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-- 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 > > > >> > > > >> _______________________________________________ > > > >> 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Mar 03 2020 - 19:30:02 PST