Dear Renato,
I have recently succeeded to install Amber22 and AmberTools22 on Ubuntu 22.
The same principles hold for the version you want to install. Please see if this may help you? Not sure if the Attached file will get thorugh the Amber Mailing list system?
Best wishes
gert Kruger
On Thu, 2023-02-16 at 09:55 -0300, Renato Freitas via AMBER wrote:
Dear Amber users/developers
I am trying to install Amber20 and AmberTools21 on my machine but it
failed after about 74% of the installation.
My specifications:
- Ubuntu 20.04.5
- gcc version 9.4.0
#####################################
[ 74%] Built target mmpbsa_py_energy
set rpath to /usr/local/amber/amber20_src/build/AmberTools/src/cpptraj/src
running build
running build_py
copying pytraj/version.py ->
/usr/local/amber/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-3.10/pytraj
running build_ext
building 'pytraj.analysis.c_analysis.c_analysis' extension
/usr/bin/gcc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall
-fPIC -O2 -isystem
/usr/local/amber/amber20_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/usr/local/amber/amber20_src/build/CMakeFiles/miniconda/install/include
-fPIC -I/usr/local/amber/amber20_src/AmberTools/src/pytraj/../cpptraj/src
-I/usr/local/amber/amber20_src/AmberTools/src/pytraj/pytraj
-I/usr/local/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10
-c pytraj/analysis/c_analysis/c_analysis.cpp -o
/usr/local/amber/amber20_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/temp.linux-x86_64-3.10/pytraj/analysis/c_analysis/c_analysis.o
-O0 -ggdb
-Wl,-rpath=/usr/local/amber/amber20_src/build/AmberTools/src/cpptraj/src
In file included from
/usr/local/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/Python.h:74,
from pytraj/analysis/c_analysis/c_analysis.cpp:18:
pytraj/analysis/c_analysis/c_analysis.cpp: In function ‘void
__pyx_tp_dealloc_6pytraj_8analysis_10c_analysis_10c_analysis_Analysis(PyObject*)’:
/usr/local/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/object.h:133:58:
error: lvalue required as increment operand
133 | #define Py_REFCNT(ob) _Py_REFCNT(_PyObject_CAST_CONST(ob))
| ^
pytraj/analysis/c_analysis/c_analysis.cpp:28873:7: note: in expansion of
macro ‘Py_REFCNT’
28873 | ++Py_REFCNT(o);
| ^~~~~~~~~
/usr/local/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/object.h:133:58:
error: lvalue required as decrement operand
133 | #define Py_REFCNT(ob) _Py_REFCNT(_PyObject_CAST_CONST(ob))
| ^
....
Error: Symbol ‘atompositions_fce’ at (1) has no IMPLICIT type
/usr/local/amber/amber20_src/AmberTools/src/rism/amber_rism_interface.F90:1476:24:
1476 | atomPositions_fce = atomPositions_md
| 1
Error: Symbol ‘atompositions_fce’ at (1) has no IMPLICIT type; did you mean
‘atompositions_md’?
/usr/local/amber/amber20_src/AmberTools/src/rism/amber_rism_interface.F90:1344:26:
1344 | atomPositions_fce => safemem_realloc(atomPositions_fce, 3,
rism_3d%solute%numAtoms)
| 1
Error: Symbol ‘atompositions_fce’ at (1) has no IMPLICIT type
make[2]: ***
[AmberTools/src/rism/CMakeFiles/sander_rism_interface.dir/build.make:63:
AmberTools/src/rism/CMakeFiles/sander_rism_interface.dir/amber_rism_interface.F90.o]
Error 1
make[1]: *** [CMakeFiles/Makefile2:5148:
AmberTools/src/rism/CMakeFiles/sander_rism_interface.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
error: command '/usr/bin/gcc' failed with exit code 1
make[2]: *** [AmberTools/src/pytraj/CMakeFiles/pytraj.dir/build.make:620:
AmberTools/src/pytraj/CMakeFiles/python-build/pytraj-build.stamp] Error 1
make[1]: *** [CMakeFiles/Makefile2:6734:
AmberTools/src/pytraj/CMakeFiles/pytraj.dir/all] Error 2
make: *** [Makefile:152: all] Error 2
#################################################
Any suggestions?
Thanks,
Renato
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Received on Thu Feb 16 2023 - 06:00:02 PST
