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
Received on Tue Mar 03 2020 - 14:00:01 PST
