Re: [gmx-users] Compilation issue with F77_FUNC functions?
And looks like the solution was to make sure that mpic++ was used as the compiler instead of mpicc. On Mon, Dec 9, 2013 at 5:22 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Dec 9, 2013 at 1:44 AM, Michael Shirts mrshi...@gmail.com wrote: So, I'm trying to compile with MPI using mpich3. Previous installations worked, and installations without MPI worked. I'm getting errors like: /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:53: warning: parameter names (without types) in function declaration Apparently F77_FUNC is getting #defined by someone else after config.h, because vec.h transitively #includes the entire world, including mpi.h. That could be proved by inspecting the preprocessed source, e.g. by hacking the command you can get from make VERBOSE=1. Assigning blame there would tax Solomon. Possible fixes include trying a more recent compiler, hacking out the #include vec.h (which I think is even superfluous), or getting rid of the F77_FUNC stuff there (which is probably a relic from when some fortran kernel needed the data). Mark /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:53: error: function ‘F77_FUNC’ is initialized like a variable /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:56: warning: braces around scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:56: warning: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: error: invalid initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: error: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: excess elements in scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: excess elements in scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: (near initialization for ‘F77_FUNC’) And it keeps on like that for a long while. Any suggestions? Perhaps something wrong in the way mpicc is handling Fortran code? -- 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.
Re: [gmx-users] Compilation issue with F77_FUNC functions?
Hi, what compiler is used by mpicc? What does mpicc -showme and mpicc --version show? Does it help to uncomment the line containing F77_FUNC int src/config.h.cmakein? Roland On Sun, Dec 8, 2013 at 7:44 PM, Michael Shirts mrshi...@gmail.com wrote: So, I'm trying to compile with MPI using mpich3. Previous installations worked, and installations without MPI worked. I'm getting errors like: /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:53: warning: parameter names (without types) in function declaration /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:53: error: function ‘F77_FUNC’ is initialized like a variable /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:56: warning: braces around scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:56: warning: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: error: invalid initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: error: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: excess elements in scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: excess elements in scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: (near initialization for ‘F77_FUNC’) And it keeps on like that for a long while. Any suggestions? Perhaps something wrong in the way mpicc is handling Fortran code? -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Compilation issue with F77_FUNC functions?
Apologies! I certainly didn't post enough information. mpicc is using: gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) Which is exactly what the non-mpi versions used, which did not have this problem. I ran cmake with: cmake ../gromacs -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_DOUBLE=ON -DGMX_CPU_ACCELERATION=AVX_256 -DCMAKE_INSTALL_PREFIX=/h3/n1/shirtsgroup/gromacs_46/install -DFFTW_INCLUDE_DIR=/h3/n1/shirtsgroup/software/fft3w/include -DFFTW_LIBRARY='/h3/n1/shirtsgroup/software/fft3w/lib/libfftw3.a;/h3/n1/shirtsgroup/software/fft3w/lib/libfftw3.so;/usr/lib64/libm.so;/share/apps/mpich3/gnu/lib/libmpich.so;' All the extra libraries for FFTWF appear to be necessary for some reason, but I don't think that's it . . . Commentinf out the line F77_FUNC int src/config.h.cmakein and rerunning cmake did not change anything. On Sun, Dec 8, 2013 at 10:29 PM, Roland Schulz rol...@utk.edu wrote: Hi, what compiler is used by mpicc? What does mpicc -showme and mpicc --version show? Does it help to uncomment the line containing F77_FUNC int src/config.h.cmakein? Roland On Sun, Dec 8, 2013 at 7:44 PM, Michael Shirts mrshi...@gmail.com wrote: So, I'm trying to compile with MPI using mpich3. Previous installations worked, and installations without MPI worked. I'm getting errors like: /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:53: warning: parameter names (without types) in function declaration /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:53: error: function ‘F77_FUNC’ is initialized like a variable /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:56: warning: braces around scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:56: warning: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: error: invalid initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: error: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: excess elements in scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: excess elements in scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: (near initialization for ‘F77_FUNC’) And it keeps on like that for a long while. Any suggestions? Perhaps something wrong in the way mpicc is handling Fortran code? -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Compilation issue with F77_FUNC functions?
And FWIW, it's being compiled on CentOS 6.4. On Sun, Dec 8, 2013 at 11:16 PM, Michael Shirts mrshi...@gmail.com wrote: Apologies! I certainly didn't post enough information. mpicc is using: gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) Which is exactly what the non-mpi versions used, which did not have this problem. I ran cmake with: cmake ../gromacs -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_DOUBLE=ON -DGMX_CPU_ACCELERATION=AVX_256 -DCMAKE_INSTALL_PREFIX=/h3/n1/shirtsgroup/gromacs_46/install -DFFTW_INCLUDE_DIR=/h3/n1/shirtsgroup/software/fft3w/include -DFFTW_LIBRARY='/h3/n1/shirtsgroup/software/fft3w/lib/libfftw3.a;/h3/n1/shirtsgroup/software/fft3w/lib/libfftw3.so;/usr/lib64/libm.so;/share/apps/mpich3/gnu/lib/libmpich.so;' All the extra libraries for FFTWF appear to be necessary for some reason, but I don't think that's it . . . Commentinf out the line F77_FUNC int src/config.h.cmakein and rerunning cmake did not change anything. On Sun, Dec 8, 2013 at 10:29 PM, Roland Schulz rol...@utk.edu wrote: Hi, what compiler is used by mpicc? What does mpicc -showme and mpicc --version show? Does it help to uncomment the line containing F77_FUNC int src/config.h.cmakein? Roland On Sun, Dec 8, 2013 at 7:44 PM, Michael Shirts mrshi...@gmail.com wrote: So, I'm trying to compile with MPI using mpich3. Previous installations worked, and installations without MPI worked. I'm getting errors like: /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:53: warning: parameter names (without types) in function declaration /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:53: error: function ‘F77_FUNC’ is initialized like a variable /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:56: warning: braces around scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:56: warning: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: error: invalid initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: error: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: excess elements in scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: (near initialization for ‘F77_FUNC’) /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: excess elements in scalar initializer /h3/n1/shirtsgroup/gromacs_46/gromacs/src/gmxlib/cinvsqrtdata.c:57: warning: (near initialization for ‘F77_FUNC’) And it keeps on like that for a long while. Any suggestions? Perhaps something wrong in the way mpicc is handling Fortran code? -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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.
