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
Received on Sun Mar 25 2012 - 05:00:03 PDT
