Console Output

Started by user Greg Bauer
Running as SYSTEM
Building in workspace /var/lib/jenkins/jobs/qmcpack-jyc/workspace
[SSH] 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}'

[SSH] executing...
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_1.0502.8871.44.1-1.0502.21728.75.3
  6) udreg/2.3.2-1.0502.10518.2.17.gem
  7) ugni/6.0-1.0502.10863.8.28.gem
  8) gni-headers/4.0-1.0502.10859.9.26.gem
  9) dmapp/7.0.1-1.0502.11080.8.74.gem
 10) xpmem/0.1-2.0502.64982.7.26.gem
 11) hss-llm/7.2.0
 12) Base-opts/1.0.2-1.0502.60680.2.4.gem
 13) cce/8.7.7
 14) craype-network-gemini
 15) craype/2.5.16
 16) cray-libsci/18.12.1
 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/6.1.2
 23) craype-interlagos
 24) cray-mpich/7.7.4
 25) java/jdk1.8.0_51
 26) globus/6.0
 27) gsissh/7.5p1b
 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
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rm: cannot remove `/tmp/tmpclusters/tetramer-guah-tip3-guah-tip3-026-049-010-039.pdb': Permission denied
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rm: cannot remove `/tmp/trqauthd-unix': Operation not permitted
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_1.0502.8871.44.1-1.0502.21728.75.3
  6) udreg/2.3.2-1.0502.10518.2.17.gem
  7) ugni/6.0-1.0502.10863.8.28.gem
  8) gni-headers/4.0-1.0502.10859.9.26.gem
  9) dmapp/7.0.1-1.0502.11080.8.74.gem
 10) xpmem/0.1-2.0502.64982.7.26.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/2.5.16
 16) moab/9.1.2.h2-sles11
 17) torque/6.1.2
 18) cray-mpich/7.7.4
 19) java/jdk1.8.0_51
 20) globus/6.0
 21) gsissh/7.5p1b
 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/6.3.0
 32) cray-libsci/18.12.1
 33) pmi/5.0.11
 34) atp/2.1.0
 35) PrgEnv-gnu/5.2.82
 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 6.3.0
-- The CXX compiler identification is GNU 6.3.0
-- 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
-- Configuring done
-- Generating done
-- Build files have been written to: /mnt/abc/u/system/bwjenkins/qmcpack-spp/qmcpack-3.2.0/build
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[ 92%] Building CXX object src/QMCWaveFunctions/CMakeFiles/qmcwfs.dir/BasisSetFactory.cpp.o
[ 93%] Building CXX object src/QMCDrivers/CMakeFiles/qmcdriver.dir/DMC/WalkerReconfigurationMPI.cpp.o
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[ 96%] Built target qmcham
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[ 96%] [ 97%] [ 97%] Building CXX object src/QMCDrivers/tests/CMakeFiles/test_drivers.dir/test_vmc.cpp.o
Building CXX object src/QMCDrivers/tests/CMakeFiles/test_drivers.dir/test_dmc.cpp.o
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Building CXX object src/QMCApp/tests/CMakeFiles/test_qmcapp.dir/test_rng_control.cpp.o
Building CXX object src/Estimators/tests/CMakeFiles/test_estimators.dir/test_accumulator.cpp.o
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[ 98%] Building CXX object src/QMCHamiltonians/tests/CMakeFiles/test_hamiltonian.dir/test_coulomb_pbcAB.cpp.o
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[100%] Building CXX object src/QMCHamiltonians/tests/CMakeFiles/test_hamiltonian.dir/test_coulomb_pbcAA.cpp.o
[100%] Building CXX object src/QMCHamiltonians/tests/CMakeFiles/test_hamiltonian.dir/test_force.cpp.o
[100%] Building CXX object src/Estimators/tests/CMakeFiles/test_estimators.dir/test_manager.cpp.o
[100%] Building CXX object src/QMCApp/tests/CMakeFiles/test_qmcapp.dir/test_wavefunction_pool.cpp.o
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[100%] Building CXX object src/QMCHamiltonians/tests/CMakeFiles/test_hamiltonian.dir/test_ecp.cpp.o
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[100%] Built target qmcpack
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[100%] Built target test_estimators
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[100%] Built target test_drivers
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[100%] Built target test_hamiltonian
INFO: Job submitted to account: jnc
MYJOBID=262966.jyc
=== RUNNING /u/staff/arnoldg/ior/wait_for.sh ===
Fri Mar 15 13:48:29 CDT 2019: waiting for 262966.jyc to finish
Fri Mar 15 13:53:29 CDT 2019: waiting for 262966.jyc to finish
Fri Mar 15 13:58:29 CDT 2019: waiting for 262966.jyc to finish
Fri Mar 15 14:03:29 CDT 2019: waiting for 262966.jyc to finish
Fri Mar 15 14:08:29 CDT 2019: waiting for 262966.jyc to finish
Fri Mar 15 14:13:29 CDT 2019: waiting for 262966.jyc to finish
Fri Mar 15 14:18:29 CDT 2019: waiting for 262966.jyc to finish
qstat: Unknown Job Id Error 262966.nid00030
Cannot open file gr4x4x1.p400x8.s001.scalar.dat
262966.jyc finished
MYREAL=1754.39

[SSH] completed
[SSH] exit-status: 0

[workspace] $ /bin/sh -xe /tmp/jenkins4870135396212950272.sh
+ rm -rf '/var/lib/jenkins/jobs/qmcpack-jyc/workspace/*'
+ scp 'JYC_REMOTE:~/qmcpack-spp/*.txt' /var/lib/jenkins/jobs/qmcpack-jyc/workspace
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/jobs/qmcpack-jyc/workspace/realtime.txt
Finished: SUCCESS