![[PukiWiki]](image/picc.png "[PukiWiki]")
#author("2024-01-16T07:32:35+00:00","default:sysosa","sysosa") #author("2024-01-16T08:05:52+00:00","default:sysosa","sysosa") 本家様 [[http://sphire.mpg.de/wiki/doku.php?id=gpu_isac>+http://sphire.mpg.de/wiki/doku.php?id=gpu_isac]] #code(nonumber){{ ISAC (Iterative Stable Alignment and Clustering) is a 2D classification algorithm. It sorts a given stack of cryo-EM particles into different classes that share the same view of a target protein. ISAC is based around iterations of alternating equal size k-means clustering and repeated 2D alignment routines. (deepL様翻訳) ISAC（Iterative Stable Alignment and Clustering）は、2次元分類アルゴリズムである。 与えられた低温電子顕微鏡粒子のスタックを、ターゲットタンパク質の同じビューを共有する異なるクラスにソートする。 ISACは、等しいサイズのk-meansクラスタリングと2Dアライメントルーチンを交互に繰り返し行うことに基づいています。 }} SPHIRE のadd-onになるのですが、SPHIRE はeman2に含まれている. このeman2のSPHIRE に当てることとします. まずはISACのパッケージをダウンロードして展開しておきます #code(nonumber){{ [root@rockylinux ~]# cd /apps/src/ [root@rockylinux src]# unzip /Public/em/gpu_isac_2.3.4.zip [root@rockylinux src]# cd gpu_isac_2.3.4/ [root@rockylinux gpu_isac_2.3.4]# ls -lF total 4 drwxr-xr-x. 3 root root 17 Feb 22 2021 bin/ drwxr-xr-x. 2 root root 26 Jan 16 15:50 checks/ drwxr-xr-x. 2 root root 102 Feb 22 2021 cuda/ drwxr-xr-x. 3 root root 32 Feb 22 2021 examples/ -rw-r--r--. 1 root root 1517 Jan 16 15:59 install.sh [root@rockylinux gpu_isac_2.3.4]# }} ここにある install.sh をたたけばいいのですが、SPHIREの稼働環境を用意してから実行します ここにある install.sh をたたけばいいのですが、SPHIRE(eman2)の稼働環境を用意してから実行します #code(nonumber){{ [root@rockylinux ~]# module use /apps/modulefiles/ [root@rockylinux ~]# module load eman2/2.91 [root@rockylinux ~]# which mpirun /apps/eman2.91/bin/mpirun [root@rockylinux ~]# which python /apps/eman2.91/bin/python [root@rockylinux ~]# }} 一応version確認をしてみます #code(nonumber){{ [root@rockylinux ~]# e2version.py EMAN 2.91 final ( GITHUB: 2021-03-08 11:36 - commit: 81caed2 ) Your Python version is: 3.7.9 [root@rockylinux ~]# sphire --version SPHIRE v1.4.1 (GitHub: 2021-03-08 11:36) [root@rockylinux ~]# export PATH=/usr/local/cuda/bin:$PATH [root@rockylinux ~]# nvcc --version nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2022 NVIDIA Corporation Built on Tue_May__3_18:49:52_PDT_2022 Cuda compilation tools, release 11.7, V11.7.64 Build cuda_11.7.r11.7/compiler.31294372_0 [root@rockylinux ~]# }} それで #code(nonumber){{ [root@rockylinux ~]# cd /apps/src/gpu_isac_2.3.4/ [root@rockylinux gpu_isac_2.3.4]# [root@rockylinux gpu_isac_2.3.4]# bash ./install.sh Checking libraries.. SPHIRE installation: .................................................check SPARX v5.0 (GITHUB: 2021-03-08 11:36) [rockylinux:33855] *** Process received signal *** [rockylinux:33855] Signal: Segmentation fault (11) [rockylinux:33855] Signal code: Address not mapped (1) [rockylinux:33855] Failing at address: 0x5604233896a0 [rockylinux:33855] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f56f0d97cf0] [rockylinux:33855] [ 1] /lib64/libc.so.6(+0xcbe57)[0x7f56f0a8be57] [rockylinux:33855] [ 2] /lib64/libc.so.6(+0x66095)[0x7f56f0a26095] [rockylinux:33855] [ 3] /lib64/libc.so.6(_IO_vfprintf+0x20c)[0x7f56f0a26bdc] [rockylinux:33855] [ 4] /lib64/libc.so.6(__vasprintf_chk+0xcc)[0x7f56f0afe4bc] [rockylinux:33855] [ 5] /lib64/libc.so.6(__asprintf_chk+0x93)[0x7f56f0afe3d3] [rockylinux:33855] [ 6] /apps/eman2.91/lib/python3.7/site-packages/../.././libopen-pal.so.40(opal_setenv+0x53)[0x7f56d00b1e33] [rockylinux:33855] [ 7] /apps/eman2.91/lib/python3.7/site-packages/../../libmpi.so.40(ompi_mpi_init+0x897)[0x7f56d025dc37] [rockylinux:33855] [ 8] /apps/eman2.91/lib/python3.7/site-packages/../../libmpi.so.40(PMPI_Init+0x71)[0x7f56d0287cb1] [rockylinux:33855] [ 9] /apps/eman2.91/lib/python3.7/site-packages/mpi.so(+0x7a41)[0x7f56d031ba41] [rockylinux:33855] [10] python(_PyMethodDef_RawFastCallKeywords+0x1e4)[0x560141a4b884] [rockylinux:33855] [11] python(_PyCFunction_FastCallKeywords+0x21)[0x560141a4ba31] [rockylinux:33855] [12] python(_PyEval_EvalFrameDefault+0x4e1d)[0x560141ab7ebd] [rockylinux:33855] [13] python(_PyFunction_FastCallKeywords+0xfb)[0x560141a4ae7b] [rockylinux:33855] [14] python(_PyEval_EvalFrameDefault+0x416)[0x560141ab34b6] [rockylinux:33855] [15] python(_PyEval_EvalCodeWithName+0x2f9)[0x5601419fa829] [rockylinux:33855] [16] python(PyEval_EvalCodeEx+0x44)[0x5601419fb714] [rockylinux:33855] [17] python(PyEval_EvalCode+0x1c)[0x5601419fb73c] [rockylinux:33855] [18] python(+0x22cf14)[0x560141b12f14] [rockylinux:33855] [19] python(PyRun_FileExFlags+0xa1)[0x560141b1d331] [rockylinux:33855] [20] python(PyRun_SimpleFileExFlags+0x1c3)[0x560141b1d523] [rockylinux:33855] [21] python(+0x238655)[0x560141b1e655] [rockylinux:33855] [22] python(_Py_UnixMain+0x3c)[0x560141b1e77c] [rockylinux:33855] [23] /lib64/libc.so.6(__libc_start_main+0xe5)[0x7f56f09fad85] [rockylinux:33855] [24] python(+0x1dcff0)[0x560141ac2ff0] [rockylinux:33855] *** End of error message *** ./install.sh: line 5: 33855 Segmentation fault (core dumped) python ./checks/lib_check.py Compiling CUDA code.. Configuring files for your system.. Linking GPU ISAC with the SPHIRE GUI.. GPU ISAC installation complete! Good luck with your project :) [root@rockylinux gpu_isac_2.3.4]# }} と一応インストールは完了します. っが、その前段でエラーが発生します. これは「install.sh」にある「python ./checks/lib_check.py」で発生します こちらは別途 #code(nonumber){{ OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 mpirun --allow-run-as-root python ./checks/lib_check.py }} にて実行できます 下記はその実行例となります. これで確認ができたので前段で「bash ./install.sh」のエラー該当部分にコメントを入れて実行させないでインストールを行ってもいいのかなと思います #code(nonumber){{ [root@rockylinux gpu_isac_2.3.4]# OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 mpirun --allow-run-as-root python ./checks/lib_check.py SPHIRE installation: .................................................check SPARX v5.0 (GITHUB: 2021-03-08 11:36) SPHIRE installation: .................................................check SPARX v5.0 (GITHUB: 2021-03-08 11:36) SPHIRE installation: .................................................check SPARX v5.0 (GITHUB: 2021-03-08 11:36) SPHIRE installation: .................................................check SPARX v5.0 (GITHUB: 2021-03-08 11:36) MPI available: .......................................................check pydusa 1.15 py37h4a2f2b1_17 cryoem MPI available: .......................................................check pydusa 1.15 py37h4a2f2b1_17 cryoem MPI available: .......................................................check pydusa 1.15 py37h4a2f2b1_17 cryoem MPI available: .......................................................check pydusa 1.15 py37h4a2f2b1_17 cryoem CUDA available: ......................................................check nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2022 NVIDIA Corporation Built on Tue_May__3_18:49:52_PDT_2022 Cuda compilation tools, release 11.7, V11.7.64 Build cuda_11.7.r11.7/compiler.31294372_0 Looks like all the libraries we need are available, huzzah! CUDA available: ......................................................check nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2022 NVIDIA Corporation Built on Tue_May__3_18:49:52_PDT_2022 Cuda compilation tools, release 11.7, V11.7.64 Build cuda_11.7.r11.7/compiler.31294372_0 Looks like all the libraries we need are available, huzzah! CUDA available: ......................................................check nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2022 NVIDIA Corporation Built on Tue_May__3_18:49:52_PDT_2022 Cuda compilation tools, release 11.7, V11.7.64 Build cuda_11.7.r11.7/compiler.31294372_0 Looks like all the libraries we need are available, huzzah! CUDA available: ......................................................check nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2022 NVIDIA Corporation Built on Tue_May__3_18:49:52_PDT_2022 Cuda compilation tools, release 11.7, V11.7.64 Build cuda_11.7.r11.7/compiler.31294372_0 Looks like all the libraries we need are available, huzzah! [root@rockylinux gpu_isac_2.3.4]# }}
