Difference between revisions of "CHARMM"
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[[Category:Applications]] | [[Category:Applications]] | ||
| + | |||
| + | ==Background== | ||
==Building CHARMM== | ==Building CHARMM== | ||
| − | 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>' | ||
| + | |||
| + | <pre> | ||
| + | %> 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 | ||
| + | ATOMID | ||
| + | CHARMM => ATOMID | ||
| + | CHARMM => CMAPSPI | ||
| + | CHARMM => GENIC::SUB600 | ||
| + | CHARMM => GETRES | ||
| + | CHARMM => GETSEG | ||
| + | CHARMM => HYDROG | ||
| + | CHARMM => INITIA | ||
| + | CHARMM => LONE | ||
| + | CHARMM => MATOM | ||
| + | CHARMM => WRNDIE | ||
| + | CMAPSPI | ||
| + | CNVTUC | ||
| + | EQST | ||
| + | EQSTA | ||
| + | GENIC::SUB600 | ||
| + | GETRES | ||
| + | GETSEG | ||
| + | HYDROG | ||
| + | INITIA | ||
| + | LONE | ||
| + | MATOM | ||
| + | TRIME | ||
| + | WRNDIE | ||
| + | |||
| + | # new routines | ||
| + | CHARMM => EQSTWC | ||
| + | CHARMM => EQSTWC::SUB10 | ||
| + | EQSTWC | ||
| + | EQSTWC::SUB10 | ||
| + | MPI_Comm_rank() | ||
| + | MPI_Comm_size() | ||
| + | PMEUTIL::XY_ZX_TR_RCV | ||
| + | PMEUTIL::ZX_TRANS_RECV | ||
| + | |||
| + | |||
| + | END_EXCLUDE_LIST | ||
| + | </pre> | ||
| + | |||
| + | 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. | ||
Latest revision as of 21:55, 27 February 2012
Background
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 ATOMID CHARMM => ATOMID CHARMM => CMAPSPI CHARMM => GENIC::SUB600 CHARMM => GETRES CHARMM => GETSEG CHARMM => HYDROG CHARMM => INITIA CHARMM => LONE CHARMM => MATOM CHARMM => WRNDIE CMAPSPI CNVTUC EQST EQSTA GENIC::SUB600 GETRES GETSEG HYDROG INITIA LONE MATOM TRIME WRNDIE # new routines CHARMM => EQSTWC CHARMM => EQSTWC::SUB10 EQSTWC EQSTWC::SUB10 MPI_Comm_rank() MPI_Comm_size() PMEUTIL::XY_ZX_TR_RCV PMEUTIL::ZX_TRANS_RECV 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.
