Re: [AMBER] Amber installation problems

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 10 Apr 2013 09:55:36 -0500

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
>> 
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>> 
>> 
> 
> 
> 
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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Received on Wed Apr 10 2013 - 08:00:04 PDT
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