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:
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
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
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.