SPIDER Compilation and Linking on GNU/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_mpfftw_opt64	SGI	AMD Opteron	FFTW	Makefile_linux_mpfftw_opt64	pgf90	64 bit OS
  spider_linux_mpfftw	SGI	AMD	FFTW	Makefile_linux_mpfftw	pgf90
  spider_linux_mpfftw_intel	SGI	Intel	FFTW	Makefile_linux_mpfftw_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_mpfftw_altix	SGI	Intel Itanium2	FFTW	Makefile_linux_mpfftw_altix	ifort
  spider_ibm_mpi	SGI	IBM SP3	FFTW	Makefile_linux_mpfftw_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_mpfftw, ... .

  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 being left on your device I suggest you 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_LIBFFTW	cpp flag for FFTW compilation
  -DSP_LIBFFTWMP	cpp flag for FFTW use with OMP compilation (not recommended)
  -O2	optimization level
  -g	for debug use
  -mp	for OMP parallel compilation & linking
  -Openmp	for OMP parallel compilation & linking with Intel compiler
  -Openmp	cpp flag for MPI parallel compilation
  -byteswapio	for SGI byte order on IA32 or IA64

• Shared Run-Time Libraries

  -lsrfftw	FFTW library
  -lsfftw	FFTW library
  -lsrfftw_threads	FFTW OMP library
  -lsfftw_threads	FFTW OMP library
  -lpthreads	OMP thread library
  -lm	math library

  
  
  

  static and dynamic library dependencies

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

• 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: 20 Sept. 2006     ArDean Leith