No Dice.
attached is the Log file.
below is what I did...
jonathan.jonathan-M-601A:~$ echo $LD_LIBRARY_PATH
/usr/local/cuda/lib64:/usr/local/cuda/lib:
jonathan.jonathan-M-601A:~$ cd amber12/
jonathan.jonathan-M-601A:~/amber12$ make clean
.
.
.
jonathan.jonathan-M-601A:~/amber12$ ./configure -cuda gnu
Checking for updates...
AmberTools12 is up to date
Amber12 is up to date
Searching for python2... Found python2.7: /usr/bin/python2.7
Obtaining the gnu suite version:
gcc -v
The version is 4.6.3
Testing the gcc compiler:
gcc -DSYSV -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 -DSYSV -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 -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
testp.c.o testp.f.o -lgfortran -w
OK
Testing pointer size:
gcc -DSYSV -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: OK
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.
jonathan.jonathan-M-601A:~/amber12$ make >& compile_log.txt
jonathan.jonathan-M-601A:~/amber12$ ls
On Wed, May 30, 2012 at 12:39 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Jonathan,
>
> Sorry. I meant change it from:
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64
>
> to
>
> export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
> export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
>
> But make sure you logout and log back in again so it inherits this change.
> You can check with:
>
> echo $LD_LIBRARY_PATH
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Jonathan Gough [mailto:jonathan.d.gough.gmail.com]
> > Sent: Wednesday, May 30, 2012 9:30 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Trouble compiling cuda, need help.
> >
> > forgive me for my newbie-ness
> >
> > what exactly do you mean by "Try swapping this so the CUDA lib paths
> > are at
> > the beginning of your
> > LD_LIBRARY_PATH"
> >
> > moving it to the top of the .bashrc file? Or rearranging something?
> > Can
> > you give me an example of what you mean?
> >
> > THanks for trying to help me out.
> >
> > Best,
> > Jonathan
> >
> > On Wed, May 30, 2012 at 12:23 PM, Ross Walker <ross.rosswalker.co.uk>
> > wrote:
> >
> > > Hi Jonathan,
> > >
> > > I can't see anything obviously wrong with your setup so I can't see
> > why
> > > this
> > > would be failing. One thing to try:
> > >
> > > export LD_LIBRARY_PATH=$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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
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Received on Wed May 30 2012 - 10:00:04 PDT
