Date: Wed, 4 Mar 2020 11:24:59 -0500
Good Morning,
So I tried all the recommendations that were suggested and i was able to
install with CUDA 9.2 but when i try and make test i get the following
errors that look pretty similar. Any suggestions on why im able to build
and install amber with this but all tests fail? I also reinstalled amber
and everything looks fine as far as I can tell but clearly something is
wrong. Thanks again for all the help!
[image: image.png]
On Wed, Mar 4, 2020 at 4:22 AM Ruxi Qi <ruxiq.uci.edu> wrote:
> Sorry, typo, should be /usr/lib/x86_64-linux-gnu.
>
> BTW, we will add a handling to this in the AmberTools 20 release.
>
> Ruxi
> On 3/4/20 5:05 PM, Ruxi Qi wrote:
>
> Hi Nicholas,
>
> The issue was because from CUDA 10.1 some libraries including the CUBLAS
> are installed in the system standard locations rather than in the Toolkit
> installation directory. Depending on distribution these installed locations
> can be either /usr/lib/x84_64-linux-gnu as with Ubuntu 18.04, or /usr/lib64
> as with Centos 7, or /usr/lib. You can check this by executing:
>
> *sudo find /usr -name libcublas**
>
> So the solution is to either create a symlink in the CUDA Toolkit library
> path to the library file missing, or more handily add the location to your
> library searching path in your .bashrc:
>
> export LD_LIBRARY_PATH=/usr/lib/x84_64-linux-gnu:$LD_LIBRARY_PATH
>
> Hope it helps.
>
> Best,
>
> Ruxi
> On 3/4/20 6:04 AM, Nicholas Moyer wrote:
>
> This is the closest error that i've seen to date, i will have to try CUDA
> 9.2, I had been trying to get 10 to work so I wouldn't have to reinstall on
> a bunch of machines but that looks like my only option. Thank you very much
> I will let you know if that works tomorrow!
>
> On Tue, Mar 3, 2020 at 4:58 PM Abhilash J <md.scfbio.gmail.com> <md.scfbio.gmail.com> wrote:
>
>
> Hi Everyone,
>
> I am also having a similar (but not exact issue) with installing AMBER
> 18. The compile seems to complete without glitch if i use CUDA 9.2. Error
> occurs if i use CUDA 10.2. Did you give CUDA 9.2 a shot.
> The error i am dealing with is as follows.
> Any comments will be useful.
>
> ============error file======================
> Warning: Deleted feature: ASSIGN statement at (1)
> /bin/ld: cannot find -lcublas
> collect2: error: ld returned 1 exit status
> make[2]: *** [pbsa.cuda] Error 1
> make[1]: *** [cuda_serial] Error 2
> make: *** [install] Error 2
> ===========================================
>
> ========out file====================
> /usr/local/cuda-10.2/bin/nvcc -gencode arch=compute_30,code=sm_30 -gencode
> arch=compute_35,code=sm_35 -gencode arch=compute_37,code=sm_37 -gencode
> arch=compute_50,code=sm_50 -gencode arch=compute_52,code=sm_52 -gencode
> arch=compute_53,code=sm_53 -gencode arch=compute_60,code=sm_60 -gencode
> arch=compute_61,code=sm_61 -gencode arch=compute_60,code=sm_70, -gencode
> arch=compute_61,code=sm_70 -Wno-deprecated-declarations -use_fast_math -O3
> -ccbin g++ -I../cusplibrary-cuda9 -o cusp_LinearSolvers.o -c
> cusp_LinearSolvers.cu -DDIA
> [PBSA] FC pbsa.cuda
> make[2]: Leaving directory
> `/home33/ajayaraj/AMBER/amber18/AmberTools/src/pbsa'
> make[1]: Leaving directory `/home33/ajayaraj/AMBER/amber18/AmberTools/src'
> =================================
>
>
> On Tue, Mar 3, 2020 at 1:27 PM Ray Luo <rluo.uci.edu> <rluo.uci.edu> wrote:
>
>
> Nicholas,
>
> Any CUDA version higher than 10.0 could be a problem. We only tested
> version 10 and older releases when the amber19 was released earlier
> last year.
>
> Right now we are testing the current release of 10.2 on one of our GPU
> boxes.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical Physics, Biomedical Engineering, and Chemical Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
> On Tue, Mar 3, 2020 at 10:20 AM Nicholas Moyer<nmoyer.broadinstitute.org> <nmoyer.broadinstitute.org> wrote:
>
> Good Afternoon,
>
> I have tried make install in the src/pmemd and it seems to install
>
> but
>
> then if I try and make test it fails each one. I am currently
>
> re-installing
>
> from scratch as you had suggested as it still had several cuda.mpi in
>
> some
>
> of the folders after the clean command. Here is some info I forgot to add
> in my original email. Thank you for all the suggestions so far !
>
> OS: Ubuntu 18.04
> shell: bash
> compiler: gnu
> CUDA toolkit: 10.1.243
> amber: 18
> amber-toolkit: 19
>
>
> On Tue, Mar 3, 2020 at 10:09 AM David A Case <david.case.rutgers.edu> <david.case.rutgers.edu>
>
> wrote:
>
> On Tue, Mar 03, 2020, Nicholas Moyer wrote:
>
>
> so ive been having an error with CUDA. I have been dealing with an
>
> annoying
>
> CUDA issue where basically i have Amber18/ambertools19 installed and
>
> set
>
> with multiple gpu's but when i try to configure amber for single GPU
>
> usage
>
> compiles but when trying to make install it gives me a huge error
>
> block
>
> The error involves pbsa.cuda, which may not be the program you really
> want (most people are more eager to run pmemd.cuda). If that is the
> case, after the configure step, do this:
>
> cd src/pmemd
> make install
>
> That will install just pmemd.cuda, whose installation is better
>
> tested.
>
> (Of course, you may still have problems, since for most people,
>
> building
>
> pbsa.cuda gives no problems. If things still don't work, provide some
> details about your OS, compiler and CUDA toolkit versions. Also,
>
> since
>
> you apparently previously installed the cuda.MPI versions, and are now
> trying to get the cuda serial codes, start from a completely fresh
> directory tree, just in case something left over from the MPI install
> is causing problems.)
>
> I'm cc-ing this to Ray Luo, in case he may have a better handle on
> recognizing the problem.
>
> ...good luck...dac
>
>
>
> /usr/bin/ld: warning: libcublasLt.so.10, needed by
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so, not
>
> found
>
> (try using -rpath or -rpath-link)
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `cublasLtShutdownCtx.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `cublasLtGetProperty.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `init_gemm_select.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `runGemmShortApi.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `cublasLtMatmulAlgoGetHeuristic.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `gemm_utilization.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `cublasLtMatmul.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `free_gemm_select.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `cublasLtCtxInit.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `cublasLtMatmulAlgoInit.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `runGemmApi.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `cublasLtGetCudartVersion.libcublasLt.so.10'
> /opt/CUDA/cuda-toolkit/targets/x86_64-linux/lib/libcublas.so:
>
> undefined
>
> reference to `cublasLtGetVersion.libcublasLt.so.10'
> collect2: error: ld returned 1 exit status
> Makefile:156: recipe for target 'pbsa.cuda' failed
> make[2]: *** [pbsa.cuda] Error 1
> make[2]: Leaving directory '/opt/amber18/AmberTools/src/pbsa'
> Makefile:447: recipe for target 'cuda_serial' failed
> make[1]: *** [cuda_serial] Error 2
> make[1]: Leaving directory '/opt/amber18/AmberTools/src'
> Makefile:7: recipe for target 'install' failed
> make: *** [install] Error 2
>
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