Installation Error
Closed this issue · 8 comments
I am trying to install gromacs-ramd-release-2023 version with the following command;
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10
with Cuda compilation tools, release 11.5, V11.5.119
however i am getting following error;
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp: In constructor ‘gmx::RAMD::RAMD(const gmx::RAMDParams&, pull_t*, int64_t*, gmx::StartingBehavior, const t_commrec*, int, const t_filenm*, const gmx_output_env_t*, FILE*)’:
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:89:9: error: ‘MASTER’ was not declared in this scope
89 | if (MASTER(cr) and opt2bSet("-ramd", nfile, fnm))
| ^~~~~~
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp: In member function ‘virtual void gmx::RAMD::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)’:
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:119:9: error: ‘MASTER’ was not declared in this scope
119 | if (MASTER(cr) and out and (*pstep % params.eval_freq == 0))
| ^~~~~~
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:132:17: error: ‘MASTER’ was not declared in this scope
132 | if (MASTER(cr) and out)
| ^~~~~~
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:143:13: error: ‘MASTER’ was not declared in this scope
143 | if (MASTER(cr) and debug)
| ^~~~~~
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:155:17: error: ‘MASTER’ was not declared in this scope
155 | if (MASTER(cr) and debug)
| ^~~~~~
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:167:17: error: ‘MASTER’ was not declared in this scope
167 | if (MASTER(cr) and out)
| ^~~~~~
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:178:21: error: ‘MASTER’ was not declared in this scope
178 | if (MASTER(cr))
| ^~~~~~
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:192:17: error: ‘MASTER’ was not declared in this scope
192 | if (MASTER(cr) and debug)
| ^~~~~~
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:207:21: error: ‘MASTER’ was not declared in this scope
207 | if (MASTER(cr) and debug)
| ^~~~~~
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:219:9: error: ‘MASTER’ was not declared in this scope
219 | if (MASTER(cr) and (pstep % params.eval_freq == 0))
| ^~~~~~
/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:114:54: warning: unused parameter ‘forceProviderOutput’ [�]8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-parameter-Wunused-parameter�]8;;]
114 | ForceProviderOutput forceProviderOutput)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
At global scope:
cc1plus: note: unrecognized command-line option ‘-Wno-cast-function-type-strict’ may have been intended to silence earlier diagnostics
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/build.make:5634: src/gromacs/CMakeFiles/libgromacs.dir/ramd/ramd.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:4331: src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [Makefile:166: all] Error 2
i could not figure out what is wrong. could you please check?
Thanks for the report. I will check it.
Sorry for the late reply. I just realized that you are trying to compile gromacs-ramd-2023. This version is not released yet and still under development. The latest stable version is gromacs-2020.5-ramd-2.0. There is also a release candidate available gromacs-2022.5-ramd-2.1-rc1. Further updates are planned for next year at the earliest.
Hi @BerndDoser
I have compiled GROMACS-RAMD 2022.5 and used the 3htb structure with the jz4 ligand. I have also modified the ligand name in the MDP file. However, I encountered an error. Could you please tell me why?.
I'm wondering if there is a newer version available.
The annual updates up to GROMACS 2024 are available in the corresponding branches.
For the official release of "GROMACS-2022.6-RAMD-2.1" and subsequent versions, I also need to wait for permission from the scientific users.
For your specific issue, I need additional details. The screenshot appears to be broken.
The annual updates up to GROMACS 2024 are available in the corresponding branches. For the official release of "GROMACS-2022.6-RAMD-2.1" and subsequent versions, I also need to wait for permission from the scientific users. For your specific issue, I need additional details. The screenshot appears to be broken.
I have recompiled gromacs-RAMD 2024. I have used complex system, i.e. protein (3HTB) and ligand (JZ4). I have preformed energy minimization and NVT/NPT equilibrations. For RAMD simulation, I have used npt.tpr, npt.cpt, index.ndx, ramd.mdp (I have modified for LIG), and toppol.top, but I got error. The error stated that Group INH in mdp file was not in the list of index file. As I know INH ligand is the ligand from the RAMD tutorial at kbbox.h-its.org, so I am confused why I got this error.
Please use the new MDP parameters introduced in RAMD v2 (see #15). Since the correct MDP parameter 'ramd-group1-ligand' is not found, the default value 'INH' is used.
Please use the new MDP parameters introduced in RAMD v2 (see #15). Since the correct MDP parameter 'ramd-group1-ligand' is not found, the default value 'INH' is used.
Thank you. It's working now.
You're welcome. Thank you for using RAMD!