SPIDER Compilation and Linking on Linux and AIX

CONTENTS

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

• EXECUTABLES

  Executable	Optimal byte-order	Optimal Processor	Fourier Library	Makefile	Compiler	Notes
  spider_linux_mp	SGI	AMD	SPIDER	Makefile_linux_mp	pgf90
  spider_linux_mp_opt64	SGI	AMD Opteron	FFTW	Makefile_linux_mp_opt64	pgf90	64 bit OS
  spider_linux_mp_intel64	SGI	Intel 64	FFTW	Makefile_linux_mp_intel64	pgf90	64 bit OS
  spider_linux_mp	SGI	AMD	FFTW	Makefile_linux_mp	pgf90
  spider_linux_mp_intel	SGI	Intel	FFTW	Makefile_linux_mp_intel	pgf90
  -	SGI	Intel	FFTW	Makefile_linux_ifc	ifc
  -	SGI	Intel P4	FFTW	Makefile_linux_ifc_p4	ifc
  -	SGI	2xIntel	FFTW	Makefile_linux_mp_ifc	ifc
  -	SGI	2xIntel P4	FFTW	Makefile_linux_mp_ifc_p4	ifc
  spider_linux_mp_altix	SGI	Intel Itanium2	FFTW	Makefile_linux_mp_altix	ifort
  spider_ibm_mpi	SGI	IBM SP3	FFTW	Makefile_linux_mp_ibm	ifort
  spider_ibm_mpi	SGI	IBM SP3	FFTW	Makefile_ibm_mpi	ifort	MPI

• 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 directory: SPIDER_DIR/src 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).
  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.
     
     
  4. Note: The archive ar command in the Makefile will use a lot of space in your TMPDIR. If you get a message about no space left on your device you can redefine TMPDIR to a directory that has space (e.g.):
     setenv TMPDIR /usr/tmp
     
     

• Some Compilation and Linking flags

  -DSP_LINUX	cpp flag for LINUX compilation
  -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	comile/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	FFTW library
  -lfftw3f_threads	FFTW threaded library
  -lpthreads	OMP thread library for Intel compiler
  -lm	math library for both PGI & Intel compilers

  
  
  

  static and dynamic library dependencies

  To see library dependencies use ldd e.g.:
  ldd spider_linux_mp

• BUGS, SUGGESTIONS

  In the event that you have questions or wish to report bugs, please send us complete info on what you are trying to do, including any error messages.

  Send such info to:

  ArDean Leith
  Wadsworth Labs, P.O. Box 509, Albany, New York 12201
  phone: 518-486-5604
  fax: 518-474-7992
  email: spider@wadsworth.org
  WWW: http://www.wadsworth.org/spider_doc

Source file: compile-linux.html     Updated: 13 may. 2009     ArDean Leith