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
--
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