Console Output

Started by user arnoldg
Building on master in workspace /var/lib/jenkins/workspace/rmg-spp-newpe
executing script:
PATH="/sw/tools/bin:/sw/tools/bin:$PATH"
HOME="/var/lib/jenkins"

set -v

# specify installation directory
export INSTDIR=/u/system/bwjenkins/rmg-spp
#rm -rf $INSTDIR
mkdir $INSTDIR
 
# begin newpe testing
module unload cce cray-mpich
module load cce/8.5.5
module load cray-mpich/7.5.0
# end newpe testing
 
module swap PrgEnv-cray PrgEnv-gnu
module swap gcc gcc/4.9.3
module load boost
module load cmake/3.1.3
module load fftw

export CRAYPE_LINK_TYPE=dynamic
export CRAY_ADD_RPATH=yes
 
# install openbabel library
cd $INSTDIR
wget http://downloads.sourceforge.net/project/openbabel/openbabel/2.3.2/openbabel-2.3.2.tar.gz
tar zxvf openbabel-2.3.2.tar.gz
cd openbabel-2.3.2/
mkdir build
cd build/
cmake -DCMAKE_INSTALL_PREFIX=$INSTDIR/openbabel-2.3.2/install ..
nice make -j8
make install
 
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$INSTDIR/openbabel-2.3.2/install/lib
 
export CC=cc
export CXX=CC
export FC=ftn
 
# install plplot library
cd $INSTDIR
git clone git://git.code.sf.net/p/plplot/plplot plplot.git
cd plplot.git/
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=$INSTDIR/plplot.git/install ..
make
make install
 
# install CPU-version of RMG
cd $INSTDIR
wget http://downloads.sourceforge.net/project/rmgdft/Releases/2.1/Sources/rmg-release_2.1.tar.gz
tar zxvf rmg-release_2.1.tar.gz
cd rmg-release_2.1
mkdir build-cpu; cd build-cpu
cmake -DOPENBABEL_INCLUDES=$INSTDIR/openbabel-2.3.2/install/include/openbabel-2.0 -DOPENBABEL_LIBRARIES=$INSTDIR/openbabel-2.3.2/install/lib/libopenbabel.so.4.0.2 -DPLplot_INCLUDE_DIR=$INSTDIR/plplot.git/install/include -DPLplot_cxx_LIBRARY=$INSTDIR/plplot.git/install/lib/libplplotcxx.so -DPLplot_LIBRARY=$INSTDIR/plplot.git/install/lib/libplplot.so ..
nice make -j12 rmg-cpu

rm -rf /u/system/bwjenkins/scratch/rmg-spp
mkdir -p /u/system/bwjenkins/scratch/rmg-spp
#cp /projects/bluewaters/benchmarking/SPP/rmg/test-0100-cpu/run.pbs /u/system/bwjenkins/scratch/rmg-spp/run.pbs
#cp /projects/bluewaters/benchmarking/SPP/rmg/test-0100-cpu/302waters.rmg_cpu /u/system/bwjenkins/scratch/rmg-spp/
cp /projects/bluewaters/benchmarking/SPP/rmg/small/* /u/system/bwjenkins/scratch/rmg-spp/
cd /u/system/bwjenkins/scratch/rmg-spp
cp /u/system/bwjenkins/rmg-spp/rmg-release_2.1/build-cpu/rmg-cpu ./
cat run.pbs | sed -e "s/aprun/time aprun/g"  > myrunA.pbs
cat myrunA.pbs | sed -e "s/OMP_NUM_THREADS=1/OM_NUM_THREADS=1\nexport LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:\$HOME\/rmg-spp\/openbabel-2.3.2\/install\/lib/g" > myrun.pbs

cat -n myrun.pbs

MYJOBID=`qsub myrun.pbs`
echo MYJOBID=$MYJOBID
~arnoldg/ior/wait_for.sh $MYJOBID
tail *.log > ~/rmg-spp/rmg.logtail.txt

grep "real" z302water_cpu100.o*
MYREALTIME=`egrep "real\s" z302water_cpu100.o* | cut -dl -f2 | cut -dm -f1` 
echo "YVALUE= $MYREALTIME" > ~/rmg-spp/rmg.realtime
cat -n ~/rmg-spp/rmg.realtime
[SSH] Exception:verify: false
com.jcraft.jsch.JSchException: verify: false
	at com.jcraft.jsch.Session.connect(Session.java:295)
	at com.jcraft.jsch.Session.connect(Session.java:150)
	at org.jvnet.hudson.plugins.SSHSite.createSession(SSHSite.java:141)
	at org.jvnet.hudson.plugins.SSHSite.executeCommand(SSHSite.java:151)
	at org.jvnet.hudson.plugins.SSHBuilder.perform(SSHBuilder.java:60)
	at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
	at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:779)
	at hudson.model.Build$BuildExecution.build(Build.java:205)
	at hudson.model.Build$BuildExecution.doRun(Build.java:162)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
	at hudson.model.Run.execute(Run.java:1728)
	at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
	at hudson.model.ResourceController.execute(ResourceController.java:98)
	at hudson.model.Executor.run(Executor.java:404)
Build step 'Execute shell script on remote host using ssh' marked build as failure
Recording plot data
Saving plot series data from: /var/lib/jenkins/workspace/rmg-spp-newpe/rmg.realtime
Finished: FAILURE