Dear list,
I am installing amber22 on my ubuntu22.04 system. I have successfully installed run_cmake in the package without any modifications. I have add cmake path to my bashrc file and can access camke in any command window. But I got the below errors while running make install:
[ 26%] Building C object AmberTools/src/arpack/CMakeFiles/arpack.dir/wallclock.c.o
[ 26%] Linking Fortran shared library libarpack.so
[ 26%] Built target arpack
[ 26%] Boostrapping Boost.Build (using machine default toolset)
Building Boost.Build engine with toolset gcc... tools/build/src/engine/bin.linuxx86_64/b2
Unicode/ICU support for Boost.Regex?... not found.
Backing up existing Boost.Build configuration in project-config.jam.2
Generating Boost.Build configuration in project-config.jam...
Bootstrapping is done. To build, run:
./b2
To adjust configuration, edit 'project-config.jam'.
Further information:
- Command line help:
./b2 --help
- Getting started guide:
http://www.boost.org/more/getting_started/unix-variants.html
- Boost.Build documentation:
http://www.boost.org/build/doc/html/index.html
/bin/sh: 1: cmake: not found
make[2]: *** [AmberTools/src/boost/CMakeFiles/boost_build.dir/build.make:88: AmberTools/src/boost/Stamp/boost_build/boost_build-bootstrap] Error 127
make[1]: *** [CMakeFiles/Makefile2:4290: AmberTools/src/boost/CMakeFiles/boost_build.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
I failed to solve the problem. Then, I used make followed by make install. it worked and make test.serial command gave me the below message:
==============================================================
export TESTsander='/home/tm/Downloads/amber22///bin/pmemd'; cd middle-scheme/ETH && ./Run.ETH_middle_scheme
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG
diffing mdout.ETH_middle_scheme.save with mdout.ETH_middle_scheme
PASSED
==============================================================
make[2]: Leaving directory '/home/tm/Downloads/amber22/test'
make[2]: Entering directory '/home/tm/Downloads/amber22/test'
Finished serial test suite for Amber 22 at Tue Jan 23 03:49:03 PM CST 2024.
make[2]: Leaving directory '/home/tm/Downloads/amber22/test'
171 file comparisons passed
6 file comparisons failed (1 of which can be ignored)
0 tests experienced errors
Test log file saved as /home/tm/Downloads/amber22/logs/test_amber_serial/2024-01-23_15-42-06.log
Test diffs file saved as /home/tm/Downloads/amber22/logs/test_amber_serial/2024-01-23_15-42-06.diff
make[1]: *** [Makefile:15: test] Error 1
make[1]: Leaving directory '/home/tm/Downloads/amber22/test'
Summary of AmberTools serial tests:
2934 file comparisons passed
3 file comparisons failed (3 of which can be ignored)
0 tests experienced errors
Test log file saved as /home/tm/Downloads/amber22///logs/test_at_serial/2024-01-23_14-39-20.log
Test diffs file saved as /home/tm/Downloads/amber22///logs/test_at_serial/2024-01-23_14-39-20.diff
may I ask is my amber installed properly? pmemd, cpptraj and pdb4amber are working.
Thanks,
Ming
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Received on Tue Jan 23 2024 - 16:00:02 PST
