RE: [gmx-users] Building Single and Double Precision in 4.6.1?
Thanks, I've posted a summary of my build process (OpenMPI and Gromacs 4.6.1 using Intel compilers) in case it's helpful to anyone else: http://flakrat.blogspot.com/2013/04/how-to-compile-gromacs-461-with-openmpi.html Mike -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Szilárd Páll Sent: Thursday, April 18, 2013 12:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Building Single and Double Precision in 4.6.1? On Thu, Apr 18, 2013 at 6:17 PM, Mike Hanby mha...@uab.edu wrote: Thanks for the reply, so the next question, after I finish building single precision non parallel, is there an efficient way to kick off the double precision build, then the single precision mpi and so on? Or do I need to delete everything from my build directory before running cmake again? Well, most setting can just be changed in the build tree and rerunning cmake build trigger a rebuild, e.g.: $ cmake path/to/source -DGMX_DOUBLE=OFF -DCMAKE_INSTALL_PREFIX=/my/install/path; make install -j; cmake .-DGMX_DOUBLE=ON; make install -j; However, I recommend that you do your builds outside the source tree in separate build directories - or at least in separate directories in the source tree - and just use the same CMAKE_INSTALL_PREFIX for every build. One concern is that each time I run cmake, it will download fftw and the regression tests. If you want to do regression tests of multiple builds, to avoid the downloading, you should download the regressiontests tarball manually and just point cmake to it instead of having it download every time. While you'll need a different FFTW build for double precision, you are right that single precision MPI vs thread-MPI builds would not need a different FFTW. If you want to avoid this (IMHO minor) overhead, compile FFTW manually and just point CMake to it (via CMAKE_PREFIX_PATH). Cheers, -- Szilárd -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Monday, April 15, 2013 11:05 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Building Single and Double Precision in 4.6.1? That's best. GROMACS will take care of a _d suffix for double precision for you. Mark On Mon, Apr 15, 2013 at 5:39 PM, Mike Hanby mha...@uab.edu wrote: Howdy, What's the proper procedure for building both single and double precision and installing them to the same directory? For example, is this the proper set of steps? #Build and install single precision cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DGMX_DOUBLE=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install Or is there a more efficient way? Thanks, Mike -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Building Single and Double Precision in 4.6.1?
Thanks for the reply, so the next question, after I finish building single precision non parallel, is there an efficient way to kick off the double precision build, then the single precision mpi and so on? Or do I need to delete everything from my build directory before running cmake again? One concern is that each time I run cmake, it will download fftw and the regression tests. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Monday, April 15, 2013 11:05 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Building Single and Double Precision in 4.6.1? That's best. GROMACS will take care of a _d suffix for double precision for you. Mark On Mon, Apr 15, 2013 at 5:39 PM, Mike Hanby mha...@uab.edu wrote: Howdy, What's the proper procedure for building both single and double precision and installing them to the same directory? For example, is this the proper set of steps? #Build and install single precision cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DGMX_DOUBLE=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install Or is there a more efficient way? Thanks, Mike -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Building Single and Double Precision in 4.6.1?
On Thu, Apr 18, 2013 at 6:17 PM, Mike Hanby mha...@uab.edu wrote: Thanks for the reply, so the next question, after I finish building single precision non parallel, is there an efficient way to kick off the double precision build, then the single precision mpi and so on? Or do I need to delete everything from my build directory before running cmake again? Well, most setting can just be changed in the build tree and rerunning cmake build trigger a rebuild, e.g.: $ cmake path/to/source -DGMX_DOUBLE=OFF -DCMAKE_INSTALL_PREFIX=/my/install/path; make install -j; cmake .-DGMX_DOUBLE=ON; make install -j; However, I recommend that you do your builds outside the source tree in separate build directories - or at least in separate directories in the source tree - and just use the same CMAKE_INSTALL_PREFIX for every build. One concern is that each time I run cmake, it will download fftw and the regression tests. If you want to do regression tests of multiple builds, to avoid the downloading, you should download the regressiontests tarball manually and just point cmake to it instead of having it download every time. While you'll need a different FFTW build for double precision, you are right that single precision MPI vs thread-MPI builds would not need a different FFTW. If you want to avoid this (IMHO minor) overhead, compile FFTW manually and just point CMake to it (via CMAKE_PREFIX_PATH). Cheers, -- Szilárd -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Monday, April 15, 2013 11:05 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Building Single and Double Precision in 4.6.1? That's best. GROMACS will take care of a _d suffix for double precision for you. Mark On Mon, Apr 15, 2013 at 5:39 PM, Mike Hanby mha...@uab.edu wrote: Howdy, What's the proper procedure for building both single and double precision and installing them to the same directory? For example, is this the proper set of steps? #Build and install single precision cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DGMX_DOUBLE=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install Or is there a more efficient way? Thanks, Mike -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Building Single and Double Precision in 4.6.1?
Howdy, What's the proper procedure for building both single and double precision and installing them to the same directory? For example, is this the proper set of steps? #Build and install single precision cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DGMX_DOUBLE=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install Or is there a more efficient way? Thanks, Mike -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Building Single and Double Precision in 4.6.1?
That's best. GROMACS will take care of a _d suffix for double precision for you. Mark On Mon, Apr 15, 2013 at 5:39 PM, Mike Hanby mha...@uab.edu wrote: Howdy, What's the proper procedure for building both single and double precision and installing them to the same directory? For example, is this the proper set of steps? #Build and install single precision cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DGMX_DOUBLE=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install Or is there a more efficient way? Thanks, Mike -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
