installing QE-GPU binaries In recent ubuntu systems using > > Nvidia Cuda, Intel MKL, Intel MPI software and NVIDIA GPU kepler-model > > cards hardware, since i think this might be useful for any of you > > fellow scientists struggling to get working their quantum espresso > > GPU-enabled installations. > > > > I, by no means, do pretend to offer an in-depth description of every > > and all given steps, since i?m no a technology expert; in fact, much > > of this are referred to mail discussions, Urls and documentation > > readings found out inside the same used installation packages. > > > > *The only purpose of this post* is to give some useful advice and, > > mainly, to unify and share to whom may be interested all the available > > information I?ve found in order to get, to the present extent of my > > technology skills, a more-or-less complete and comprehensive tutorial > > containing all what it?s needed to get success about QE-GPU > > installation and usage. > > > > A big *thank you* to the following scholars for all of your highly > > valuable advice and key assistance to get this done: > > > > > > *Ari Paavo Seitsonen* > > *Claudio Quarti* > > and all of you > > *PW_FORUM FELLOWS* > > * > > * > > * > > * > > All trademarks, copyrights and author ownerships over texts, codes and > > original information links *are respected and are the exclusive > > property of their rightfully legitimate owners*. > > > > I apologize for any typos or vocabulary/redaction errors; I?m not a > > native english speaker. > > > > > > All said above, in the attached file I share what I did to get a > > flawless compilation. > > > > *Best regards, * > > > > Josu? Clavijo, Dr. Sc. in Chemistry > > Assistant Professor > > Universidad Nacional de Colombia > > Science College > > Chemistry Department > > > > > > _______________________________________________ > > Pw_forum mailing list > > [email protected] > > http://pwscf.org/mailman/listinfo/pw_forum > > -- > PhD. Research Fellow, > Dept. of Physics & Materials Science, > City University of Hong Kong > Tel: +852 3442 4000 > Fax: +852 3442 0538 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://pwscf.org/pipermail/pw_forum/attachments/20160825/ > 6f3a4400/attachment-0001.html > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > End of Pw_forum Digest, Vol 109, Issue 25 > ***************************************** >
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