Hi,
Was your MPI built with support for C++? If it wasn't, I think you
need to recompile your MPI with C++ support. If it was, try adding
'-lmpi_cxx' to the PMEMD_CU_LIBS variable in your config.h file.
Hope this helps,
-Dan
On Wed, Apr 10, 2013 at 7:48 AM, Donato Pera <donato.pera.dm.univaq.it> wrote:
> Dear Developers,
>
> We have had some problems during Amber12 installation with MPI.
> (We doesn't have problems on a single GPU).
>
> This is our make install results:
>
>
>
> [montagna.compute-1-6 amber12_GPU]$ ./configure -cuda -mpi gnu
> Checking for updates...
> AmberTools12 is up to date
> Amber12 is up to date
>
> Searching for python2... Found python2.4: /usr/bin/python2.4
>
> Obtaining the gnu suite version:
> gcc -v
> The version is 4.1.2
>
> Testing the gcc compiler:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> OK
>
> Testing the gfortran compiler:
> gfortran -O0 -o testp testp.f
> OK
>
> Testing mixed C/Fortran compilation:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
> testp.c gfortran -O0 -c -o testp.f.o testp.f
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o
> testp.f.o -lgfortran -w
> OK
>
> Testing pointer size:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size
> test_pointer_size.c
> Detected 64 bit operating system.
>
> Testing flex: OK
>
> Configuring NetCDF (may be time-consuming)...
>
> NetCDF configure succeeded.
>
> Checking for zlib: OK
>
> Checking for libbz2: testp.c:2:19: error: bzlib.h: No such file or
> directory testp.c: In function 'main':
> testp.c:5: error: 'BZFILE' undeclared (first use in this function)
> testp.c:5: error: (Each undeclared identifier is reported only once
> testp.c:5: error: for each function it appears in.)
> testp.c:5: error: 'infile' undeclared (first use in this function)
> ./configure2: line 1897: ./testp: No such file or directory
> Not found.
> Skipping configuration of FFTW3
>
> The configuration file, config.h, was successfully created.
>
> The next step is to type 'make install'
>
> Cleaning the src directories. This may take a few moments.
> Configure complete.
> [montagna.compute-1-6 amber12_GPU]$ make install
> cd AmberTools/src && make install
> make[1]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/AmberTools/src' AmberTools12 has no
> CUDA-enabled components
> (cd ../../src && make cuda_parallel )
> make[2]: Entering directory `/home/SWcbbc/Amber12/amber12_GPU/src'
> Starting installation of Amber12 (cuda parallel) at Wed Apr 10 15:39:18
> CEST 2013.
> cd pmemd && make cuda_parallel
> make[3]: Entering directory `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd'
> make -C src/ cuda_parallel
> make[4]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src' mpif90 -DMPI -DBINTRAJ
> -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT
> -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -Duse_SPFP
> -I/home/SWcbbc/Amber12/amber12_GPU/include -c gbl_constants.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c gbl_datatypes.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c state_info.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c file_io_dat.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pmemd_lib.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c parallel_dat.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c file_io.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c mdin_ctrl_dat.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c axis_optimize.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c fft1d.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c charmm.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c
> nextprmtop_section.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c prmtop_dat.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c
> mdin_ewald_dat.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c
> mdin_debugf_dat.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c remd.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c binrestart.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c inpcrd_dat.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c constraints.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c mol_list.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c
> extra_pnts_nb14.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c prfs.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c dynamics_dat.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c random.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c dynamics.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pbc.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c img.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c timers.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c bspline.F90
> In file bspline.F90:89
>
> if (ibcbeg - 1) 11, 15, 16
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file bspline.F90:144
>
> if (ibcend - 1) 21, 30, 24
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file bspline.F90:176
>
> 25 if (ibcend-1) 26, 30, 24
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pme_recip_dat.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pme_fft_dat.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pme_blk_fft.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pme_slab_fft.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c shake.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c nmr_lib.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c nmr_calls.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c angles.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c angles_ub.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c cmap.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c bonds.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c cit.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c dihedrals.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c dihedrals_imp.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c nb_exclusions.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c parallel.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c
> ene_frc_splines.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c nb_pairlist.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c nbips.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c gb_parallel.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c loadbal.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pme_blk_recip.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c
> pme_slab_recip.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pme_direct.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c bintraj.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c runfiles.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c amd.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pme_force.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c degcnt.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c gbsa.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c gb_ene.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c gb_force.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c get_cmdline.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c multipmemd.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c remd_exchg.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c runmd.F90
> In file runmd.F90:2323
>
> if (abs(biga) - abs(a(ij))) 15, 20, 20
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file runmd.F90:2332
>
> if (j - k) 35, 35, 25
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file runmd.F90:2345
>
> if (i - k) 45, 45, 38
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file runmd.F90:2356
>
> 45 if (biga) 48, 46, 48
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file runmd.F90:2360
>
> if (i - k) 50, 55, 50
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file runmd.F90:2373
>
> if (i - k) 60, 65, 60
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file runmd.F90:2374
>
> 60 if (j - k) 62, 65, 62
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file runmd.F90:2384
>
> if (j - k) 70, 75, 70
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file runmd.F90:2402
>
> if (k) 150, 150, 105
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file runmd.F90:2404
>
> if (i - k) 120, 120, 108
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file runmd.F90:2414
>
> if (j - k) 100, 100, 125
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c runmin.F90
> In file runmin.F90:409
>
> if (fch) 100, 90, 130
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c veclib.F90 mpicc
> -O3 -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pmemd_clib.c
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c
> gb_alltasks_setup.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c
> pme_alltasks_setup.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pme_setup.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c findmask.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c master_setup.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c pmemd.F90 mpif90
> -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c erfcfun.F90
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/home/SWcbbc/Amber12/amber12_GPU/include -c charmm_gold.F90
> make -C ./cuda
> make[5]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c cuda_info.F90
> mpicc -O3 -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c gpu.cpp
> mpicc -O3 -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c gputypes.cpp
> /usr/local/cuda-5.0/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c kForcesUpdate.cu
> ./kForcesUpdate.cu(87): Advisory: Loop was not unrolled, cannot deduce
> loop trip count
> ./kForcesUpdate.cu(127): Advisory: Loop was not unrolled, cannot deduce
> loop trip count
> /usr/local/cuda-5.0/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c kCalculateLocalForces.cu
> /usr/local/cuda-5.0/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c kCalculateGBBornRadii.cu
> /usr/local/cuda-5.0/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c kCalculatePMENonbondEnergy.cu
> /usr/local/cuda-5.0/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c kCalculateGBNonbondEnergy1.cu
> /usr/local/cuda-5.0/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c kNLRadixSort.cu
> B40C/radix_sort/../radix_sort/../radix_sort/upsweep/../../radix_sort/upsweep/cta.cuh(127):
> Advisory: Loop was not unrolled, unexpected control flow construct
> B40C/radix_sort/../radix_sort/../radix_sort/upsweep/../../radix_sort/upsweep/cta.cuh(127):
> Advisory: Loop was not unrolled, unexpected control flow construct
> B40C/radix_sort/../radix_sort/../util/kernel_props.cuh: In member function
> 'int b40c::util::KernelProps::OversubscribedGridSize(int, int, int)
> const':
> B40C/radix_sort/../radix_sort/../util/kernel_props.cuh:140: warning:
> converting to 'int' from 'double'
> /usr/local/cuda-5.0/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c kCalculateGBNonbondEnergy2.cu
> /usr/local/cuda-5.0/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c kShake.cu
> /usr/local/cuda-5.0/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c kNeighborList.cu
> /usr/local/cuda-5.0/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/include -c kPMEInterpolation.cu
> /usr/local/cuda-5.0/bin/nvcc -use_fast_math -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -Duse_SPFP -I/usr/local/cuda-5.0/include -IB40C -IB40C/KernelCommon
> -I/opt/openmpi/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
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make -C ./cuda
> make[5]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make[5]: `cuda.a' is up to date.
> make[5]: Leaving directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make -C ./cuda
> make[5]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make[5]: `cuda.a' is up to date.
> make[5]: Leaving directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make -C ./cuda
> make[5]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make[5]: `cuda.a' is up to date.
> make[5]: Leaving directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make -C ./cuda
> make[5]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make[5]: `cuda.a' is up to date.
> make[5]: Leaving directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make -C ./cuda
> make[5]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make[5]: `cuda.a' is up to date.
> make[5]: Leaving directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> mpif90 -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -Duse_SPFP -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 gbsa.o \
> ./cuda/cuda.a -L/usr/local/cuda-5.0/lib64 -L/usr/local/cuda-5.0/lib
> -lcurand -lcufft -lcudart -L/home/SWcbbc/Amber12/amber12_GPU/lib
> -L/home/SWcbbc/Amber12/amber12_GPU/lib -lnetcdf
> ./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)]+0x19):
> undefined reference to `ompi_mpi_cxx_op_intercept'
> ./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Create(MPI::Group
> const&) const':
> gpu.cpp:(.text._ZNK3MPI9Intracomm6CreateERKNS_5GroupE[MPI::Intracomm::Create(MPI::Group
> const&) const]+0x2a): 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]+0x25): 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]+0x8f): undefined reference to
> `MPI::Comm::Comm()'
> ./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]+0x2b): undefined reference to
> `MPI::Comm::Comm()'
> ./cuda/cuda.a(gpu.o): In function `MPI::Cartcomm::Clone() const':
> gpu.cpp:(.text._ZNK3MPI8Cartcomm5CloneEv[MPI::Cartcomm::Clone()
> const]+0x25): undefined reference to `MPI::Comm::Comm()'
> ./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZN3MPI8Cartcomm3SubEPKb[MPI::Cartcomm::Sub(bool
> const*)]+0x76): 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
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src' make[3]: ***
> [cuda_parallel] Error 2
> make[3]: Leaving directory `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd'
> make[2]: *** [cuda_parallel] Error 2
> make[2]: Leaving directory `/home/SWcbbc/Amber12/amber12_GPU/src'
> make[1]: [cuda_parallel] Error 2 (ignored)
> make[1]: Leaving directory
> `/home/SWcbbc/Amber12/amber12_GPU/AmberTools/src' make[1]: Entering
> directory `/home/SWcbbc/Amber12/amber12_GPU/src' Starting installation of
> Amber12 (cuda parallel) at Wed Apr 10 15:44:42 CEST 2013.
> cd pmemd && make cuda_parallel
> make[2]: Entering directory `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd'
> make -C src/ cuda_parallel
> make[3]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src' make -C ./cuda
> make[4]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make[4]: `cuda.a' is up to date.
> make[4]: Leaving directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make -C ./cuda
> make[4]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make[4]: `cuda.a' is up to date.
> make[4]: Leaving directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make -C ./cuda
> make[4]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make[4]: `cuda.a' is up to date.
> make[4]: Leaving directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make -C ./cuda
> make[4]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make[4]: `cuda.a' is up to date.
> make[4]: Leaving directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make -C ./cuda
> make[4]: Entering directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> make[4]: `cuda.a' is up to date.
> make[4]: Leaving directory
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src/cuda'
> mpif90 -O3 -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK -Duse_SPFP -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 gbsa.o \
> ./cuda/cuda.a -L/usr/local/cuda-5.0/lib64 -L/usr/local/cuda-5.0/lib
> -lcurand -lcufft -lcudart -L/home/SWcbbc/Amber12/amber12_GPU/lib
> -L/home/SWcbbc/Amber12/amber12_GPU/lib -lnetcdf
> ./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)]+0x19):
> undefined reference to `ompi_mpi_cxx_op_intercept'
> ./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Create(MPI::Group
> const&) const':
> gpu.cpp:(.text._ZNK3MPI9Intracomm6CreateERKNS_5GroupE[MPI::Intracomm::Create(MPI::Group
> const&) const]+0x2a): 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]+0x25): 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]+0x8f): undefined reference to
> `MPI::Comm::Comm()'
> ./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]+0x2b): undefined reference to
> `MPI::Comm::Comm()'
> ./cuda/cuda.a(gpu.o): In function `MPI::Cartcomm::Clone() const':
> gpu.cpp:(.text._ZNK3MPI8Cartcomm5CloneEv[MPI::Cartcomm::Clone()
> const]+0x25): undefined reference to `MPI::Comm::Comm()'
> ./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZN3MPI8Cartcomm3SubEPKb[MPI::Cartcomm::Sub(bool
> const*)]+0x76): 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
> `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd/src' make[2]: ***
> [cuda_parallel] Error 2
> make[2]: Leaving directory `/home/SWcbbc/Amber12/amber12_GPU/src/pmemd'
> make[1]: *** [cuda_parallel] Error 2
> make[1]: Leaving directory `/home/SWcbbc/Amber12/amber12_GPU/src'
> make: *** [install] Error 2
>
> Regards Donato.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 10 2013 - 07:30:03 PDT
