Hi ,<br />
I want to install gromacs 4.0.7 in double precision in a 64 bit Mac computer with 8 <br />
nodes.<br />
I got the lam7.1.4 source code files and installed them using the following commands<br />
./configure --without-fc ( it was giving an error for the fortran compiler)<br />
make<br />
make install<br />
<br />
then I get the gromacs 4.0.7 source code files and installed it as<br />
./configure --disable-float<br />
make<br />
make install<br />
<br />
After that I try get the "mpi " version for mdrun<br />
make clean<br />
./configure --enable-mpi --disable-nice --program-suffix="_mpi"<br />
make mdrun<br />
I GET ERROR IN THIS STEP , With error message<br />
undefined symbols:<br />
"_lam_mpi_double", referenced from:<br />
_gmx_sumd_sim in libgmx_mpi.a(network.o)<br />
_gmx_sumd in libgmx_mpi.a(network.o)<br />
_gmx_sumd in libgmx_mpi.a(network.o)<br />
_wallcycle_sum in libmd_mpi.a(gmx_wallcycle.o)<br />
"_lam_mpi_byte", referenced from:<br />
_exchange_rvecs in repl_ex.o<br />
_replica_exchange in repl_ex.o<br />
_replica_exchange in repl_ex.o<br />
_replica_exchange in repl_ex.o<br />
_finish_run in libmd_mpi.a(sim_util.o)<br />
_dd_collect_vec in libmd_mpi.a(domdec.o)<br />
_dd_collect_vec in libmd_mpi.a(domdec.o)<br />
_set_dd_cell_sizes in libmd_mpi.a(domdec.o)<br />
_dd_distribute_vec in libmd_mpi.a(domdec.o)<br />
_dd_distribute_vec in libmd_mpi.a(domdec.o)<br />
_dd_partition_system in libmd_mpi.a(domdec.o)<br />
_partdec_init_local_state in libmd_mpi.a(partdec.o)<br />
_partdec_init_local_state in libmd_mpi.a(partdec.o)<br />
_gmx_rx in libmd_mpi.a(partdec.o)<br />
_gmx_tx in libmd_mpi.a(partdec.o)<br />
_gmx_bcast_sim in libgmx_mpi.a(network.o)<br />
_gmx_bcast in libgmx_mpi.a(network.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_gmx_pme_do in libmd_mpi.a(pme.o)<br />
_write_traj in libmd_mpi.a(stat.o)<br />
_write_traj in libmd_mpi.a(stat.o)<br />
_gmx_pme_receive_f in libmd_mpi.a(pme_pp.o)<br />
_gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o)<br />
_gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o)<br />
_gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o)<br />
_gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o)<br />
_gmx_pme_send_force_vir_ener in libmd_mpi.a(pme_pp.o)<br />
_gmx_pme_send_force_vir_ener in libmd_mpi.a(pme_pp.o)<br />
_gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o)<br />
_gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o)<br />
_gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o)<br />
_gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o)<br />
_dd_gatherv in libmd_mpi.a(domdec_network.o)<br />
_dd_scatterv in libmd_mpi.a(domdec_network.o)<br />
_dd_gather in libmd_mpi.a(domdec_network.o)<br />
_dd_scatter in libmd_mpi.a(domdec_network.o)<br />
_dd_bcastc in libmd_mpi.a(domdec_network.o)<br />
_dd_bcast in libmd_mpi.a(domdec_network.o)<br />
_dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o)<br />
_dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o)<br />
_dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o)<br />
_dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o)<br />
_dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o)<br />
_dd_sendrecv_rvec in libmd_mpi.a(domdec_network.o)<br />
_dd_sendrecv_rvec in libmd_mpi.a(domdec_network.o)<br />
_dd_sendrecv_rvec in libmd_mpi.a(domdec_network.o)<br />
_dd_sendrecv_int in libmd_mpi.a(domdec_network.o)<br />
_dd_sendrecv_int in libmd_mpi.a(domdec_network.o)<br />
_dd_sendrecv_int in libmd_mpi.a(domdec_network.o)<br />
"_lam_mpi_prod", referenced from:<br />
_gprod in do_gct.o<br />
_do_coupling in do_gct.o<br />
_do_coupling in do_gct.o<br />
_do_coupling in do_gct.o<br />
"_lam_mpi_float", referenced from:<br />
_gprod in do_gct.o<br />
_do_coupling in do_gct.o<br />
_do_coupling in do_gct.o<br />
_do_coupling in do_gct.o<br />
_gmx_tx_rx_real in libmd_mpi.a(partdec.o)<br />
_gmx_sumf_sim in libgmx_mpi.a(network.o)<br />
_gmx_sumf in libgmx_mpi.a(network.o)<br />
_gmx_sumf in libgmx_mpi.a(network.o)<br />
_gmx_sum_qgrid_dd in libmd_mpi.a(pme.o)<br />
_gmx_sum_qgrid_dd in libmd_mpi.a(pme.o)<br />
_gmx_sum_qgrid_dd in libmd_mpi.a(pme.o)<br />
_gmx_sum_qgrid_dd in libmd_mpi.a(pme.o)<br />
_gmx_sum_qgrid_dd in libmd_mpi.a(pme.o)<br />
_gmx_sum_qgrid_dd in libmd_mpi.a(pme.o)<br />
_pmeredist in libmd_mpi.a(pme.o)<br />
_gmx_pme_init in libmd_mpi.a(pme.o)<br />
_gmx_sum_qgrid in libmd_mpi.a(pme.o)<br />
_gmx_sum_qgrid in libmd_mpi.a(pme.o)<br />
_gmx_parallel_transpose_xy in libmd_mpi.a(gmx_parallel_3dfft.o)<br />
_gmx_parallel_transpose_xy in libmd_mpi.a(gmx_parallel_3dfft.o)<br />
"_lam_mpi_int", referenced from:<br />
_make_dd_communicators in libmd_mpi.a(domdec.o)<br />
_make_dd_communicators in libmd_mpi.a(domdec.o)<br />
_make_dd_communicators in libmd_mpi.a(domdec.o)<br />
_gmx_sumi_sim in libgmx_mpi.a(network.o)<br />
_gmx_sumi in libgmx_mpi.a(network.o)<br />
_gmx_sumi in libgmx_mpi.a(network.o)<br />
_pmeredist in libmd_mpi.a(pme.o)<br />
"_lam_mpi_sum", referenced from:<br />
_make_dd_communicators in libmd_mpi.a(domdec.o)<br />
_make_dd_communicators in libmd_mpi.a(domdec.o)<br />
_make_dd_communicators in libmd_mpi.a(domdec.o)<br />
_gmx_sumi_sim in libgmx_mpi.a(network.o)<br />
_gmx_sumf_sim in libgmx_mpi.a(network.o)<br />
_gmx_sumd_sim in libgmx_mpi.a(network.o)<br />
_gmx_sumi in libgmx_mpi.a(network.o)<br />
_gmx_sumi in libgmx_mpi.a(network.o)<br />
_gmx_sumf in libgmx_mpi.a(network.o)<br />
_gmx_sumf in libgmx_mpi.a(network.o)<br />
_gmx_sumd in libgmx_mpi.a(network.o)<br />
_gmx_sumd in libgmx_mpi.a(network.o)<br />
_gmx_sum_qgrid in libmd_mpi.a(pme.o)<br />
_wallcycle_sum in libmd_mpi.a(gmx_wallcycle.o)<br />
"_lam_mpi_comm_world", referenced from:<br />
_init_par in libgmx_mpi.a(main.o)<br />
_init_multisystem in libgmx_mpi.a(main.o)<br />
_gmx_finalize in libgmx_mpi.a(network.o)<br />
_gmx_abort in libgmx_mpi.a(network.o)<br />
_gmx_node_num in libgmx_mpi.a(network.o)<br />
_gmx_node_rank in libgmx_mpi.a(network.o)<br />
_gmx_setup in libgmx_mpi.a(network.o)<br />
ld: symbol(s) not found<br />
collect2: ld returned 1 exit status<br />
<br />
<br />
I am not being able to solve this problem.<br />
I know that in gromacs 4 "grompp" command does not take np flag. but then i will have to <br />
specify no. of nodes to mpirun. <br />
It could be that the "mpi" environment has not been set up correctly.<br />
Any suggestion regarding this will be very helpful.<br />
Thanks in advance<br />
Sarbani<br />
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