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> 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
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Received on Wed Mar 04 2020 - 01:30:04 PST
