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-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x00.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x01.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x02.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x03.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x04.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x05.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x06.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x07.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x08.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x09.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x10.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x11.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x12.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x13.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x14.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x15.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x16.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x17.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x18.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x19.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x20.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x21.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x22.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x23.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x24.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x25.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x26.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x27.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x28.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x29.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x30.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x31.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x33.tcl
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x00
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x01
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x02
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x03
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x04
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x05
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x06
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x07
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x08
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x09
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x10
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x11
-- Up-to-da 
# install CPU-version of RMG
cd $INSTDIR
wget http://downloads.sourceforge.net/project/rmgdft/Releases/2.1/Sources/rmg-release_2.1.tar.gz
--2017-02-14 13:38:38--  http://downloads.sourceforge.net/project/rmgdft/Releases/2.1/Sources/rmg-release_2.1.tar.gz
Resolving downloads.sourceforge.net... 216.34.181.59
Connecting to downloads.sourceforge.net|216.34.181.59|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://svwh.dl.sourceforge.net/project/rmgdft/Releases/2.1/Sources/rmg-release_2.1.tar.gz [following]
--2017-02-14 13:38:38--  https://svwh.dl.sourceforge.net/project/rmgdft/Releases/2.1/Sources/rmg-release_2.1.tar.gz
Resolving svwh.dl.sourceforge.net... 72.5.72.15, 2606:c680:0:b:3830:34ff:fe66:6663
Connecting to svwh.dl.sourceforge.net|72.5.72.15|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 42363399 (40M) [application/x-gzip]
Saving to: `rmg-release_2.1.tar.gz.10'

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-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x26
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x27
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x28
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x29
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x30
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x31
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/x33
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/pltcl_standard_examples.in
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/tclsh_standard_examples.in
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/CMakeLists.txt
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/plplot5.11.1/examples/tcl/mktclIndex
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/man/man1/pltek.1
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/man/man1/plserver.1
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/man/man1/pltcl.1
-- Up-to-date: /u/system/bwjenkins/rmg-spp/plplot.git/install/share/doc/plplot/README.pkg-config
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2017-02-14 13:39:52 (560 KB/s) - `rmg-release_2.1.tar.gz.10' saved [42363399/42363399]

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cd rmg-release_2.1
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mkdir: cannot create directory `build-cpu': File exists
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rmg-release_2.1/Headers/my_scalapack.h
rmg-release_2.1/Headers/Plots.h
rmg-release_2.1/Headers/RmgGemm.h
rmg-release_2.1/Headers/init_var.h
rmg-release_2.1/Headers/CheckValue.h
rmg-release_2.1/Headers/svn-commit.tmp
rmg-release_2.1/Headers/Solvers.h
rmg-release_2.1/Headers/rmg_control.h
rmg-release_2.1/Headers/svnrev.h
rmg-release_2.1/Headers/BesselRoots.h
rmg-release_2.1/Headers/RmgShm.h
rmg-release_2.1/Headers/Subdiag.h
rmg-release_2.1/Headers/mg.h
rmg-release_2.1/Headers/pe_control.h
rmg-release_2.1/Headers/rmgtypedefs.h
rmg-release_2.1/Headers/input.h
rmg-release_2.1/Headers/pack_3d.h
rmg-release_2.1/Headers/Pw.h
rmg-release_2.1/Headers/RmgException.h
rmg-release_2.1/Headers/cnpy.h
rmg-release_2.1/Headers/BesselRoots.h.sav
rmg-release_2.1/Headers/blas.h
rmg-release_2.1/Headers/RmgInputFile.h
rmg-release_2.1/Headers/Atomic.h
rmg-release_2.1/Headers/rmgthreads.h
rmg-release_2.1/Headers/grid.h
rmg-release_2.1/Headers/lbfgs.h
rmg-release_2.1/Headers/common_prototypes.h
rmg-release_2.1/Headers/macros.h
rmg-release_2.1/Headers/make_conf.h
rmg-release_2.1/Headers/GpuAlloc.h
rmg-release_2.1/Headers/InternalPseudo.h
rmg-release_2.1/Headers/common_prototypes1.h
rmg-release_2.1/Headers/State.h
rmg-release_2.1/Headers/main.h
rmg-release_2.1/Headers/rmg_alloc.h
rmg-release_2.1/Headers/const.h
rmg-release_2.1/Headers/typedefs.h
rmg-release_2.1/Headers/remap_3d.h
rmg-release_2.1/Headers/InputOpts.h
rmg-release_2.1/Headers/Scalapack.h
rmg-release_2.1/Headers/RmgThread.h
rmg-release_2.1/Headers/MapElements.h
rmg-release_2.1/Headers/AtomicInterpolate.h
rmg-release_2.1/Headers/params.h
-- Boost version: 1.53.0
-- Found the following Boost libraries:
--   thread
--   system
--   iostreams
--   program_options
--   filesystem
CMake Warning (dev) at SubprojectIncludes/CMakeLists.txt.rmg.inc:5 (add_dependencies):
  Policy CMP0046 is not set: Error on non-existent dependency in
  add_dependencies.  Run "cmake --help-policy CMP0046" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  The dependency target "libspg" of target "rmg-cpu" does not exist.
Call Stack (most recent call first):
  CMakeLists.txt:589 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Configuring done
nice make -j12 rmg-cpu
-- Generating done
-- Build files have been written to: /u/system/bwjenkins/rmg-spp/rmg-release_2.1/build-cpu
[  0%] [  1%] Built target MG
Built target InternalPseudo
[  5%] Built target XC1
[  7%] Built target Force
[  8%] Built target RMG_Spin
[ 17%] [ 20%] Built target RmgLib
Built target XC
[ 24%] Built target RMG_Subdiag
[ 29%] Built target Finite_diff
[ 34%] Built target Input
[ 40%] Built target RMG_Spin_XC
[ 49%] Built target US_PP
[ 72%] Built target Misc
[ 98%] Built target RMG_Common

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/
cp /projects/bluewaters/benchmarking/SPP/rmg/small/* ~/scratch/rmg-spp/
[100%] Built target rmg-cpu
cd ~/scratch/rmg-spp
cp ~/rmg-spp/rmg-release_2.1/build-cpu/rmg-cpu ./
cat run.pbs | sed -e "s/aprun/time aprun/g"  > myrun.pbs

cat -n myrun.pbs

MYJOBID=`qsub myrun.pbs`
qsub myrun.pbs
     1	#!/bin/bash
     2	#PBS -N zsmall
     3	#PBS -j oe
     4	#PBS -l walltime=2:00:00
     5	#PBS -l nodes=20:ppn=32:xe
     6	
     7	source /opt/modules/default/init/bash
     8	module swap PrgEnv-cray PrgEnv-gnu
     9	module load boost
    10	module unload darshan
    11	module list
    12	
    13	cd $PBS_O_WORKDIR
    14	
    15	export MPICH_MAX_THREAD_SAFETY=serialized
    16	export OMP_WAIT_POLICY=passive
    17	export MPICH_ENV_DISPLAY=1
    18	ulimit -a
    19	export MPICH_GNI_MBOX_PLACEMENT=nic
    20	export MPICH_GNI_RDMA_THRESHOLD=1024
    21	export MPICH_GNI_NUM_BUFS=512
    22	export MPICH_GNI_MAX_EAGER_MSG_SIZE=65536
    23	
    24	export OMP_NUM_THREADS=1
    25	time aprun -n 640 -N 32 rmg-cpu 302waters.rmg_cpu
    26	
Job submitted to account: jnc
echo MYJOBID=$MYJOBID
~arnoldg/ior/wait_for.sh $MYJOBID
MYJOBID=6148331.bw
=== RUNNING /u/staff/arnoldg/ior/wait_for.sh ===
Tue Feb 14 13:40:19 CST 2017: waiting for 6148331.bw to finish
Tue Feb 14 13:45:19 CST 2017: waiting for 6148331.bw to finish
Tue Feb 14 13:50:19 CST 2017: waiting for 6148331.bw to finish
Tue Feb 14 13:55:19 CST 2017: waiting for 6148331.bw to finish
Tue Feb 14 14:00:20 CST 2017: waiting for 6148331.bw to finish
qstat: Unknown Job Id Error 6148331.bw
tail *.log > ~/rmg-spp/rmg.logtail.txt
tail: cannot open `*.log' for reading: No such file or directory

grep "real" z302water_cpu100.o*
grep: z302water_cpu100.o*: No such file or directory
MYREALTIME=`egrep "real\s" z302water_cpu100.o* | cut -dl -f2 | cut -dm -f1` 
egrep "real\s" z302water_cpu100.o* | cut -dl -f2 | cut -dm -f1
egrep: z302water_cpu100.o*: No such file or directory
echo "YVALUE= $MYREALTIME" > ~/rmg-spp/rmg.realtime
cat -n ~/rmg-spp/rmg.realtime
6148331.bw finished
     1	YVALUE= 
[SSH] exit-status: 0
[rmg-spp-newpe] $ /bin/sh -xe /tmp/hudson5324226827270353638.sh
+ scp 'BW_REMOTE:~/rmg-spp/*.txt' /var/lib/jenkins/workspace/rmg-spp-newpe

Access by OTP or Two Factor Certificate Authority only.
Use myproxy-logon -s tfca.ncsa.illinois.edu -p 7512 for gsissh access.
gsissh or ssh -o PreferredAuthentications=keyboard-interactive for otp access.

Blue Water Admin Team

+ scp 'BW_REMOTE:~/rmg-spp/rmg.realtime' /var/lib/jenkins/workspace/rmg-spp-newpe

Access by OTP or Two Factor Certificate Authority only.
Use myproxy-logon -s tfca.ncsa.illinois.edu -p 7512 for gsissh access.
gsissh or ssh -o PreferredAuthentications=keyboard-interactive for otp access.

Blue Water Admin Team

Recording plot data
Saving plot series data from: /var/lib/jenkins/workspace/rmg-spp-newpe/rmg.realtime
Finished: SUCCESS