Hi again,
I forgot to mention that using the old ./configure method it works but I
have this error at some compilation stage:
/usr/lib64/gcc/x86_64-suse-linux/9/../../../../lib64/crti.o: file not
recognized: file format not recognized
collect2: error: ld returned 1 exit status
error: command 'g++' failed with exit status 1
make[2]: *** [Makefile:529: parmed] Error 1
make[2]: Leaving directory '/home/kometata/amber20_src/AmberTools/src'
make[1]: *** [Makefile:258: parallel] Error 2
make[1]: Leaving directory '/home/kometata/amber20_src/AmberTools/src'
make: *** [Makefile:7: install] Error 2
kometata.localhost:~/amber20_src>
Regards,
Filip
На 17-May-20 в 06:13, fratev.biomed.bas.bg написа:
> Hi,
> Thank you for your respond!
>
> I have default mpich installation as it is provided by my Linux
> distribution (Suse)and cmake can not find it.
>
> Then I installed mpich from their website in the specified folder in
> Amber_scr/AmberTols/scr..and used
> cd $AMBERHOME/AmberTools/src
> ./configure_mpich <compiler>
> This script installed the mpich in amber20/bin folder. However, cmake
> gives the same error, e.g is not able to find MPICH.
>
> Further I tried with openmpi3 as it was specified and have the
> same/similar error (please see below).
>
> I also tried to set MPI_C_INCLUDE_PATH and MPI_C_LIBRARIES variables,
> which gave me the same error again (a bit different output log).
>
> Finally, I was almost completely sure that your solution with
> -DCMAKE_PREFIX_PATH=/home/case/mpich will work and installed mpich in my
> home folder /home/fratev/mpich. However, it gave me the same error message
> and I really need of help. I saw that similar problems have been detected
> during the development v4 and v5 versions.
>
> About the cuda my gcc version is higher that 8 and I remember that you
> have already provided solution for that for the previous Amber versions. I
> am not sure how to point the Cmake to some folder with older gcc version
> or something similar.
>
> Regards,
> Filip
>
> These are the outputs:
> MPICH
> -- **************************************************************************
> -- Starting configuration of Amber version 20.0.0...
> -- CMake Version: 3.17.2
> -- For how to use this build system, please read this wiki:
> -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
> -- For a list of important CMake variables, check here:
> -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
> -- **************************************************************************
> -- Amber source found, building AmberTools and Amber
> CMake Warning (dev) at
> /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272
> (message):
> The package name passed to `find_package_handle_standard_args` (OpenMP_C)
> does not match the name of the calling package (OpenMPFixed). This can
> lead to problems in calling code that expects `find_package` result
> variables (e.g., `_FOUND`) to follow a certain pattern.
> Call Stack (most recent call first):
> cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
> (find_package_handle_standard_args)
> cmake/OpenMPConfig.cmake:11 (find_package)
> CMakeLists.txt:117 (include)
> This warning is for project developers. Use -Wno-dev to suppress it.
>
> CMake Warning (dev) at
> /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272
> (message):
> The package name passed to `find_package_handle_standard_args` (OpenMP_CXX)
> does not match the name of the calling package (OpenMPFixed). This can
> lead to problems in calling code that expects `find_package` result
> variables (e.g., `_FOUND`) to follow a certain pattern.
> Call Stack (most recent call first):
> cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
> (find_package_handle_standard_args)
> cmake/OpenMPConfig.cmake:11 (find_package)
> CMakeLists.txt:117 (include)
> This warning is for project developers. Use -Wno-dev to suppress it.
>
> CMake Warning (dev) at
> /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272
> (message):
> The package name passed to `find_package_handle_standard_args`
> (OpenMP_Fortran) does not match the name of the calling package
> (OpenMPFixed). This can lead to problems in calling code that expects
> `find_package` result variables (e.g., `_FOUND`) to follow a certain
> pattern.
> Call Stack (most recent call first):
> cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
> (find_package_handle_standard_args)
> cmake/OpenMPConfig.cmake:11 (find_package)
> CMakeLists.txt:117 (include)
> This warning is for project developers. Use -Wno-dev to suppress it.
>
> -- Could NOT find MPI_C (missing: MPI_mpi_LIBRARY MPI_C_WORKS)
> -- Could NOT find MPI_CXX (missing: MPI_mpicxx_LIBRARY MPI_mpi_LIBRARY
> MPI_CXX_WORKS)
> -- Could NOT find MPI_Fortran (missing: MPI_mpifort_LIBRARY
> MPI_mpi_LIBRARY MPI_Fortran_WORKS)
> -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND MPI_Fortran_FOUND)
> CMake Error at cmake/MPIConfig.cmake:12 (message):
> You requested MPI, but the MPI C library was not found. Please install one
> and try again, or set MPI_C_INCLUDE_PATH and MPI_C_LIBRARIES to point to
> your MPI.
> Call Stack (most recent call first):
> CMakeLists.txt:118 (include)
>
> OpenMPI
>
> Running: cmake /home/fratev/amber20_src
> -DCMAKE_INSTALL_PREFIX=/home/fratev/amber20
> -DCMAKE_PREFIX_PATH=/home/kometata/mpich
> ./quick_cmake_install: line 168: -DCOMPILER=GNU: command not found
> -- **************************************************************************
> -- Starting configuration of Amber version 20.0.0...
> -- CMake Version: 3.17.2
> -- For how to use this build system, please read this wiki:
> -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
> -- For a list of important CMake variables, check here:
> -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
> -- **************************************************************************
> -- Amber source found, building AmberTools and Amber
> CMake Warning (dev) at
> /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272
> (message):
> The package name passed to `find_package_handle_standard_args` (OpenMP_C)
> does not match the name of the calling package (OpenMPFixed). This can
> lead to problems in calling code that expects `find_package` result
> variables (e.g., `_FOUND`) to follow a certain pattern.
> Call Stack (most recent call first):
> cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
> (find_package_handle_standard_args)
> cmake/OpenMPConfig.cmake:11 (find_package)
> CMakeLists.txt:117 (include)
> This warning is for project developers. Use -Wno-dev to suppress it.
>
> CMake Warning (dev) at
> /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272
> (message):
> The package name passed to `find_package_handle_standard_args` (OpenMP_CXX)
> does not match the name of the calling package (OpenMPFixed). This can
> lead to problems in calling code that expects `find_package` result
> variables (e.g., `_FOUND`) to follow a certain pattern.
> Call Stack (most recent call first):
> cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
> (find_package_handle_standard_args)
> cmake/OpenMPConfig.cmake:11 (find_package)
> CMakeLists.txt:117 (include)
> This warning is for project developers. Use -Wno-dev to suppress it.
>
> CMake Warning (dev) at
> /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272
> (message):
> The package name passed to `find_package_handle_standard_args`
> (OpenMP_Fortran) does not match the name of the calling package
> (OpenMPFixed). This can lead to problems in calling code that expects
> `find_package` result variables (e.g., `_FOUND`) to follow a certain
> pattern.
> Call Stack (most recent call first):
> cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
> (find_package_handle_standard_args)
> cmake/OpenMPConfig.cmake:11 (find_package)
> CMakeLists.txt:117 (include)
> This warning is for project developers. Use -Wno-dev to suppress it.
>
> -- Could NOT find MPI_C (missing: MPI_mpi_LIBRARY MPI_C_WORKS)
> -- Could NOT find MPI_CXX (missing: MPI_mpicxx_LIBRARY MPI_mpi_LIBRARY
> MPI_CXX_WORKS)
> -- Could NOT find MPI_Fortran (missing: MPI_mpifort_LIBRARY
> MPI_mpi_LIBRARY MPI_Fortran_WORKS)
> -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND MPI_Fortran_FOUND)
> CMake Error at cmake/MPIConfig.cmake:12 (message):
> You requested MPI, but the MPI C library was not found. Please install one
> and try again, or set MPI_C_INCLUDE_PATH and MPI_C_LIBRARIES to point to
> your MPI.
> Call Stack (most recent call first):
> CMakeLists.txt:118 (include)
>
>
>
>
>
>
>> On Sat, May 16, 2020, Filip Fratev wrote:
>>> I have a problem with MPIC location during Amber20 installation. I did
>>> everything according to the manual, created suggested paths and also
>>> many other things but without any success.
>> It's not clear what you actually did; "everything according to the
>> manual" is a little vague. If your MPICH is installed in some
>> non-standard location (such as /home/case/mpich), it should be possible
>> to just add '-DCMAKE_PREFIX_PATH=/home/case/mpich' to your run_cmake
>> file. This will tell cmake to look there for the mpi codes it needs.
>>
>> ....good luck....dac
>>
>>> Indeed, I also have a problem with cuda (10.2 in my case).
>>>
>> Can't help much here, given no details. Is your CUDA_HOME environment
>> variable set?
>>
>> ....good luck....dac
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Sun May 17 2020 - 01:30:01 PDT
