Well I unistall ubuntu, even from the powershell wsl --unregister
And install everything again, and now I couldn’t install gromacs, I had error, and now I do not have gromacs. I would appreciate any advice
This is my information. Could I fix it?
nvidia-smi
nvcc --version
Command ‘nvcc’ not found, but can be installed with:
sudo apt install nvidia-cuda-toolkit
###CUDA Toolkit Installer
wget https://developer.download.nvidia.com/compute/cuda/12.6.2/local_installers/cuda_12.6.2_560.35.03_linux.run
sudo sh cuda_12.6.2_560.35.03_linux.run
= Summary =
Driver: Not Selected
Toolkit: Installed in /usr/local/cuda-12.6/
Please make sure that
- PATH includes /usr/local/cuda-12.6/bin
- LD_LIBRARY_PATH includes /usr/local/cuda-12.6/lib64, or, add /usr/local/cuda-12.6/lib64 to /etc/ld.so.conf and run ldconfig as root
To uninstall the CUDA Toolkit, run cuda-uninstaller in /usr/local/cuda-12.6/bin
***WARNING: Incomplete installation! This installation did not install the CUDA Driver. A driver of version at least 560.00 is required for CUDA 12.6 functionality to work.
To install the driver using this installer, run the following command, replacing with the name of this run file:
sudo .run --silent --driver
Logfile is /var/log/cuda-installer.log
#after installing
sudo apt install nvidia-cuda-toolkit
sudo apt install build-essential
sudo apt update
sudo apt upgrade
#now nvcc is recognized
$whereis nvcc
nvcc: /usr/bin/nvcc
$nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2023 NVIDIA Corporation
Built on Fri_Jan__6_16:45:21_PST_2023
Cuda compilation tools, release 12.0, V12.0.140
Build cuda_12.0.r12.0/compiler.32267302_0
$gcc --version
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
$lspci
4eab:00:00.0 System peripheral: Red Hat, Inc. Virtio file system (rev 01)
b311:00:00.0 3D controller: Microsoft Corporation Basic Render Driver
b6ab:00:00.0 SCSI storage controller: Red Hat, Inc. Virtio 1.0 console (rev 01)
c2bf:00:00.0 3D controller: Microsoft Corporation Basic Render Driver
$sudo apt install cmake
$cmake --version
cmake version 3.28.3
I tried to install gromacs
mkdir gromacs
cd gromacs
wget https://ftp.gromacs.org/gromacs/gromacs-2024.4.tar.gz
tar xfz gromacs-2024.4.tar.gz
cd gromacs-2024.4
mkdir build
cd build
cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA
###and it returned:
– The C compiler identification is GNU 13.2.0
– The CXX compiler identification is GNU 13.2.0
– Detecting C compiler ABI info
– Detecting C compiler ABI info - done
– Check for working C compiler: /usr/bin/cc - skipped
– Detecting C compile features
– Detecting C compile features - done
– Detecting CXX compiler ABI info
– Detecting CXX compiler ABI info - done
– Check for working CXX compiler: /usr/bin/c++ - skipped
– Detecting CXX compile features
– Detecting CXX compile features - done
– Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Development Development.Module Development.Embed) (found suitable version “3.12.3”, minimum required is “3.7”)
– Selected GPU FFT library - cuFFT
– Found OpenMP_C: -fopenmp (found version “4.5”)
– Found OpenMP_CXX: -fopenmp (found version “4.5”)
– Found OpenMP: TRUE (found version “4.5”)
– Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
– Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
– Performing Test CFLAGS_EXCESS_PREC
– Performing Test CFLAGS_EXCESS_PREC - Success
– Performing Test CFLAGS_COPT
– Performing Test CFLAGS_COPT - Success
– Performing Test CFLAGS_NOINLINE
– Performing Test CFLAGS_NOINLINE - Success
– Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
– Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
– Performing Test CXXFLAGS_EXCESS_PREC
– Performing Test CXXFLAGS_EXCESS_PREC - Success
– Performing Test CXXFLAGS_COPT
– Performing Test CXXFLAGS_COPT - Success
– Performing Test CXXFLAGS_NOINLINE
– Performing Test CXXFLAGS_NOINLINE - Success
– Looking for include file unistd.h
– Looking for include file unistd.h - found
– Looking for include file pwd.h
– Looking for include file pwd.h - found
– Looking for include file dirent.h
– Looking for include file dirent.h - found
– Looking for include file time.h
– Looking for include file time.h - found
– Looking for include file sys/time.h
– Looking for include file sys/time.h - found
– Looking for include file io.h
– Looking for include file io.h - not found
– Looking for include file sched.h
– Looking for include file sched.h - found
– Looking for include file xmmintrin.h
– Looking for include file xmmintrin.h - found
– Looking for gettimeofday
– Looking for gettimeofday - found
– Looking for sysconf
– Looking for sysconf - found
– Looking for nice
– Looking for nice - found
– Looking for fsync
– Looking for fsync - found
– Looking for _fileno
– Looking for _fileno - not found
– Looking for fileno
– Looking for fileno - found
– Looking for _commit
– Looking for _commit - not found
– Looking for sigaction
– Looking for sigaction - found
– Performing Test HAVE_BUILTIN_CLZ
– Performing Test HAVE_BUILTIN_CLZ - Success
– Performing Test HAVE_BUILTIN_CLZLL
– Performing Test HAVE_BUILTIN_CLZLL - Success
– Looking for clock_gettime in rt
– Looking for clock_gettime in rt - found
– Looking for feenableexcept in m
– Looking for feenableexcept in m - found
– Looking for fedisableexcept in m
– Looking for fedisableexcept in m - found
– Checking for sched.h GNU affinity API
– Performing Test sched_affinity_compile
– Performing Test sched_affinity_compile - Success
– Looking for include file mm_malloc.h
– Looking for include file mm_malloc.h - found
– Looking for include file malloc.h
– Looking for include file malloc.h - found
– Checking for _mm_malloc()
– Checking for _mm_malloc() - supported
– Looking for posix_memalign
– Looking for posix_memalign - found
– Looking for memalign
– Looking for memalign - not found
– Using default binary suffix: “”
– Using default library suffix: “”
– Performing Test CMAKE_HAVE_LIBC_PTHREAD
– Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
– Found Threads: TRUE
– Looking for C++ include pthread.h
– Looking for C++ include pthread.h - found
– Performing Test TEST_ATOMICS
– Performing Test TEST_ATOMICS - Success
– Atomic operations found
– Performing Test PTHREAD_SETAFFINITY
– Performing Test PTHREAD_SETAFFINITY - Success
– Detecting best SIMD instructions for this CPU
– Checking for GCC x86 inline asm
– Checking for GCC x86 inline asm - supported
– Detected build CPU features - aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
– Detected build CPU brand - 12th Gen Intel(R) Core™ i5-12500H
– Detected best SIMD instructions for this CPU - AVX2_256
– Performing Test C_mavx2_mfma_FLAG_ACCEPTED
– Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success
– Performing Test C_mavx2_mfma_COMPILE_WORKS
– Performing Test C_mavx2_mfma_COMPILE_WORKS - Success
– Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED
– Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success
– Performing Test CXX_mavx2_mfma_COMPILE_WORKS
– Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success
– Enabling 256-bit AVX2 SIMD instructions using CXX flags: -mavx2 -mfma
– Detecting flags to enable runtime detection of AVX-512 units on newer CPUs
– Performing Test C_march_skylake_avx512_FLAG_ACCEPTED
– Performing Test C_march_skylake_avx512_FLAG_ACCEPTED - Success
– Performing Test C_march_skylake_avx512_COMPILE_WORKS
– Performing Test C_march_skylake_avx512_COMPILE_WORKS - Success
– Performing Test CXX_march_skylake_avx512_FLAG_ACCEPTED
– Performing Test CXX_march_skylake_avx512_FLAG_ACCEPTED - Success
– Performing Test CXX_march_skylake_avx512_COMPILE_WORKS
– Performing Test CXX_march_skylake_avx512_COMPILE_WORKS - Success
– Detecting flags to enable runtime detection of AVX-512 units on newer CPUs - -march=skylake-avx512
– Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED
– Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success
– Performing Test _callconv___vectorcall
– Performing Test _callconv___vectorcall - Failed
– Performing Test _callconv___regcall
– Performing Test _callconv___regcall - Failed
– Performing Test callconv
– Performing Test callconv - Success
– Found CUDA: /usr (found suitable version “12.0”, minimum required is “11.0”)
– Adding work-around for issue compiling CUDA code with glibc 2.23 string.h
– Check for working NVCC/C++ compiler combination with nvcc ‘/usr/bin/nvcc’
– Check for working NVCC/C compiler combination - broken
– /usr/bin/nvcc standard output: ‘’
– /usr/bin/nvcc standard error: 'In file included from /usr/include/cuda_runtime.h:83,
from :
/usr/include/crt/host_config.h:132:2: error: #error – unsupported GNU version! gcc versions later than 12 are not supported! The nvcc flag ‘-allow-unsupported-compiler’ can be used to override this version check; however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.
132 | #error – unsupported GNU version! gcc versions later than 12 are not supported! The nvcc flag ‘-allow-unsupported-compiler’ can be used to override this version check; however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.
| ^~~~~
’
CMake Error at cmake/gmxManageNvccConfig.cmake:101 (if):
if given arguments:
"In file included from /usr/include/cuda_runtime.h:83,
from <command-line>:
/usr/include/crt/host_config.h:132:2: error: #error – unsupported GNU
version! gcc versions later than 12 are not supported! The nvcc flag
‘-allow-unsupported-compiler’ can be used to override this version check" "
however, using an unsupported host compiler may cause compilation failure
or incorrect run time execution. Use at your own risk.
132 | #error -- unsupported GNU version! gcc versions later than 12 are not supported! The nvcc flag '-allow-unsupported-compiler' can be used to override this version check" " however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.
| ^~~~~
" “MATCHES” “nsupported”
Unknown arguments specified
Call Stack (most recent call first):
cmake/gmxManageCuda.cmake:110 (include)
CMakeLists.txt:700 (include)
– Configuring incomplete, errors occurred!
