A well known bug (see e.g. end of Top Ten Reasons not to use the C shell) but you have to be aware of it:
If the last line of the C shell script does not have a new line character, it never gets exeucted!
vi and emacs allways (?) add the EOL at the end; namo seems to be a bad guy, so just add an empty line at the end to be on the save side.
Contributors to the KONWIHR-Workshop:
Notes:
More information and a registration form can be found at the official KONWIHR/EIHECS web page !
The collected presentations of the KONWIHR Results Workshop are available online as PDF file (10.5 MB)!
Just as an internal information for ourselves: mvapich and mvapich2 heavily depend on the underlaying Infiniband stack. Therefore, both MPI libraries had to be recompiled while changing from Voltaire IBHOST-3.4.5 stack to GridStack 4.1.5 (aka OFED-1.1).
As mvapich/mvapich2 are statically linked into executables, probably those applications have to be recompiled, too.
On the other side, Intel-MPI (which is the default on woody) is not affected, thus, most of the users’ applications will not require recompilation.
The RRZE versions of mvapich-0.9.8 and mvapich2-0.9.8 were now compiled using:
module load intel64-c/9.1.049, intel64-f/9.1.045 export CC=icc export CXX=icpc export F77=ifort export F90=ifort export ARCH=_EM64T_ export OPEN_IB_HOME=/usr/local/ofed export PREFIX=/apps/mvapich2/0.9.8-gridstack-4.1.5 ./make.mvapich[2].gen2
During ParCFD2007 there was a short course on lattice Boltzmann methods. The slides are made available on the tutorials web page of Parallel CFD 2007. Please come back and check for updates as some parts are still missing.
The next lattice Boltzmann short course will take place at the beginning of ICMMES 2007 taking place in Munich from June 16-20.
At both conferences, RRZE is in charge of the HPC aspects of implementing lattice Boltzmann methods.
some notes on using Intel Trace Collector (ITC/ITA)
Preliminary note: these are just some “random” notes for myself …
-tcollect switch
-g and set VT_PCTRACE to some value (either ON or the call level to be recorded (with optional skip levels); see ITC-RefGuide Sec. 3.8, p. 19/20 and 95VT_COUNTER variable has to be set accordingly; see ITC-RefGuide Sec. 3.10, p. 22VT_LOGFILE_NAME can be used to specify the name of the tracefilempiexec + taskset: code snippet to generate config file
We usually use Pete Wyckoff’s mpiexec to start MPI processes from within batch jobs. The following code snippet may be used to pin individual MPI processes to their CPU. A similar snippet could be used to allow round-robin distribution of the MPI processes …
[shell]
#!/bin/bash
# usage: run.sh 8 “0 2 4 6” ./a.out “-b -c”
# start a.out with arguments -b -c
# use 4 MPI processes
# pin processes to CPUs 0,2,4,6
NUMPROC=$1
TASKCPUS=”$2″
EXE=$3
ARGS=$4
TASKS=`echo $TASKCPUS | wc -w`
echo “running $NUMPROC MPI processes with $TASKS per node”
cat /dev/null > cfg.$PBS_JOBID
for node in `uniq $PBS_NODEFILE`; do
for cpu in $TASKCPUS; do
echo “$node : taskset -c $cpu $EXE $ARGS” >> cfg.$PBS_JOBID
NUMPROC=$((NUMPROC – 1))
if [ $NUMPROC -eq 0 ]; then
break 2
fi
done
done
mpiexec -comm pmi -kill -config cfg.$PBS_JOBID
[/shell]