[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