Installing Gemma

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Use an SFTP tool to upload the Gemma installation package to the /path/to/GEMMA directory.
3. Run the following command to install dependencies:

   yum install blas-devel lapack-devel -y

4. Run the following command to decompress the installation package:

   cd /path/to/GEMMA && tar -zxf GEMMA-0.96.tar.gz

5. Run the following command to go to the directory generated after the decompression:

   cd GEMMA-0.96

6. Run the following command to modify compilation optimization parameters:

   sed -i 's/\-O3/-O3 -march=armv8.2-a -mtune=tsv110/' Makefile

7. Run the following command to replace the parameter -m64 by -mabi=lp64:

   sed -i 's/\-m64/\-mabi=lp64/g' Makefile

8. Run the following commands to change the value of the compilation parameter LIBS_LNX_S_LAPACK and delete the compilation parameter static:

   sed -i 's/LIBS_LNX_S_LAPACK = /# LIBS_LNX_S_LAPACK = /' Makefile
   sed -i '/LIBS_LNX_S_LAPACK = /a LIBS_LNX_S_LAPACK = -lgfortran -lopenblas -llapack -lblas -lgfortran' Makefile
   sed -i 's/CPPFLAGS += -static/#CPPFLAGS += -static/' Makefile

9. Run the following commands to set the environment variables:

   export LIBRARY_PATH=/path/to/OPENBLAS/lib:/path/to/GSL/lib:$LIBRARY_PATH
   export LD_LIBRARY_PATH=/path/to/OPENBLAS/lib:/path/to/GSL/lib:$LD_LIBRARY_PATH
   export CPLUS_INCLUDE_PATH=/path/to/OpenBLAS/include:/path/to/EIGEN/include/eigen3:/path/to/GSL/include:$CPLUS_INCLUDE_PATH
   export C_INCLUDE_PATH=/path/to/OpenBLAS/include:/path/to/EIGEN/include/eigen3:/path/to/GSL/include:$C_INCLUDE_PATH

10. Run the following commands to perform the compilation and installation:

    make -j