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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 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/amberReceived on Tue Mar 03 2020 - 10:30:03 PST