GROMACS version: 2021.5
GROMACS modification: No
Hi there!
I’m having trouble installing GROMACS on the LTS version of Ubuntu 24. It seems the issue might be related to CUDA drivers and the compatible compilers, GCC and G++.
I’ll provide my system configuration and the errors displayed below:
nvidia-smi
Fri Nov 8 17:50:09 2024
±----------------------------------------------------------------------------------------+
| NVIDIA-SMI 560.35.03 Driver Version: 560.35.03 CUDA Version: 12.6 |
|-----------------------------------------±-----------------------±---------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+========================+======================|
| 0 NVIDIA GeForce RTX 3080 Ti Off | 00000000:01:00.0 On | N/A |
| 32% 47C P8 37W / 350W | 378MiB / 12288MiB | 0% Default |
| | | N/A |
±----------------------------------------±-----------------------±---------------------+±----------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=========================================================================================|
| 0 N/A N/A 2336 G /usr/lib/xorg/Xorg 124MiB |
| 0 N/A N/A 2623 G /usr/bin/gnome-shell 25MiB |
| 0 N/A N/A 3425 G …irefox/4793/usr/lib/firefox/firefox 0MiB |
| 0 N/A N/A 4530 G /usr/bin/nautilus 17MiB |
| 0 N/A N/A 44973 G nvidia-settings 0MiB |
±----------------------------------------------------------------------------------------+
For the installation commands I added one flag for a previous error at the 27% of the "Building CXX object " but it stopped at 71% this time.
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DGMX_CUDA_TARGET_SM=86
[ 69%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o
[ 69%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o
[ 69%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o
[ 69%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o
[ 71%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o
[ 71%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o
[ 71%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o
[ 71%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o
[ 71%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o
[ 71%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o
[ 71%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o
In file included from /home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/analysisdata/dataframe.h:49,
from /home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/analysisdata/dataframe.cpp:44:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:126:5: error: ‘uint64_t’ does not name a type
126 | uint64_t flags_;
| ^~~~~~~~
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:1:1: note: ‘uint64_t’ is defined in header ‘’; did you forget to ‘#include ’?
+++ |+#include
1 | /*
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h: In constructor ‘gmx::FlagsTemplate::FlagsTemplate()’:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:73:23: error: class ‘gmx::FlagsTemplate’ does not have any field named ‘flags_’
73 | FlagsTemplate() : flags_(0) {}
| ^~~~~~
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h: In constructor ‘gmx::FlagsTemplate::FlagsTemplate(FlagType)’:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:75:36: error: class ‘gmx::FlagsTemplate’ does not have any field named ‘flags_’
75 | FlagsTemplate(FlagType flag) : flags_(flag) {}
| ^~~~~~
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h: In member function ‘bool gmx::FlagsTemplate::test(FlagType) const’:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:83:46: error: ‘flags_’ was not declared in this scope; did you mean ‘flag’?
83 | bool test(FlagType flag) const { return (flags_ & flag) != 0; }
| ^~~~~~
| flag
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h: In member function ‘void gmx::FlagsTemplate::clearAll()’:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:85:23: error: ‘flags_’ was not declared in this scope
85 | void clearAll() { flags_ = 0; }
| ^~~~~~
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h: In member function ‘void gmx::FlagsTemplate::set(FlagType)’:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:87:31: error: ‘flags_’ was not declared in this scope; did you mean ‘flag’?
87 | void set(FlagType flag) { flags_ |= flag; }
| ^~~~~~
| flag
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h: In member function ‘void gmx::FlagsTemplate::clear(FlagType)’:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:89:33: error: ‘flags_’ was not declared in this scope; did you mean ‘flag’?
89 | void clear(FlagType flag) { flags_ &= ~flag; }
| ^~~~~~
| flag
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h: In member function ‘gmx::FlagsTemplate gmx::FlagsTemplate::operator|(const gmx::FlagsTemplate&) const’:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:106:40: error: ‘flags_’ was not declared in this scope
106 | return FlagsTemplate(flags_ | other.flags_);
| ^~~~~~
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h: In member function ‘gmx::FlagsTemplate& gmx::FlagsTemplate::operator|=(const gmx::FlagsTemplate&)’:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:111:9: error: ‘flags_’ was not declared in this scope
111 | flags_ |= other.flags_;
| ^~~~~~
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h: In member function ‘gmx::FlagsTemplate gmx::FlagsTemplate::operator&(const gmx::FlagsTemplate&) const’:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:117:40: error: ‘flags_’ was not declared in this scope
117 | return FlagsTemplate(flags_ & other.flags_);
| ^~~~~~
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h: In member function ‘gmx::FlagsTemplate gmx::FlagsTemplate::operator~() const’:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:120:81: error: ‘flags_’ was not declared in this scope
120 | FlagsTemplate operator~() const { return FlagsTemplate(~flags_); }
| ^~~~~~
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h: In constructor ‘gmx::FlagsTemplate::FlagsTemplate(long unsigned int)’:
/home/masisrodriguez/Downloads/gromacs-2021.5/src/gromacs/utility/flags.h:124:51: error: class ‘gmx::FlagsTemplate’ does not have any field named ‘flags_’
124 | explicit FlagsTemplate(unsigned long flags) : flags_(flags) {}
| ^~~~~~
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/build.make:7195: src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:4433: src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [Makefile:166: all] Error 2
I would be really grateful if someone can lend me a hand!!
Thanks!!
Marcos