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Started by user Greg Bauer
Building on master in workspace /var/lib/jenkins/workspace/qmcpack-jyc
executing script:


module list
rm -rf qmcpack-spp
tar xzf ~arnoldg/qmcpack_spp_20180222_jyc.tgz
cd qmcpack-spp/qmcpack-3.2.0/build
module unload PrgEnv-cray
module use /u/vendor/cray/dalton/modulefiles
rm -rf /tmp/*
./build_script_cpu_complex
cd ../../runs/cpu_4

MYJOBID=`qsub bw.pbs`
echo MYJOBID=$MYJOBID
~arnoldg/ior/wait_for.sh $MYJOBID

MYREAL=`grep real qmcpack.err | cut -d' ' -f2`
echo MYREAL=$MYREAL
echo YVALUE=$MYREAL > ~/qmcpack-spp/realtime.txt
./energy.pl gr4x4x1.p400x8.s001.scalar.dat 0 | grep LocalEnergy | awk '{print $3}'
Currently Loaded Modulefiles:
  1) modules/3.2.10.5
  2) nodestat/2.2-1.0502.60539.1.31.gem
  3) sdb/1.1-1.0502.63652.4.27.gem
  4) alps/5.2.4-2.0502.9774.31.12.gem
  5) lustre-cray_gem_s/2.5_3.0.101_0.46.1_1.0502.8871.38.1-1.0502.21728.74.1
  6) udreg/2.3.2-1.0502.10518.2.17.gem
  7) ugni/6.0-1.0502.10863.8.28.gem
  8) gni-headers/4.0-1.0502.10859.9.19.gem
  9) dmapp/7.0.1-1.0502.11080.8.74.gem
 10) xpmem/0.1-2.0502.64982.7.19.gem
 11) hss-llm/7.2.0
 12) Base-opts/1.0.2-1.0502.60680.2.4.gem
 13) cce/8.5.8
 14) craype-network-gemini
 15) craype/2.5.9
 16) cray-libsci/16.11.1
 17) pmi/5.0.11
 18) rca/1.0.0-2.0502.60530.1.63.gem
 19) atp/2.1.0
 20) PrgEnv-cray/5.2.82
 21) moab/9.1.2.h2-sles11
 22) torque/6.0.4
 23) craype-interlagos
 24) cray-mpich/7.5.3
 25) java/jdk1.8.0_51
 26) globus/5.2.5
 27) gsissh/6.2p2
 28) xalt/0.7.6.local
 29) scripts
 30) OpenSSL/1.0.2m
 31) cURL/7.59.0
 32) git/2.17.0
 33) wget/1.19.4
 34) user-paths
 35) gnuplot/5.0.5
 36) darshan/3.1.3
rm: cannot remove `/tmp/DzTx9oWmwT': Permission denied
rm: cannot remove `/tmp/intelremotemonagent.21412.log': Operation not permitted
rm: cannot remove `/tmp/stunnel.log': Operation not permitted
rm: cannot remove `/tmp/trqauthd-unix': Operation not permitted
rm: cannot remove `/tmp/VElO11Yyq3': Permission denied
Currently Loaded Modulefiles:
  1) modules/3.2.10.5
  2) nodestat/2.2-1.0502.60539.1.31.gem
  3) sdb/1.1-1.0502.63652.4.27.gem
  4) alps/5.2.4-2.0502.9774.31.12.gem
  5) lustre-cray_gem_s/2.5_3.0.101_0.46.1_1.0502.8871.38.1-1.0502.21728.74.1
  6) udreg/2.3.2-1.0502.10518.2.17.gem
  7) ugni/6.0-1.0502.10863.8.28.gem
  8) gni-headers/4.0-1.0502.10859.9.19.gem
  9) dmapp/7.0.1-1.0502.11080.8.74.gem
 10) xpmem/0.1-2.0502.64982.7.19.gem
 11) hss-llm/7.2.0
 12) Base-opts/1.0.2-1.0502.60680.2.4.gem
 13) craype-network-gemini
 14) craype-interlagos
 15) craype/2.5.15
 16) moab/9.1.2.h2-sles11
 17) torque/6.0.4
 18) cray-mpich/7.7.1
 19) java/jdk1.8.0_51
 20) globus/5.2.5
 21) gsissh/6.2p2
 22) xalt/0.7.6.local
 23) scripts
 24) OpenSSL/1.0.2m
 25) cURL/7.59.0
 26) git/2.17.0
 27) wget/1.19.4
 28) user-paths
 29) gnuplot/5.0.5
 30) darshan/3.1.3
 31) gcc/7.3.0
 32) cray-libsci/18.04.1
 33) pmi/5.0.14
 34) atp/2.1.2
 35) PrgEnv/gnu-7.3.0-cuda-9.1
 36) cray-hdf5/1.10.0.1
 37) fftw/3.3.4.11
 38) boost/1.53.0
 39) cmake/3.1.3
 40) craype-hugepages2M
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Check for working C compiler: /opt/cray/craype/default/bin/cc
-- Check for working C compiler: /opt/cray/craype/default/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /opt/cray/craype/default/bin/CC
-- Check for working CXX compiler: /opt/cray/craype/default/bin/CC -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
   Base precision = double
   Full precision = double
-- Detecting CXX compile features - done
-- QMC_SYMLINK_TEST_FILES = TRUE.  Using symbolic links for large test files may cause test failures if the build is installed on a separate filesystem from the source.  For example, Titan at OLCF.
-- CMAKE_BUILD_TYPE is 
-- defining the float point precision
-- Looking for sincos
-- Looking for sincos - found
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for dlfcn.h
-- Looking for dlfcn.h - found
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Looking for memory.h
-- Looking for memory.h - found
-- Looking for sys/stat.h
-- Looking for sys/stat.h - found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Found Git: /sw/EasyBuild/software/git/2.17.0/bin/git (found version "2.17.0") 
-- Using /mnt/abc/u/system/bwjenkins/qmcpack-spp/qmcpack-3.2.0/config/attic/BWGNU.cmake toolchain 
-- Performing Test CXX_COMPILER_SUPPORT_CXX11
-- Performing Test CXX_COMPILER_SUPPORT_CXX11 - Success
-- MPI runner is mpirun
-- CXX compiler flags: -std=c++11 
-- CC  compiler flags: 
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE  
-- FFTW_INCLUDE_DIR=/opt/cray/fftw/default/interlagos/include
-- FFTW_LIBRARIES=/opt/cray/fftw/default/interlagos/lib/libfftw3.a
-- Found FFTW
-- Found ZLIB: /usr/lib64/libz.a (found version "1.2.7") 
-- Trying libxml2 via LIBXML2_HOME
-- LIBXML2_INCLUDE_DIR=/usr/include/libxml2/libxml
-- LIBXML2_LIBRARIES=/usr/lib64/libxml2.a
-- Libxml2 found by FindLibxml2QMC
-- Found HDF5: /opt/cray/hdf5/default/GNU/4.9/lib/libhdf5.a  
-- Using HDF5 non-scalable serial I/O due to the lack of library support for parallel
-- Boost version: 1.53.0
-- Setting Boost_INCLUDE_DIRS=/sw/xe/boost/default/sles11.1_gnu4.8.2/include
-- Disabling CUDA
-- Ready to build qmcpack
Adding tests for QMCPACK
Skipping all gaussian basis tests because they are not supported by complex build (QMC_COMPLEX=1)
Adding test short-LiH_solid_1x1x1_pp-gamma-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-gamma-drift-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-x-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-x-drift-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-arb-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-arb-drift-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-gamma-dmc-hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-x-dmc-hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-arb-dmc-hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-gamma-dmcnl-hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-x-dmcnl-hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-arb-dmcnl-hf_noj-1-16
Adding test short-bccH_1x1x1_ae-vmc_sdj-1-16
Adding test short-bccH_1x1x1_ae-dmc_sdj-1-16
Adding test short-bccH_1x1x1_ae-vmc-all-nodrift_sdj-1-16
Adding test short-bccH_1x1x1_ae-vmc-all_sdj-1-16
Adding test short-bccH_1x1x1_ae-dmc-all_sdj-1-16
Adding test short-bccH_1x1x1_ae-csvmc-pbyp-nodrift_sdj-16-1
Adding test short-bccH_1x1x1_ae-csvmc-all-nodrift_sdj-16-1
Adding test short-bccH_1x1x1_ae-csvmc-all_sdj-16-1
Adding test short-bccH_1x1x1_ae-rmc_sdj-1-16
Adding test short-bccH_1x1x1_ae-rmc_sdj-4-4
Adding test short-bccH_1x1x1_ae-vmc_sdj-pw-1-16
Adding test short-diamondC_1x1x1_pp-vmc_sdj-1-16
Adding test short-diamondC_1x1x1_pp-vmc_sdj-meshf-1-16
Adding test short-diamondC_1x1x1_pp-opt_sdj-1-16
Adding test short-diamondC_1x1x1_pp-dmc_sdj-1-16
Adding test short-diamondC_2x1x1_pp-vmc_sdj-1-16
Adding test short-diamondC_2x1x1_pp-dmc_sdj-1-16
Adding test short-hcpBe_1x1x1_pp-vmc_sdj-1-16
Adding test short-monoO_1x1x1_pp-vmc_sdj-1-16
Adding test long-bccH_1x1x1_ae-vmc_sdj-1-16
Adding test long-bccH_1x1x1_ae-dmc_sdj-1-16
Adding test long-bccH_1x1x1_ae-rmc_sdj-1-16
Adding test long-diamondC_1x1x1_pp-vmc_sdj-1-16
Adding test long-diamondC_1x1x1_pp-vmc_sdj-meshf-1-16
Adding test long-diamondC_1x1x1_pp-dmc_sdj-1-16
Adding test long-diamondC_2x1x1_pp-vmc_sdj-1-16
Adding test long-diamondC_2x1x1_pp-dmc_sdj-1-16
Adding test long-hcpBe_1x1x1_pp-vmc_sdj-1-16
Adding test long-monoO_1x1x1_pp-vmc_sdj-1-16
Adding estimator tests for QMCPACK
Missing python module h5py, not adding test estimator-skinetic
Missing python module pandas, not adding test estimator-latdev
Missing python module h5py, not adding test estimator-latdev
Adding I/O tests for QMCPACK
Adding test restart-8-2
Adding test restart-1-16
Adding performance tests for QMCPACK
QMC_DATA not set. Performance tests not added.
QMC_DATA not set. Performance tests not added.
Adding example tests for QMCPACK
-- Configuring done
-- Generating done
-- Build files have been written to: /mnt/abc/u/system/bwjenkins/qmcpack-spp/qmcpack-3.2.0/build
   Base precision = double
   Full precision = double
-- QMC_SYMLINK_TEST_FILES = TRUE.  Using symbolic links for large test files may cause test failures if the build is installed on a separate filesystem from the source.  For example, Titan at OLCF.
-- CMAKE_BUILD_TYPE is 
-- defining the float point precision
-- Using ../config/attic/BWGNU.cmake toolchain 
-- MPI runner is mpirun
-- CXX compiler flags: -std=c++11 -march=bdver1 -msse -msse2 -msse3 -msse4.1 -D_CRAYMPI -fopenmp -O3 -Drestrict=__restrict__ -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -Wno-deprecated -ffast-math -funroll-loops -fomit-frame-pointer -malign-double -DDISABLE_TIMER=1 -DHAVE_FMA4=1 -DHAVE_AMDLIBM=1 -DENABLE_SOA=1 -DQMC_MIXED_PRECISION=1 -D__forceinline="__attribute__((always_inline))" -ftemplate-depth-60 -DADD_ -DINLINE_ALL=inline
-- CC  compiler flags: -march=bdver1 -msse -msse2 -msse3 -msse4.1 -D_CRAYMPI -fopenmp -O3 -Drestrict=__restrict__ -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -Wno-deprecated -ffast-math -funroll-loops -fomit-frame-pointer -malign-double -DDISABLE_TIMER=1 -DHAVE_FMA4=1 -DHAVE_AMDLIBM=1 -DENABLE_SOA=1 -DQMC_MIXED_PRECISION=1 -D__forceinline="__attribute__((always_inline))" -std=c99
-- FFTW_INCLUDE_DIR=/opt/cray/fftw/default/interlagos/include
-- FFTW_LIBRARIES=/opt/cray/fftw/default/interlagos/lib/libfftw3.a
-- Found FFTW
-- Trying libxml2 via LIBXML2_HOME
-- LIBXML2_INCLUDE_DIR=/usr/include/libxml2/libxml
-- LIBXML2_LIBRARIES=/usr/lib64/libxml2.a
-- Libxml2 found by FindLibxml2QMC
-- Using HDF5 non-scalable serial I/O due to the lack of library support for parallel
-- Boost version: 1.53.0
-- Setting Boost_INCLUDE_DIRS=/sw/xe/boost/default/sles11.1_gnu4.8.2/include
-- Disabling CUDA
-- Ready to build qmcpack
Adding tests for QMCPACK
Skipping all gaussian basis tests because they are not supported by complex build (QMC_COMPLEX=1)
Adding test short-LiH_solid_1x1x1_pp-gamma-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-gamma-drift-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-x-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-x-drift-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-arb-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-arb-drift-vmc_hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-gamma-dmc-hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-x-dmc-hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-arb-dmc-hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-gamma-dmcnl-hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-x-dmcnl-hf_noj-1-16
Adding test short-LiH_solid_1x1x1_pp-arb-dmcnl-hf_noj-1-16
Adding test short-bccH_1x1x1_ae-vmc_sdj-1-16
Adding test short-bccH_1x1x1_ae-dmc_sdj-1-16
Adding test short-bccH_1x1x1_ae-vmc-all-nodrift_sdj-1-16
Adding test short-bccH_1x1x1_ae-vmc-all_sdj-1-16
Adding test short-bccH_1x1x1_ae-dmc-all_sdj-1-16
Adding test short-bccH_1x1x1_ae-csvmc-pbyp-nodrift_sdj-16-1
Adding test short-bccH_1x1x1_ae-csvmc-all-nodrift_sdj-16-1
Adding test short-bccH_1x1x1_ae-csvmc-all_sdj-16-1
Adding test short-bccH_1x1x1_ae-rmc_sdj-1-16
Adding test short-bccH_1x1x1_ae-rmc_sdj-4-4
Adding test short-bccH_1x1x1_ae-vmc_sdj-pw-1-16
Adding test short-diamondC_1x1x1_pp-vmc_sdj-1-16
Adding test short-diamondC_1x1x1_pp-vmc_sdj-meshf-1-16
Adding test short-diamondC_1x1x1_pp-opt_sdj-1-16
Adding test short-diamondC_1x1x1_pp-dmc_sdj-1-16
Adding test short-diamondC_2x1x1_pp-vmc_sdj-1-16
Adding test short-diamondC_2x1x1_pp-dmc_sdj-1-16
Adding test short-hcpBe_1x1x1_pp-vmc_sdj-1-16
Adding test short-monoO_1x1x1_pp-vmc_sdj-1-16
Adding test long-bccH_1x1x1_ae-vmc_sdj-1-16
Adding test long-bccH_1x1x1_ae-dmc_sdj-1-16
Adding test long-bccH_1x1x1_ae-rmc_sdj-1-16
Adding test long-diamondC_1x1x1_pp-vmc_sdj-1-16
Adding test long-diamondC_1x1x1_pp-vmc_sdj-meshf-1-16
Adding test long-diamondC_1x1x1_pp-dmc_sdj-1-16
Adding test long-diamondC_2x1x1_pp-vmc_sdj-1-16
Adding test long-diamondC_2x1x1_pp-dmc_sdj-1-16
Adding test long-hcpBe_1x1x1_pp-vmc_sdj-1-16
Adding test long-monoO_1x1x1_pp-vmc_sdj-1-16
Adding estimator tests for QMCPACK
Missing python module h5py, not adding test estimator-skinetic
Missing python module pandas, not adding test estimator-latdev
Missing python module h5py, not adding test estimator-latdev
Adding I/O tests for QMCPACK
Adding test restart-8-2
Adding test restart-1-16
Adding performance tests for QMCPACK
QMC_DATA not set. Performance tests not added.
QMC_DATA not set. Performance tests not added.
Adding example tests for QMCPACK
CMake Error at src/CMakeLists.txt:174 (ADD_LIBRARY):
  Cannot find source file:

    /mnt/abc/u/system/bwjenkins/qmcpack-spp/qmcpack-3.2.0/build/src/git-rev-tmp.h

  Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp
  .hxx .in .txx


-- Configuring done
CMake Error: Cannot determine link language for target "qmcutil".
CMake Error: CMake can not determine linker language for target: qmcutil
-- Generating done
-- Build files have been written to: /mnt/abc/u/system/bwjenkins/qmcpack-spp/qmcpack-3.2.0/build
make[2]: *** No rule to make target `src/CMakeFiles/qmcutil.dir/build'.  Stop.
make[1]: *** [src/CMakeFiles/qmcutil.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Scanning dependencies of target qmcutil
Scanning dependencies of target qmcfakerng
[  0%] Building CXX object src/CMakeFiles/qmcfakerng.dir/Utilities/FakeRandom.cpp.o
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Building C object src/einspline/CMakeFiles/einspline.dir/bspline_data.c.o
Scanning dependencies of target oompi
[  1%] Building CXX object src/OOMPI/CMakeFiles/oompi.dir/Cart_comm.cc.o
Linking CXX static library ../lib/libqmcfakerng.a
[  1%] Building C object src/einspline/CMakeFiles/einspline.dir/multi_bspline_create.c.o
[  1%] Built target qmcfakerng
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[  3%] Building C object src/einspline/CMakeFiles/einspline.dir/nubasis.c.o
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Building CXX object src/OOMPI/CMakeFiles/oompi.dir/Environment.cc.o
[  5%] [  5%] Building CXX object src/OOMPI/CMakeFiles/oompi.dir/Error_table.cc.o
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Building CXX object src/einspline/CMakeFiles/einspline.dir/bspline_eval_d_std.cpp.o
[  6%] Building CXX object src/OOMPI/CMakeFiles/oompi.dir/Group.cc.o
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[  8%] Building CXX object src/OOMPI/CMakeFiles/oompi.dir/Intra_comm.cc.o
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Building CXX object src/einspline/CMakeFiles/einspline.dir/multi_nubspline_eval_z_std.cpp.o
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Scanning dependencies of target adios_config
Linking CXX static library ../../lib/liboompi.a
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Linking CXX static library ../../lib/libqmcwfs.a
make: *** [all] Error 2
mv: cannot stat `qmcpack': No such file or directory
[ 42%] Built target qmcwfs
INFO: Job submitted to account: jnc
MYJOBID=243645.jyc
=== RUNNING /u/staff/arnoldg/ior/wait_for.sh ===
Thu Jul 12 09:44:54 CDT 2018: waiting for 243645.jyc to finish
Thu Jul 12 09:49:54 CDT 2018: waiting for 243645.jyc to finish
qstat: Unknown Job Id Error 243645.nid00030
Cannot open file gr4x4x1.p400x8.s001.scalar.dat
243645.jyc finished
MYREAL=0.93
[SSH] exit-status: 0
[qmcpack-jyc] $ /bin/sh -xe /tmp/jenkins7228165837602907442.sh
+ rm -rf /var/lib/jenkins/workspace/qmcpack-jyc/realtime.txt
+ scp 'JYC_REMOTE:~/qmcpack-spp/*.txt' /var/lib/jenkins/workspace/qmcpack-jyc
NCSA JYC System 
Access status: User Access UnRestricted.

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.

Restricted access during weekly scheduled maintenance on Wednesdays 10AM - 6PM

Recording plot data
Saving plot series data from: /var/lib/jenkins/workspace/qmcpack-jyc/realtime.txt
Finished: SUCCESS