GisSPA

Time for compling: short
No need to install

Introduction

GPU parallel for isSPA, pick particle with CC.
CPU version from CJ, BeiJing

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This site is no longer updated, please check "https://www.x-mol.com/groups/Zhang_Xinzheng" for subsequent updates.
Please find the test data on this website.

pipeline

see GisSPA-protocal.pdf

structure

./deprated_code/:ignored this file
./EMReader/: read .hdf and .mrc file(just read data). Extracted from EMAN1.9.
./main.cu: main function
./GPU_func.cu(h): function processed on GPU
./Makefile: complier
./hdf5: the source package of hdf5
temp file:
./Data_TEST: test data
./Output: res for test data and obj files.
./Config_example: configure file to run test data.

Install

0. install git lfs to get the test_Data
1. install hdf5 1.8 (https://portal.hdfgroup.org/display/support/HDF5+1.8.21), the source is attached at ./hdf5
2. Fill the "LIB_HDF5" and "INCLUDE_HDF5" (row 4 & 5) in Makefile with your install path to set hdf5 available.
3. complie with Makefile.
4. write a config file
5. ./main + config_file

Quick start

-> inatll git lfs

1. sudo apt-get update
2. sudo apt-get install git-lfs
3. git lfs install
4. git lfs clone https://github.com/Autumn1998/GisSPA.git

-> install hdf5

0. cd GisSPA
1. cd ./hdf5
2. tar zvxf hdf5-1.8.21.tar.gz
3. cd hdf5-1.8.21
4. ./configure --prefix="your hdf5 install path"
5. make
6. make install
7. export LD_LIBRARY_PATH="your hdf5 install path"/lib:$LD_LIBRARY_PATH
   at /etc/profile or ~/.bashrc
8. source /etc/profile or ~/.bashrc

-> run GisSPA

0. cd GisSPA
1. vim Makfile, set LIB_HDF5="your hdf5 install path"/lib, set INCLUDE_HDF5="your hdf5 install path"/include
2. make clean
3. make
   If "can not create /Output/Objects/main.o", mkdir /Output/Objects
4. ./main ./Data_TEST/config

WARNING:The Data_TEST need at least 13GB memory at GPU!
If error occurred and temp_size = 10,10 and img_size = 10,10, check the git lfs.
If "error while loading shared libraries", check your LD_LIBRARY_PATH, and source. If it not work, do
cp "your hdf5 install path"/lib/libhdf5.so.10 .
Make ./main and libhdf5.so.10 in the same path.

How to use this problem: "./main config_file"
use "./main -h" to get help msg

contributor

LT & CJ.