本家様 https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Main_Page

180802にRelion-3.0 beta-2がリリースされました。ここではこのRelion-3.0を取り上げます。
対象マシンは CentOS7 です。

Relion/GPU
Relion/qsub, Relion/qsub.sh
Relion/icc

過去ページ Relion2.180803

入手方法

ソースコードを展開したい場所を掘ってそこにgitコマンドで入手します

mkdir /Appl/src/relion3
cd /Appl/src/relion3
git clone https://bitbucket.org/scheres/relion-3.0_beta.git

コンパイル環境の準備

https://bitbucket.org/scheres/relion-3.0_beta/overviewによれば、
GPU-acceleration版、CPU-acceleration版(AVX2向け, AVX512向け, Xeon Phi向け)、acceleration機能なし版が作れるそうな。
nvidiaのカードで計算を速めたいならGPU-acceleration --> 早くなるのは relion_refine と relion_autopick
持ってなくCPUの拡張命令で早めたいならCPU-acceleration --> 早くなるのは relion_refine のみ

ここではgccで 「acceleration機能なし版」 を用意してみます。

yumで開発環境と必要なパッケージをインストールします

[root@c ~]# yum groupinstall "Development Tools"
[root@c ~]# yum --enablerepo=epel install cmake openmpi-devel openmpi libpng12 \
              fltk-devel fltk-fluid fftw-devel \
              compat-libtiff3 \
              evince \
              texlive-latex \
              ghostscript \
              texlive-latex-bin \
              libtiff-devel
[root@c ~]#

コンパイル

繰り返しますが、ここではgccで 「acceleration機能なし版」です。
インストール先は「/Appl/relion-3.0-beta-2」

[root@c relion3]# cd relion-3.0_beta/
 
[root@c relion-3.0_beta]# mkdir b-180803
[root@c relion-3.0_beta]# cd b-180803
 
[root@c b-180803]# export PATH=/usr/lib64/openmpi/bin:$PATH
[root@c b-180803]# export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:$LD_LIBRARY_PATH
 
[root@c b-180803]# cmake -DCUDA=OFF -DCMAKE_INSTALL_PREFIX=/Appl/relion-3.0-beta-2 ..
 
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /bin/cc
-- Check for working C compiler: /bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /bin/c++
-- Check for working CXX compiler: /bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- BUILD TYPE set to the default type:  'Release'
-- Setting fallback CUDA_ARCH=35
-- Setting cpu precision to double
-- Setting accelerated code precision to single
-- Using non-cuda compilation....
-- CMAKE_C_COMPILER : /bin/cc
-- CMAKE_CXX_COMPILER : /bin/c++
-- MPI_C_COMPILER :
-- MPI_CXX_COMPILER :
-- CMAKE_CXX_COMPILER_ID : GNU
-- Found MPI_C: /usr/lib64/openmpi/lib/libmpi.so
-- Found MPI_CXX: /usr/lib64/openmpi/lib/libmpi_cxx.so;/usr/lib64/openmpi/lib/libmpi.so
-- MPI_INCLUDE_PATH : /usr/include/openmpi-x86_64
-- MPI_LIBRARIES : /usr/lib64/openmpi/lib/libmpi_cxx.so;/usr/lib64/openmpi/lib/libmpi.so
-- MPI_CXX_INCLUDE_PATH : /usr/include/openmpi-x86_64
-- MPI_CXX_LIBRARIES : /usr/lib64/openmpi/lib/libmpi_cxx.so;/usr/lib64/openmpi/lib/libmpi.so
-- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so
-- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /usr/lib64/libX11.so
-- Could NOT find FLTK (missing:  FLTK_FLUID_EXECUTABLE)
-- No FLTK installation was found
-- Found previously built non-system FLTK libraries that will be used.
-- FLTK_INCLUDE_DIR: /usr/include
-- FLTK_LIBRARIES:   /usr/lib64/libfltk_images.so;/usr/lib64/libfltk_forms.so;/usr/lib64/libfltk.so
-- Found FFTW
-- FFTW_PATH: /usr/include
-- FFTW_INCLUDES: /usr/include
-- FFTW_LIBRARIES: /usr/lib64/libfftw3f.so;/usr/lib64/libfftw3.so
-- Looking for sincos
-- Looking for sincos - found
-- Looking for __sincos
-- Looking for __sincos - not found
-- Found TIFF: /usr/lib64/libtiff.so (found version "4.0.3")
BUILD_SHARED_LIBS = OFF
-- Building static libs (larger build size and binaries)
Running apps/CMakeLists.txt...
-- CMAKE_BINARY_DIR:/Appl/src/relion3/relion-3.0_beta/b-180803
TIFF FOUND
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
OPENMP FOUND
-- Configuring done
-- Generating done
-- Build files have been written to: /Appl/src/relion3/relion-3.0_beta/b-180803
 
[root@c b-180803]# make && make install
[root@c b-180803]# ( cd /Appl; rm relion; ln -s relion-3.0-beta-2 relion )

起動

各自の.bashrc/.cshrcにPATH環境変数とLD_LIBRARY_PATH環境変数を加えておきます

(bash)
export PATH=/Appl/relion/bin:$PATH
export LD_LIBRARY_PATH=/Appl/relion/lib:$LD_LIBRARY_PATH
 
(csh/tcsh)
setenv PATH /Appl/relion/bin:$PATH
setenv LD_LIBRARY_PATH /Appl/relion/lib:$LD_LIBRARY_PATH

そうした上で relion とターミナルに入力させて起動する

relion

2018y08m03d_111426957.png
外見的には従来と同じですが、計算項目が増えましたね。

メモ

まだbeta-2だからだろうか、もしOS提供のfltkライブラリでコンパイルされると、make installの際に

 :
-- Installing: /Appl/relion-3.0-beta-2/bin/relion_qsub.csh
-- Installing: /Appl/relion-3.0-beta-2/lib/gui_background.xpm
CMake Error at cmake_install.cmake:52 (FILE):
  file INSTALL cannot find
  "/Appl/src/relion3/relion-3.0_beta/external/fltk/lib".
 
 
make: *** [install] エラー 1

と言われる。「fltk-fluid」パッケージをインストールすれば治まります


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Last-modified: 2018-08-07 (火) 16:11:14 (10d)