Dear Dan,
It doesn't work also adding
'-lmpi_cxx' to the PMEMD_CU_LIBS
Thanks Donato
> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
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> believed to be clean.
>
>
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Received on Wed Apr 10 2013 - 08:00:03 PDT
