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.
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Received on Wed Apr 10 2013 - 07:00:04 PDT
