Started by user tbouvet
[EnvInject] - Loading node environment variables.
Building on master in workspace /var/lib/jenkins/workspace/rmg-spp
executing script:
PATH="/sbin:/usr/sbin:/bin:/usr/bin"

set -v

# specify installation directory
export INSTDIR=~/rmg-spp
#rm -rf $INSTDIR
mkdir $INSTDIR
 
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/openbabel -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 ~/scratch/rmg-spp
mkdir -p ~/scratch/rmg-spp
cp /projects/bluewaters/benchmarking/SPP/rmg/test-0100-cpu/run.pbs ~/scratch/rmg-spp/run.pbs
cp /projects/bluewaters/benchmarking/SPP/rmg/test-0100-cpu/302waters.rmg_cpu ~/scratch/rmg-spp/
cd ~/scratch/rmg-spp
cat run.pbs | grep -v aprun > myrun.pbs
echo "time aprun -n 400 -N 4 -d 8 -cc numa_node  ~/rmg-spp/rmg-release_2.1/build-cpu/rmg-cpu 302waters.rmg_cpu" >> 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:java.net.NoRouteToHostException: No route to host
com.jcraft.jsch.JSchException: java.net.NoRouteToHostException: No route to host
	at com.jcraft.jsch.Util.createSocket(Util.java:341)
	at com.jcraft.jsch.Session.connect(Session.java:182)
	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$BuildExecution.build(Build.java:206)
	at hudson.model.Build$BuildExecution.doRun(Build.java:163)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
	at hudson.model.Run.execute(Run.java:1733)
	at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:405)
Caused by: java.net.NoRouteToHostException: No route to host
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:579)
	at java.net.Socket.connect(Socket.java:528)
	at java.net.Socket.<init>(Socket.java:425)
	at java.net.Socket.<init>(Socket.java:208)
	at com.jcraft.jsch.Util.createSocket(Util.java:335)
	... 14 more
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/rmg.realtime
Finished: FAILURE