forgive me for my newbie-ness
what exactly do you mean by "Try swapping this so the CUDA lib paths are at
the beginning of your
LD_LIBRARY_PATH"
moving it to the top of the .bashrc file? Or rearranging something? Can
you give me an example of what you mean?
THanks for trying to help me out.
Best,
Jonathan
On Wed, May 30, 2012 at 12:23 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Jonathan,
>
> I can't see anything obviously wrong with your setup so I can't see why
> this
> would be failing. One thing to try:
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64
>
> Try swapping this so the CUDA lib paths are at the beginning of your
> LD_LIBRARY_PATH, just in case there is an older cuda library lying
> somewhere. Then try:
>
> cd $AMBERHOME
> make clean
> ./configure -cuda gnu
> make >& compile_log.txt
>
> Then if it fails please post (gzipped) the compile_log.txt file.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Jonathan Gough [mailto:jonathan.d.gough.gmail.com]
> > Sent: Wednesday, May 30, 2012 5:26 AM
> > To: amber
> > Subject: [AMBER] Trouble compiling cuda, need help.
> >
> > First a big thanks to the amber team, Jason Swails and his wiki (and of
> > course google) that helped me successfully compile amber in serial and
> > parallel (without needing to reach out for help)
> >
> > That being said, i finally have hit a wall.
> >
> > After doing the configuration, make install seems to fall apart and I
> > get
> > the full series of "undefined reference to ' ** ' " right after the
> > following command:
> >
> > gfortran -O3 -mtune=native -DCUDA -o pmemd.cuda 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 \
> > -L/usr/local/cuda/lib64 -L/usr/local/cuda/lib -lcurand -lcufft
> > -lcudart ./cuda/cuda.a -L/home/jonathan/amber12/lib
> > -L/home/jonathan/amber12/lib -lnetcdf
> >
> > I thought that I have everything set up correctly... but who knows....
> > What
> > follows are, as best as I can tell the necessary details re: my setup.
> >
> > uname -m && cat /etc/*release
> > x86_64
> > DISTRIB_ID=Ubuntu
> > DISTRIB_RELEASE=12.04
> > DISTRIB_CODENAME=precise
> > DISTRIB_DESCRIPTION="Ubuntu 12.04 LTS"
> >
> > intel i7
> >
> > gcc --version
> > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
> >
> > gfortran --version
> > GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
> >
> > nvcc --version
> > nvcc: NVIDIA (R) Cuda compiler driver
> > Copyright (c) 2005-2012 NVIDIA Corporation
> > Built on Thu_Apr__5_00:24:31_PDT_2012
> > Cuda compilation tools, release 4.2, V0.2.1221
> >
> > cat /proc/driver/nvidia/version
> > NVRM version: NVIDIA UNIX x86_64 Kernel Module 295.41 Fri Apr 6
> > 23:18:58
> > PDT 2012
> > GCC version: gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
> >
> > .bashrc has the following present.
> >
> > export AMBERHOME=/home/jonathan/amber12
> > export PATH=$PATH:/usr/local/cuda/bin
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64
> > export CUDA_HOME=/usr/local/cuda
> > export PATH=$PATH:/$CUDA_HOME/bin
> >
> > /usr/local/cuda/
> > has the following:
> > bin/ doc/ extras/ include/ lib/ lib64/ libnvvp/ nvvm/
> > open64/ src/ tools/
> >
> >
> > the SDK is at:
> > /NVIDIA_GPU_Computing_SDK$ pwd
> > /home/jonathan/NVIDIA_GPU_Computing_SDK
> >
> > amber12 is at:
> > /amber12$ pwd
> > /home/jonathan/amber12
> > jonathan.jonathan-M-601A:~/amber12$ ls
> > AmberTools bin configure doc include lib64 Makefile
> > README src
> > benchmarks config.h dat GNU_LGPL_v2 lib logs
> > patch_amber.py share test
> >
> > deviceQuery gives:
> >
> > /deviceQuery
> > [deviceQuery] starting...
> >
> > ./deviceQuery Starting...
> >
> > CUDA Device Query (Runtime API) version (CUDART static linking)
> >
> > Found 2 CUDA Capable device(s)
> >
> > Device 0: "Tesla C1060"
> > CUDA Driver Version / Runtime Version 4.2 / 4.2
> > CUDA Capability Major/Minor version number: 1.3
> > Total amount of global memory: 4096 MBytes
> > (4294770688
> > bytes)
> > (30) Multiprocessors x ( 8) CUDA Cores/MP: 240 CUDA Cores
> > GPU Clock rate: 1296 MHz (1.30 GHz)
> > Memory Clock rate: 800 Mhz
> > Memory Bus Width: 512-bit
> > Max Texture Dimension Size (x,y,z) 1D=(8192),
> > 2D=(65536,32768), 3D=(2048,2048,2048)
> > Max Layered Texture Size (dim) x layers 1D=(8192) x 512,
> > 2D=(8192,8192) x 512
> > Total amount of constant memory: 65536 bytes
> > Total amount of shared memory per block: 16384 bytes
> > Total number of registers available per block: 16384
> > Warp size: 32
> > Maximum number of threads per multiprocessor: 1024
> > Maximum number of threads per block: 512
> > Maximum sizes of each dimension of a block: 512 x 512 x 64
> > Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
> > Maximum memory pitch: 2147483647 bytes
> > Texture alignment: 256 bytes
> > Concurrent copy and execution: Yes with 1 copy
> > engine(s)
> > Run time limit on kernels: No
> > Integrated GPU sharing Host Memory: No
> > Support host page-locked memory mapping: Yes
> > Concurrent kernel execution: No
> > Alignment requirement for Surfaces: Yes
> > Device has ECC support enabled: No
> > Device is using TCC driver mode: No
> > Device supports Unified Addressing (UVA): No
> > Device PCI Bus ID / PCI location ID: 2 / 0
> > Compute Mode:
> > < Default (multiple host threads can use ::cudaSetDevice() with
> > device
> > simultaneously) >
> >
> > Device 1: "GeForce 9500 GT"
> > CUDA Driver Version / Runtime Version 4.2 / 4.2
> > CUDA Capability Major/Minor version number: 1.1
> > Total amount of global memory: 1024 MBytes
> > (1073414144
> > bytes)
> > ( 4) Multiprocessors x ( 8) CUDA Cores/MP: 32 CUDA Cores
> > GPU Clock rate: 1350 MHz (1.35 GHz)
> > Memory Clock rate: 400 Mhz
> > Memory Bus Width: 128-bit
> > Max Texture Dimension Size (x,y,z) 1D=(8192),
> > 2D=(65536,32768), 3D=(2048,2048,2048)
> > Max Layered Texture Size (dim) x layers 1D=(8192) x 512,
> > 2D=(8192,8192) x 512
> > Total amount of constant memory: 65536 bytes
> > Total amount of shared memory per block: 16384 bytes
> > Total number of registers available per block: 8192
> > Warp size: 32
> > Maximum number of threads per multiprocessor: 768
> > Maximum number of threads per block: 512
> > Maximum sizes of each dimension of a block: 512 x 512 x 64
> > Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
> > Maximum memory pitch: 2147483647 bytes
> > Texture alignment: 256 bytes
> > Concurrent copy and execution: Yes with 1 copy
> > engine(s)
> > Run time limit on kernels: Yes
> > Integrated GPU sharing Host Memory: No
> > Support host page-locked memory mapping: Yes
> > Concurrent kernel execution: No
> > Alignment requirement for Surfaces: Yes
> > Device has ECC support enabled: No
> > Device is using TCC driver mode: No
> > Device supports Unified Addressing (UVA): No
> > Device PCI Bus ID / PCI location ID: 3 / 0
> > Compute Mode:
> > < Default (multiple host threads can use ::cudaSetDevice() with
> > device
> > simultaneously) >
> >
> > deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 4.2, CUDA
> > Runtime
> > Version = 4.2, NumDevs = 2, Device = Tesla C1060, Device = GeForce 9500
> > GT
> > [deviceQuery] test results...
> > PASSED
> >
> > > exiting in 3 seconds: 3...2...1...done!
> >
> >
> >
> > and config.h has the following:
> >
> > # Amber configuration file, created with: ./configure -cuda gnu
> >
> > #######################################################################
> > ########
> >
> > # (1) Location of the installation
> >
> > BASEDIR=/home/jonathan/amber12
> > BINDIR=/home/jonathan/amber12/bin
> > LIBDIR=/home/jonathan/amber12/lib
> > INCDIR=/home/jonathan/amber12/include
> > DATDIR=/home/jonathan/amber12/dat
> > LOGDIR=/home/jonathan/amber12/logs
> >
> > #######################################################################
> > ########
> >
> >
> > # (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= -lsff -lpbsa -larpack -llapack -lblas -L$(BASEDIR)/lib -
> > lnetcdf
> > -lgfortran -w
> > FLIBS_PTRAJ= -larpack -llapack -lblas -lgfortran -w
> > FLIBSF= -larpack -llapack -lblas
> > FLIBS_FFTW3=
> > #######################################################################
> > ########
> >
> > # (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
> > BUILDAMBER=amber
> >
> > # Set the C compiler, etc.
> >
> > # The configure script should be fine, but if you need to hand-edit,
> > # here is some info:
> >
> > # Example: CC-->gcc; LEX-->flex; YACC-->yacc (built in byacc)
> > # Note: If your lexer is "really" flex, you need to set
> > # LEX=flex below. For example, on some 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=gcc
> > CFLAGS= -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
> > $(CUSTOMBUILDFLAGS)
> > CNOOPTFLAGS=
> > COPTFLAGS=-O3 -mtune=native -DBINTRAJ -DHASGZ -DHASBZ2
> > AMBERCFLAGS= $(AMBERBUILDFLAGS)
> >
> > CXX=g++
> > CPLUSPLUS=g++
> > CXXFLAGS= $(CUSTOMBUILDFLAGS)
> > CXXNOOPTFLAGS=
> > CXXOPTFLAGS=-O3
> > AMBERCXXFLAGS= $(AMBERBUILDFLAGS)
> >
> > NABFLAGS=
> > PBSAFLAG=
> >
> > LDFLAGS= $(CUSTOMBUILDFLAGS)
> > AMBERLDFLAGS=$(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= 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=gfortran
> > FFLAGS= $(LOCALFLAGS) $(CUSTOMBUILDFLAGS) -I$(INCDIR) $(NETCDFINC)
> > FNOOPTFLAGS= -O0
> > FOPTFLAGS= -O3 -mtune=native
> > AMBERFFLAGS=$(AMBERBUILDFLAGS)
> > FREEFORMAT_FLAG= -ffree-form
> > LM=-lm
> > FPP=cpp -traditional -P
> > FPPFLAGS= -DBINTRAJ $(CUSTOMBUILDFLAGS)
> > AMBERFPPFLAGS=$(AMBERBUILDFLAGS)
> > FCREAL8=-fdefault-real-8
> >
> > XHOME= /usr
> > XLIBS= -L/usr/lib/x86_64-linux-gnu -L/usr/lib64 -L/usr/lib
> > MAKE_XLEAP=install_xleap
> >
> > NETCDF=$(BASEDIR)/include/netcdf.mod
> > NETCDFLIB=-L$(BASEDIR)/lib -lnetcdf
> > NETCDFINC=-I$(BASEDIR)/include
> > PNETCDF=
> > PNETCDFLIB=
> > FFTWLIB=
> >
> > ZLIB=-lz
> > BZLIB=-lbz2
> >
> > HASFC=yes
> > MTKPP=
> > XBLAS=
> > FFTW3=
> > MDGX=no
> >
> > COMPILER=gnu
> > MKL=
> > MKL_PROCESSOR=
> >
> > #CUDA Specific build flags
> > NVCC=$(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$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon
> > PMEMD_CU_LIBS=-L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft
> > -lcudart ./cuda/cuda.a
> > PMEMD_CU_DEFINES=-DCUDA
> >
> > #PMEMD Specific build flags
> > PMEMD_F90=gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
> > -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT
> > PMEMD_FOPTFLAGS=-O3 -mtune=native
> > PMEMD_CC=gcc
> > PMEMD_COPTFLAGS=-O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64
> > -D_LARGEFILE_SOURCE -DBINTRAJ
> > PMEMD_FLIBSF=
> > PMEMD_LD= gfortran
> > LDOUT= -o
> >
> > #for NAB:
> > MPI=
> >
> > #1D-RISM
> > RISM=no
> >
> > #3D-RISM NAB
> > RISMSFF=
> > SFF_RISM_INTERFACE=
> > TESTRISMSFF=
> >
> > #3D-RISM SANDER
> > RISMSANDER=
> > SANDER_RISM_INTERFACE=
> > FLIBS_RISMSANDER=
> > TESTRISMSANDER=
> >
> > #PUPIL
> > PUPILLIBS=-lrt -lm -lc -L${PUPIL_PATH}/lib -lPUPIL -lPUPILBlind
> >
> > #Python interpreter we are using
> > PYTHON=/usr/bin/python2.7
> >
> >
> > if you need any other info, please let me know...
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 30 2012 - 09:30:04 PDT
