Galaxy Software

Software Issues

Linux Programming

• Optimization flags.

GCC compiler (gcc, g++)

• -O2 -fomit-frame-pointer -funroll-loops -malign-double
• PGI compiler (pgcc, pgCC)

  -O2 -Mvect -tp p6

• Optimized libraries

  BLAS, FFT, etc.

• Common problems with floating point operations.

  The way to reset the precision of FPU operations is

  #ifdef __linux__ __setfpucw( (unsigned short)((_FPU_DEFAULT & 0xF0FF) | _FPU_DOUBLE) ); #endif

• Data Display Debugger.
  
  
• Several benchmarks.

  User's Guide for mpich (A 48-page PS file)

• MPI in Practice: A Slide Show (A 147-page PS file)
• A roundup of advanced LAM tools. Includes an overview and an example of a simple project.
• Communication primitives in MPI and on Paragon
  

Operation	MPI	Paragon
Initialization	MPI_Init()	-
Shutdown	MPI_Finalize()	-
Blocking Comm.	MPI_Send(), MPI_Recv()	csend(), crecv()
Non-blocking Comm.	MPI_ISend(), MPI_IRecv()	isend(), irecv()
Asynchronous Comm.	none	hrecv()
Collective Comm.	MPI_Scatter(), MPI_Gather(),  MPI_Reduce()
		none