++ pwd + OLD_PWD=/home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003 +++ dirname /home/jb/workspace/flow123d/bin/fterm ++ cd /home/jb/workspace/flow123d/bin/.. ++ pwd + ABS_FLOW_DIR=/home/jb/workspace/flow123d +++ pwd ++ realpath --relative-to=/home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003 /home/jb/workspace/flow123d + REL_FLOW_DIR=../../../../../flow123d + CFG=../../../../../flow123d/config + image_version=dbg + image_tag=latest + DOCKER_TAG=../../../../../flow123d/config/docker/image_tag + [[ -f ../../../../../flow123d/config/docker/image_tag ]] ++ cat ../../../../../flow123d/config/docker/image_tag + image_tag=4.0.1 + [[ -z '' ]] + test -t 1 ++ id -g + gid=1000 ++ id -u + uid=1000 + uname=flow + autopull=1 + theme=light + DCFG=../../../../../flow123d/config/docker.cfg + [[ -f ../../../../../flow123d/config/docker.cfg ]] + privileged=0 + verbose=1 + action=shell ++ get_mount_dir /home/jb/workspace/flow123d ++ [[ -n '' ]] ++ local workdir=/home/jb/workspace/flow123d ++ local workdir_tmp= ++ (( i = 0 )) ++ (( i < 10 )) +++ dirname /home/jb/workspace/flow123d ++ workdir_tmp=/home/jb/workspace ++ [[ /home/jb/workspace == \/\h\o\m\e\/\j\b ]] ++ workdir=/home/jb/workspace ++ (( i++ )) ++ (( i < 10 )) +++ dirname /home/jb/workspace ++ workdir_tmp=/home/jb ++ [[ /home/jb == \/\h\o\m\e\/\j\b ]] ++ echo /home/jb/workspace ++ return + work=/home/jb/workspace + contname= + docker_terminal=-it + [[ 3 -gt 0 ]] + key=--no-term + case $key in + docker_terminal= + shift + [[ 2 -gt 0 ]] + key=run + case $key in + action=run + shift + rest=/home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/transport_fullscale.yaml + break + image_kind=dbg + image_env=dbg + '[' dbg = dbg ']' + image_env=gnu + '[' -z '' ']' + flow123d_images='flow-dev-gnu-dbg flow-dev-gnu-rel' + base_image=flow123d/flow-dev-gnu-dbg:4.0.1 + dbg 'base_image = flow123d/flow-dev-gnu-dbg:4.0.1' + [[ 1 -eq 1 ]] + echo -e '[DBG] base_image = flow123d/flow-dev-gnu-dbg:4.0.1' + dbg 'image_tag = 4.0.1' + [[ 1 -eq 1 ]] + echo -e '[DBG] image_tag = 4.0.1' + dbg 'image_kind = dbg' + [[ 1 -eq 1 ]] + echo -e '[DBG] image_kind = dbg' + dbg 'image_env = gnu' + [[ 1 -eq 1 ]] + echo -e '[DBG] image_env = gnu' + dbg 'action = run' + [[ 1 -eq 1 ]] + echo -e '[DBG] action = run' + dbg 'mount dirs - /home/jb/workspace' + [[ 1 -eq 1 ]] + echo -e '[DBG] mount dirs - /home/jb/workspace' + dbg ' - /home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003' + [[ 1 -eq 1 ]] + echo -e '[DBG] - /home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003' + dbg 'user = flow(1000:1000)' + [[ 1 -eq 1 ]] + echo -e '[DBG] user = flow(1000:1000)' + dbg 'theme = light' + [[ 1 -eq 1 ]] + echo -e '[DBG] theme = light' + dbg 'autopull = 1' + [[ 1 -eq 1 ]] + echo -e '[DBG] autopull = 1' + dbg 'privileged = 0' + [[ 1 -eq 1 ]] + echo -e '[DBG] privileged = 0' + envarg='-euid=1000 -egid=1000 -etheme=light -ewho=flow -ehome=/mnt//home/jb -v //home/jb:/mnt//home/jb' + mountargs='-w //home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003 -v //home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003://home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003 -v //home/jb/workspace://home/jb/workspace' + [[ 0 == \1 ]] + case $action in + update_image flow123d/flow-dev-gnu-dbg:4.0.1 1 + pull_image=flow123d/flow-dev-gnu-dbg:4.0.1 + autopull=1 + [[ 1 == \1 ]] + docker pull flow123d/flow123d/flow-dev-gnu-dbg:4.0.1:4.0.1 invalid reference format + dbg2 'Executing flow123d with args /home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/transport_fullscale.yaml' + [[ 1 -eq 1 ]] + echo -e '[DBG] Executing flow123d with args /home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/transport_fullscale.yaml' + dbgc docker run --rm -euid=1000 -egid=1000 -etheme=light -ewho=flow -ehome=/mnt//home/jb -v //home/jb:/mnt//home/jb -w //home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003 -v //home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003://home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003 -v //home/jb/workspace://home/jb/workspace flow123d/flow-dev-gnu-dbg:4.0.1 ../../../../../flow123d/bin/flow123d /home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/transport_fullscale.yaml + [[ 1 -eq 1 ]] + echo -e '[RUN] docker' run --rm -euid=1000 -egid=1000 -etheme=light -ewho=flow -ehome=/mnt//home/jb -v //home/jb:/mnt//home/jb -w //home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003 -v //home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003://home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003 -v //home/jb/workspace://home/jb/workspace flow123d/flow-dev-gnu-dbg:4.0.1 ../../../../../flow123d/bin/flow123d /home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/transport_fullscale.yaml + docker run --rm -euid=1000 -egid=1000 -etheme=light -ewho=flow -ehome=/mnt//home/jb -v //home/jb:/mnt//home/jb -w //home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003 -v //home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003://home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003 -v //home/jb/workspace://home/jb/workspace flow123d/flow-dev-gnu-dbg:4.0.1 ../../../../../flow123d/bin/flow123d /home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/transport_fullscale.yaml 00:00:01.886 WARNING.Unprocessed key 'n_schurs' in Record '/problem/flow_equation'. 00:00:01.886 WARNING.Unprocessed key 'dt_max' in Tuple '/problem/solute_equation/time/dt_limits/0'. 00:00:01.886 WARNING.Unprocessed key 'dt_max' in Tuple '/problem/solute_equation/time/dt_limits/1'. 00:00:01.886 WARNING.Unprocessed key 'dt_max' in Tuple '/problem/solute_equation/time/dt_limits/2'. 00:00:01.886 WARNING.Unprocessed key 'dt_max' in Tuple '/problem/solute_equation/time/dt_limits/3'. 00:00:01.887 WARNING.Remaining token 'time', file '/home/jb/workspace/Endorse/tests/test_data/conc_flux_UOS_[kg:y].csv', line 1 after token #0 00:00:01.891 WARNING.Input file with version: '3.1.0' is no compatible with the program version: '4.0.0a' 00:00:03.021 WARNING.Renaming output file: /home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/output/flow_fields to /home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/output/flow_fields.pvd 00:00:04.429 WARNING.In file '/home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/input_fields.msh2', '$ElementData' section for field 'cross_section', time: 0. Different number of entities: 78949, computation needs 63050. 00:00:04.594 WARNING.In file '/home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/input_fields.msh2', '$ElementData' section for field 'conductivity', time: 0. Different number of entities: 78949, computation needs 63050. 00:00:30.731 WARNING. Used default values of Fields for equation HC explicit sequential: ---------------------------------------------------------------------------------------------------- Field name Default value Apply on regions anisotropy 1.0 fractures box sigma 1.0 fractures box water_source_density 0.0 fractures box bc_type "none" .fr_bore .box_boreholes .box_tunnel .IMPLICIT_BOUNDARY init_pressure 0.0 fractures box storativity 0.0 fractures box extra_storativity 0.0 fractures box extra_water_source_density 0.0 fractures box init_piezo_head 0.0 fractures box bc_piezo_head 0.0 .fr_bore .box_boreholes .box_tunnel .IMPLICIT_BOUNDARY bc_switch_piezo_head 0.0 .fr_outer .fr_bore .box_outer .box_boreholes .box_tunnel .IMPLICIT_BOUNDARY ---------------------------------------------------------------------------------------------------- 00:00:30.933 WARNING.Renaming output file: /home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/output/solute_fields to /home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/output/solute_fields.pvd 00:00:36.005 WARNING.In file '/home/jb/workspace/Endorse/tests/sandbox/output/L00_S0000003/input_fields.msh2', '$ElementData' section for field 'porosity', time: 0. Different number of entities: 78949, computation needs 63050. 00:00:36.206 WARNING. Used default values of Fields for equation transport DG: ---------------------------------------------------------------------------------------------------- Field name Default value Apply on regions U235_sources_density 0.0 fractures box U235_sources_sigma 0.0 fractures box U235_sources_conc 0.0 fractures box U235_bc_type "inflow" .fr_outer .box_outer .box_tunnel .IMPLICIT_BOUNDARY U235_bc_conc 0.0 .fr_outer .fr_bore .box_outer .box_boreholes .box_tunnel .IMPLICIT_BOUNDARY U235_bc_robin_sigma 0.0 .fr_bore .box_boreholes U235_init_conc 0.0 fractures box rock_density 0.0 fractures box U235_sorption_coefficient 0.0 fractures box U235_fracture_sigma 1.0 fractures box U235_dg_penalty 1.0 fractures box ---------------------------------------------------------------------------------------------------- [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Argument out of range [0]PETSC ERROR: New nonzero at (4139,4131) caused a malloc Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn off this check [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.17.0, Mar 30, 2022 [0]PETSC ERROR: /home/jb/workspace/flow123d/bin/../build_tree/bin/flow123d on a named 55c2a0fb62fb by Unknown Sun Dec 4 23:18:31 2022 [0]PETSC ERROR: Configure options PETSC_ARCH=flow123d_Debug --prefix=/usr/local/petsc_3.17.0 --with-mpi-dir=/usr/local/mpich_3.4.2 --download-metis=yes --download-parmetis=yes --download-blacs=yes --download-scalapack=yes --download-mumps=yes --download-hypre=https://github.com/hypre-space/hypre/archive/v2.24.0.tar.gz --with-debugging=1 --with-shared-libraries=1 --with-make-np 5 --CFLAGS=-O --CXXFLAGS="-O -Wall -Wno-unused-local-typedefs -std=c++11" [0]PETSC ERROR: #1 MatSetValues_SeqAIJ() at /libs-build-gnu/petsc/build_Debug/src/mat/impls/aij/seq/aij.c:478 [0]PETSC ERROR: #2 MatSetValues() at /libs-build-gnu/petsc/build_Debug/src/mat/interface/matrix.c:1343 00:00:53.378 [0] ERROR.-------------------------------------------------------- Program Error: [63] ** Diagnosting info ** /home/jb/workspace/flow123d/src/system/system.hh(144): Throw in function void chkerr(unsigned int) Dynamic exception type: boost::wrapexcept [EI_ErrCode_TAG*] = 63 ** Stacktrace ** 0 _Z6chkerrj 1 _ZN12LinSys_PETSC14mat_set_valuesEiPiiS0_Pd 2 _ZN19StiffnessAssemblyDGILj3E27ConcentrationTransportModelE13edge_integralE12RangeConvertI10DHEdgeSide10DHCellSideE 3 _ZN12AssemblyBaseILj3EE23assemble_edge_integralsERK14RevertableListIN19GenericAssemblyBase16EdgeIntegralDataEE 4 _ZN15GenericAssemblyIN11TransportDGI27ConcentrationTransportModelE20StiffnessAssemblyDimEE18assemble_integralsEv 5 _ZN15GenericAssemblyIN11TransportDGI27ConcentrationTransportModelE20StiffnessAssemblyDimEE8assembleESt10shared_ptrI18DOFHandlerMultiDimE 6 _ZN11TransportDGI27ConcentrationTransportModelE15update_solutionEv 7 _ZN26TransportOperatorSplitting15update_solutionEv 8 _ZN21HC_ExplicitSequential22advection_process_stepERNS_13AdvectionDataE 9 _ZN21HC_ExplicitSequential14run_simulationEv 10 _ZN11Application3runEv 11 main -------------------------------------------------------- + exit 1