I just want to attach the full error message to you beside part of it in the earlier mail.
Thank you.
[root.gpucc amber12]# make install
cd AmberTools/src && make install
make[1]: Entering directory `/usr/local/apps/amber12/AmberTools/src'
AmberTools12 has no CUDA-enabled components
(cd ../../src && make cuda_parallel )
make[2]: Entering directory `/usr/local/apps/amber12/src'
Starting installation of Amber12 (cuda parallel) at Tue Apr 17 15:41:05 MYT 2012.
cd pmemd && make cuda_parallel
make[3]: Entering directory `/usr/local/apps/amber12/src/pmemd'
make -C src/ cuda_parallel
make[4]: Entering directory `/usr/local/apps/amber12/src/pmemd/src'
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c gbl_constants.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c gbl_datatypes.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c state_info.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c file_io_dat.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pmemd_lib.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c parallel_dat.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c file_io.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c mdin_ctrl_dat.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c axis_optimize.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c fft1d.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c charmm.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c nextprmtop_section.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c prmtop_dat.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c mdin_ewald_dat.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c mdin_debugf_dat.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c remd.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c binrestart.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c inpcrd_dat.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c constraints.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c mol_list.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c extra_pnts_nb14.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c prfs.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c dynamics_dat.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c random.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c dynamics.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pbc.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c img.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c timers.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c bspline.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pme_recip_dat.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pme_fft_dat.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pme_blk_fft.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pme_slab_fft.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c shake.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c nmr_lib.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c nmr_calls.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c angles.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c angles_ub.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c cmap.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c bonds.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c cit.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c dihedrals.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c dihedrals_imp.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c nb_exclusions.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c parallel.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c ene_frc_splines.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c nb_pairlist.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c nbips.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c gb_parallel.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c loadbal.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pme_blk_recip.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pme_slab_recip.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pme_direct.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c bintraj.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c runfiles.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c amd.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pme_force.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c degcnt.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c gb_ene.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c gb_force.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c get_cmdline.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c multipmemd.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c remd_exchg.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c runmd.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c runmin.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c veclib.F90
mpicc -O3 -mtune=native -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pmemd_clib.c
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c gb_alltasks_setup.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pme_alltasks_setup.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pme_setup.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c findmask.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c master_setup.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c pmemd.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c erfcfun.F90
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/apps/amber12/include -c charmm_gold.F90
make -C ./cuda
make[5]: Entering directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c cuda_info.F90
mpicc -O3 -mtune=native -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c gpu.cpp
mpicc -O3 -mtune=native -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c gputypes.cpp
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c kForcesUpdate.cu
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c kCalculateLocalForces.cu
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c kCalculateGBBornRadii.cu
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c kCalculatePMENonbondEnergy.cu
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c kCalculateGBNonbondEnergy1.cu
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c kNLRadixSort.cu
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c kCalculateGBNonbondEnergy2.cu
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c kShake.cu
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c kNeighborList.cu
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c kPMEInterpolation.cu
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/local/bin//include -c kCalculateAMDWeights.cu
ar rvs cuda.a cuda_info.o gpu.o gputypes.o kForcesUpdate.o kCalculateLocalForces.o kCalculateGBBornRadii.o kCalculatePMENonbondEnergy.o kCalculateGBNonbondEnergy1.o kNLRadixSort.o kCalculateGBNonbondEnergy2.o kShake.o kNeighborList.o kPMEInterpolation.o kCalculateAMDWeights.o
ar: creating cuda.a
a - cuda_info.o
a - gpu.o
a - gputypes.o
a - kForcesUpdate.o
a - kCalculateLocalForces.o
a - kCalculateGBBornRadii.o
a - kCalculatePMENonbondEnergy.o
a - kCalculateGBNonbondEnergy1.o
a - kNLRadixSort.o
a - kCalculateGBNonbondEnergy2.o
a - kShake.o
a - kNeighborList.o
a - kPMEInterpolation.o
a - kCalculateAMDWeights.o
make[5]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
mpif90 -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -o pmemd.cuda.MPI gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o nbips.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o bintraj.o binrestart.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o charmm_gold.o findmask.o remd.o
multipmemd.o remd_exchg.o amd.o \
-L/usr/local/cuda/lib64 -L/usr/local/cuda/lib -lcurand -lcufft -lcudart ./cuda/cuda.a -L/usr/local/apps/amber12/lib -L/usr/local/apps/amber12/lib -lnetcdf
./cuda/cuda.a(gpu.o): In function `MPI::Cartcomm::Clone() const':
gpu.cpp:(.text._ZNK3MPI8Cartcomm5CloneEv[MPI::Cartcomm::Clone() const]+0x24): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Graphcomm::Clone() const':
gpu.cpp:(.text._ZNK3MPI9Graphcomm5CloneEv[MPI::Graphcomm::Clone() const]+0x24): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intercomm::Merge(bool)':
gpu.cpp:(.text._ZN3MPI9Intercomm5MergeEb[MPI::Intercomm::Merge(bool)]+0x26): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)':
gpu.cpp:(.text._ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb[MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)]+0x1f): undefined reference to `ompi_mpi_cxx_op_intercept'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const':
gpu.cpp:(.text._ZNK3MPI9Intracomm12Create_graphEiPKiS2_b[MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const]+0x27): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Create_cart(int, int const*, bool const*, bool) const':
gpu.cpp:(.text._ZNK3MPI9Intracomm11Create_cartEiPKiPKbb[MPI::Intracomm::Create_cart(int, int const*, bool const*, bool) const]+0x124): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Cartcomm::Sub(bool const*)':
gpu.cpp:(.text._ZN3MPI8Cartcomm3SubEPKb[MPI::Cartcomm::Sub(bool const*)]+0x7b): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Clone() const':
gpu.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone() const]+0x27): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Split(int, int) const':
gpu.cpp:(.text._ZNK3MPI9Intracomm5SplitEii[MPI::Intracomm::Split(int, int) const]+0x24): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI9Intracomm6CreateERKNS_5GroupE[MPI::Intracomm::Create(MPI::Group const&) const]+0x27): more undefined references to `MPI::Comm::Comm()' follow
./cuda/cuda.a(gpu.o):(.rodata._ZTVN3MPI3WinE[vtable for MPI::Win]+0x48): undefined reference to `MPI::Win::Free()'
./cuda/cuda.a(gpu.o):(.rodata._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
collect2: ld returned 1 exit status
make[4]: *** [pmemd.cuda.MPI] Error 1
make[4]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src'
make[3]: *** [cuda_parallel] Error 2
make[3]: Leaving directory `/usr/local/apps/amber12/src/pmemd'
make[2]: *** [cuda_parallel] Error 2
make[2]: Leaving directory `/usr/local/apps/amber12/src'
make[1]: [cuda_parallel] Error 2 (ignored)
make[1]: Leaving directory `/usr/local/apps/amber12/AmberTools/src'
make[1]: Entering directory `/usr/local/apps/amber12/src'
Starting installation of Amber12 (cuda parallel) at Tue Apr 17 15:44:54 MYT 2012.
cd pmemd && make cuda_parallel
make[2]: Entering directory `/usr/local/apps/amber12/src/pmemd'
make -C src/ cuda_parallel
make[3]: Entering directory `/usr/local/apps/amber12/src/pmemd/src'
make -C ./cuda
make[4]: Entering directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src/cuda'
mpif90 -O3 -mtune=native -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -o pmemd.cuda.MPI gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o nbips.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o bintraj.o binrestart.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o charmm_gold.o findmask.o remd.o
multipmemd.o remd_exchg.o amd.o \
-L/usr/local/cuda/lib64 -L/usr/local/cuda/lib -lcurand -lcufft -lcudart ./cuda/cuda.a -L/usr/local/apps/amber12/lib -L/usr/local/apps/amber12/lib -lnetcdf
./cuda/cuda.a(gpu.o): In function `MPI::Cartcomm::Clone() const':
gpu.cpp:(.text._ZNK3MPI8Cartcomm5CloneEv[MPI::Cartcomm::Clone() const]+0x24): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Graphcomm::Clone() const':
gpu.cpp:(.text._ZNK3MPI9Graphcomm5CloneEv[MPI::Graphcomm::Clone() const]+0x24): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intercomm::Merge(bool)':
gpu.cpp:(.text._ZN3MPI9Intercomm5MergeEb[MPI::Intercomm::Merge(bool)]+0x26): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)':
gpu.cpp:(.text._ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb[MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)]+0x1f): undefined reference to `ompi_mpi_cxx_op_intercept'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const':
gpu.cpp:(.text._ZNK3MPI9Intracomm12Create_graphEiPKiS2_b[MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const]+0x27): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Create_cart(int, int const*, bool const*, bool) const':
gpu.cpp:(.text._ZNK3MPI9Intracomm11Create_cartEiPKiPKbb[MPI::Intracomm::Create_cart(int, int const*, bool const*, bool) const]+0x124): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Cartcomm::Sub(bool const*)':
gpu.cpp:(.text._ZN3MPI8Cartcomm3SubEPKb[MPI::Cartcomm::Sub(bool const*)]+0x7b): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Clone() const':
gpu.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone() const]+0x27): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Split(int, int) const':
gpu.cpp:(.text._ZNK3MPI9Intracomm5SplitEii[MPI::Intracomm::Split(int, int) const]+0x24): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI9Intracomm6CreateERKNS_5GroupE[MPI::Intracomm::Create(MPI::Group const&) const]+0x27): more undefined references to `MPI::Comm::Comm()' follow
./cuda/cuda.a(gpu.o):(.rodata._ZTVN3MPI3WinE[vtable for MPI::Win]+0x48): undefined reference to `MPI::Win::Free()'
./cuda/cuda.a(gpu.o):(.rodata._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
collect2: ld returned 1 exit status
make[3]: *** [pmemd.cuda.MPI] Error 1
make[3]: Leaving directory `/usr/local/apps/amber12/src/pmemd/src'
make[2]: *** [cuda_parallel] Error 2
make[2]: Leaving directory `/usr/local/apps/amber12/src/pmemd'
make[1]: *** [cuda_parallel] Error 2
make[1]: Leaving directory `/usr/local/apps/amber12/src'
make: *** [install] Error 2
[root.gpucc amber12]# echo $MPI_HOME
/usr/local/bin/
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 16 April 2012, 21:19
Subject: Re: [AMBER] error installing Amber12-gpu version
On Mon, Apr 16, 2012, Vijay Manickam Achari wrote:
>
> I tried to compile the serial version of amber12 and I installed
> openmpi-1.5.4. from Ambertools/src by executing ./configure-openmpi
> script. All the installation went on smoothly.
>
> Then in execute 'make install' command to install amber12 parallel
> version and I got stuck again. The errors are as below;
> /usr/local/apps/amber12/bin/yacc -d nabgrm.y
> /usr/local/apps/amber12/bin/yacc: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
Does your LD_LIBRARY_PATH variable include $AMBERHOME/lib? Or have you set
MPI_HOME to $AMBERHOME? Also, make sure that "which mpicc" returns the
executable in $AMBERHOME/bin.
...good luck...dac
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Received on Tue Apr 17 2012 - 01:00:04 PDT
