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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 Wed, Mar 4, 2020 at 10:03 AM Ray Luo <rluo.uci.edu> wrote: > > Hi Abhilash, > > We'll need to reinstall cuda 9.2 to reproduce what you are seeing. For > now, please stay with cuda 10.0 for your amber installation. > > 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 Wed, Mar 4, 2020 at 9:37 AM Abhilash J <md.scfbio.gmail.com> wrote: > > > > Hi Everyone, > > > > I tried what Ruxi had suggested. But i could not find *libcublas* in > > /usr/lib64 or /usr/lib for CUDA 10.2. But i tried to use these *libcublas* > > files from CUDA 9.2 installation (Just thinking if they are compatible and > > useful). > > That did not go well and i ended up with the same error (/usr/bin/ld: > > cannot find -lcublas). I did add the path to the *libcublas* files to my > > LD_PATH_LIBRARY. I am using CentOS 7 > > I also tried what David suggested earlier in the thread to compile > > pmemd.cuda only with CUDA 10.2 and was able to get that. I did not get any > > appreciable change in the speed. And pmemd.cuda is what i use most of the > > times. > > I was wondering what is the performance gain if I manage to get it > > compiled to 10.2. Should i wait for AMBER20 given that its only few months > > ahead. > > It will be great if someone can share some expected numbers. > > > > Regards > > > > Abhilash > > > > On Wed, Mar 4, 2020 at 11:25 AM Nicholas Moyer <nmoyer.broadinstitute.org> > > wrote: > > > > > Good Morning, > > > > > > So I tried all the recommendations that were suggested and i was able to > > > install with CUDA 9.2 but when i try and make test i get the following > > > errors that look pretty similar. Any suggestions on why im able to build > > > and install amber with this but all tests fail? I also reinstalled amber > > > and everything looks fine as far as I can tell but clearly something is > > > wrong. Thanks again for all the help! > > > > > > [image: image.png] > > > > > > On Wed, Mar 4, 2020 at 4:22 AM Ruxi Qi <ruxiq.uci.edu> wrote: > > > > > > > Sorry, typo, should be /usr/lib/x86_64-linux-gnu. > > > > > > > > BTW, we will add a handling to this in the AmberTools 20 release. > > > > > > > > Ruxi > > > > On 3/4/20 5:05 PM, Ruxi Qi wrote: > > > > > > > > Hi Nicholas, > > > > > > > > The issue was because from CUDA 10.1 some libraries including the CUBLAS > > > > are installed in the system standard locations rather than in the Toolkit > > > > installation directory. Depending on distribution these installed > > > locations > > > > can be either /usr/lib/x84_64-linux-gnu as with Ubuntu 18.04, or > > > /usr/lib64 > > > > as with Centos 7, or /usr/lib. You can check this by executing: > > > > > > > > *sudo find /usr -name libcublas** > > > > > > > > So the solution is to either create a symlink in the CUDA Toolkit library > > > > path to the library file missing, or more handily add the location to > > > your > > > > library searching path in your .bashrc: > > > > > > > > export LD_LIBRARY_PATH=/usr/lib/x84_64-linux-gnu:$LD_LIBRARY_PATH > > > > > > > > Hope it helps. > > > > > > > > Best, > > > > > > > > Ruxi > > > > On 3/4/20 6:04 AM, Nicholas Moyer 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> < > > > 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> <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> > > > <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> < > > > 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 listAMBER.ambermd.orghttp:// > > > lists.ambermd.org/mailman/listinfo/amber > > > > > > > > _______________________________________________ > > > > AMBER mailing listAMBER.ambermd.orghttp:// > > > lists.ambermd.org/mailman/listinfo/amber > > > > > > > > _______________________________________________ > > > > AMBER mailing listAMBER.ambermd.orghttp:// > > > lists.ambermd.org/mailman/listinfo/amber > > > > > > > > _______________________________________________ > > > > AMBER mailing listAMBER.ambermd.orghttp:// > > > 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 Thu Mar 05 2020 - 23:00:02 PST