Compilation and Installation

Procedure

1. Decompress the installation package.

   unzip hmmer-h3-arm.zip -d /path/to/hmmer
   unzip easel-master.zip -d /path/to/hmmer/hmmer-h3-arm

2. Go to the source code directory and change the related directory name.

   cd /path/to/hmmer
   mv hmmer-h3-arm/ hmmer-3.3.2/
   cd hmmer-3.3.2/
   mv easel-master/ easel/

3. Set the environment variables.

   export MPICC=mpicc
   export MPICXX=mpicxx
   export MPIFC=mpifort
   export CC=$MPICC
   export CXX=$MPICXX
   export FC=$MPIFC

4. Generate Makefile and modify the related file.

   autoconf
   ./configure --prefix=/path/to/hmmer/hmmer --enable-mpi --enable-neon CC=$MPICC CXX=$MPICXX FC=$MPIFC F77=$MPIFC
   sed -i 's/esl_FCompare/esl_FCompareNew/g' src/p7_domain.c
   sed -i 's/esl_DCompare/esl_DCompareNew/g' src/p7_domain.c
   sed -i 's/esl_FCompare/esl_FCompareNew/g' src/p7_hit.c
   sed -i 's/esl_DCompare/esl_DCompareNew/g' src/p7_hit.c
   sed -i 's/esl_FCompare_old/esl_FCompare/g' src/p7_hmm.c
   sed -i 's/esl_FCompare_old/esl_FCompare/g' src/p7_trace.c
   sed -i 's/esl_FCompare_old/esl_FCompare/g' src/impl_neon/p7_oprofile.c
   sed -i 's/esl_FCompare_old/esl_FCompare/g' src/generic_vtrace.c
   sed -i 's/esl_FCompare_old/esl_FCompare/g' src/p7_bg.c
   sed -i 's/esl_FCompare_old/esl_FCompare/g' src/p7_gmx.c
   sed -i '41 d' src/impl_neon/impl_neon.h
   sed -i '29c static inline float' src/impl_neon/impl_neon.h
   sed -i 's/esl_FCompare_old/esl_FCompare/g' src/./generic_stotrace.c
   sed -i 's/esl_FCompare_old/esl_FCompare/g' src/./generic_viterbi.c
   sed -i 's/esl_FCompare_old/esl_FCompare/g' src/./modelconfig.c
   sed -i 's/esl_FCompare_old/esl_FCompare/g' src/impl_neon/./stotrace.c
   sed -i 's/esl_FCompare_old/esl_FCompare/g' src/impl_neon/./optacc.c

5. Perform the compilation and installation.

   make -j$(nproc)
   make check
   make -j$(nproc) install

6. Load the HMMER environment variable.

   export PATH=/path/to/hmmer/hmmer/bin:$PATH

7. (Optional) Install the Easel library.

   cd easel/
   make install