Dear Jason,
I have the C++ MPI support but AMBER doesn't work
Regards Donato.
> Then you will need to build your MPI with C++ support. You can download
> mpich2 in the $AMBERHOME/AmberTools/src folder and use the
> configure_mpich2 script to build a compatible MPICH2 installation in
> AMBERHOME/bin.
>
> Then make sure you add AMBERHOME/bin to the beginning of your PATH so that
> the MPI you just built is used.
>
> HTH,
> Jason
>
> --
> Jason Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Apr 10, 2013, at 9:32 AM, "Donato Pera" <donato.pera.dm.univaq.it>
> wrote:
>
>> Dear Dan,
>>
>> It doesn't work also adding
>>
>> '-lmpi_cxx' to the PMEMD_CU_LIBS
>>
>> Thanks Donato
>>
>>
>>> Hi,
>>>
>>> Was your MPI built with support for C++? If it wasn't, I think you
>>> need to recompile your MPI with C++ support. If it was, try adding
>>> '-lmpi_cxx' to the PMEMD_CU_LIBS variable in your config.h file.
>>>
>>> Hope this helps,
>>>
>>> -Dan
>>>
>>> On Wed, Apr 10, 2013 at 7:48 AM, Donato Pera <donato.pera.dm.univaq.it>
>>> wrote:
>>>> Dear Developers,
>>>>
>>>> We have had some problems during Amber12 installation with MPI.
>>>> (We doesn't have problems on a single GPU).
>>>>
>>>> This is our make install results:
>>>>
>>>>
>>>>
>>>> [montagna.compute-1-6 amber12_GPU]$ ./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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>>> This message has been scanned for viruses and
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>>> believed to be clean.
>>>
>>>
>>
>>
>>
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>
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Received on Fri Apr 12 2013 - 00:30:02 PDT
