[gmx-users] gromacs-2020 build gcc/nvcc error
Szilárd Páll
pall.szilard at gmail.com
Fri Jan 31 20:01:23 CET 2020
Dear Ryan,
On Thu, Jan 30, 2020 at 11:31 PM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:
> Dear Szilárd,
>
> Thank you so much for your help. I performed the following steps
> and it seems to have built successfully, I'll let you know if it does not
> run correctly as well.
>
> rm -r gromacs-2020/
> sudo apt-get install gcc-8 g++-8
> tar -xvzf gromacs-2020.tar.gz
> cd gromacs-2020/
> mkdir build
> cd build
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release
>
Note that you are still using the _default_ gcc installation, that is gcc 7
on Ubuntu 18.04. You should see on the first line on the console when you
run cmake something like:
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
which will clearly indicate the version of the compiler detected.
Unless you tell cmake to use the apt-get installed gcc-8, it will not use
it (and you can also verify that by inspecting the CMAKE_CXX_COMPILER
string in the CMakeCache.txt file).
make
> make check
> sudo make install
> source /usr/local/gromacs/bin/GMXRC
>
> Lastly, when I was building in default and ran into trouble I like to build
> in debug so it gives details about building and helps me identify source of
> the problems or identify relevant information to pass to you so you can
> better help me. I appreciate your comment about not building in debugging
> mode, but is there a way to run release in verbose mode? When I had
> problems with other programs I'd usually build my first time in debugger
> mode so I can monitor the process, then make clean and rebuild in default.
> Is there a better way to do this?
>
A "Debug" build (i.e. when you use CMAKE_BUILD_TYPE=Debug), is useful to
compile a program for running in a debugger (like gdb). You seem to instead
want a way to "debug" build-time issues. A debug build will not help in
that, you will not get additional information about compilation issues. You
can run "make VERBOSE=1" (regadless of the build type) with makefiles
generated by cmake to get a detailed information on the commands executed
during the build, but unless you have a compile- or link-time failure that
you want to track down that sea of output is generally not too useful.
Configure-time errors are stored by cmake in files listed after the usual
"-- Configuring incomplete, errors occurred!" error (files called
CMakeOutput/CMakeError.txt).
> Once again you help was greatly appreciated,
>
> Ryan
>
> PS again a few notes (if you have time to comment on anything incorrect) I
> have for people needing a fix in the future and maybe myself if I do this
> again in a few years and forget how.
>
> CUDA version (nvcc --version) is 9.1. This is a little confusing to me
> because you referenced CUDA 10.1 and I completely rebuilt this computer in
> September 2019, so unless there is a new driver since then it should be
> 10.1? I grabbed the newest drivers I could find but my computer is
> outputting 9.1 so I guess that is my version.
>
CUDA is not (just) the drivers, it is a number of software components that
allow compiling for and runnig computation on the GPU:
- the CUDA toolkit, latest of which is version 10.2 (as you can see here:
https://developer.nvidia.com/cuda-downloads?target_os=Linux), but the
Ubuntu 18.04 repositories seem to only have 9.1
- a display driver, confusingly versioned with numbers like 418.88 or
430.35, the Ubuntu packages are called "nvidia-driver-VERSION"
These two of course have to be compatible, so if you decide to download the
CUDA 10.2 installer from NVIDIA, this will include a compatible driver. Be
careful to completely remove the NVIDIA drivers installed from the Ubuntu
repositories prior to installing sofware with the NVIDIA installer!
when building gromacs and I specify gcc/g++ verison 5, 8, or 9 it fails
> with the original error message regarding glibc 23.2.
>
> CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-8 -DCUDA_HOST_COMPILER=gcc-8
> -DCMAKE_CXX_COMPILER=g++-8 -DCMAKE_C_COMPILER=/usr/bin/gcc-8
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release
>
Not sure, but if you want to investigate further, I suggest to start with
installing a more recent CUDA toolkit version, 9.1 is already about two
years old.
Cheers,
--
Szilárd
> Do you know why this is? When I started this adventure I just had sudo
> apt-get install gcc g++ build-essentials. Then I used gcc-5 g++-5 and
> specified the version in the build step, which failed. after taking that
> out and running sudo apt-get install gcc-9 g++-9 it passes "CMAKE" but
> fails in "make". Based on your suggestions I ran the commands at the top of
> the email to which then worked. Would this have worked if I had just
> installed gcc-8 g++-8 from the beginning and ran CMAKE with no version
> specification?
>
>
> On Thu, Jan 30, 2020 at 5:50 AM Szilárd Páll <pall.szilard at gmail.com>
> wrote:
>
> > Dear Ryan,
> >
> > On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz <rlwoltz at ucdavis.edu> wrote:
> >
> > > Dear Szilárd,
> > >
> > > Thank you for your quick response. You are correct, after
> > > issuing sudo apt-get install gcc-9 g++-9 CMake was run with:
> > >
> >
> > gcc 9 is not supported with CUDA, as far as I know version 8 is the
> latest
> > supported gcc in CUDA 10.2 (officially "native support" whatever they
> mean
> > by that is for 7.3 on Ubuntu 18.04.3, see
> > https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)
> >
> > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> -DGMX_BUILD_OWN_FFTW=ON
> > > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> > >
> >
> > Don't use a Debug build unless you want to debug the GROMACS tools (it's
> > slow).
> >
> > Make sure that you cmake configuration does actually use the gcc version
> > you intend to use. The default invocation as above will pick up the
> default
> > compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by
> > opening the CMakeCache.txt file or using ccmake) -- and I think the lack
> of
> > proper AVX512 support in your default gcc 5 (which you are stil; using)
> is
> > the source of the issues you report below.
> >
> > You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the
> > configure step; for details see
> >
> >
> http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20compiler#typical-installation
> >
> > Cheers,
> > --
> > Szilárd
> >
> >
> > > However now I'm getting an error in make
> > >
> > > make VERBOSE=1
> > >
> > > error:
> > >
> > > [ 25%] Building CXX object
> > >
> > >
> >
> src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o
> > > In file included from
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0,
> > > from
> > >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146,
> > > from
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40,
> > > from
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49:
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:
> > > In function ‘void gmx::gatherLoadTransposeHsimd(const float*, const
> > float*,
> > > const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2;
> > > int32_t = int]’:
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28:
> > > error: the last argument must be scale 1, 2, 4, 8
> > > tmp1 = _mm512_castpd_ps(
> > > ^
> > >
> > >
> >
> /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28:
> > > error: the last argument must be scale 1, 2, 4, 8
> > > tmp2 = _mm512_castpd_ps(
> > > ^
> > > src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for
> target
> > >
> > >
> >
> 'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o'
> > > failed
> > > make[2]: ***
> > >
> > >
> >
> [src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o]
> > > Error 1
> > > CMakeFiles/Makefile2:2910: recipe for target
> > > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > > Makefile:162: recipe for target 'all' failed
> > > make: *** [all] Error 2
> > >
> > > after doing a 1 hour google I found discussions saying that the error
> > > (Makefile:162: recipe for target 'all' failed) is too vague with no
> > general
> > > solution. I found fixes for headers and other files for other programs
> > but
> > > not fixes for this file. The fix linked below is for gromacs-2018 and a
> > > different file but the general problem seems to suggest it still is a
> > > gcc/g++ version compatibility error correct? Any suggestions for this
> > > error?
> > >
> > > https://redmine.gromacs.org/issues/2312
> > >
> > >
> > > Thank you so much,
> > >
> > > Ryan
> > >
> > > PS Just to document for anyone else going through what I did for
> > > Gromacs-2020 these were my steps.
> > >
> > > sudo apt-get install gcc g++
> > > cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > -DGMX_GPU=ON
> > >
> > > I then received multiple errors complaining about nvcc/C++
> > > incompatibility. After researching found errors for previous gromacs
> > > versions suggesting to use gcc-5 (but as you suggested this error has
> > been
> > > patched).
> > >
> > > sudo apt-get install gcc-5 g++-5
> > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> > > -D_FORCE_INLINES=OFF
> > >
> > > Received different error described in previous email and solved with
> your
> > > suggested solution. The key might be to specifically install latest
> > version
> > > number i.e.
> > >
> > > sudo apt-get install gcc-X g++-X (with X being the largest number
> > > available).
> > >
> > >
> > >
> > >
> > > On Wed, Jan 29, 2020 at 2:05 AM Szilárd Páll <pall.szilard at gmail.com>
> > > wrote:
> > >
> > > > Hi Ryan,
> > > >
> > > > The issue you linked has been worked around in the build system, so
> my
> > > > guess is that the issue you are seeing is not related.
> > > >
> > > > I would recommend that you update your software stack to the latest
> > > version
> > > > (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you
> > should
> > > > be able to get gcc 8 through the package manager. Together with
> > > > upgrading to the latest CUDA might well solve your issues.
> > > >
> > > > Let us know if that worked!
> > > >
> > > > Cheers,
> > > > --
> > > > Szilárd
> > > >
> > > >
> > > > On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwoltz at ucdavis.edu>
> > wrote:
> > > >
> > > > > Hello Gromacs experts,
> > > > >
> > > > > First things first, I apologize for any double post but I
> > > just
> > > > > joined the community so I'm very new and only found 1-2 posts
> related
> > > to
> > > > my
> > > > > problem but the solutions did not work. I have been doing MD for
> > about
> > > > > 6-months using NAMD but want to also try out Gromacs. That being
> > said I
> > > > am
> > > > > slightly familiar with CPU modeling programs like Rosetta, but I am
> > > > totally
> > > > > lost when it comes to fixing errors using GPU accelerated code for
> > > CUDA.
> > > > I
> > > > > did find that at one point my error was fixed for an earlier
> version
> > of
> > > > > Gromacs but Gromacs-2020 may have resurfaced the same error again,
> > here
> > > > is
> > > > > what I think my error is:
> > > > >
> > > > > https://redmine.gromacs.org/issues/1982
> > > > >
> > > > > I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did
> > initially
> > > > have
> > > > > the gcc/nvcc incompatible but I think installing and using
> > gcc-5/g++-5
> > > > > version command in cmake has fixed that issue. I have a NVIDIA card
> > > with
> > > > > CUDA-9.1 driver when I type nvcc --version.
> > > > >
> > > > > my cmake command is as follows:
> > > > >
> > > > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../
> > > > > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5
> > > > > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5
> > > > > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug
> (I
> > > did
> > > > > try adding -D_FORCE_INLINES= based on the link above in my running
> > > > command
> > > > > but it did not work). I did look at the error log but it is way
> over
> > my
> > > > > head. I have in addition deleted the CMakeCache.txt file or the
> > > unpacked
> > > > > Gromacs and re-unzipped it to restart the cmake process to make
> sure
> > it
> > > > was
> > > > > starting "clean". Is there any additional information I could
> > provide?
> > > > Does
> > > > > anyone have a suggestion? Again I'm sorry if this is a duplicate,
> > > > > everything I found on other sites was way over my head and I
> > generally
> > > > > understand what is going on but the forums I read on possible
> > solutions
> > > > > seem way over my head and I'm afraid I will break the driver if I
> > > attempt
> > > > > them (which has happened to me already and the computer required a
> > full
> > > > > reinstall).
> > > > >
> > > > > here is last lines from the build:
> > > > >
> > > > > -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found
> suitable
> > > > > version "1.11.6", minimum required is "1.5")
> > > > > -- Looking for C++ include pthread.h
> > > > > -- Looking for C++ include pthread.h - found
> > > > > -- Atomic operations found
> > > > > -- Performing Test PTHREAD_SETAFFINITY
> > > > > -- Performing Test PTHREAD_SETAFFINITY - Success
> > > > > -- Adding work-around for issue compiling CUDA code with glibc 2.23
> > > > > string.h
> > > > > -- Check for working NVCC/C++ compiler combination with nvcc
> > > > > '/usr/local/cuda/bin/nvcc'
> > > > > -- Check for working NVCC/C compiler combination - broken
> > > > > -- /usr/local/cuda/bin/nvcc standard output: ''
> > > > > -- /usr/local/cuda/bin/nvcc standard error:
> > > > > '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such
> > file
> > > > or
> > > > > directory
> > > > > '
> > > > > CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message):
> > > > > CUDA compiler does not seem to be functional.
> > > > > Call Stack (most recent call first):
> > > > > cmake/gmxManageGPU.cmake:207 (include)
> > > > > CMakeLists.txt:577 (gmx_gpu_setup)
> > > > >
> > > > >
> > > > > -- Configuring incomplete, errors occurred!
> > > > > See also
> > > > >
> > > > >
> > > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log".
> > > > > See also
> > > > >
> > > > >
> > > >
> > >
> >
> "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log".
> > > > > --
> > > > > Gromacs Users mailing list
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