Hi, I use the following combination with Intel PSXE. It works and your problem is likely related to the name of the Intel CXX compiler.
source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64 source /opt/intel/impi/2018.4.274/bin64/mpivars.sh source /opt/intel/mkl/bin/mklvars.sh intel64 FLAGS="-xCORE-AVX2"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS; cmake .. -DCMAKE_C_COMPILER=mpiicc \ -DCMAKE_CXX_COMPILER=mpiicpc \ -DCMAKE_INSTALL_PREFIX=/home/user/Gromacs/gromacs-2020/install \ -DGMX_FFT_LIBRARY=mkl \ -DGMX_MPI=ON \ -DGMX_SIMD=AVX2_256 \ -DMPIEXEC=srun \ -DMPIEXEC_NUMPROC_FLAG=-n \ -DMPIEXEC_PREFLAGS= \ -DMPIEXEC_POSTFLAGS= make -j 16 make install On Fri, Mar 27, 2020 at 12:35 AM Schulz, Roland <roland.sch...@intel.com> wrote: > This isn't really a GROMACS question. You might need to set > LD_LIBRARY_PATH manual. If you don't know how you should ask e.g. your > cluster admin. Or you could use a static build (see GROMACS install guide). > > Roland > > > -----Original Message----- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Harry > > Mark Greenblatt > > Sent: Thursday, March 26, 2020 12:11 AM > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] compile with intel compiler > > > > BS"D > > > > > > Yes, indeed, that was the error. I did try to define the > > GMX_GPLUSPLUS_PATH, and have that point to a local install of gcc 6.4; > that > > worked to compile and install gromacs. But when it came to executing the > > program it couldn't find the libstdc++ for gcc 6.4. This is on a > cluster, and > > when I have compiled gromacs in the past with gcc 6.4, I can set up the > > environment by loading the gcc 6.4 module, but this of course displaces > the > > intel compiler module. If I add the gcc 6.4 library path in the GMXRC > file, > > would that interfere with the intel stuff? > > > > > > Thanks > > > > > > Harry > > > > > > > > > > > > Harry M. Greenblatt > > Associate Staff Scientist > > Dept of Structural Biology > > harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs > > 5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.& > > URL=mailto%3aharry.greenblatt%40weizmann.ac.il> > > Weizmann Institute of Science Phone: 972-8-934-3625 > > 234 Herzl St. Facsimile: 972-8-934-4159 > > Rehovot, 76100 > > Israel > > ________________________________ > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Schulz, > > Roland <roland.sch...@intel.com> > > Sent: Wednesday, March 25, 2020 10:25:24 PM > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] compile with intel compiler > > > > Hi, > > > > > > Are you referring to this type of error: > > > > -- Performing Test USING_LIBSTDCXX > > -- Performing Test USING_LIBSTDCXX - Success CMake Error at > > cmake/FindLibStdCpp.cmake:119 (message): > > Found g++ at /usr/bin/g++. Its version is 4.8.5. GROMACS requires at > > least version 5.1. Please specify a different g++ using > > GMX_GPLUSPLUS_PATH, PATH or CMAKE_PREFIX_PATH. > > > > This is because GROMACS needs both a C++ compiler and a C++ standard > > library. The Intel compiler doesn't come with a standard library but > utilizes > > libstdc++ for that. GROMACS automatically looks for the right version of > g++ > > to find the proper version of libstdc++ > > > > If you are referring to a different error please be more specific and > post the > > exact error. > > > > Roland > > > > > -----Original Message----- > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Harry > > > Mark Greenblatt > > > Sent: Wednesday, March 25, 2020 3:46 AM > > > To: gmx-us...@gromacs.org > > > Subject: [gmx-users] compile with intel compiler > > > > > > BS"D > > > > > > Dear All, > > > > > > I would like to compile Gromacs 2020 with an intel compiler; I set > > > the > > > following: > > > > > > -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc - > > DGMX_MPI=on > > > -DGMX_BUILD_OWN_FFTW=OFF - DGMX_FFT_LIBRARY=mkl > > > -DMKL_LIBRARIES=$MKLROOT/lib/intel64 - > > > DMKL_INCLUDE_DIR=$MKLROOT/include > > > > > > Despite the fact that I have told it to use the Intel C++ compile is > > > (which it finds), it still looks and finds the system g++, which, of > > > course is quite old. If I have given it the name of a C++ compiler, > why is it > > looking for g++? > > > > > > > > > > > > Thanks > > > > > > Harry > > > > > > > > > > > > -------------------------------------------------------------------- > > > Harry M. Greenblatt > > > Associate Staff Scientist > > > Dept of Structural Biology > > > harry.greenbl...@weizmann.ac.il<mailto:harry.greenbl...@weizmann.ac.il > > > > > Weizmann Institute of Science Phone: 972-8-934-6340 > > > 234 Herzl St. Facsimile: 972-8-934-3361 > > > Rehovot, 7610001 > > > Israel > > > > > > -- > > > 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. > > -- > > 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. > -- 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.
