ubuntu18.04の構築はこちら参照ubuntu/18.04

ubuntu18.04だとリポジトリの「universe」が既定で有効ではない。
なので「/etc/apt/sources.list」を修正して「universe」を追加させる。その後の「apt update」は必須です

root@ubuntu:~# cat /etc/apt/sources.list
deb http://archive.ubuntu.com/ubuntu bionic main universe
deb http://archive.ubuntu.com/ubuntu bionic-security main universe
deb http://archive.ubuntu.com/ubuntu bionic-updates main universe
 
root@ubuntu:~# apt update

コンパイル環境を整備します。

root@ubuntu:~# apt install build-essential
 
root@ubuntu:~# apt install cmake build-essential mpi-default-bin mpi-default-dev libfftw3-dev \
   xserver-xorg-dev fluid libtiff-dev

そしてRelionの本体を召還

root@ubuntu:~# git clone https://bitbucket.org/scheres/relion-3.0_beta.git

buildディレクトリを作って cmake でconfigを行う

root@e:~# cd relion-3.0_beta/
 
root@e:~/relion-3.0_beta# mkdir build
root@e:~/relion-3.0_beta# cd build
 
root@e:~/relion-3.0_beta/build# cmake -DCUDA=ON -DCudaTexture=ON -DCMAKE_INSTALL_PREFIX=/Appl/relion-3.0-beta-2 ..

っでmakeを行う

root@e:~/relion-3.0_beta/build# make
 :
[ 98%] Built target run_motioncorr
Scanning dependencies of target maingui
[ 98%] Building CXX object src/apps/CMakeFiles/maingui.dir/maingui.cpp.o
[ 99%] Linking CXX executable ../../bin/relion_maingui
[ 99%] Built target maingui
Scanning dependencies of target prepare_subtomo
[100%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o
[100%] Linking CXX executable ../../bin/relion_prepare_subtomo
[100%] Built target prepare_subtomo
root@e:~/relion-3.0_beta/build#

と一見makeに成功したと見えるのだが、、、
再度make もしくはそのまま make installすると

root@e:~/relion-3.0_beta/build# make
-- BUILD TYPE set to the default type:  'Release'
-- Setting fallback CUDA_ARCH=35
-- CUDA enabled - Building CUDA-accelerated version of RELION
-- Setting cpu precision to double
-- Setting accelerated code precision to single
-- Using cuda wrapper to compile....
-- Cuda version is >= 7.5 and single-precision build, enable double usage warning.
-- CMAKE_C_COMPILER : /usr/bin/cc
-- CMAKE_CXX_COMPILER : /usr/bin/c++
-- MPI_C_COMPILER : /usr/bin/mpicc
-- MPI_CXX_COMPILER : /usr/bin/mpicxx
-- CMAKE_CXX_COMPILER_ID : GNU
-- Could NOT find MPI_C (missing: MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS)
CMake Error at /usr/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
  /usr/share/cmake-3.10/Modules/FindMPI.cmake:1444 (find_package_handle_standard_args)
  CMakeLists.txt:242 (find_package)
 
 
-- Configuring incomplete, errors occurred!
See also "/root/relion-3.0_beta/build/CMakeFiles/CMakeOutput.log".
See also "/root/relion-3.0_beta/build/CMakeFiles/CMakeError.log".
Makefile:894: recipe for target 'cmake_check_build_system' failed
make: *** [cmake_check_build_system] Error 1
root@e:~/relion-3.0_beta/build#

と駄目みたい...

っで回避方法ですが、cmakeを古くする。
ubuntu18.04で提供されているcmakeは

root@e:~# cmake -version
cmake version 3.10.2
 
CMake suite maintained and supported by Kitware (kitware.com/cmake).
root@e:~#

これをCentOS7で提供されている「2.8.12.2」にします。
https://cmake.org/files/v2.8/から「cmake-2.8.12.2.tar.gz」を得てバイナリを作ります。

root@e:~# curl -O https://cmake.org/files/v2.8/cmake-2.8.12.2.tar.gz
 
root@e:~# gzip -cd cmake-2.8.12.2.tar.gz | tar xf -
root@e:~# cd cmake-2.8.12.2/
 
root@e:~/cmake-2.8.12.2# ./configure
root@e:~/cmake-2.8.12.2# make && make install

作ったcmake-2.8.12.2を使って再度Relionを作ります。

#code(nonumber){{
root@e:~# cd relion-3.0_beta/build
 
root@e:~/relion-3.0_beta/build# rm -rf ./*
 
root@e:~/relion-3.0_beta/build# /usr/local/bin/cmake -DCUDA=ON -DCudaTexture=ON -DCMAKE_INSTALL_PREFIX=/Appl/relion-3.0-beta-2 ..
 
root@e:~/relion-3.0_beta/build# make && make install
 
root@e:~/relion-3.0_beta/build# ( cd /Appl && ln -s relion-3.0-beta-2 relion )

環境設定を施します

export PATH=/Appl/relion/bin:$PATH
export LD_LIBRARY_PATH=/usr/relion/lib

これでrelionが利用可能になります


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Last-modified: 2018-10-23 (火) 02:51:28 (26d)