Internal compiler error while installing gromacs

User discussions
1

GROMACS version: 2024.1

Hi everyone,

I am trying to install gromacs in my machine. But while running the make command after running the cmake command, I get an internal compiler error.

The commands and their outputs are as follows:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA :
– Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version “4.0.0”)
– Configuring done
– Generating done
– Build files have been written to: /home/sudeeplab/softwares/gromacs-2024.1/build

make :
/home/sudeeplab/softwares/gromacs-2024.1/build/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/libbench2/mp.c:444:13: internal compiler error: Segmentation fault
444 | static void fft0(int n, N *a, int sign)
| ^~~~

The machine has following configurations:
compiler: gnu-11.4.0
cuda toolkit: 12.2
nvidia drivers: 535.171.04
gpu: NVIDIA GeForce RTX 4070
ubuntu: 22.04

I do not even know where to begin with this. The machine had gromacs earlier, but since there is some issue in the installation, I am trying to re-install gromacs.

I hope someone can help me with this.

Thanks and regards,
Chaitanya

2

Hi,

why not try out a different compiler (or compiler version)? That might already solve the issue.

Best,
Carsten

3

Hi, Carsten

I tried to use intel one api compilers, icx and icpx, but then it gives me some other error in the installation related to nvidia/cuda. This maybe because the nvidia drivers were installed based on gnu compilers.

I am not sure it the updating of the gnu compilers may cause an issue with the nvidia drivers. Hence, was avoiding to try that.

But if there is no other work around, I will be forced to do so.

Let me know what you think.

Thanks,
Chaitanya

4

You could try another GCC, e.g. GCC 12.2, if you have. Or, alternatively, as the error occurs during the compilation of FFTW, you could first build FFTW yourself with some compiler that works (even older GCCs) and then let GROMACS use that precompiled FFTW version.

5

Okay Carsten.

I will try that out and get back to you.

Thanks for your inputs.

Regards,
Chaitanya

6

Hello Carsten,

I tried your suggestions and built the FFTW library separately.
I also tried using the gcc-12 and gcc-11 and gcc-10 compilers.
I am

I am still getting error or the other. I am pasting those below for your reference:

gcc-10: cmake command runs, but error during make command

/home/sudeeplab/softwares/gromacs-2024.1/src/external/colvars/colvar.cpp: In member function ‘int colvar::set_state_params(const string&)’:

/home/sudeeplab/softwares/gromacs-2024.1/src/external/colvars/colvar.cpp:2383:1: internal compiler error: in try_forward_edges, at cfgcleanup.c:581

gcc-11: cmake command gives error

CMake Error at cmake/gmxManageNvccConfig.cmake:110 (message):
  CUDA compiler does not seem to be functional or is not compatible with the
  host compiler.  Set the GMX_NVCC_WORKS CMake cache variable to bypass this
  check if you know what you are doing.
Call Stack (most recent call first):
  cmake/gmxManageCuda.cmake:110 (include)
  CMakeLists.txt:704 (include)

gcc-12: cmake command gives error

CMake Error at cmake/gmxManageNvccConfig.cmake:104 (if):
  if given arguments:

    "In file included from /usr/include/cuda_runtime.h:83,
                   from <command-line>:

  /usr/include/crt/host_config.h:139:2: error: #error -- unsupported GNU
  version! gcc versions later than 11 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.

    139 | #error -- unsupported GNU version! gcc versions later than 11 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:703 (include)

I humbly request you to help me with this. It has taken up a lot of my time.

Regards,
Chaitanya

7

Hi Chaitanya,

regarding the last error: “unsupported GNU version” - could you re-check that you used the correct combination of GCC and CUDA Versions? I can compile GROMACS 2024 with GCC 12.2 and CUDA 12.2, so it should work on your machine as well.

Best,
Carsten

8

Thanks for your kind reply Carsten.

I will check it, but as fas as I know, I did take care of that.

Thanks again,

Chaitanya