error with running gromcs-2022.5 patched with plumed-2.8.2

[Kami Kahzadi]

Dear all,

I am trying to run a Modelling Concentration-driven processes with PLUMED (gmx_mpi-plumed-2.8.2) but I come to the segmentation fault error. I can't even run simple processes when plumed and grpmacs are patched. gromacs runs without plumed, and also plumed without gmx. I have tried to run an empty .dat and then it asks for .tpr so it is not about the installation issue.

the codes are as below:

1) this is the link of github repository, and I downloaded it's content:

https://github.com/mme-ucl/CmuMD/Example1_methane_permeation_in_ZIF-8_membrane

then run the followings:

gmx_mpi grompp -f NEMD.mdp -c md1.gro -r md1.gro -p ZIF8.top -o topol.tpr -maxwarn 3
gmx_mpi mdrun -s topol.tpr -plumed plumed2.dat -nb gp

and get this error:

*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0x440000e9
[ 0] /lib/x86_64-linux-gnu/libc.so.6

2) also, I run the exercise 3 of the git repository: https://github.com/mme-ucl/PLUMED_MClass_22-08

the code is as it is mentioned in plumed tutorial : gmx_mpi mdrun --plumed cmumd_diff.dat

and still the same error comes up, in this run also shows "note:the file tpx version 112, software tpx version 127" which I rectified this in the first process by generating .tpr with my version.

I have attached the log files for both processes (1 & 2) and also .txt contains the full script of the error.

additionally, I have installed plumed-2.8.2 with mpi support with no errors also first add CMUMD.cpp file to root/src/colvar then compiled it. for gromacs installation, before compilation, in its root directory, patched it with plumed (no errors occurred).

the installation codes are as below:

cd plumed-2.8.2/

 ./configure --enable-mpi --enable-shared
 make -j 4
sudo make install

cd gromacs-2022.5/
plumed-patch -p -f  #then choose the gromacs version and patched.

mkdir build
cd build/
cmake '.../gromacs-2022.5' -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
make -j 4
sudo make install.

Finally, I tried all this steps for plumed-2.8.0 patched with gromacs-2021.4 and also plumed-2.8.0 patched with gromacs 2020.6 and still get the segmentation fault.

any suggestions?!!

Thanks in advance,

[Shenghui Zhong]

Hi，

Have you solved this problem?

I encounter the same issue,.

BR//Shenghui