「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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(普通は上記だけでlibtiffをリンクしたRELIONをビルドできるはずです。ただ、minicondaやanacondaを使ってEMAN2をビルドした環境とかでは、[[minicondaにCMakeの検索パスを持ってかれる]]というつらい現象が起きるかもしれません。) | (普通は上記だけでlibtiffをリンクしたRELIONをビルドできるはずです。ただ、minicondaやanacondaを使ってEMAN2をビルドした環境とかでは、[[minicondaにCMakeの検索パスを持ってかれる]]というつらい現象が起きるかもしれません。) | ||
+ | |||
+ | |||
+ | == 2D classification == | ||
+ | ===<u>[[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129</u>=== | ||
+ | ==== 症状 ==== | ||
+ | 2019/5/21, v3.0.5, build from source in Ubuntu 16.04.6 LTS | ||
+ | |||
+ | RELION3チュートリアルで最初の2D classificationを実行したらMPI関連のエラーが出て異常終了した。 | ||
+ | |||
+ | エラー全文は以下。DL-Boxはホストマシン名。 | ||
+ | <pre> | ||
+ | [DL-Box:00925] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129 | ||
+ | [DL-Box:00926] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129 | ||
+ | [DL-Box:00927] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129 | ||
+ | [DL-Box:00928] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129 | ||
+ | *** An error occurred in MPI_Init | ||
+ | *** on a NULL communicator | ||
+ | *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | ||
+ | *** and potentially your MPI job) | ||
+ | *** An error occurred in MPI_Init | ||
+ | *** on a NULL communicator | ||
+ | *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | ||
+ | *** and potentially your MPI job) | ||
+ | *** An error occurred in MPI_Init | ||
+ | *** on a NULL communicator | ||
+ | *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | ||
+ | *** and potentially your MPI job) | ||
+ | *** An error occurred in MPI_Init | ||
+ | *** on a NULL communicator | ||
+ | *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | ||
+ | *** and potentially your MPI job) | ||
+ | [DL-Box:926] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! | ||
+ | [DL-Box:925] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! | ||
+ | [DL-Box:928] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! | ||
+ | [DL-Box:927] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! | ||
+ | [DL-Box:00929] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129 | ||
+ | *** An error occurred in MPI_Init | ||
+ | *** on a NULL communicator | ||
+ | *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | ||
+ | *** and potentially your MPI job) | ||
+ | [DL-Box:929] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! | ||
+ | </pre> | ||
+ | |||
+ | |||
+ | ジョブのパラメータのうちMPIに関係するかもしれない部分は以下(I/Oとかも含め) | ||
+ | <pre> | ||
+ | Combine iterations through disc? == No | ||
+ | Use parallel disc I/O? == Yes | ||
+ | Pre-read all particles into RAM? == Yes | ||
+ | Which GPUs to use: == 0:1:2:3 | ||
+ | Minimum dedicated cores per node: == 1 | ||
+ | Number of MPI procs: == 5 | ||
+ | Number of pooled particles: == 30 | ||
+ | Number of threads: == 3 | ||
+ | Copy particles to scratch directory: == | ||
+ | Use GPU acceleration? == Yes | ||
+ | </pre> |
2019年5月21日 (火) 08:36時点における版
目次
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入れる必要がある。
- Issue上がってた。 https://github.com/3dem/relion/issues/383
- relion.gitのreadmeにも書いてある。 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。マニュアルはちゃんと読もう。
# 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
(普通は上記だけでlibtiffをリンクしたRELIONをビルドできるはずです。ただ、minicondaやanacondaを使ってEMAN2をビルドした環境とかでは、minicondaにCMakeの検索パスを持ってかれるというつらい現象が起きるかもしれません。)
2D classification
[[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129
症状
2019/5/21, v3.0.5, build from source in Ubuntu 16.04.6 LTS
RELION3チュートリアルで最初の2D classificationを実行したらMPI関連のエラーが出て異常終了した。
エラー全文は以下。DL-Boxはホストマシン名。
[DL-Box:00925] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129 [DL-Box:00926] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129 [DL-Box:00927] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129 [DL-Box:00928] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129 *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [DL-Box:926] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! [DL-Box:925] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! [DL-Box:928] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! [DL-Box:927] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! [DL-Box:00929] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 129 *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [DL-Box:929] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
ジョブのパラメータのうちMPIに関係するかもしれない部分は以下(I/Oとかも含め)
Combine iterations through disc? == No Use parallel disc I/O? == Yes Pre-read all particles into RAM? == Yes Which GPUs to use: == 0:1:2:3 Minimum dedicated cores per node: == 1 Number of MPI procs: == 5 Number of pooled particles: == 30 Number of threads: == 3 Copy particles to scratch directory: == Use GPU acceleration? == Yes