Error in Downloading 2020 version of Gromacs

User discussions
1

GROMACS version: 2020

Hi,

I am trying to download the 2020 version of Gromacs through Linux. I have completed a majority of the steps for installation listed below:

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install gcc
sudo apt-get install cmake
sudo apt-get install build-essential
sudo apt-get install libfftw3
sudo apt-get install doxygen

Download Regression Test
wget https://ftp.gromacs.org/regressiontests/regressiontests-2020.tar.gz
tar xvzf regressiontests-2020.tar.gz

Download Gromacs Version
wget https://ftp.gromacs.org/pub/gromacs/gromacs-2020.tar.gz
tar xvzf gromacs-2020.tar.gz

cd gromacs-2020
mkdir build
cd build

When I enter this next line of code I receive an error:
sudo cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF -DREGRESSIONTEST_PATH=/home/bioresearchlab/regressiontests-2020 -DCMAKE_INSTALL_PREFIX=/opt/gromcs -DGMX_GPU=off -DGMX_USE_TNG=off -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=ON

The error is this:

– The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2;–enable-avx;–enable-avx2
CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.

Update the VERSION argument value or use a … suffix to tell
CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:41 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.

Update the VERSION argument value or use a … suffix to tell
CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:48 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.

Update the VERSION argument value or use a … suffix to tell
CMake that the project does not need compatibility with older versions.

CMake Error at tests/CMakeLists.txt:103 (message):
REGRESSIONTEST_PATH invalid. The path needs to contain gmxtest.pl.

– Configuring incomplete, errors occurred!
See also “/home/bioreasearchlab/gromacs-2020/build/CMakeFiles/CMakeOutput.log”.
See also “/home/bioreasearchlab/gromacs-2020/build/CMakeFiles/CMakeError.log”.

I would greatly appreciate advice on what I can do so that I can successfully download the 2020 version of Gromacs.

Thank you in advance.

2

It looks like you made a typo in one of your paths (please check them again so that they are consistent).

Other than fixing that, what you ought to do is NEVER using sudo before a complex command like cmake. In this case, a new folder was probably created in a place that you did not expect.

Giacomo

1 Like
3

Thank you so much! I was able to find the typo and correct it which included the missing file from the folder I was trying to reach.

4

Please how did you solve this prb (i have the same)

5

When I execute this command: sudo cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF -DREGRESSIONTEST_PATH=/home/fatima/egressiontests-2020/ -DCMAKE_INSTALL_PREFIX=/opt/gromacs -DGMX_GPU=off -DGMX_USE_TNG=off -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=0N
Iget this error:
– The C compiler identification is GNU 11.4.0
– The CXX compiler identification is GNU 11.4.0
– 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
– 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_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_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
– Looking for HWLOC
– Looking for hwloc – hwloc.h not found
– Looking for hwloc – lib hwloc not found
– Could NOT find HWLOC (missing: HWLOC_LIBRARIES HWLOC_INCLUDE_DIRS) (Required is at least version “1.5”)
– Looking for pthread.h
– Looking for pthread.h - found
– 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
– Atomic operations found
– Performing Test PTHREAD_SETAFFINITY
– Performing Test PTHREAD_SETAFFINITY - Success
– Checking for GCC x86 inline asm
– Checking for GCC x86 inline asm - supported
– Detected build CPU vendor - Intel
– Detected build CPU brand - 12th Gen Intel(R) Core™ i7-1260P
– Detected build CPU family - 6
– Detected build CPU model - 154
– Detected build CPU stepping - 3
– Detected build CPU features - apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
– Enabling RDTSCP support - detected on the build host
– Checking for 64-bit off_t
– Checking for 64-bit off_t - present
– Checking for fseeko/ftello
– Checking for fseeko/ftello - present
– Checking for SIGUSR1
– Checking for SIGUSR1 - found
– Checking for pipe support
– Checking for system XDR support
– Checking for system XDR support - not present
– Detecting best SIMD instructions for this CPU
– 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_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
– Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
– Performing Test C_xCORE_AVX512_FLAG_ACCEPTED
– Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed
– Performing Test C_mavx512f_mfma_FLAG_ACCEPTED
– Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Success
– Performing Test C_mavx512f_mfma_COMPILE_WORKS
– Performing Test C_mavx512f_mfma_COMPILE_WORKS - Success
– Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
– Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
– Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED
– Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed
– Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED
– Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Success
– Performing Test CXX_mavx512f_mfma_COMPILE_WORKS
– Performing Test CXX_mavx512f_mfma_COMPILE_WORKS - Success
– Detecting flags to enable runtime detection of AVX-512 units on newer CPUs - -mavx512f -mfma
– 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
– The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2;–enable-avx;–enable-avx2
– Using external FFT library - FFTW3 build managed by GROMACS
– Looking for sgemm
– Looking for sgemm - not found
– Could NOT find BLAS (missing: BLAS_LIBRARIES)
– Using GROMACS built-in BLAS.
– Could NOT find LAPACK (missing: LAPACK_LIBRARIES)
Reason given by package: LAPACK could not be found because dependency BLAS could not be found.

– Using GROMACS built-in LAPACK.
– Checking for dlopen
– Performing Test HAVE_DLOPEN
– Performing Test HAVE_DLOPEN - Success
– Checking for dlopen - found
– Using dynamic plugins (e.g VMD-supported file formats)
– Checking for suitable VMD version
– VMD version of /usr/local/lib/vmd/plugins/LINUXAMD64/molfile is suitable
– Using default binary suffix: “”
– Using default library suffix: “”
– Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/posts/2018/fixing-imagick-error-unauthorized
Traceback (most recent call last):
File “”, line 1, in
ModuleNotFoundError: No module named ‘pygments’
– Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version “1.6.1”)
CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.

Update the VERSION argument value or use a … suffix to tell
CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:41 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.

Update the VERSION argument value or use a … suffix to tell
CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:48 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.

Update the VERSION argument value or use a … suffix to tell
CMake that the project does not need compatibility with older versions.

– Performing Test HAVE_NO_DEPRECATED_COPY
– Performing Test HAVE_NO_DEPRECATED_COPY - Success
– Performing Test HAS_NO_STRINGOP_TRUNCATION
– Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
– Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
– Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
– Performing Test HAS_NO_REDUNDANT_MOVE
– Performing Test HAS_NO_REDUNDANT_MOVE - Success
– Performing Test HAS_NO_UNUSED
– Performing Test HAS_NO_UNUSED - Success
– Performing Test HAS_NO_UNUSED_PARAMETER
– Performing Test HAS_NO_UNUSED_PARAMETER - Success
– Performing Test HAS_NO_MISSING_DECLARATIONS
– Performing Test HAS_NO_MISSING_DECLARATIONS - Success
– Performing Test HAS_DECL_IN_SOURCE
– Performing Test HAS_DECL_IN_SOURCE - Failed
– Performing Test HAS_NO_CLASS_MEMACCESS
– Performing Test HAS_NO_CLASS_MEMACCESS - Success
– Found Doxygen: /usr/bin/doxygen (found version “1.9.1”) found components: doxygen missing components: dot
CMake Error at tests/CMakeLists.txt:103 (message):
REGRESSIONTEST_PATH invalid. The path needs to contain gmxtest.pl.

– Configuring incomplete, errors occurred!
See also “/home/fatima/gromacs-2020/build/CMakeFiles/CMakeOutput.log”.
See also “/home/fatima/gromacs-2020/build/CMakeFiles/CMakeError.log”.

6

Is the path really correct? If you do ls /home/fatima/egressiontests-2020/ is the gmxtest.pl file there?

Could it be a typo in your path (quite probable)? Try cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF -DREGRESSIONTEST_PATH=/home/fatima/regressiontests-2020/ -DCMAKE_INSTALL_PREFIX=/opt/gromacs -DGMX_GPU=off -DGMX_USE_TNG=off -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=0N.

And by the way, do not run cmake with sudo. You should not run make with sudo either, except make install` (if you are installing to a directory where you need superuser privileges).