Re: [gmx-users] problem compiling gromacs 5.1
HI, I was able to compile gromacs 5.1 via: cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include" -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/ginstall -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a -DCMAKE_SKIP_RPATH=ON -DGMX_BUILD_SHARED_EXE=OFF -DSPHINX_EXECUTABLE=OFF Thank you for all your help and patience with mine somewhat basic questions! Cheers, Ana On Sat, Oct 24, 2015 at 9:31 PM, Mark Abraham wrote: > Hi, > > The purpose of using a wrapper compiler is that it handles linking all the > right stuff. MPI_LIBRARY was a thing from a cmake module we used only in > Gromacs 4.5, before we removed it when we decided that wrapper compilers do > a better job. So there's nothing that replaces it. That the recent > installation guides make zero mention of linking MPI libraries is a big > clue... > > Mark > > On Sat, 24 Oct 2015 22:05 Ana Marija wrote: > >> For 4.6.7 gromacs MPI_Library flag was necessary as well as for 4.5.5. >> What I am asking here is not weather my admins are doing a good job,and >> also as you know some things you just got with machine,and sometimes things >> are not great,so you have to make a workaround. What I am asking here is >> what is the function and is there is a function of mpi_Library flag in >> gromacs 5.1 and was that flag replaced with a different one in that version? >> On Oct 24, 2015 2:07 PM, "Mark Abraham" wrote: >> >>> Hi, >>> >>> On Sat, Oct 24, 2015 at 8:22 PM Ana Marija >>> wrote: >>> so I managed to install gromacs via: #in ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2" -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include" -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/ginstall -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a -DCMAKE_SKIP_RPATH=ON -DGMX_BUILD_SHARED_EXE=OFF -DSPHINX_EXECUTABLE=OFF on the and of the installation it was reported that: GMX_FORCE_CXX MPI_LIBRARY flags were not used. What I am worried about is MPI_LIBRARY flag. Does this means that gromacs just found on it's own MPI libraries or? >>> >>> What's more likely? That I said earlier that the point of the modules >>> you loaded is that you are using the magic wrapper compilers Cray provides >>> to handle MPI for you, or that I'm wrong about that *and* about my >>> assertion that MPI_LIBRARY was useless? :-) >>> >>> Not needing to know about such garbage is why you should be asking your >>> system administators to do these infrastructure things for you... >>> >>> Mark >>> >> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem compiling gromacs 5.1
Hi, The purpose of using a wrapper compiler is that it handles linking all the right stuff. MPI_LIBRARY was a thing from a cmake module we used only in Gromacs 4.5, before we removed it when we decided that wrapper compilers do a better job. So there's nothing that replaces it. That the recent installation guides make zero mention of linking MPI libraries is a big clue... Mark On Sat, 24 Oct 2015 22:05 Ana Marija wrote: > For 4.6.7 gromacs MPI_Library flag was necessary as well as for 4.5.5. > What I am asking here is not weather my admins are doing a good job,and > also as you know some things you just got with machine,and sometimes things > are not great,so you have to make a workaround. What I am asking here is > what is the function and is there is a function of mpi_Library flag in > gromacs 5.1 and was that flag replaced with a different one in that version? > On Oct 24, 2015 2:07 PM, "Mark Abraham" wrote: > >> Hi, >> >> On Sat, Oct 24, 2015 at 8:22 PM Ana Marija >> wrote: >> >>> so I managed to install gromacs via: >>> >>> #in ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> >>> >>> cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include >>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a >>> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2" >>> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include" >>> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON >>> -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON >>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/ginstall >>> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a >>> -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a >>> -DCMAKE_SKIP_RPATH=ON -DGMX_BUILD_SHARED_EXE=OFF -DSPHINX_EXECUTABLE=OFF >>> >>> on the and of the installation it was reported that: >>> GMX_FORCE_CXX >>> MPI_LIBRARY >>> >>> flags were not used. What I am worried about is MPI_LIBRARY flag. Does >>> this means that gromacs just found on it's own MPI libraries or? >>> >> >> What's more likely? That I said earlier that the point of the modules you >> loaded is that you are using the magic wrapper compilers Cray provides to >> handle MPI for you, or that I'm wrong about that *and* about my assertion >> that MPI_LIBRARY was useless? :-) >> >> Not needing to know about such garbage is why you should be asking your >> system administators to do these infrastructure things for you... >> >> Mark >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem compiling gromacs 5.1
For 4.6.7 gromacs MPI_Library flag was necessary as well as for 4.5.5. What I am asking here is not weather my admins are doing a good job,and also as you know some things you just got with machine,and sometimes things are not great,so you have to make a workaround. What I am asking here is what is the function and is there is a function of mpi_Library flag in gromacs 5.1 and was that flag replaced with a different one in that version? On Oct 24, 2015 2:07 PM, "Mark Abraham" wrote: > Hi, > > On Sat, Oct 24, 2015 at 8:22 PM Ana Marija > wrote: > >> so I managed to install gromacs via: >> >> #in ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> >> >> cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include >> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a >> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2" >> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include" >> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON >> -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON >> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/ginstall >> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a >> -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a >> -DCMAKE_SKIP_RPATH=ON -DGMX_BUILD_SHARED_EXE=OFF -DSPHINX_EXECUTABLE=OFF >> >> on the and of the installation it was reported that: >> GMX_FORCE_CXX >> MPI_LIBRARY >> >> flags were not used. What I am worried about is MPI_LIBRARY flag. Does >> this means that gromacs just found on it's own MPI libraries or? >> > > What's more likely? That I said earlier that the point of the modules you > loaded is that you are using the magic wrapper compilers Cray provides to > handle MPI for you, or that I'm wrong about that *and* about my assertion > that MPI_LIBRARY was useless? :-) > > Not needing to know about such garbage is why you should be asking your > system administators to do these infrastructure things for you... > > Mark > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem compiling gromacs 5.1
Hi, On Sat, Oct 24, 2015 at 8:22 PM Ana Marija wrote: > so I managed to install gromacs via: > > #in ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> > > cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include > -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a > -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2" > -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include" > -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON > -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON > -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/ginstall > -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a > -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a > -DCMAKE_SKIP_RPATH=ON -DGMX_BUILD_SHARED_EXE=OFF -DSPHINX_EXECUTABLE=OFF > > on the and of the installation it was reported that: > GMX_FORCE_CXX > MPI_LIBRARY > > flags were not used. What I am worried about is MPI_LIBRARY flag. Does > this means that gromacs just found on it's own MPI libraries or? > What's more likely? That I said earlier that the point of the modules you loaded is that you are using the magic wrapper compilers Cray provides to handle MPI for you, or that I'm wrong about that *and* about my assertion that MPI_LIBRARY was useless? :-) Not needing to know about such garbage is why you should be asking your system administators to do these infrastructure things for you... Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem compiling gromacs 5.1
so I managed to install gromacs via: #in ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2" -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include" -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/ginstall -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a -DCMAKE_SKIP_RPATH=ON -DGMX_BUILD_SHARED_EXE=OFF -DSPHINX_EXECUTABLE=OFF on the and of the installation it was reported that: GMX_FORCE_CXX MPI_LIBRARY flags were not used. What I am worried about is MPI_LIBRARY flag. Does this means that gromacs just found on it's own MPI libraries or? also gmx_mpi is there: ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build/bin> ls gmx_mpi template On Sat, Oct 24, 2015 at 11:39 AM, Mark Abraham wrote: > Hi, > > On Sat, Oct 24, 2015 at 6:32 PM Ana Marija > wrote: > >> Hay Mark, >> >> is it -DSPHINX_EXECUTABLE=OFF >> > > They're equivalent - cmake regards both of them as equivalent to "not > found." > > >> also just curious would commenting out that 62 line in >> /lustre/beagle2/ams/new/gromacs/gromacs-5.1/docs/CMakeLists.txt >> solve the problem as well? >> > > Looks like it, but not touching the source code is generally a good > strategy. It's much easier to record a cmake command than to record how the > source code was patched. > > >> can you please tell me what other flags I need in cmake or you are saying >> that I just have some redundant stuff there? >> > > I can't tell what you need, that's between you, the machine, the sysadmins > and their docs. I've said you have a bunch of things that don't exist / > don't exist any more and that makes your life more complex than you want it > to be. > > Mark > > >> Ana >> >> On Sat, Oct 24, 2015 at 11:29 AM, Mark Abraham >> wrote: >> >>> Hi, >>> >>> That one's our fault, sorry :-( It'll be fixed in 5.1.1 out shortly, but >>> you can work around it by adding >>> >>> -DSPHINX_EXECUTABLE=no >>> >>> to your cmake call (which, by the way, still has a lot of stuff in it >>> that I've said you don't want to have) >>> >>> Mark >>> >>> On Sat, Oct 24, 2015 at 6:14 PM Ana Marija >>> wrote: >>> HI, I tried to configure gromacs 5.1 via: ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2" -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include" -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/ginstall -DGMX_X11=OFF -DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF But I am getting this error: -- Found PythonInterp: /usr/bin/python (found version "2.6.9") CMake Error at cmake/FindSphinx.cmake:52 (string): string sub-command REGEX, mode REPLACE needs at least 6 arguments total to command. Call Stack (most recent call first): docs/CMakeLists.txt:62 (find_package) line 62 in /lustre/beagle2/ams/new/gromacs/gromacs-5.1/docs/CMakeLists.txt looks like this: find_package(Sphinx 1.2.3 QUIET COMPONENTS pygments) can
Re: [gmx-users] problem compiling gromacs 5.1
Hi, That one's our fault, sorry :-( It'll be fixed in 5.1.1 out shortly, but you can work around it by adding -DSPHINX_EXECUTABLE=no to your cmake call (which, by the way, still has a lot of stuff in it that I've said you don't want to have) Mark On Sat, Oct 24, 2015 at 6:14 PM Ana Marija wrote: > HI, > > I tried to configure gromacs 5.1 via: > > ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> cmake .. > -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include > -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a > > -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2" > -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include" > -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON > -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON > -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/ginstall > -DGMX_X11=OFF -DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF > > > But I am getting this error: > -- Found PythonInterp: /usr/bin/python (found version "2.6.9") > CMake Error at cmake/FindSphinx.cmake:52 (string): > string sub-command REGEX, mode REPLACE needs at least 6 arguments total > to > command. > Call Stack (most recent call first): > docs/CMakeLists.txt:62 (find_package) > > line 62 in /lustre/beagle2/ams/new/gromacs/gromacs-5.1/docs/CMakeLists.txt > looks like this: > > find_package(Sphinx 1.2.3 QUIET COMPONENTS pygments) > > can you please advise me on what to do? > > Thanks > Ana > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem compiling Gromacs 5.1
On 8/21/15 11:18 AM, Atsutoshi Okabe wrote:
Thanks, Mark.
I inserted quotation in line 52 as Mark suggested.
I tried cmake again and got the only error.
Boost >= 1.44 not found. Using minimal internal version. This may cause trouble
if you plan on compiling/linking other software that uses Boost against GROMACS.
I don't know what the error means, but I did make and make install.
After finished, I checked /bin directory. But almost all commands which we need
to execute(i.g mdrun, trjconv...) were not generated.
Actually, onlyI the following file were generated in bin directory.
bin/
bin/xplor2gmx.pl
bin/GMXRC.bash
bin/gmx-completion-gmx_mpi.bash
bin/demux.pl
bin/GMXRC.zsh
bin/GMXRC
bin/gmx-completion.bash
bin/GMXRC.csh
bin/gmx_mpi
What causes this problem?
There is no problem. This is the new convention - one binary, called gmx (in
this case gmx_mpi since you compiled with MPI) and everything is a module of
that binary:
gmx grompp ...
gmx mdrun ...
(etc)
-Justin
2015/08/20 21:44、Mark Abraham のメール：
Hi,
You should change line 52 from what it is, to what I suggested - which
inserts quotation marks around one of the variable interpolations.
Mark
On Thu, Aug 20, 2015 at 2:43 PM 岡部篤俊 wrote:
Thanks, Peter.
But , I mean I don’t know what line I should change to from line 52 of
cmake/FindPhinx.cmake to solve this error.
Leucer
2015/08/20 16:02、Kroon, P.C. のメール：
Just use your favourite text editor.
Peter
On Thu, Aug 20, 2015 at 3:10 AM, wrote:
Line 52 of cmake/FindSphinx.cmake file is written below.
string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
Can you tell me how I can change the line?
Bests,
Leucer
2015/08/19 23:11、Mark Abraham のメッセージ:
Hi,
On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 wrote:
Hi,
I am unable to compile Gromamcs 5.1 using the following cmake
command.
cmake .. -DGMX_FFT_LIBRARY=fftpack
-DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
-DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
effect.
-DGMX_USE_RDTSCP=off
Then I got the error message.
Boost >= 1.44 not found. Using minimal internal version. This may
cause
trouble if you plan on compiling/linking other software that uses
Boost
against GROMACS.
CMake Error at cmake/FindSphinx.cmake:52 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments
total
to
command.
Call Stack (most recent call first):
docs/CMakeLists.txt:62 (find_package)
Could you advice what could be causing this error?
We try to find Sphinx in case people want to build the new
documentation,
but it looks like some part of the detection isn't reliable enough. Can
you
please try changing line 52 of cmake/FindSphinx.cmake to read
string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
and let us know how you go?
Mark
I was able to compile Gromacs 5.0 using same cmake command….
Bests,
Leucer
--
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posting!
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Re: [gmx-users] Problem compiling Gromacs 5.1
Thanks, Mark.
I inserted quotation in line 52 as Mark suggested.
I tried cmake again and got the only error.
Boost >= 1.44 not found. Using minimal internal version. This may cause trouble
if you plan on compiling/linking other software that uses Boost against GROMACS.
I don't know what the error means, but I did make and make install.
After finished, I checked /bin directory. But almost all commands which we need
to execute(i.g mdrun, trjconv...) were not generated.
Actually, onlyI the following file were generated in bin directory.
bin/
bin/xplor2gmx.pl
bin/GMXRC.bash
bin/gmx-completion-gmx_mpi.bash
bin/demux.pl
bin/GMXRC.zsh
bin/GMXRC
bin/gmx-completion.bash
bin/GMXRC.csh
bin/gmx_mpi
What causes this problem?
2015/08/20 21:44、Mark Abraham のメール：
> Hi,
>
> You should change line 52 from what it is, to what I suggested - which
> inserts quotation marks around one of the variable interpolations.
>
> Mark
>
> On Thu, Aug 20, 2015 at 2:43 PM 岡部篤俊 wrote:
>
>> Thanks, Peter.
>> But , I mean I don’t know what line I should change to from line 52 of
>> cmake/FindPhinx.cmake to solve this error.
>>
>> Leucer
>>
>> 2015/08/20 16:02、Kroon, P.C. のメール：
>>
>>> Just use your favourite text editor.
>>>
>>> Peter
>>>
>>> On Thu, Aug 20, 2015 at 3:10 AM, wrote:
>>>
Line 52 of cmake/FindSphinx.cmake file is written below.
string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
Can you tell me how I can change the line?
Bests,
Leucer
2015/08/19 23:11、Mark Abraham のメッセージ:
> Hi,
>> On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 wrote:
>>
>> Hi,
>>
>> I am unable to compile Gromamcs 5.1 using the following cmake
>> command.
>> cmake .. -DGMX_FFT_LIBRARY=fftpack
>> -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
>> -DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
>
>
> Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
> effect.
>
>
>> -DGMX_USE_RDTSCP=off
>>
>> Then I got the error message.
>> Boost >= 1.44 not found. Using minimal internal version. This may
>> cause
>> trouble if you plan on compiling/linking other software that uses
>> Boost
>> against GROMACS.
>> CMake Error at cmake/FindSphinx.cmake:52 (string):
>> string sub-command REGEX, mode REPLACE needs at least 6 arguments
>> total
>> to
>> command.
>> Call Stack (most recent call first):
>> docs/CMakeLists.txt:62 (find_package)
>>
>> Could you advice what could be causing this error?
>
> We try to find Sphinx in case people want to build the new
>> documentation,
> but it looks like some part of the detection isn't reliable enough. Can
you
> please try changing line 52 of cmake/FindSphinx.cmake to read
>
> string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
> SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
>
> and let us know how you go?
>
> Mark
>
> I was able to compile Gromacs 5.0 using same cmake command….
>>
>> Bests,
>> Leucer
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
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send a mail to gmx-users-requ...@gromacs.org.
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> htt
Re: [gmx-users] Problem compiling Gromacs 5.1
Hi,
You should change line 52 from what it is, to what I suggested - which
inserts quotation marks around one of the variable interpolations.
Mark
On Thu, Aug 20, 2015 at 2:43 PM 岡部篤俊 wrote:
> Thanks, Peter.
> But , I mean I don’t know what line I should change to from line 52 of
> cmake/FindPhinx.cmake to solve this error.
>
> Leucer
>
> 2015/08/20 16:02、Kroon, P.C. のメール：
>
> > Just use your favourite text editor.
> >
> > Peter
> >
> > On Thu, Aug 20, 2015 at 3:10 AM, wrote:
> >
> >> Line 52 of cmake/FindSphinx.cmake file is written below.
> >> string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
> >> SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
> >>
> >> Can you tell me how I can change the line?
> >>
> >> Bests,
> >> Leucer
> >>
> >>
> >> 2015/08/19 23:11、Mark Abraham のメッセージ:
> >>
> >>> Hi,
> On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 wrote:
>
> Hi,
>
> I am unable to compile Gromamcs 5.1 using the following cmake
> command.
> cmake .. -DGMX_FFT_LIBRARY=fftpack
> -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
> -DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
> >>>
> >>>
> >>> Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
> >>> effect.
> >>>
> >>>
> -DGMX_USE_RDTSCP=off
>
> Then I got the error message.
> Boost >= 1.44 not found. Using minimal internal version. This may
> cause
> trouble if you plan on compiling/linking other software that uses
> Boost
> against GROMACS.
> CMake Error at cmake/FindSphinx.cmake:52 (string):
> string sub-command REGEX, mode REPLACE needs at least 6 arguments
> total
> to
> command.
> Call Stack (most recent call first):
> docs/CMakeLists.txt:62 (find_package)
>
> Could you advice what could be causing this error?
> >>>
> >>> We try to find Sphinx in case people want to build the new
> documentation,
> >>> but it looks like some part of the detection isn't reliable enough. Can
> >> you
> >>> please try changing line 52 of cmake/FindSphinx.cmake to read
> >>>
> >>> string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
> >>> SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
> >>>
> >>> and let us know how you go?
> >>>
> >>> Mark
> >>>
> >>> I was able to compile Gromacs 5.0 using same cmake command….
>
> Bests,
> Leucer
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >> --
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Re: [gmx-users] Problem compiling Gromacs 5.1
On 8/20/15 8:42 AM, 岡部篤俊 wrote:
Thanks, Peter.
But , I mean I don’t know what line I should change to from line 52 of
cmake/FindPhinx.cmake to solve this error.
Mark's message provided the corrected line. Just replace whatever is on line 52
with that.
-Justin
Leucer
2015/08/20 16:02、Kroon, P.C. のメール：
Just use your favourite text editor.
Peter
On Thu, Aug 20, 2015 at 3:10 AM, wrote:
Line 52 of cmake/FindSphinx.cmake file is written below.
string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
Can you tell me how I can change the line?
Bests,
Leucer
2015/08/19 23:11、Mark Abraham のメッセージ:
Hi,
On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 wrote:
Hi,
I am unable to compile Gromamcs 5.1 using the following cmake command.
cmake .. -DGMX_FFT_LIBRARY=fftpack
-DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
-DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
effect.
-DGMX_USE_RDTSCP=off
Then I got the error message.
Boost >= 1.44 not found. Using minimal internal version. This may cause
trouble if you plan on compiling/linking other software that uses Boost
against GROMACS.
CMake Error at cmake/FindSphinx.cmake:52 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total
to
command.
Call Stack (most recent call first):
docs/CMakeLists.txt:62 (find_package)
Could you advice what could be causing this error?
We try to find Sphinx in case people want to build the new documentation,
but it looks like some part of the detection isn't reliable enough. Can
you
please try changing line 52 of cmake/FindSphinx.cmake to read
string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
and let us know how you go?
Mark
I was able to compile Gromacs 5.0 using same cmake command….
Bests,
Leucer
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Department of Pharmaceutical Sciences
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University of Maryland, Baltimore
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Re: [gmx-users] Problem compiling Gromacs 5.1
Thanks, Peter.
But , I mean I don’t know what line I should change to from line 52 of
cmake/FindPhinx.cmake to solve this error.
Leucer
2015/08/20 16:02、Kroon, P.C. のメール：
> Just use your favourite text editor.
>
> Peter
>
> On Thu, Aug 20, 2015 at 3:10 AM, wrote:
>
>> Line 52 of cmake/FindSphinx.cmake file is written below.
>> string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
>> SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
>>
>> Can you tell me how I can change the line?
>>
>> Bests,
>> Leucer
>>
>>
>> 2015/08/19 23:11、Mark Abraham のメッセージ:
>>
>>> Hi,
On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 wrote:
Hi,
I am unable to compile Gromamcs 5.1 using the following cmake command.
cmake .. -DGMX_FFT_LIBRARY=fftpack
-DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
-DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
>>>
>>>
>>> Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
>>> effect.
>>>
>>>
-DGMX_USE_RDTSCP=off
Then I got the error message.
Boost >= 1.44 not found. Using minimal internal version. This may cause
trouble if you plan on compiling/linking other software that uses Boost
against GROMACS.
CMake Error at cmake/FindSphinx.cmake:52 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total
to
command.
Call Stack (most recent call first):
docs/CMakeLists.txt:62 (find_package)
Could you advice what could be causing this error?
>>>
>>> We try to find Sphinx in case people want to build the new documentation,
>>> but it looks like some part of the detection isn't reliable enough. Can
>> you
>>> please try changing line 52 of cmake/FindSphinx.cmake to read
>>>
>>> string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
>>> SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
>>>
>>> and let us know how you go?
>>>
>>> Mark
>>>
>>> I was able to compile Gromacs 5.0 using same cmake command….
Bests,
Leucer
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Re: [gmx-users] Problem compiling Gromacs 5.1
Just use your favourite text editor.
Peter
On Thu, Aug 20, 2015 at 3:10 AM, wrote:
> Line 52 of cmake/FindSphinx.cmake file is written below.
> string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
> SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
>
> Can you tell me how I can change the line?
>
> Bests,
> Leucer
>
>
> 2015/08/19 23:11、Mark Abraham のメッセージ:
>
> > Hi,
> >> On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 wrote:
> >>
> >> Hi,
> >>
> >> I am unable to compile Gromamcs 5.1 using the following cmake command.
> >> cmake .. -DGMX_FFT_LIBRARY=fftpack
> >> -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
> >> -DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
> >
> >
> > Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
> > effect.
> >
> >
> >> -DGMX_USE_RDTSCP=off
> >>
> >> Then I got the error message.
> >> Boost >= 1.44 not found. Using minimal internal version. This may cause
> >> trouble if you plan on compiling/linking other software that uses Boost
> >> against GROMACS.
> >> CMake Error at cmake/FindSphinx.cmake:52 (string):
> >> string sub-command REGEX, mode REPLACE needs at least 6 arguments total
> >> to
> >> command.
> >> Call Stack (most recent call first):
> >> docs/CMakeLists.txt:62 (find_package)
> >>
> >> Could you advice what could be causing this error?
> >
> > We try to find Sphinx in case people want to build the new documentation,
> > but it looks like some part of the detection isn't reliable enough. Can
> you
> > please try changing line 52 of cmake/FindSphinx.cmake to read
> >
> >string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
> > SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
> >
> > and let us know how you go?
> >
> > Mark
> >
> > I was able to compile Gromacs 5.0 using same cmake command….
> >>
> >> Bests,
> >> Leucer
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Problem compiling Gromacs 5.1
Line 52 of cmake/FindSphinx.cmake file is written below.
string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
Can you tell me how I can change the line?
Bests,
Leucer
2015/08/19 23:11、Mark Abraham のメッセージ:
> Hi,
>> On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 wrote:
>>
>> Hi,
>>
>> I am unable to compile Gromamcs 5.1 using the following cmake command.
>> cmake .. -DGMX_FFT_LIBRARY=fftpack
>> -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
>> -DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
>
>
> Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
> effect.
>
>
>> -DGMX_USE_RDTSCP=off
>>
>> Then I got the error message.
>> Boost >= 1.44 not found. Using minimal internal version. This may cause
>> trouble if you plan on compiling/linking other software that uses Boost
>> against GROMACS.
>> CMake Error at cmake/FindSphinx.cmake:52 (string):
>> string sub-command REGEX, mode REPLACE needs at least 6 arguments total
>> to
>> command.
>> Call Stack (most recent call first):
>> docs/CMakeLists.txt:62 (find_package)
>>
>> Could you advice what could be causing this error?
>
> We try to find Sphinx in case people want to build the new documentation,
> but it looks like some part of the detection isn't reliable enough. Can you
> please try changing line 52 of cmake/FindSphinx.cmake to read
>
>string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
> SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
>
> and let us know how you go?
>
> Mark
>
> I was able to compile Gromacs 5.0 using same cmake command….
>>
>> Bests,
>> Leucer
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Problem compiling Gromacs 5.1
Yeah sorry, I realized later that I did not read the complete thing... Bad habit. On 19/08/15 16:18, Mark Abraham wrote: Hi, No, the warning about Boost versions is unrelated and just happens to precede the issue. Mark On Wed, Aug 19, 2015 at 4:13 PM Felipe Merino < felipe.mer...@mpi-dortmund.mpg.de> wrote: Hi, As the error says you should get a version >=1.44 for the boost libraries On 19/08/15 15:49, 岡部篤俊 wrote: g minimal internal version. T -- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133 2306 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133 2306 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem compiling Gromacs 5.1
Hi, No, the warning about Boost versions is unrelated and just happens to precede the issue. Mark On Wed, Aug 19, 2015 at 4:13 PM Felipe Merino < felipe.mer...@mpi-dortmund.mpg.de> wrote: > Hi, > > As the error says you should get a version >=1.44 for the boost libraries > > On 19/08/15 15:49, 岡部篤俊 wrote: > > g minimal internal version. T > > -- > Felipe Merino > Max Planck Institute for Molecular Physiology > Department of Structural Biochemistry > Otto-Hahn-Str. 11 > 44227 Dortmund > Phone: +49 231 133 2306 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem compiling Gromacs 5.1
Hi, As the error says you should get a version >=1.44 for the boost libraries On 19/08/15 15:49, 岡部篤俊 wrote: g minimal internal version. T -- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133 2306 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem compiling Gromacs 5.1
Hi,
On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 wrote:
> Hi,
>
> I am unable to compile Gromamcs 5.1 using the following cmake command.
> cmake .. -DGMX_FFT_LIBRARY=fftpack
> -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
> -DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
effect.
> -DGMX_USE_RDTSCP=off
>
> Then I got the error message.
> Boost >= 1.44 not found. Using minimal internal version. This may cause
> trouble if you plan on compiling/linking other software that uses Boost
> against GROMACS.
> CMake Error at cmake/FindSphinx.cmake:52 (string):
> string sub-command REGEX, mode REPLACE needs at least 6 arguments total
> to
> command.
> Call Stack (most recent call first):
> docs/CMakeLists.txt:62 (find_package)
>
> Could you advice what could be causing this error?
>
We try to find Sphinx in case people want to build the new documentation,
but it looks like some part of the detection isn't reliable enough. Can you
please try changing line 52 of cmake/FindSphinx.cmake to read
string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
and let us know how you go?
Mark
I was able to compile Gromacs 5.0 using same cmake command….
>
> Bests,
> Leucer
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Problem compiling Gromacs 5.1 with XL Compiler
Hi, That all seems wildly unlikely, particularly as you say you can compile earlier GROMACS versions with the same toolchain. The errors are caused by the compiler interpreting gmx_unused as a variable name, instead of a portable way to suppress compiler warnings about variables that are unused on some code paths. But the source file is correctly including the header that declares gmx_unused (and in any case, if there was a compiler problem, gmx_unused should preprocess to something that triggers a different compiler error, or to nothing). Can you please email me (off list) your CMakeCache.txt, src/config.h src/buildinfo.h from the build directory? Thanks, Mark On Mon, Aug 17, 2015 at 8:43 AM Jernej Zidar wrote: > Hi, > I am unable to compile Gromacs 5.1 using the XL compiler (version 12.1.0) > on our BlueGene/Q cluster. > > Before starting I set the relevant paths like so: > export PATH=/bgsys/drivers/ppcfloor/comm/xl/bin/:$PATH > export > LD_LIBRARY_PATH=/bgsys/drivers/ppcfloor/comm/xl/lib/:$LD_LIBRARY_PATH > export CXX=/bgsys/drivers/ppcfloor/comm/xl/bin/mpicxx > export CC=/bgsys/drivers/ppcfloor/comm/xl/bin/mpicc > > Gromacs is configured like so: > cmake ../gromacs-5.1 \ > -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C \-DGMX_MPI=ON \ > -DCMAKE_INSTALL_PREFIX=/home/ihpczidj/scratch/ \ > -DGMX_BUILD_OWN_FFTW=ON -DGMX_BUILD_MDRUN_ONLY=ON > > The whole list of errors: > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 181.76: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 201.79: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 281.72: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 302.75: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 1472.77: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 1486.80: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 1575.73: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 1589.76: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 2810.92: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 2824.95: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 2904.88: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 2918.91: 1540-0063 (S) The text "m" is unexpected. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 326.36: 1540-0274 (S) The name lookup for "gmx_simd_invsqrt_notmaskfpe_f" > did not find a declaration. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 541.15: 1540-0274 (S) The name lookup for "gmx_simd_inv_notmaskfpe_f" did > not find a declaration. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 688.15: 1540-0274 (S) The name lookup for "gmx_simd_inv_notmaskfpe_f" did > not find a declaration. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 999.37: 1540-0274 (S) The name lookup for "gmx_simd_inv_maskfpe_f" did not > find a declaration. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 1031.32: 1540-0274 (S) The name lookup for "gmx_simd_invsqrt_notmaskfpe_f" > did not find a declaration. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 1080.31: 1540-0274 (S) The name lookup for "gmx_simd_invsqrt_notmaskfpe_f" > did not find a declaration. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 1120.34: 1540-0274 (S) The name lookup for "gmx_simd_inv_maskfpe_f" did not > find a declaration. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 1174.41: 1540-0274 (S) The name lookup for "gmx_simd_inv_notmaskfpe_f" did > not find a declaration. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 1609.36: 1540-0274 (S) The name lookup for "gmx_simd_invsqrt_notmaskfpe_d" > did not find a declaration. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 1851.40: 1540-0274 (S) The name lookup for "gmx_simd_inv_maskfpe_d" did not > find a declaration. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 1887.41: 1540-0274 (S) The name lookup for "gmx_simd_inv_notmaskfpe_d" did > not find a declaration. > "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line > 2036.40: 1540-0274 (S) The name looku
