Installing CTFFIND

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Obtain the CTFFIND installation package.

   wget https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-4.1.14.tar.gz&file=1&type=node&id=26

3. Decompress the CTFFIND installation package.

   tar -zxvf  ctffind-4.1.14.tar.gz

4. Go to the directory generated after the decompression.

   cd ctffind-4.1.14

5. Modify the src/core/matrix.cpp file.
   1. Open src/core/matrix.cpp.

      vi src/core/matrix.cpp

   2. Press i to enter the insert mode and modify the content in line 7:

      Before the modification:

      7  #define _AL_SINCOS(x, s, c)  __asm__ ("fsincos" : "=t" (c), "=u" (s) : "0" (x))

      After the modification:

      7 #define _AL_SINCOS(x, s, c)   s = sinf(x);  c = cosf(x);

      

      After performing 5.a, press Esc, type :set nu, and press Enter to display the line number.

   3. Press Esc, type :wq!, and press Enter to save the file and exit.
6. Perform the compilation and installation.

   yum install -y libjpeg* libtiff* fftw*
   autoreconf -f -i
   ./configure --prefix=/path/to/ctffind --disable-mkl --enable-openmp --enable-debugmode

7. Modify the Makefile file.
   1. Open Makefile.

      vi Makefile

   2. Press i to enter the insert mode and change -O2 in CFLAGS CPPFLAGS CXXFLAGS to -O0.

      Before the modification:

      296 CFLAGS = -g -O2
      297 CPP = clang -E
      298 CPPFLAGS = -O2 -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DDEBUG
      299 CXX = clang++
      300 CXXCPP = clang++ -E
      301 CXXDEPMODE = depmode=gcc3
      302 CXXFLAGS = -O2 -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DDEBUG  -fopenmp

      After the modification:

      296 CFLAGS = -g –O0
      297 CPP = clang -E
      298 CPPFLAGS = -O0 -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DDEBUG
      299 CXX = clang++
      300 CXXCPP = clang++ -E
      301 CXXDEPMODE = depmode=gcc3
      302 CXXFLAGS = -O0 -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DDEBUG  -fopenmp

   3. Press Esc, type :wq!, and press Enter to save the file and exit.
8. Perform the compilation and installation.

   make & make install

9. Set the environment variables.

   export PATH=/path/to/install/ctffind/bin:$PATH