Difficulty installing

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
wynton@wyntonnewlaptop:~ sudo apt install build-essential cmake git libfftw3-dev libgsl-dev Reading package lists... Done Building dependency tree... Done Reading state information... Done E: Unable to locate package build-essential E: Unable to locate package cmake E: Unable to locate package libfftw3-dev E: Unable to locate package libgsl-dev wynton@wyntonnewlaptop:~ sudo apt install build-essential cmake git libfftw3-dev libgsl-dev
Reading package lists… Done
Building dependency tree… Done
Reading state information… Done
E: Unable to locate package build-essential
E: Unable to locate package cmake
E: Unable to locate package libfftw3-dev
E: Unable to locate package libgsl-dev

Rgds,

Wynton

2

Hi,
This problem is not related to GROMACS installation as such. You are having difficulties installing the required packages. What Linux distribution are you using and which version?

3

Ok, successfully installed. but gmx.exe is not found in the bin.

4

By “bin” do you mean the installation directory? To which directory did you install? Is there a gmx file there?

5

yes, the folder bin in it. i installed to C:\Softwares\gromacs-2024.3\fftw-install.

6

no there is no gmx file

7

So is CMAKE_INSTALL_PREFIX set to C:\Softwares\gromacs-2024.3\fftw-install? Or is that just the directory where you ran the compilation? The installed files should be in the bin/ subdirectory in the directory specified by CMAKE_INSTALL_PREFIX.

8

C:\Softwares\gromacs-2024.3\cmake, no CMAKE_INSTALL_PREFIX present.

9

If there is no CMAKE_INSTALL_PREFIX it will be installed in the default system-wide installation directory. I presume that would be C:\Program Files\gromacs (or something similar) on Windows.

10

C:\Program Files\CMake\bin

(Attachment Outlook-3dhisnbk.webp is missing)

(Attachment Outlook-rdwgtlaa.webp is missing)

(Attachment Outlook-kpsh5bus.webp is missing)

11

cmake.exe

12

I don’t understand. You should not be looking for GROMACS installations in the system-wide cmake directory.

I think it would be easier if you describe your installation procedure (of GROMACS) all the way from the start. Please provide the exact commands that you have used and the current working directories when you executed those commands.

13

cmake …\gromacs-2024.3 ^
-G “Visual Studio 17 2022” ^
-A x64 ^
-DGMX_DOUBLE=ON ^
-DGMX_BUILD_OWN_FFTW=OFF ^
-DREGRESSIONTEST_DOWNLOAD=ON ^
-DFFTW_INCLUDE_DIR=“C:\Softwares\gromacs-2024.3\fftw-install\include” ^
-DFFTW_LIBRARY=“C:\Softwares\gromacs-2024.3\fftw-install\lib\fftw3.lib”
current working directories when you executed those commands: C:\Program Files\CMake\bin, C:\Softwares\gromacs-2024.3, C:\Users\wyntonlam\gromacs-2024.3, C:\Users\wyntonlam\gmxapi_env, C:\gromacs-2024.3

14

So, have you run make and make install to actually build and install GROMACS? make install would need admin privileges, unless you specify a CMAKE_INSTALL_PREFIX that is in your user home directory. You might want to run make check as well to verify that the tests are passing.

15

C:\Softwares\gromacs-2024.3\build>cmake … -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=fftw3 -DFFTW_INCLUDE_DIR=“C:\Softwares\gromacs-2024.3\fftw-install\include” -DFFTW_LIBRARY=“C:\Softwares\gromacs-2024.3\fftw-install\lib\libfftw3.lib” -DGMX_BUILD_SHARED_EXE=ON -DGMX_USE_OPENMP=ON -DCMAKE_INSTALL_PREFIX=“C:\Softwares\gromacs-2024.3\install” -DCMAKE_VERBOSE_MAKEFILE=ON
– Selecting Windows SDK version 10.0.22621.0 to target Windows 10.0.19045.
– Could not identify number of AVX-512 units - detection program missing compilation prerequisites
CMake Error at cmake/FindFFTW.cmake:104 (message):
Could not find fftw_plan_many_[r2c|c2r] in
C:/Softwares/gromacs-2024.3/fftw-install/lib/libfftw3.lib, take a look at
the error message in
C:/Softwares/gromacs-2024.3/build/CMakeFiles/CMakeError.log to find out
what went wrong. If you are using a static lib (.a) make sure you have
specified all dependencies of fftw3 in FFTW_LIBRARY by hand (e.g.
-DFFTW_LIBRARY=‘/path/to/libfftw3.so;/path/to/libm.so’) !
Call Stack (most recent call first):
cmake/gmxManageFFTLibraries.cmake:64 (find_package)
CMakeLists.txt:872 (include)

– Configuring incomplete, errors occurred!

16

So, it fails during compilation. It seems like your FFTW library doesn’t work.

17

so what should i do?

18

I haven’t built GROMACS or FFTW on Windows for a very long time, so I might not be the best person to help you.

But following the instructions at Installation guide - GROMACS 2024.3 documentation. How did you build the FFTW library? Did you follow the instructions at Installation guide - GROMACS 2024.3 documentation, Installation and Customization (FFTW 3.3.10) and Installation on non-Unix systems (FFTW 3.3.10)? Otherwise, can you use the built-in fftpack instead?