Gromacs 2021.3 installation error

User discussions
1

GROMACS version: 2021.3
GROMACS modification: No
Here post your question

I was trying to install gromacs new version 2021.3 (also same for 2021.2 same error) in cluster with CENTOS 7.

Version of other tools:
CMAKE = 3.2
GCC = 11.2
Python = 3.9

cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/home/khademul/bin/gromacs -DCMAKE_C_COMPILER=/home/khademul/bin/gcc11/bin/gcc -DCMAKE_CXX_COMPILER=/home/khademul/bin/gcc11/bin/g++

make

…
…
…

[100%] Built target nblib
[100%] Building CXX object api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o
[100%] Linking CXX executable …/…/…/bin/argon-forces-integration
/home/khademul/bin/gromacs-2021.2/build/lib/libgromacs.so.6: undefined reference to GOMP_loop_nonmonotonic_dynamic_next@GOMP_4.5' /home/khademul/bin/gromacs-2021.2/build/lib/libgromacs.so.6: undefined reference to GOMP_loop_nonmonotonic_dynamic_start@GOMP_4.5’
collect2: error: ld returned 1 exit status
make[2]: *** [bin/argon-forces-integration] Error 1
make[1]: *** [api/nblib/samples/CMakeFiles/argon-forces-integration.dir/all] Error 2
make: *** [all] Error 2

Can anyone help how to fix

2

This looks like you are using an incompatible linker.
What is CMAKE_LINKER set to? You can check in CMakeCache.txt.
Try setting that to, I guess, /home/khademul/bin/gcc11/bin/ld

3

Hi,

Many thanks for your response.

CMAKE_LINKER was

CMAKE_LINKER:FILEPATH=/usr/bin/ld

Then I have changed it to, as you suggested (though here is no ld file)

CMAKE_LINKER:FILEPATH=/home/khademul/bin/gcc11/bin/ld
//ADVANCED property for variable: CMAKE_LINKER
CMAKE_LINKER-ADVANCED:INTERNAL=1

However the problem persists and remains the same.

cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DMPI_C_COMPILER=mpicc -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX=/home/khademul/bin/gromacs -DCMAKE_C_COMPILER=/home/khademul/bin/gcc11/bin/gcc -DCMAKE_CXX_COMPILER=/home/khademul/bin/gcc11/bin/g++ -DCMAKE_LINKER=/home/khademul/bin/gcc11/bin/ld

…
…

make

…
…

[ 98%] Built target nblib
[ 98%] Building CXX object api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o
[100%] Linking CXX executable …/…/…/bin/argon-forces-integration
/home/khademul/bin/gromacs-2021.3/build/lib/libgromacs_mpi.so.6: undefined reference to GOMP_loop_nonmonotonic_dynamic_next@GOMP_4.5' /home/khademul/bin/gromacs-2021.3/build/lib/libgromacs_mpi.so.6: undefined reference to GOMP_loop_nonmonotonic_dynamic_start@GOMP_4.5’
collect2: error: ld returned 1 exit status
make[2]: *** [bin/argon-forces-integration] Error 1
make[1]: *** [api/nblib/samples/CMakeFiles/argon-forces-integration.dir/all] Error 2
make: *** [all] Error 2

I do not have root permission and CMAKE, GCC etc installed locally. (default things are tool old version)

module load openmpi-1.8-x86_64
module load tools/openBLAS-0.2.18
module load lib/OpenBLAS-0.3.9
module load compilers/python-3.6.2-gcc

cmake version 3.20.0-rc4

gcc version 11.2.0

thanks, # any more suggestions?

4

Perhaps try without MPI and if that works, build MPI with the same gcc
compiler you are using.