Hi Adam,
The scripts are not designed to be used directly.
Do
Export DO_PARALLEL='mpirun -np 2'
Make test.cuda.parallel
All the best
Ross
On Mar 25, 2012, at 4:51, Adam Jion <adamjion.yahoo.com> wrote:
> Hi all,
>
> I'm having a nightmare making Amber11 fully-functional.
> Anyone able to help??
>
>
> I managed to compile, install and test the parallel version of Amber 11.
> I'm also able to compile, install and test the serial version of Amber11-GPU (i.e. pmemd.cuda)
>
> After installing mpich2, I am able to compile and install Amber 11-MultiGPU (i.e.pmemd.cuda.mpi)
> All this was done without tweaking the config.h file.
>
> However, for some reasons, I cannot run tests on pmemd.cuda.mpi.
> Here's the error log:
>
> adam.adam-MS-7750:~/amber11/test$ ./test_amber_cuda_parallel.sh
> [: 50: unexpected operator
> [: 57: unexpected operator
> cd cuda && make -k test.pmemd.cuda.MPI GPU_ID= PREC_MODEL=
> make[1]: Entering directory `/home/adam/amber11/test/cuda'
> ------------------------------------
> Running CUDA Implicit solvent tests.
> Precision Model =
> GPU_ID =
> ------------------------------------
> cd trpcage/ && ./Run_md_trpcage netcdf.mod
> [proxy:0:0.adam-MS-7750] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ../../../bin/pmemd.cuda_.MPI (No such file or directory)
> [proxy:0:0.adam-MS-7750] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ../../../bin/pmemd.cuda_.MPI (No such file or directory)
> ./Run_md_trpcage: Program error
> make[1]: *** [test.pmemd.cuda.gb] Error 1
> ------------------------------------
> Running CUDA Explicit solvent tests.
> Precision Model =
> GPU_ID =
> ------------------------------------
> cd 4096wat/ && ./Run.pure_wat netcdf.mod
> [proxy:0:0.adam-MS-7750] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ../../../bin/pmemd.cuda_.MPI (No such file or directory)
> [proxy:0:0.adam-MS-7750] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ../../../bin/pmemd.cuda_.MPI (No such file or directory)
> ./Run.pure_wat: Program error
> make[1]: *** [test.pmemd.cuda.pme] Error 1
> make[1]: Target `test.pmemd.cuda.MPI' not remade because of errors.
> make[1]: Leaving directory `/home/adam/amber11/test/cuda'
> make: *** [test.pmemd.cuda.MPI] Error 2
> make: Target `test.parallel.cuda' not remade because of errors.
> 0 file comparisons passed
> 0 file comparisons failed
> 11 tests experienced errors
> Test log file saved as logs/test_amber_cuda_parallel/2012-03-25_19-35-37.log
> No test diffs to save!
>
> Appreciate any help,
> Adam
>
> ps. Using compilers gcc-4.4.6, gfortran-4.4.6, mpicc,mpif90
> pps. The config.h file is given below:
>
> #MODIFIED FOR AMBERTOOLS 1.5
> # Amber configuration file, created with: ./configure -cuda -mpi gnu
>
> ###############################################################################
>
> # (1) Location of the installation
>
> BINDIR=/home/adam/amber11/bin
> LIBDIR=/home/adam/amber11/lib
> INCDIR=/home/adam/amber11/include
> DATDIR=/home/adam/amber11/dat
>
> ###############################################################################
>
>
> # (2) If you want to search additional libraries by default, add them
> # to the FLIBS variable here. (External libraries can also be linked into
> # NAB programs simply by including them on the command line; libraries
> # included in FLIBS are always searched.)
>
> FLIBS= -L$(LIBDIR) -lsff_mpi -lpbsa $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a $(LIBDIR)/libnetcdf.a -lgfortran
> FLIBS_PTRAJ= $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a -lgfortran
> FLIBSF= $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a
> FLIBS_FFTW2=-L$(LIBDIR)
> ###############################################################################
>
> # (3) Modify any of the following if you need to change, e.g. to use gcc
> # rather than cc, etc.
>
> SHELL=/bin/sh
> INSTALLTYPE=cuda_parallel
>
> # Set the C compiler, etc.
>
> # For GNU: CC-->gcc; LEX-->flex; YACC-->bison -y -t;
> # Note: If your lexer is "really" flex, you need to set
> # LEX=flex below. For example, on many linux distributions,
> # /usr/bin/lex is really just a pointer to /usr/bin/flex,
> # so LEX=flex is necessary. In general, gcc seems to need flex.
>
> # The compiler flags CFLAGS and CXXFLAGS should always be used.
> # By contrast, *OPTFLAGS and *NOOPTFLAGS will only be used with
> # certain files, and usually at compile-time but not link-time.
> # Where *OPTFLAGS and *NOOPTFLAGS are requested (in Makefiles,
> # makedepend and depend), they should come before CFLAGS or
> # CXXFLAGS; this allows the user to override *OPTFLAGS and
> # *NOOPTFLAGS using the BUILDFLAGS variable.
> CC=mpicc
> CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI $(CUSTOMBUILDFLAGS) $(AMBERCFLAGS)
> OCFLAGS= $(COPTFLAGS) $(AMBERCFLAGS)
> CNOOPTFLAGS=
> COPTFLAGS=-O3 -mtune=generic -DBINTRAJ -DHASGZ -DHASBZ2
> AMBERCFLAGS= $(AMBERBUILDFLAGS)
>
> CXX=g++
> CPLUSPLUS=g++
> CXXFLAGS= -DMPI $(CUSTOMBUILDFLAGS)
> CXXNOOPTFLAGS=
> CXXOPTFLAGS=-O3
> AMBERCXXFLAGS= $(AMBERBUILDFLAGS)
>
> NABFLAGS=
>
> LDFLAGS= $(CUSTOMBUILDFLAGS) $(AMBERLDFLAGS)
> AMBERLDFLAGS=$(AMBERBUILDFLAGS)
>
> LEX= flex
> YACC= $(BINDIR)/yacc
> AR= ar rv
> M4= m4
> RANLIB=ranlib
>
> # Set the C-preprocessor. Code for a small preprocessor is in
> # ucpp-1.3; it gets installed as $(BINDIR)/ucpp;
> # this can generally be used (maybe not on 64-bit machines like altix).
>
> CPP= $(BINDIR)/ucpp -l
>
> # These variables control whether we will use compiled versions of BLAS
> # and LAPACK (which are generally slower), or whether those libraries are
> # already available (presumably in an optimized form).
>
> LAPACK=install
> BLAS=install
> F2C=skip
>
> # These variables determine whether builtin versions of certain components
> # can be used, or whether we need to compile our own versions.
>
> UCPP=install
> C9XCOMPLEX=skip
>
> # For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty:
> # Set OBJSFX to ".obj" instead of ".o" on Windows:
>
> SFX=
> OSFX=.o
> MV=mv
> RM=rm
> CP=cp
>
> # Information about Fortran compilation:
>
> FC=mpif90
> FFLAGS= $(LOCALFLAGS) $(CUSTOMBUILDFLAGS) $(FNOOPTFLAGS)
> FNOOPTFLAGS= -O0
> FOPTFLAGS= -O3 -mtune=generic $(LOCALFLAGS) $(CUSTOMBUILDFLAGS)
> AMBERFFLAGS=$(AMBERBUILDFLAGS)
> FREEFORMAT_FLAG= -ffree-form
> LM=-lm
> FPP=cpp -traditional $(FPPFLAGS) $(AMBERFPPFLAGS)
> FPPFLAGS=-P -DBINTRAJ -DMPI $(CUSTOMBUILDFLAGS)
> AMBERFPPFLAGS=$(AMBERBUILDFLAGS)
>
>
> BUILD_SLEAP=install_sleap
> XHOME=
> XLIBS= -L/lib64 -L/lib
> MAKE_XLEAP=skip_xleap
>
> NETCDF=netcdf.mod
> NETCDFLIB=$(LIBDIR)/libnetcdf.a
> PNETCDF=yes
> PNETCDFLIB=$(LIBDIR)/libpnetcdf.a
>
> ZLIB=-lz
> BZLIB=-lbz2
>
> HASFC=yes
> MDGX=yes
> CPPTRAJ=yes
> MTKPP=
>
> COMPILER=gnu
> MKL=
> MKL_PROCESSOR=
>
> #CUDA Specific build flags
> NVCC=$(CUDA_HOME)/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20
> PMEMD_CU_INCLUDES=-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon -I/usr/include
> PMEMD_CU_LIBS=-L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart ./cuda/cuda.a
> PMEMD_CU_DEFINES=-DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
>
> #PMEMD Specific build flags
> PMEMD_FPP=cpp -traditional -DMPI -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT
> PMEMD_NETCDFLIB= $(NETCDFLIB)
> PMEMD_F90=mpif90
> PMEMD_FOPTFLAGS=-O3 -mtune=generic
> PMEMD_CC=mpicc
> PMEMD_COPTFLAGS=-O3 -mtune=generic -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI
> PMEMD_FLIBSF=
> PMEMD_LD= mpif90
> LDOUT= -o
>
> #3D-RISM MPI
> RISMSFF=
> SANDER_RISM_MPI=sander.RISM.MPI$(SFX)
> TESTRISM=
>
> #PUPIL
> PUPILLIBS=-lrt -lm -lc -L${PUPIL_PATH}/lib -lPUPIL -lPUPILBlind
>
> #Python
> PYINSTALL=
>
>
>
>
>
>
>
>
> adam.adam-MS-7750:~/amber11/test$ ./test_amber_cuda_parallel.sh
> [: 50: unexpected operator
> [: 57: unexpected operator
> cd cuda && make -k test.pmemd.cuda.MPI GPU_ID= PREC_MODEL=
> make[1]: Entering directory `/home/adam/amber11/test/cuda'
> ------------------------------------
> Running CUDA Implicit solvent tests.
> Precision Model =
> GPU_ID =
> ------------------------------------
> cd trpcage/ && ./Run_md_trpcage netcdf.mod
> [proxy:0:0.adam-MS-7750] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ../../../bin/pmemd.cuda_.MPI (No such file or directory)
> [proxy:0:0.adam-MS-7750] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ../../../bin/pmemd.cuda_.MPI (No such file or directory)
> ./Run_md_trpcage: Program error
> make[1]: *** [test.pmemd.cuda.gb] Error 1
> ------------------------------------
> Running CUDA Explicit solvent tests.
> Precision Model =
> GPU_ID =
> ------------------------------------
> cd 4096wat/ && ./Run.pure_wat netcdf.mod
> [proxy:0:0.adam-MS-7750] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ../../../bin/pmemd.cuda_.MPI (No such file or directory)
> [proxy:0:0.adam-MS-7750] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ../../../bin/pmemd.cuda_.MPI (No such file or directory)
> ./Run.pure_wat: Program error
> make[1]: *** [test.pmemd.cuda.pme] Error 1
> make[1]: Target `test.pmemd.cuda.MPI' not remade because of errors.
> make[1]: Leaving directory `/home/adam/amber11/test/cuda'
> make: *** [test.pmemd.cuda.MPI] Error 2
> make: Target `test.parallel.cuda' not remade because of errors.
> 0 file comparisons passed
> 0 file comparisons failed
> 11 tests experienced errors
> Test log file saved as logs/test_amber_cuda_parallel/2012-03-25_19-35-37.log
> No test diffs to save!
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Mar 25 2012 - 07:30:03 PDT
