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
> > >>
> > >> _______________________________________________
> > >> 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 Tue Mar 03 2020 - 14:30:02 PST
