autumn1998 / gisspa

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This site is no longer updated, please check "https://www.x-mol.com/groups/Zhang_Xinzheng" for subsequent updates.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.

gisspa's Issues

Not able to run the program in Centos 7 workstation

Hi Jing and Tong,

We have a workstation with the following information:
Centos 7
4GPU: RTX2080Ti
CUDA11.6

I have installed the program and downloaded the test data. When I tried to run the program, I had the following error:

$ ~/GisSPA/main config1
Undefined option: .Abort.
Undefined option: .Abort.
Parameter requested:
--input micrographs_ctf.lst
--template 2D_projections.hdf
--eulerfile euler_C1_step5.lst
--angpix 2.720000
--phistep 3.000000
--kk 3.000000
--energy 300.000000
--cs 2.700000
--Highres 8.000000
--Lowres 400.000000
--diameter 160.000000
Parameter optional:
--threshold 6.800000
--output TestData_output.lst
--first 0
--last 20
--window_size 512
--GPU_ID 2
--phase_flip 1
--overlap 160
--norm_type 1
--invert 1
Parameter fixed:
--a -9.320000
--b 2.650000
--b2 0.019080
--bfactor -78.775703
--bfactor2 -12.912100
--bfactor3 1.287320

Error => Open euler file failed : euler_C1_step5.lst

' not founds_ctf.lst
Error -3 occured in readRawImage!
Cannot open MRC file
IMG size: 10 10
Number of template:0
Cannot open MRC file
Temp size: 10 10
Error invalid configuration argument at main.cu:331

我应该怎么正确使用jspr来消除相位残差

开发者你好：
protocol中的最后一步我不知道如何使用，按照protocal我输入了：
jspr_refine_2_relion_class3d.py 00p1.lst 324 1.5 001.star 0/1 0/1/2
但是它反应的是：

请问我应该如何正确使用呢
祝好！

relion2lst_dont_write_mics.py with error