I did installed Amber18/AmberTools19 on ubuntu 18.04 with cuda 10.2. The
test_amber_cuda log file says as
>233 file comparisons passed
>0 file comparisons failed (0 ignored)
>0 tests experienced errors
Regards
Manish
On Wed, Mar 4, 2020 at 8:37 AM Ray Luo <rluo.uci.edu> wrote:
> Abhilash,
>
> Yes, CUDA 10.2 is too new as it was not available when we announced
> Amber 19 ... Please use CUDA 10.0 and CUDA 9.2 for Amber 19 ...
>
> We are testing CUDA 10.2 right now ... and will support it in Amber 20.
>
> 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 2:07 PM Nicholas Moyer <nmoyer.broadinstitute.org>
> 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> 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> 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> 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>
> > > > 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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> > > >
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Received on Tue Mar 03 2020 - 22:00:02 PST
