[gmx-users] GROMACS Installation error on domdec.cpp

[Benson Muite]

What version of MPI do you have? It may be helpful to indicate exact 
location of MPI if the paths are not automatically found.


On 08/03/2018 02:43 PM, 郭聪 wrote:
> Hi All,
>
>
>
> I wanted to build GROMACS-2016.4 on hpc clusters but I got error with domdec.cpp. Could anyone helps me with that? Thanks!
>
>
> ps: I succeeded to build it on my lab pc. I am wondering if something is wrong with GROMACS code or the compiler. I used gnu and openmpi.
>
>
>
> tar -zxvf gromacs-2016.4.tar.gz
> cd gromacs-2016.4/
> mkdir build
> cd build
> cmake .. -DGMX_BUILD_OWN_FFTW=on -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX=~/
> gromacs-2016.4/
> make
>
> *********************************error message************************
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In function ‘int ddcoord2ddnodeid(gmx_domdec_t*, int*)’:
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:233:53: error: ‘MPI_Cart_rank’ was not declared in this scope
>           MPI_Cart_rank(dd->mpi_comm_all, c, &ddnodeid);
>                                                       ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In function ‘void dd_collect_vec_sendrecv(gmx_domdec_t*, real (*)[3], real (*)[3])’:
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1185:47: error: ‘MPI_STATUS_IGNORE’ was not declared in this scope
>                            n, dd->mpi_comm_all, MPI_STATUS_IGNORE);
>                                                 ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In function ‘void dd_distribute_vec_sendrecv(gmx_domdec_t*, t_block*, real (*)[3], real (*)[3])’:
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1472:49: error: ‘MPI_STATUS_IGNORE’ was not declared in this scope
>                    MPI_ANY_TAG, dd->mpi_comm_all, MPI_STATUS_IGNORE);
>                                                   ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In function ‘int ddcoord2simnodeid(t_commrec*, int, int, int)’:
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1937:58: error: ‘MPI_Cart_rank’ was not declared in this scope
>           MPI_Cart_rank(cr->mpi_comm_mysim, coords, &nodeid);
>                                                            ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In function ‘int dd_simnode2pmenode(const gmx_domdec_t*, const t_commrec*, int)’:
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1976:67: error: ‘MPI_Cart_coords’ was not declared in this scope
>           MPI_Cart_coords(cr->mpi_comm_mysim, sim_nodeid, DIM, coord);
>                                                                     ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:1981:66: error: ‘MPI_Cart_rank’ was not declared in this scope
>               MPI_Cart_rank(cr->mpi_comm_mysim, coord_pme, &pmenode);
>                                                                    ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In function ‘gmx_bool receive_vir_ener(const gmx_domdec_t*, const t_commrec*)’:
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:2106:76: error: ‘MPI_Cart_coords’ was not declared in this scope
>               MPI_Cart_coords(cr->mpi_comm_mysim, cr->sim_nodeid, DIM, coords);
>                                                                              ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:2111:64: error: ‘MPI_Cart_rank’ was not declared in this scope
>                   MPI_Cart_rank(cr->mpi_comm_mysim, coords, &rank);
>                                                                  ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In function ‘void make_pp_communicator(FILE*, gmx_domdec_t*, t_commrec*, int)’:
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5642:35: error: ‘MPI_Cart_create’ was not declared in this scope
>                           &comm_cart);
>                                     ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5682:64: error: ‘MPI_Cart_coords’ was not declared in this scope
>           MPI_Cart_coords(dd->mpi_comm_all, dd->rank, DIM, dd->ci);
>                                                                  ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5706:79: error: ‘MPI_Cart_rank’ was not declared in this scope
>                   MPI_Cart_rank(dd->mpi_comm_all, dd->master_ci, &dd->masterrank);
>                                                                                 ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp: In function ‘void split_communicator(FILE*, t_commrec*, gmx_domdec_t*, int, int)’:
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5862:35: error: ‘MPI_Cart_create’ was not declared in this scope
>                           &comm_cart);
>                                     ^
> /gpfs/home/XXX/software/gromacs-2016.4/src/gromacs/domdec/domdec.cpp:5875:72: error: ‘MPI_Cart_coords’ was not declared in this scope
>           MPI_Cart_coords(cr->mpi_comm_mysim, cr->sim_nodeid, DIM, dd->ci);
>                                                                          ^
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o] Error 1
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error