Hi Gert,
thanks for your very detailed tutorial.
Following your instructions, I updated my gcc/g++/gfortran to version 10
and tried to install Amber again. As David suggested I used "make install"
to have a clear log. This time, the installation stops at 95%, but
basically, it gives the same error as before:
error: command '/usr/bin/gcc' failed with exit code 1
make[2]: *** [AmberTools/src/pytraj/CMakeFiles/pytraj.dir/build.make:522:
AmberTools/src/pytraj/CMakeFiles/python-build/pytraj-build.stamp] Error 1
make[1]: *** [CMakeFiles/Makefile2:6738:
AmberTools/src/pytraj/CMakeFiles/pytraj.dir/all] Error 2
make: *** [Makefile:152: all] Error 2
In case it helps, the attached file has the results of "make install".
Best,
Renato
On Thu, Feb 16, 2023 at 10:45 AM Gert Kruger via AMBER <amber.ambermd.org>
wrote:
> 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 - 15:00:03 PST
