SPIDER Compilation and Linking on Linux

CONTENTS

1. EXECUTABLES
2. COMPILING & LINKING
3. COMPILATION FLAGS
4. SHARED RUN-TIME LIBRARIES

• EXECUTABLES

  The SPIDER distribution may contain the following executable files in the spider/bin directory and Makefiles in the spider/src directory.

  In addition the spider/src/Makefile_samples directory contains a number of other sample Makefiles for AIX, legacy systems, and alternative compilers.

  All executables use: FFTW3.

  Precompiled executable	Optimal byte-order	Optimal Processor	Parallelization	Makefile	Compiler	Notes
  -none-	Big-endian	AMD Opteron	-	Makefile_linux	pgf90	32 bit OS
  spider_linux_mp_intel	Big-endian	Intel Xeon	OMP	Makefile_linux_mp_intel	pgf90
  spider_linux_mp_intel64	Big-endian	Intel Xeon 64	OMP	Makefile_linux_mp_intel64.ifort	Intel ifort	64 bit OS
  spider_linux_mp_opt64	Big-endian	AMD Opteron	OMP	Makefile_linux_mp_opt64	pgf90	64 bit OS
  -none-	Big-endian	AMD Opteron	MPI	Makefile_linux_mpi_opt64	pgf90	64 bit OS
  -none-	Little-endian	Compilation Host	-	Makefile_linux.gfort	gfortran	Compilation Host OS
  -none-	Little-endian	Compilation Host	OMP	Makefile_linux_mp_opt64.gfort	gfortran	Compilation Host OS

• Compiling and Linking

  In the documention that follows SPIDER_DIR refers to the location of SPIDER on your system and a '?' inside a filename refers to the suffix of one of the specific SPIDER distributions available e.g. _linux, _linux_mp, ... .

  The SPIDER_DIR/src directory or the SPIDER_DIR//src/Makefile_samples directory contains Makefiles listed above. These makefiles can be used to compile the source code, place the object code in an object library, link the object code with system object libraries, and create an executable binary file.

  1. Save copies of the original executables and libraries under an alternative name, e.g.

     cd SPIDER_DIR/bin
     mv spider? spider?_orig
     cd SPIDER_DIR/src
     mv spider?.a spider?_orig.a
     

  2. Edit Makefile? as necessary (e.g. change processor or optimization levels). (Make sure that any existing .mod files in your directory have been removed prior to compilation. These files are not compatible across different compilers.)
  3. Compile and /or link SPIDER using the provided Makefiles e.g.

     make -f Makefile?
     

     If the make operation fails or the new executable does not run contact us at the address below.
     

• Some Compilation and Linking flags (for PGI compiler)

  -DSP_IFC	cpp flag for Intel Fortran compilation
  -DSP_MP	cpp flag for OMP compilation
  -DSP_LIBFFTW3	cpp flag for FFTW3 compilation
  -O2	optimization level
  -g	compile/link for debug use
  -mp	for OMP parallel compilation & linking with PGI compiler
  -Openmp	for OMP parallel compilation & linking with Intel compiler
  -byteswapio	flag for Big-endian byte order on IA32 or IA64 with PGI compiler

• Libraries

  -lfftw3f	FFTW3 library
  -lfftw3f_threads	FFTW3 threaded library
  -lpthreads	OMP thread library for Intel compiler
  -lm	Math library for both PGI & Intel compilers

  Dynamic library dependencies

  To see dynamic library dependencies when not linking code statically use ldd e.g.:
  ldd spider_linux_mp

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Source file: compile-linux.html     Updated: 20 Feb. 2025     ArDean Leith