VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 13 2020 - 09:55:28 CDT

Oleksii,
  Is there a reason you're unable to run the VMD 1.9.4 test versions?
The error you're getting below is a known bug in recent versions of CUDA
(> 9.1 IIRC) that the new versions of VMD have workarounds for.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 13, 2020 at 05:45:11PM +0300, Oleksii Zdorevskyi wrote:
> Hi, Josh,
> Thanks for your answer.
> In my Ubuntu 18.04 I have gcc version 8.4.0. I firstly I upgraded it to
> the version 9.2.1 but during vmd compilation I got an error that my cuda
> libraries are incompatible with gcc versions 9* and older, so I returned
> back to the previous version.
> I tried to do 'make veryclean' but it didn't help.
> I even made an attempt to install older CUDA libraries (8.0) but they
> require an older nvidia driver version that has a conflict with my GPU.
> When compiling VMD, in the log-file above there is a following error:
> echo "Compiling " CUDAMarchingCubes.cu " --> " CUDAMarchingCubes.o " ...";
> \
> /usr/local/cuda-10.2/bin/nvcc --ptxas-options=-v -gencode
> arch=compute_30,code=compute_30 -gencode arch=compute_30,code=sm_35
> -gencode arch=compute_30,code=sm_37 -gencode
> arch=compute_50,code=compute_50 -gencode arch=compute_50,code=sm_50
> -gencode arch=compute_60,code=compute_60 -gencode
> arch=compute_60,code=sm_60 --ftz=true  --machine 64 -O3
> Â -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDOPENGLPBUFFER -DVMDGLXPBUFFER
> Â -DVMDACTC Â -DVMDCOLVARS -DVMDCUDA -DMSMPOT_CUDA -DVMDMPI Â -DVMDIMD
> -DVMDXINPUT -DVMDLIBTACHYON -DVMDCONTRIB -DVMDPYTHON -DVMDTHREADS
> -DWKFTHREADS -DUSEPOSIXTHREADS -D_REENTRANT -DVMDNUMPY -DVMDQUICKSURF
> -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDTCL
> -DVMDTK Â -DVMDSTATICPLUGINS Â -DVMDGUI -DVMDFLTK Â -I../lib/actc/include
>  -I/usr/include/mpich  -I../lib/tachyon/include
> Â -I/usr/include/python2.7 -I/usr/include/python2.7/numpy
> -I/usr/lib/python2.7/dist-packages/numpy/core/lib  -I/usr/include/tcl
> -I/usr/include/tk -I/usr/local/lib/vmd/plugins/include
> -I/usr/local/lib/vmd/plugins/LINUXAMD64/molfile -I./lib/netcdf/include
> -I../lib/fltk/include -I. -c CUDAMarchingCubes.cu -o
> ./LINUXAMD64/CUDAMarchingCubes.o
> Compiling  CUDAMarchingCubes.cu  -->  CUDAMarchingCubes.o  ...
> /usr/local/cuda-10.2/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/cub/block/block_scan.cuh(578):
> error: no suitable constructor exists to convert from "int" to "uint2"
> Are there any options to deal with it?
> Thanks.
> Best,
> Oleksii
> пÑ*, 10 апÑ*. 2020 г. в 19:21, Josh Vermaas
> <[1]joshua.vermaas_at_gmail.com>:
>
> Hi Oleksii,
> Were there any other errors higher up in the log? I've also seen these
> if I got halfway through a compile and then changed something. Sometimes
> CUDA can get finicky about that. Just "make clean" to remove the object
> files then "make" has solved this problem for me in the past. The other
> possibility I can think of is that your gcc version is too old for CUDA
> 10.2 (depends on your operating system.
> See [2]https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html#system-requirements).
> -Josh
> On Fri, Apr 10, 2020 at 10:03 AM Oleksii Zdorevskyi
> <[3]alzdorev_at_gmail.com> wrote:
>
> Hi all,
> I am trying to compile vmd 1.9.3 on my PC with the following options:
> LINUXAMD64 OPENGL OPENGLPBUFFER FLTK TK ACTC CUDA MPI IMD XINPUT
> LIBTACHYON NETCDF COLVARS CONTRIB TCL PYTHON PTHREADS NUMPY GCC
> But when running 'make' command I get the following error:
> 1 error detected in the compilation of
> "/tmp/tmpxft_000021ca_00000000-8_CUDAMarchingCubes.compute_60.cpp1.ii".
> Makefile:586: recipe for target 'CUDAMarchingCubes.o' failed
> make: *** [CUDAMarchingCubes.o] Error 1
> I have GPU GTX 1660 TI, the version 10.2 of cuda libraries and Nvidia
> driver 440.82.
> Could you give me an idea what's wrong?
> Thanks in advance.
> Best,
> Oleksii
>
> References
>
> Visible links
> 1. mailto:joshua.vermaas_at_gmail.com
> 2. https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html#system-requirements
> 3. mailto:alzdorev_at_gmail.com 

-- 
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