---------------------------------------- Begin Torque Prologue (Sat Jun 1 00:02:02 2019) Job ID: 8705580.cc-mgmt1.campuscluster.illinois.edu Username: xiaoma5 Group: insight Job Name: example9 Limits: nodes=5:ppn=10,walltime=01:00:00,neednodes=5:ppn=10 Job Queue: secondary Account: insight Nodes: golub033 golub034 golub035 golub037 golub038 End Torque Prologue ---------------------------------------- gcc(8):ERROR:105: Unable to locate a modulefile for 'gcc/4.9.2' ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'mvapich2/2.1rc1-gcc-4.9.2' ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'git/1.7' /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters /home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/h5py-2.7.1-py2.7-linux-x86_64.egg/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters [29]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [9]PETSC ERROR: [29]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- Error in external library [9]PETSC ERROR: [29]PETSC ERROR: Error in external library Error in HDF5 call H5Dcreate2() Status -1 [9]PETSC ERROR: [29]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [9]PETSC ERROR: [29]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [9]PETSC ERROR: [29]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub035 by xiaoma5 Sat Jun 1 00:02:01 2019 [9]PETSC ERROR: [29]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub037 by xiaoma5 Sat Jun 1 00:02:17 2019 Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [9]PETSC ERROR: [29]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith #1 VecView_MPI_HDF5() line 677 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [9]PETSC ERROR: [29]PETSC ERROR: #1 VecView_MPI_HDF5() line 677 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c #2 VecView_MPI() line 817 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [9]PETSC ERROR: [29]PETSC ERROR: #2 VecView_MPI() line 817 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c #3 VecView() line 583 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/interface/vector.c [9]PETSC ERROR: [29]PETSC ERROR: #3 VecView() line 583 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/interface/vector.c #4 virtual void pylith::meshio::DataWriterHDF5::open(const pylith::topology::Mesh&, int, const char*, int)() line 230 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc [9]PETSC ERROR: [29]PETSC ERROR: #4 virtual void pylith::meshio::DataWriterHDF5::open(const pylith::topology::Mesh&, int, const char*, int)() line 230 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc --------------------- Error Message -------------------------------------------------------------- [9]PETSC ERROR: [29]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- Error in external library [9]PETSC ERROR: [29]PETSC ERROR: Error in external library Error in HDF5 call H5Fclose() Status -1 [9]PETSC ERROR: [29]PETSC ERROR: Error in HDF5 call H5Fclose() Status -1 See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [9]PETSC ERROR: [29]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [9]PETSC ERROR: [29]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub035 by xiaoma5 Sat Jun 1 00:02:01 2019 [9]PETSC ERROR: [29]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub037 by xiaoma5 Sat Jun 1 00:02:17 2019 Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [9]PETSC ERROR: [29]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith #5 PetscViewerFileClose_HDF5() line 39 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [9]PETSC ERROR: [29]PETSC ERROR: #5 PetscViewerFileClose_HDF5() line 39 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c #6 PetscViewerDestroy_HDF5() line 49 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [9]PETSC ERROR: [29]PETSC ERROR: #6 PetscViewerDestroy_HDF5() line 49 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c #7 PetscViewerDestroy() line 100 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/interface/view.c [9]PETSC ERROR: [29]PETSC ERROR: #7 PetscViewerDestroy() line 100 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/interface/view.c #8 virtual void pylith::meshio::DataWriterHDF5::deallocate()() line 73 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc [9]PETSC ERROR: Traceback (most recent call last): #8 virtual void pylith::meshio::DataWriterHDF5::deallocate()() line 73 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc File "", line 1, in Traceback (most recent call last): File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/__init__.py", line 42, in mpistart File "", line 1, in File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/__init__.py", line 42, in mpistart kwds = kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/__init__.py", line 41, in start kwds = kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/__init__.py", line 41, in start shell.run(**kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run shell.run(**kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 49, in execute method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 49, in execute self.main(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 58, in main self.main(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 58, in main self.runSubscript(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 62, in runSubscript self.runSubscript(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 62, in runSubscript self.subscript.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Application.py", line 42, in run self.subscript.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Application.py", line 42, in run shell.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run shell.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/Application.py", line 118, in _onComputeNodes method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/Application.py", line 118, in _onComputeNodes self.onComputeNodes(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 77, in onComputeNodes self.onComputeNodes(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 77, in onComputeNodes self.cleanup() # Attempt to clean up memory. File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 109, in cleanup self.cleanup() # Attempt to clean up memory. File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 109, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 75, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 75, in cleanup subcomponent.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup subcomponent.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 77, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 77, in cleanup self._cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 88, in _cleanup self._cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 88, in _cleanup self.deallocate() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/meshio/meshio.py", line 366, in deallocate self.deallocate() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/meshio/meshio.py", line 366, in deallocate def deallocate(self): return _meshio.DataWriterHDF5_deallocate(self) RuntimeErrordef deallocate(self): return _meshio.DataWriterHDF5_deallocate(self) : RuntimeErrorError detected while in PETSc function.: Error detected while in PETSc function. [28]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [28]PETSC ERROR: Error in external library [28]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 [28]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [28]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [28]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub035 by xiaoma5 Sat Jun 1 00:02:01 2019 [28]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [28]PETSC ERROR: #1 VecView_MPI_HDF5() line 677 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [28]PETSC ERROR: #2 VecView_MPI() line 817 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [28]PETSC ERROR: #3 VecView() line 583 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/interface/vector.c [28]PETSC ERROR: #4 virtual void pylith::meshio::DataWriterHDF5::open(const pylith::topology::Mesh&, int, const char*, int)() line 230 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc [28]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [28]PETSC ERROR: Error in external library [28]PETSC ERROR: Error in HDF5 call H5Fclose() Status -1 [28]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [28]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [28]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub035 by xiaoma5 Sat Jun 1 00:02:01 2019 [28]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [28]PETSC ERROR: #5 PetscViewerFileClose_HDF5() line 39 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [28]PETSC ERROR: #6 PetscViewerDestroy_HDF5() line 49 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [28]PETSC ERROR: #7 PetscViewerDestroy() line 100 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/interface/view.c [28]PETSC ERROR: #8 virtual void pylith::meshio::DataWriterHDF5::deallocate()() line 73 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc Traceback (most recent call last): File "", line 1, in File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/__init__.py", line 42, in mpistart kwds = kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/__init__.py", line 41, in start shell.run(**kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 49, in execute self.main(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 58, in main self.runSubscript(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 62, in runSubscript self.subscript.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Application.py", line 42, in run shell.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/Application.py", line 118, in _onComputeNodes self.onComputeNodes(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 77, in onComputeNodes self.cleanup() # Attempt to clean up memory. File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 109, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 75, in cleanup subcomponent.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 77, in cleanup self._cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 88, in _cleanup self.deallocate() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/meshio/meshio.py", line 366, in deallocate def deallocate(self): return _meshio.DataWriterHDF5_deallocate(self) RuntimeError: Error detected while in PETSc function. [29]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [29]PETSC ERROR: Error in external library [29]PETSC ERROR: Error in HDF5 call H5Fclose() Status -1 [29]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [29]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [9]PETSC ERROR: [29]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub035 by xiaoma5 Sat Jun 1 00:02:01 2019 --------------------- Error Message -------------------------------------------------------------- [29]PETSC ERROR: [9]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith Error in external library [29]PETSC ERROR: [9]PETSC ERROR: #9 PetscViewerFileClose_HDF5() line 39 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c Error in HDF5 call H5Fclose() Status -1 [29]PETSC ERROR: [9]PETSC ERROR: #10 PetscViewerDestroy_HDF5() line 49 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [29]PETSC ERROR: [9]PETSC ERROR: #11 PetscViewerDestroy() line 100 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/interface/view.c Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [29]PETSC ERROR: [9]PETSC ERROR: #12 virtual void pylith::meshio::DataWriterHDF5::deallocate()() line 73 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub037 by xiaoma5 Sat Jun 1 00:02:17 2019 terminate called after throwing an instance of '[9]PETSC ERROR: std::runtime_errorConfigure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith ' [9]PETSC ERROR: what(): #9 PetscViewerFileClose_HDF5() line 39 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c Error detected while in PETSc function.[9]PETSC ERROR: #10 PetscViewerDestroy_HDF5() line 49 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [golub035:mpi_rank_29][error_sighandler] Caught error: Aborted (signal 6) [9]PETSC ERROR: #11 PetscViewerDestroy() line 100 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/interface/view.c [9]PETSC ERROR: #12 virtual void pylith::meshio::DataWriterHDF5::deallocate()() line 73 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc terminate called after throwing an instance of 'std::runtime_error' what(): Error detected while in PETSc function. [golub037:mpi_rank_9][error_sighandler] Caught error: Aborted (signal 6) [39]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [39]PETSC ERROR: Error in external library [39]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 [39]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [39]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [39]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub038 by xiaoma5 Sat Jun 1 00:02:17 2019 [39]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [39]PETSC ERROR: #1 VecView_MPI_HDF5() line 677 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [39]PETSC ERROR: #2 VecView_MPI() line 817 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [39]PETSC ERROR: #3 VecView() line 583 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/interface/vector.c [39]PETSC ERROR: #4 virtual void pylith::meshio::DataWriterHDF5::open(const pylith::topology::Mesh&, int, const char*, int)() line 230 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc [39]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [39]PETSC ERROR: Error in external library [39]PETSC ERROR: Error in HDF5 call H5Fclose() Status -1 [39]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [39]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [39]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub038 by xiaoma5 Sat Jun 1 00:02:17 2019 [39]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [39]PETSC ERROR: #5 PetscViewerFileClose_HDF5() line 39 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [39]PETSC ERROR: #6 PetscViewerDestroy_HDF5() line 49 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [39]PETSC ERROR: #7 PetscViewerDestroy() line 100 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/interface/view.c [39]PETSC ERROR: #8 virtual void pylith::meshio::DataWriterHDF5::deallocate()() line 73 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc Traceback (most recent call last): File "", line 1, in [38]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [38]PETSC ERROR: Error in external library [38]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 [38]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [38]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [38]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub038 by xiaoma5 Sat Jun 1 00:02:17 2019 [38]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [38]PETSC ERROR: #1 VecView_MPI_HDF5() line 677 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [38]PETSC ERROR: #2 VecView_MPI() line 817 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [38]PETSC ERROR: #3 VecView() line 583 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/interface/vector.c [38]PETSC ERROR: #4 virtual void pylith::meshio::DataWriterHDF5::open(const pylith::topology::Mesh&, int, const char*, int)() line 230 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/__init__.py", line 42, in mpistart kwds = kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/__init__.py", line 41, in start shell.run(**kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 49, in execute self.main(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 58, in main self.runSubscript(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 62, in runSubscript self.subscript.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Application.py", line 42, in run shell.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/Application.py", line 118, in _onComputeNodes self.onComputeNodes(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 77, in onComputeNodes self.cleanup() # Attempt to clean up memory. File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 109, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 75, in cleanup subcomponent.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 77, in cleanup self._cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 88, in _cleanup self.deallocate() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/meshio/meshio.py", line 366, in deallocate def deallocate(self): return _meshio.DataWriterHDF5_deallocate(self) RuntimeError: Error detected while in PETSc function. [38]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [38]PETSC ERROR: Error in external library [38]PETSC ERROR: Error in HDF5 call H5Fclose() Status -1 [38]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [38]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [38]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub038 by xiaoma5 Sat Jun 1 00:02:17 2019 [38]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [38]PETSC ERROR: #5 PetscViewerFileClose_HDF5() line 39 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [38]PETSC ERROR: #6 PetscViewerDestroy_HDF5() line 49 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [38]PETSC ERROR: #7 PetscViewerDestroy() line 100 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/interface/view.c [38]PETSC ERROR: #8 virtual void pylith::meshio::DataWriterHDF5::deallocate()() line 73 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc Traceback (most recent call last): File "", line 1, in File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/__init__.py", line 42, in mpistart kwds = kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/__init__.py", line 41, in start shell.run(**kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 49, in execute self.main(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 58, in main self.runSubscript(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 62, in runSubscript self.subscript.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Application.py", line 42, in run shell.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/Application.py", line 118, in _onComputeNodes self.onComputeNodes(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 77, in onComputeNodes self.cleanup() # Attempt to clean up memory. File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 109, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 75, in cleanup subcomponent.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 77, in cleanup self._cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 88, in _cleanup self.deallocate() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/meshio/meshio.py", line 366, in deallocate def deallocate(self): return _meshio.DataWriterHDF5_deallocate(self) RuntimeError: Error detected while in PETSc function. [49]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [49]PETSC ERROR: Error in external library [49]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 [49]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [49]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [49]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub034 by xiaoma5 Sat Jun 1 00:02:18 2019 [49]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [49]PETSC ERROR: #1 VecView_MPI_HDF5() line 677 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [49]PETSC ERROR: #2 VecView_MPI() line 817 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [49]PETSC ERROR: #3 VecView() line 583 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/interface/vector.c [49]PETSC ERROR: #4 virtual void pylith::meshio::DataWriterHDF5::open(const pylith::topology::Mesh&, int, const char*, int)() line 230 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc [48]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [48]PETSC ERROR: Error in external library [48]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 [48]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [48]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [48]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub034 by xiaoma5 Sat Jun 1 00:02:18 2019 [48]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [48]PETSC ERROR: #1 VecView_MPI_HDF5() line 677 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [48]PETSC ERROR: #2 VecView_MPI() line 817 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/impls/mpi/pdvec.c [48]PETSC ERROR: #3 VecView() line 583 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/vec/vec/interface/vector.c [48]PETSC ERROR: #4 virtual void pylith::meshio::DataWriterHDF5::open(const pylith::topology::Mesh&, int, const char*, int)() line 230 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc [49]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [49]PETSC ERROR: Error in external library [49]PETSC ERROR: Error in HDF5 call H5Fclose() Status -1 [49]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [49]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [49]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub034 by xiaoma5 Sat Jun 1 00:02:18 2019 [49]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [49]PETSC ERROR: #5 PetscViewerFileClose_HDF5() line 39 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [49]PETSC ERROR: #6 PetscViewerDestroy_HDF5() line 49 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [49]PETSC ERROR: #7 PetscViewerDestroy() line 100 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/interface/view.c [49]PETSC ERROR: #8 virtual void pylith::meshio::DataWriterHDF5::deallocate()() line 73 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc Traceback (most recent call last): File "", line 1, in File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/__init__.py", line 42, in mpistart kwds = kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/__init__.py", line 41, in start [39]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [39]PETSC ERROR: Error in external library [39]PETSC ERROR: Error in HDF5 call H5Fclose() Status -1 [39]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. shell.run(**kwds) [39]PETSC ERROR: File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [39]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub038 by xiaoma5 Sat Jun 1 00:02:17 2019 [39]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [39]PETSC ERROR: #9 PetscViewerFileClose_HDF5() line 39 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c method(*args, **kwds) [39]PETSC ERROR: File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 49, in execute #10 PetscViewerDestroy_HDF5() line 49 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [39]PETSC ERROR: self.main(*args, **kwds) #11 PetscViewerDestroy() line 100 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/interface/view.c File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 58, in main [39]PETSC ERROR: #12 virtual void pylith::meshio::DataWriterHDF5::deallocate()() line 73 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc self.runSubscript(*args, **kwds) terminate called after throwing an instance of ' File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 62, in runSubscript std::runtime_error ' what(): Error detected while in PETSc function. [golub038:mpi_rank_39][error_sighandler] Caught error: Aborted (signal 6) self.subscript.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Application.py", line 42, in run shell.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/Application.py", line 118, in _onComputeNodes self.onComputeNodes(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 77, in onComputeNodes self.cleanup() # Attempt to clean up memory. File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 109, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 75, in cleanup subcomponent.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup [48]PETSC ERROR: component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup --------------------- Error Message -------------------------------------------------------------- [48]PETSC ERROR: Error in external library [48]PETSC ERROR: Error in HDF5 call H5Fclose() Status -1 [48]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [48]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [48]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub034 by xiaoma5 Sat Jun 1 00:02:18 2019 [48]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [48]PETSC ERROR: #5 PetscViewerFileClose_HDF5() line 39 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [48]PETSC ERROR: #6 PetscViewerDestroy_HDF5() line 49 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [48]PETSC ERROR: #7 PetscViewerDestroy() line 100 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/interface/view.c [48]PETSC ERROR: #8 virtual void pylith::meshio::DataWriterHDF5::deallocate()() line 73 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 77, in cleanup self._cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 88, in _cleanup self.deallocate() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/meshio/meshio.py", line 366, in deallocate Traceback (most recent call last): File "", line 1, in def deallocate(self): return _meshio.DataWriterHDF5_deallocate(self) RuntimeError: Error detected while in PETSc function. File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/__init__.py", line 42, in mpistart kwds = kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/__init__.py", line 41, in start shell.run(**kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 49, in execute self.main(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 58, in main self.runSubscript(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/SuperScript.py", line 62, in runSubscript self.subscript.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Application.py", line 42, in run shell.run(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/pyre/applications/Shell.py", line 143, in run method(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pythia-0.8.1.18-py2.7.egg/mpi/Application.py", line 118, in _onComputeNodes self.onComputeNodes(*args, **kwds) File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 77, in onComputeNodes self.cleanup() # Attempt to clean up memory. File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 109, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 75, in cleanup subcomponent.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 69, in cleanup component.cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 77, in cleanup self._cleanup() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/utils/PetscComponent.py", line 88, in _cleanup self.deallocate() File "/home/xiaoma5/project-beckman/pylith_home/pylith/lib/python2.7/site-packages/pylith/meshio/meshio.py", line 366, in deallocate def deallocate(self): return _meshio.DataWriterHDF5_deallocate(self) RuntimeError: Error detected while in PETSc function. [38]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [38]PETSC ERROR: Error in external library [38]PETSC ERROR: Error in HDF5 call H5Fclose() Status -1 [38]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [38]PETSC ERROR: Petsc Development GIT revision: v3.7.6-4826-gd686aaf GIT Date: 2017-08-03 14:01:44 -0500 [38]PETSC ERROR: /home/xiaoma5/project-beckman/pylith_home/pylith/bin/mpinemesis on a arch-pylith named golub038 by xiaoma5 Sat Jun 1 00:02:17 2019 [38]PETSC ERROR: Configure options --prefix=/home/xiaoma5/project-beckman/pylith_home/pylith --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hdf5=1 --with-hdf5-dir=/home/xiaoma5/project-beckman/pylith_home/pylith --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/xiaoma5/project-beckman/pylith_home/pylith/include -I/home/xiaoma5/project-beckman/pylith_home/pylith/include " LDFLAGS="-L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib -L/home/xiaoma5/project-beckman/pylith_home/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/xiaoma5/project-beckman/pylith_home/build/pylith/petsc-pylith PETSC_ARCH=arch-pylith [38]PETSC ERROR: #9 PetscViewerFileClose_HDF5() line 39 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [38]PETSC ERROR: #10 PetscViewerDestroy_HDF5() line 49 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/impls/hdf5/hdf5v.c [38]PETSC ERROR: #11 PetscViewerDestroy() line 100 in /projects/beckman/xiaoma5/pylith_home/build/pylith/petsc-pylith/src/sys/classes/viewer/interface/view.c [38]PETSC ERROR: #12 virtual void pylith::meshio::DataWriterHDF5::deallocate()() line 73 in ../../../pylith-2.2.1/libsrc/pylith/meshio/DataWriterHDF5.cc terminate called after throwing an instance of 'std::runtime_error' what(): Error detected while in PETSc function. [golub038:mpi_rank_38][error_sighandler] Caught error: Aborted (signal 6) [proxy:0:1@golub033] HYD_pmcd_pmip_control_cmd_cb (pm/pmiserv/pmip_cb.c:911): assert (!closed) failed [proxy:0:1@golub033] HYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback returned error status [proxy:0:1@golub033] main (pm/pmiserv/pmip.c:202): demux engine error waiting for event [proxy:0:3@golub038] HYD_pmcd_pmip_control_cmd_cb (pm/pmiserv/pmip_cb.c:911): assert (!closed) failed [proxy:0:3@golub038] HYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback returned error status [proxy:0:3@golub038] main (pm/pmiserv/pmi[proxy:0:4@golub034] HYD_pmcd_pmip_control_cmd_cb (pm/pmiserv/pmip_cb.c:911): assert (!closed) failed [proxy:0:4@golub034] HYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback returned error status [proxy:0:4@golub034] main (pm/pmiserv/pmip.c:202): demux engine error waiting for event p.c:202): demux engine error waiting for event /home/xiaoma5/project-beckman/pylith_home/pylith/bin/nemesis: mpirun: exit 6 ---------------------------------------- Begin Torque Epilogue (Sat Jun 1 00:10:28 2019) Job ID: 8705580.cc-mgmt1.campuscluster.illinois.edu Username: xiaoma5 Group: insight Job Name: example9 Session: 3673 Limits: nodes=5:ppn=10,walltime=01:00:00,neednodes=5:ppn=10 Resources: cput=06:25:42,vmem=134579156kb,walltime=00:07:59,mem=130666768kb,energy_used=0 Job Queue: secondary Account: insight Nodes: golub033 golub034 golub035 golub037 golub038 End Torque Epilogue ----------------------------------------