「RELIONトラブルシューティング」の版間の差分
提供: Eospedia
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cmakeでこけた怒 | cmakeでこけた怒 | ||
+ | (出力の一部抜粋) | ||
CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): | CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): | ||
Cannot generate a safe runtime search path for target tiltpair_plot because | Cannot generate a safe runtime search path for target tiltpair_plot because | ||
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$ /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=../install .. | $ /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=../install .. | ||
+ | (出力の一部抜粋) | ||
CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): | CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): | ||
Cannot generate a safe runtime search path for target maingui because files | Cannot generate a safe runtime search path for target maingui because files | ||
行78: | 行80: | ||
$ cmake -DCMAKE_INSTALL_PREFIX=../install -DTIFF_INCLUDE_DIR=/usr/include/x86_64-linux-gnu -DTIFF_LIBRARY=/usr/lib/x86_64-linux-gnu/libtiff.so.5 .. | $ cmake -DCMAKE_INSTALL_PREFIX=../install -DTIFF_INCLUDE_DIR=/usr/include/x86_64-linux-gnu -DTIFF_LIBRARY=/usr/lib/x86_64-linux-gnu/libtiff.so.5 .. | ||
+ | (出力の一部抜粋) | ||
CMake Error at /home/kttn/softwares/relion/build/CMakeFiles/CMakeTmp/cmTC_3d3bbTargets.cmake:16 (add_library): | CMake Error at /home/kttn/softwares/relion/build/CMakeFiles/CMakeTmp/cmTC_3d3bbTargets.cmake:16 (add_library): | ||
Target "MPI::MPI_C" links to item " -Wl,-rpath,/home/kttn/miniconda2/lib | Target "MPI::MPI_C" links to item " -Wl,-rpath,/home/kttn/miniconda2/lib | ||
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/home/kttn/softwares/relion/build/CMakeFiles/CMakeTmp/CMakeLists.txt:12 (include) | /home/kttn/softwares/relion/build/CMakeFiles/CMakeTmp/CMakeLists.txt:12 (include) | ||
− | + | libtiffは解消されたけど他のライブラリが相変わらずminicondaに持ってかれている | |
$ conda remove cmake | $ conda remove cmake | ||
$ cmake -DCMAKE_INSTALL_PREFIX=../install .. | $ cmake -DCMAKE_INSTALL_PREFIX=../install .. | ||
+ | (一部抜粋) | ||
CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): | CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): | ||
Cannot generate a safe runtime search path for target tiltpair_plot because | Cannot generate a safe runtime search path for target tiltpair_plot because | ||
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minicondaの呪縛からどうやって逃れたらいいの? | minicondaの呪縛からどうやって逃れたらいいの? | ||
+ | |||
+ | |||
+ | * 色々試す | ||
+ | ** miniconda2をPATHから削除してcmakeする | ||
+ | *** (結果)相変わらずminiconda2に持ってかれたまま | ||
+ | |||
+ | |||
+ | CMakeはインクルードとライブラリを検索するとき、どの設定ファイルまたは環境変数を呼んでどこを探しに行っているのか? |
2019年5月15日 (水) 03:02時点における版
Motion Correction
ERROR: TIFF support was not enabled during compilation
症状
2019/5/14, v3.0.5, build from source in Ubuntu 16.04.6 LTS
RELIONチュートリアルでMotion correctionするとき、MoitonCor2のRELION実装使ったら表題のエラーが出た。
対処
- libtiffのdevel入れる必要があったみたいっす。
- https://github.com/3dem/relion/issues/383
- というかrelion.gitのreadmeに書いてあった。 https://github.com/3dem/relion
- sudo apt install ... のところに列挙してなかったから見落としてた。
# relionのルートディレクトリに移動 (cmakeとかsrcとかあるディレクトリ) $ rm -r build/ install/ $ sudo apt install libtiff5-dev $ mkdir build/ install/ $ cd build && cmake -DCMAKE_INSTALL_PREFIX=../install .. $ make -j10 $ make install
cmakeでこけた怒
(出力の一部抜粋)
CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): Cannot generate a safe runtime search path for target tiltpair_plot because files in some directories may conflict with libraries in implicit directories: runtime library [libtiff.so.5] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3f.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib Some of these libraries may not be found correctly.
$ which cmake /home/kttn/miniconda2/bin/cmake
EMAN2インストールするときに入れたminiconda2のbin/に、condaで入れたcmakeが入ってて、それ使ってるのが問題か
cmakeを/usr/bin/cmakeに置き換えて再ビルド
$ /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=../install ..
(出力の一部抜粋)
CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): Cannot generate a safe runtime search path for target maingui because files in some directories may conflict with libraries in implicit directories: runtime library [libtiff.so.5] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3f.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib Some of these libraries may not be found correctly.
んぁー cmakeわからん
relion.gitのreadmeに" If you installed libtiff in a non-standard location, specify the location by -DTIFF_INCLUDE_DIR=/path/to/include -DTIFF_LIBRARY=/path/to/libtiff.so.5."なる記述があったので、これを使ってみる
- includeとlibはどこですか
- https://packages.ubuntu.com/xenial/amd64/libtiff5-dev/filelist
- /usr/include/x86_64-linux-gnu と /usr/lib/x86_64-linux-gnu/ でした
$ cmake -DCMAKE_INSTALL_PREFIX=../install -DTIFF_INCLUDE_DIR=/usr/include/x86_64-linux-gnu -DTIFF_LIBRARY=/usr/lib/x86_64-linux-gnu/libtiff.so.5 ..
(出力の一部抜粋)
CMake Error at /home/kttn/softwares/relion/build/CMakeFiles/CMakeTmp/cmTC_3d3bbTargets.cmake:16 (add_library): Target "MPI::MPI_C" links to item " -Wl,-rpath,/home/kttn/miniconda2/lib -Wl,-rpath -Wl,/home/kttn/miniconda2/lib -Wl,--enable-new-dtags" which has leading or trailing whitespace. This is now an error according to policy CMP0004. Call Stack (most recent call first): /home/kttn/softwares/relion/build/CMakeFiles/CMakeTmp/CMakeLists.txt:12 (include)
libtiffは解消されたけど他のライブラリが相変わらずminicondaに持ってかれている
$ conda remove cmake $ cmake -DCMAKE_INSTALL_PREFIX=../install ..
(一部抜粋)
CMake Warning at src/apps/CMakeLists.txt:165 (add_executable): Cannot generate a safe runtime search path for target tiltpair_plot because files in some directories may conflict with libraries in implicit directories: runtime library [libtiff.so.5] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3f.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib runtime library [libfftw3.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in: /home/kttn/miniconda2/lib Some of these libraries may not be found correctly.
minicondaの呪縛からどうやって逃れたらいいの?
- 色々試す
- miniconda2をPATHから削除してcmakeする
- (結果)相変わらずminiconda2に持ってかれたまま
- miniconda2をPATHから削除してcmakeする
CMakeはインクルードとライブラリを検索するとき、どの設定ファイルまたは環境変数を呼んでどこを探しに行っているのか?