Gromacs 2022 fiase after updating Ubuntu to 22.04

User discussions
1

GROMACS version: 2022
GROMACS modification: No

I had installed and used GROMACS 2022 in my workstation w/o problems until I ungraded to Ubuntu 22.04.

Now if I try to run gmx I set the following error message:
gmx: /lib/x86_64-linux-gnu/libpthread.so.0: version `GLIBC_PRIVATE’ not found (required by gmx)

I tried to compile gmx 2022 again with the following cmake line:

CC=gcc CXX=g++ cmake …/ -DGMX_GPU=CUDA -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs2022_2/

cmake seems to work fine w/o Errors, but when I do the make part, after a while I set the following error message:

/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libopenblas.a(sormtr.o): in function sormtr_': (.text+0x34e): undefined reference to _gfortran_concat_string’
/usr/bin/ld: (.text+0x4e7): undefined reference to _gfortran_concat_string' /usr/bin/ld: (.text+0x559): undefined reference to gfortran_concat_string’
/usr/bin/ld: (.text+0x5a9): undefined reference to _gfortran_concat_string' /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libopenblas.a(sormql.o): in function sormql’:
(.text+0x5f7): undefined reference to _gfortran_concat_string' /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libopenblas.a(sormql.o):(.text+0x6be): more undefined references to _gfortran_concat_string’ follow
collect2: error: ld returned 1 exit status
make[2]: *** [src/programs/CMakeFiles/gmx.dir/build.make:100: bin/gmx] Error 1
make[1]: *** [CMakeFiles/Makefile2:6200: src/programs/CMakeFiles/gmx.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

How can I fix either of these issues?

Thanks.

Raul.

2

Hello Raul,

Were you running CMake in a clean directory, or have you just re-run it in the old build directory? If it’s the latter, I suggest fully clearing the directory and building from scratch.

If that does not help, it looks like the problem comes from libopenblas. You can try adding -DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF to your CMake call to build BLAS and LAPACK libraries bundled with GROMACS instead of trying to use the ones provided by the OS.

3

Hi,

Thanks for your answer. I tried it in a new build and that’s when I got the error message. I’m trying it again following your advice.

Actually this all issue started because after upgrading to Ubuntu 22.04 my currently installed gmx 2022 stopes working. If I try to run not I get the following error:
/lib/x86_64-linux-gnu/libpthread.so.0: version ‘GLIBC_PRIVATE’ not found (required by gmx)

I could not find any solutions so I decided to try to install GROMACS from scratch.

Do you have any idea how to solve that?

Thanks.

Raul.

4

If I try to run not I get the following error:
/lib/x86_64-linux-gnu/libpthread.so.0: version ‘GLIBC_PRIVATE’ not found (required by gmx)

The version of Glibc and other libraries supplied by your operating system got updated, so the applications that expect to have old ones won’t work. Usually, rebuilding GROMACS from scratch is the easiest course of action in such cases.

If you’re still having trouble, please also tell us which version of gcc, g++, and CUDA you’re using.

5

Hi,

I followed your advice and the installation worked!!. The I just needed to update some libraries and nos GMX is working.

Thanks so much.

Raul.