Failing plugin installation

[albertmena]

Hello, I'm @albertmena part of the xmippTeam.
After run the devel installation steps it fails in the MD-NMMD-Genesis-1.1 installation step. It also fails in the Scipion Plugin Manager GUI.

Making install in src
make[1]: Entering directory '/home/agarcia/scipion3/software/em/MD-NMMD-Genesis-1.1/src'
Making install in lib
make[2]: Entering directory '/home/agarcia/scipion3/software/em/MD-NMMD-Genesis-1.1/src/lib'
cpp -traditional-cpp -traditional -DHAVE_CONFIG_H constants.fpp constants.f90
mpif90  -I. -I../../src  -I. -O3 -ffast-math -march=native -ffree-line-length-none -fopenmp  -c constants.f90
cpp -traditional-cpp -traditional -DHAVE_CONFIG_H mpi_parallel.fpp mpi_parallel.f90
mpif90  -I. -I../../src  -I. -O3 -ffast-math -march=native -ffree-line-length-none -fopenmp  -c mpi_parallel.f90
cpp -traditional-cpp -traditional -DHAVE_CONFIG_H messages.fpp messages.f90
mpif90  -I. -I../../src  -I. -O3 -ffast-math -march=native -ffree-line-length-none -fopenmp  -c messages.f90
cpp -traditional-cpp -traditional -DHAVE_CONFIG_H random.fpp random.f90
mpif90  -I. -I../../src  -I. -O3 -ffast-math -march=native -ffree-line-length-none -fopenmp  -c random.f90
cpp -traditional-cpp -traditional -DHAVE_CONFIG_H atom_libs.fpp atom_libs.f90
mpif90  -I. -I../../src  -I. -O3 -ffast-math -march=native -ffree-line-length-none -fopenmp  -c atom_libs.f90
cpp -traditional-cpp -traditional -DHAVE_CONFIG_H math_libs.fpp math_libs.f90
mpif90  -I. -I../../src  -I. -O3 -ffast-math -march=native -ffree-line-length-none -fopenmp  -c math_libs.f90
cpp -traditional-cpp -traditional -DHAVE_CONFIG_H string.fpp string.f90
mpif90  -I. -I../../src  -I. -O3 -ffast-math -march=native -ffree-line-length-none -fopenmp  -c string.f90
cpp -traditional-cpp -traditional -DHAVE_CONFIG_H table_libs.fpp table_libs.f90
mpif90  -I. -I../../src  -I. -O3 -ffast-math -march=native -ffree-line-length-none -fopenmp  -c table_libs.f90
cpp -traditional-cpp -traditional -DHAVE_CONFIG_H timers.fpp timers.f90
mpif90  -I. -I../../src  -I. -O3 -ffast-math -march=native -ffree-line-length-none -fopenmp  -c timers.f90
cpp -traditional-cpp -traditional -DHAVE_CONFIG_H nbond_list.fpp nbond_list.f90
mpif90  -I. -I../../src  -I. -O3 -ffast-math -march=native -ffree-line-length-none -fopenmp  -c nbond_list.f90
cpp -traditional-cpp -traditional -DHAVE_CONFIG_H ffte_fft235.fpp ffte_fft235.f90
mpif90  -I. -I../../src  -I. -O3 -ffast-math -march=native -ffree-line-length-none -fopenmp  -c ffte_fft235.f90
ffte_fft235.fpp:195:30:

  195 |         CALL SETTBL0(W(J),8,L)
      |                              1
Error: Type mismatch in argument ‘w’ at (1); passed COMPLEX(8) to REAL(8)
ffte_fft235.fpp:200:30:

  200 |         CALL SETTBL0(W(J),5,L)
      |                              1
Error: Type mismatch in argument ‘w’ at (1); passed COMPLEX(8) to REAL(8)
ffte_fft235.fpp:205:30:

  205 |         CALL SETTBL0(W(J),4,L)
      |                              1
Error: Type mismatch in argument ‘w’ at (1); passed COMPLEX(8) to REAL(8)
ffte_fft235.fpp:210:30:

  210 |         CALL SETTBL0(W(J),3,L)
      |                              1
Error: Type mismatch in argument ‘w’ at (1); passed COMPLEX(8) to REAL(8)
make[2]: *** [Makefile:714: ffte_fft235.o] Error 1
make[2]: Leaving directory '/home/agarcia/scipion3/software/em/MD-NMMD-Genesis-1.1/src/lib'
make[1]: *** [Makefile:358: install-recursive] Error 1
make[1]: Leaving directory '/home/agarcia/scipion3/software/em/MD-NMMD-Genesis-1.1/src'
make: *** [Makefile:355: install-recursive] Error 1
target '/home/agarcia/scipion3/software/em/MD-NMMD-Genesis-1.1/bin/atdyn' not built (after running 'eval "$(/home/agarcia/anaconda3/bin/conda shell.bash hook)"&& conda activate continuousflex-git && git clone -b merge_genesis_1.4 https://github.com/continuousflex-org/MD-NMMD-Genesis.git . ; autoreconf -fi ; ./configure LDFLAGS=-L/home/agarcia/anaconda3/envs/continuousflex-git/lib ; make install;')

[mms29]

Hi @albertmena

Thanks for reporting,
These lines appear as warnings with GCC 8 and as errors with GCC 10
This should solve the problem #145

[albertmena]

Thanks for your quick response.

In my Ubuntu works (whitout Genesis; in init.py default=False), but in my Centos machine I have some more errors
Centos 7, gcc 10.2.1 errors related to the std library. Some examples:

      In file included from bpl-subset/bpl_subset/boost/bind/mem_fn.hpp:25,
                       from bpl-subset/bpl_subset/boost/mem_fn.hpp:22,
                       from bpl-subset/bpl_subset/boost/function/detail/prologue.hpp:18,
                       from bpl-subset/bpl_subset/boost/function/function_template.hpp:13,
                       from bpl-subset/bpl_subset/boost/function/detail/maybe_include.hpp:23,
                       from bpl-subset/bpl_subset/boost/function/function2.hpp:11,
                       from bpl-subset/bpl_subset/boost/python/object/function_object.hpp:8,
                       from bpl-subset/bpl_subset/libs/python/src/object/iterator.cpp:7:
      bpl-subset/bpl_subset/boost/get_pointer.hpp:25:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         25 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
            |                                        ^~~~~~

      In file included from bpl-subset/bpl_subset/boost/bind/bind.hpp:29,
                       from bpl-subset/bpl_subset/boost/bind.hpp:22,
                       from bpl-subset/bpl_subset/libs/python/src/object/inheritance.cpp:14:
      bpl-subset/bpl_subset/boost/bind/arg.hpp: In constructor ‘pycudaboost::arg<I>::arg(const T&)’:
      bpl-subset/bpl_subset/boost/bind/arg.hpp:37:22: warning: typedef ‘T_must_be_placeholder’ locally defined but not used [-Wunused-local-typedefs]
         37 |         typedef char T_must_be_placeholder[ I == is_placeholder<T>::value? 1: -1 ];
            |                      ^~~~~~~~~~~~~~~~~~~~~
      gcc -pthread -B /home/xmippuser/miniconda3/envs/continuousflex-git/compiler_compat -Wl,--sysroot=/ -Wsign-compare -fwrapv -Wall -O3 -DNDEBUG -fPIC -DBOOST_ALL_NO_LIB=1 -DBOOST_THREAD_BUILD_DLL=1 -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION=1 -DBOOST_PYTHON_SOURCE=1 -Dboost=pycudaboost -DBOOST_THREAD_DONT_USE_CHRONO=1 -DPYGPU_PACKAGE=pycuda -DPYGPU_PYCUDA=1 -DHAVE_CURAND=1 -Isrc/cpp -Ibpl-subset/bpl_subset -I/home/xmippuser/miniconda3/envs/continuousflex-git/lib/python3.8/site-packages/numpy/core/include -I/home/xmippuser/miniconda3/envs/continuousflex-git/include/python3.8 -c bpl-subset/bpl_subset/libs/python/src/object/iterator.cpp -o build/temp.linux-x86_64-cpython-38/bpl-subset/bpl_subset/libs/python/src/object/iterator.o

[mms29]

Hi @albertmena, can you share the entire output of the plugin installation? or maybe at which step of the installation does this error occurs ? By the way, are they shown as errors because I just see warnings here?

I don't know which protocol uses this bpl_subset package, @MohamadHarastani , @ilyes-hm any ideas?

[albertmena]

Hi again,
I could fix it. It was related with the CUDA path in bashrc.
Thanks for the fast answering!