Difference between revisions of "CHARMM"
| Line 10: | Line 10: | ||
2. CHARMM finds MPI via environment variables so: | 2. CHARMM finds MPI via environment variables so: | ||
| − | %> export MPI_INCLUDE=<mpi include dir> | + | %> export MPI_INCLUDE=<mpi include dir> |
| − | %> export MPI_LIB=<mpi include dir> | + | %> export MPI_LIB=<mpi include dir> |
3. I started with source based instrumentation (via PDT), notice the use of a | 3. I started with source based instrumentation (via PDT), notice the use of a | ||
selective instrumentation file to tune instrumentation: | selective instrumentation file to tune instrumentation: | ||
| − | %> export TAU_MAKEFILE=<tau home>/<arch>/lib/Makefile.tau-mpi-pdt | + | %> export TAU_MAKEFILE=<tau home>/<arch>/lib/Makefile.tau-mpi-pdt |
| − | %> export TAU_OPTIONS='-optKeepFiles -optVerbose -optTauSelectFile=<full path to select.tau>' | + | %> export TAU_OPTIONS='-optKeepFiles -optVerbose -optTauSelectFile=<full path to select.tau>' |
| − | %> cat select.tau | + | %> cat select.tau |
| + | <pre> | ||
BEGIN_EXCLUDE_LIST | BEGIN_EXCLUDE_LIST | ||
| Line 49: | Line 50: | ||
END_EXCLUDE_LIST | END_EXCLUDE_LIST | ||
| − | + | </pre> | |
4. Now I need to override the default mpif90 compiler with TAU's tau_f90.sh | 4. Now I need to override the default mpif90 compiler with TAU's tau_f90.sh | ||
| Line 56: | Line 57: | ||
TAU): | TAU): | ||
| − | %> sed -i 's/mpif90/tau_f90.sh/g' install.com | + | %> sed -i 's/mpif90/tau_f90.sh/g' install.com |
and compile with the xlarge version with MPI: | and compile with the xlarge version with MPI: | ||
| − | %> ./install.com gnu xlarge NOLOG M | + | %> ./install.com gnu xlarge NOLOG M |
Now when you run a simulation you will get TAU profile.* files in your current directory. | Now when you run a simulation you will get TAU profile.* files in your current directory. | ||
Revision as of 22:30, 19 August 2009
Building CHARMM
Instructions for instrumenting CHARMM with TAU:
1. My gfortran compiler had problems with some WRITE commands in source/nbond/enbips.src so I commented out line 3288 and 3301.
2. CHARMM finds MPI via environment variables so:
%> export MPI_INCLUDE=<mpi include dir> %> export MPI_LIB=<mpi include dir>
3. I started with source based instrumentation (via PDT), notice the use of a selective instrumentation file to tune instrumentation:
%> export TAU_MAKEFILE=<tau home>/<arch>/lib/Makefile.tau-mpi-pdt %> export TAU_OPTIONS='-optKeepFiles -optVerbose -optTauSelectFile=<full path to select.tau>'
%> cat select.tau
BEGIN_EXCLUDE_LIST # omit this routine, TAU has problems this some CONTINUE statements MASTER.0.TIMRB::TIMRB # omit these low level routine that contribute to excessive instrumentation # overhead ERFCD EXCH5 GAUSSI MPI_Irecv() MPI_Isend() NINDX OLDRANDOM ORDER5 PATOM PMEUTIL::CFFTB PMEUTIL::CFFTB1 PMEUTIL::CFFTF PMEUTIL::CFFTF1 PMEUTIL::FILL_BSPLINE PMEUTIL::PASSB2 PMEUTIL::PASSB4 PMEUTIL::PASSF2 PMEUTIL::PASSF4 PROCATOMS RANDOM END_EXCLUDE_LIST
4. Now I need to override the default mpif90 compiler with TAU's tau_f90.sh wrapper script. The easiest way to do this was with global replace in install.com (you may want to backup this file so you can compile CHARMM without TAU):
%> sed -i 's/mpif90/tau_f90.sh/g' install.com
and compile with the xlarge version with MPI:
%> ./install.com gnu xlarge NOLOG M
Now when you run a simulation you will get TAU profile.* files in your current directory.
