Comments (6)
JamesEMcClure
commented on August 20, 2024
Try setting the environment variable export MPI_THREAD_MULTIPLE=1
If that does not work please provide the MPI implementation (e.g. mvapich2 or openmpi) and version so that we can give good advice on how to proceed.
from lbpm.
ahmedsrizk95
commented on August 20, 2024
After setting the environment variable export MPI_THREAD_MULTIPLE=1 it gives this error:
> Program abort called in file '/apps/ku/build/lbpm/lbpm-2020/common/Database.cpp' at line 83:
> Variable FlowAdaptor was not found in database
> Bytes used = 300266512
> Stack Trace:
> [7] 0x00000046f56e: lbpm_color_simulator _start
> [7] 0x00000046eb40: lbpm_color_simulator main lbpm_color_simulator.cpp:112
> [7] 0x00000054ba0f: lbpm_color_simulator ScaLBL_ColorModel::Run(int) basic_string.h:222
> [7] 0x0000005aed7f: lbpm_color_simulator Database::getDatabase(std::string const&) shared_ptr.h:510
> [7] 0x0000005ae2cb: lbpm_color_simulator Database::getData(std::string const&) Database.cpp:83
> [1] 0x000000556696: lbpm_color_simulator StackTrace::Utilities::abort(std::string const&, std::string const&, int) stl_vector.h:108
> | [1] 0x00000055cc51: lbpm_color_simulator StackTrace::backtrace()
> | [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [6] 0x000000553682: lbpm_color_simulator StackTrace::Utilities::terminate(StackTrace::abort_error const&)
> [6] 0x000000555c45: lbpm_color_simulator StackTrace::abort_error::what() const
> [6] 0x00000055ffad: lbpm_color_simulator getRemoteCallStacks()
> [6] 0x147fc0e186bb: libc.so.6 __sched_yield
> [14] 0x14d5ff520dc3: libc.so.6 clone
> [14] 0x14d6000a014a: libpthread.so.0 pthread_create.c
> [7] 0x14d5feb58c94: libopen-pal.so.40 epoll.c:409
> | [7] 0x14d5ff5210f7: libc.so.6 epoll_wait
> | [7] 0x14d6000aab20: libpthread.so.0 sigaction.c
> | [7] 0x00000055a144: lbpm_color_simulator <artificial>
> | [7] 0x00000055a103: lbpm_color_simulator <artificial>
> [7] 0x14d5feb181fe: libopen-pal.so.40 opal_progress_threads.c:104
> [7] 0x14d5feb6553d: libopen-pal.so.40 poll.c:167
> [7] 0x14d5ff515a41: libc.so.6 __poll
> [7] 0x14d6000aab20: libpthread.so.0 sigaction.c
> [7] 0x00000055a144: lbpm_color_simulator <artificial>
> [7] 0x00000055a103: lbpm_color_simulator <artificial>
> Program abort called in file '/apps/ku/build/lbpm/lbpm-2020/common/Database.cpp' at line 83:
> Variable FlowAdaptor was not found in database
> Bytes used = 305164080
> Stack Trace:
> [2] 0x00000046f56e: lbpm_color_simulator _start
> [2] 0x00000046eb40: lbpm_color_simulator main lbpm_color_simulator.cpp:112
> [2] 0x00000054ba0f: lbpm_color_simulator ScaLBL_ColorModel::Run(int) basic_string.h:222
> [2] 0x0000005aed7f: lbpm_color_simulator Database::getDatabase(std::string const&) shared_ptr.h:510
> [2] 0x0000005ae2cb: lbpm_color_simulator Database::getData(std::string const&) Database.cpp:83
> [1] 0x000000556696: lbpm_color_simulator StackTrace::Utilities::abort(std::string const&, std::string const&, int) stl_vector.h:108
> | [1] 0x00000055cc51: lbpm_color_simulator StackTrace::backtrace()
> | [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [1] 0x000000553682: lbpm_color_simulator StackTrace::Utilities::terminate(StackTrace::abort_error const&)
> [1] 0x000000555c45: lbpm_color_simulator StackTrace::abort_error::what() const
> [1] 0x00000055ffad: lbpm_color_simulator getRemoteCallStacks()
> [1] 0x14d5ff5076bb: libc.so.6 __sched_yield
> [4] 0x14b9b7567dc3: libc.so.6 clone
> [4] 0x14b9b80e714a: libpthread.so.0 pthread_create.c
> [2] 0x14b9b6b9fc94: libopen-pal.so.40 epoll.c:409
> | [2] 0x14b9b75680f7: libc.so.6 epoll_wait
> | [2] 0x14b9b80f1b20: libpthread.so.0 sigaction.c
> | [2] 0x00000055a144: lbpm_color_simulator <artificial>
> | [2] 0x00000055a103: lbpm_color_simulator <artificial>
> [2] 0x14b9b6b5f1fe: libopen-pal.so.40 opal_progress_threads.c:104
> [2] 0x14b9b6bac53d: libopen-pal.so.40 poll.c:167
> [2] 0x14b9b755ca41: libc.so.6 __poll
> [2] 0x14b9b80f1b20: libpthread.so.0 sigaction.c
> [2] 0x00000055a144: lbpm_color_simulator <artificial>
> [2] 0x00000055a103: lbpm_color_simulator <artificial>
> Program abort called in file '/apps/ku/build/lbpm/lbpm-2020/common/Database.cpp' at line 83:
> Variable FlowAdaptor was not found in database
> Bytes used = 304768640
> Stack Trace:
> [1] 0x00000046f56e: lbpm_color_simulator _start
> [1] 0x00000046eb40: lbpm_color_simulator main lbpm_color_simulator.cpp:112
> [1] 0x00000054ba0f: lbpm_color_simulator ScaLBL_ColorModel::Run(int) basic_string.h:222
> [1] 0x0000005aed7f: lbpm_color_simulator Database::getDatabase(std::string const&) shared_ptr.h:510
> [1] 0x0000005ae2cb: lbpm_color_simulator Database::getData(std::string const&) Database.cpp:83
> [1] 0x000000556696: lbpm_color_simulator StackTrace::Utilities::abort(std::string const&, std::string const&, int) stl_vector.h:108
> [1] 0x00000055cc51: lbpm_color_simulator StackTrace::backtrace()
> [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [2] 0x14f9b021ddc3: libc.so.6 clone
> [2] 0x14f9b0d9d14a: libpthread.so.0 pthread_create.c
> [1] 0x14f9af855c94: libopen-pal.so.40 epoll.c:409
> | [1] 0x14f9b021e0f7: libc.so.6 epoll_wait
> | [1] 0x14f9b0da7b20: libpthread.so.0 sigaction.c
> | [1] 0x00000055a144: lbpm_color_simulator <artificial>
> | [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [1] 0x14f9af8151fe: libopen-pal.so.40 opal_progress_threads.c:104
> [1] 0x14f9af86253d: libopen-pal.so.40 poll.c:167
> [1] 0x14f9b0212a41: libc.so.6 __poll
> [1] 0x14f9b0da7b20: libpthread.so.0 sigaction.c
> [1] 0x00000055a144: lbpm_color_simulator <artificial>
> [1] 0x00000055a103: lbpm_color_simulator <artificial>
> Program abort called in file '/apps/ku/build/lbpm/lbpm-2020/common/Database.cpp' at line 83:
> Variable FlowAdaptor was not found in database
> Bytes used = 295198464
> Stack Trace:
> [1] 0x00000046f56e: lbpm_color_simulator _start
> [1] 0x00000046eb40: lbpm_color_simulator main lbpm_color_simulator.cpp:112
> [1] 0x00000054ba0f: lbpm_color_simulator ScaLBL_ColorModel::Run(int) basic_string.h:222
> [1] 0x0000005aed7f: lbpm_color_simulator Database::getDatabase(std::string const&) shared_ptr.h:510
> [1] 0x0000005ae2cb: lbpm_color_simulator Database::getData(std::string const&) Database.cpp:83
> [1] 0x000000556696: lbpm_color_simulator StackTrace::Utilities::abort(std::string const&, std::string const&, int) stl_vector.h:108
> [1] 0x00000055cc51: lbpm_color_simulator StackTrace::backtrace()
> [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [2] 0x147fc0e31dc3: libc.so.6 clone
> [2] 0x147fc19b114a: libpthread.so.0 pthread_create.c
> [1] 0x147fc0469c94: libopen-pal.so.40 epoll.c:409
> | [1] 0x147fc0e320f7: libc.so.6 epoll_wait
> | [1] 0x147fc19bbb20: libpthread.so.0 sigaction.c
> | [1] 0x00000055a144: lbpm_color_simulator <artificial>
> | [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [1] 0x147fc04291fe: libopen-pal.so.40 opal_progress_threads.c:104
> [1] 0x147fc047653d: libopen-pal.so.40 poll.c:167
> [1] 0x147fc0e26a41: libc.so.6 __poll
> [1] 0x147fc19bbb20: libpthread.so.0 sigaction.c
> [1] 0x00000055a144: lbpm_color_simulator <artificial>
> [1] 0x00000055a103: lbpm_color_simulator <artificial>
> Program abort called in file '/apps/ku/build/lbpm/lbpm-2020/common/Database.cpp' at line 83:
> Variable FlowAdaptor was not found in database
> Bytes used = 301353328
> Stack Trace:
> [1] 0x00000046f56e: lbpm_color_simulator _start
> [1] 0x00000046eb40: lbpm_color_simulator main lbpm_color_simulator.cpp:112
> [1] 0x00000054ba0f: lbpm_color_simulator ScaLBL_ColorModel::Run(int) basic_string.h:222
> [1] 0x0000005aed7f: lbpm_color_simulator Database::getDatabase(std::string const&) shared_ptr.h:510
> [1] 0x0000005ae2cb: lbpm_color_simulator Database::getData(std::string const&) Database.cpp:83
> [1] 0x000000556696: lbpm_color_simulator StackTrace::Utilities::abort(std::string const&, std::string const&, int) stl_vector.h:108
> [1] 0x00000055cc51: lbpm_color_simulator StackTrace::backtrace()
> [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [2] 0x14a21b475dc3: libc.so.6 clone
> [2] 0x14a21bff514a: libpthread.so.0 pthread_create.c
> [1] 0x14a21aaadc94: libopen-pal.so.40 epoll.c:409
> | [1] 0x14a21b4760f7: libc.so.6 epoll_wait
> | [1] 0x14a21bfffb20: libpthread.so.0 sigaction.c
> | [1] 0x00000055a144: lbpm_color_simulator <artificial>
> | [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [1] 0x14a21aa6d1fe: libopen-pal.so.40 opal_progress_threads.c:104
> [1] 0x14a21aaba53d: libopen-pal.so.40 poll.c:167
> [1] 0x14a21b46aa41: libc.so.6 __poll
> [1] 0x14a21bfffb20: libpthread.so.0 sigaction.c
> [1] 0x00000055a144: lbpm_color_simulator <artificial>
> [1] 0x00000055a103: lbpm_color_simulator <artificial>
> Program abort called in file '/apps/ku/build/lbpm/lbpm-2020/common/Database.cpp' at line 83:
> Variable FlowAdaptor was not found in database
> Bytes used = 284188736
> Stack Trace:
> [1] 0x00000046f56e: lbpm_color_simulator _start
> [1] 0x00000046eb40: lbpm_color_simulator main lbpm_color_simulator.cpp:112
> [1] 0x00000054ba0f: lbpm_color_simulator ScaLBL_ColorModel::Run(int) basic_string.h:222
> [1] 0x0000005aed7f: lbpm_color_simulator Database::getDatabase(std::string const&) shared_ptr.h:510
> [1] 0x0000005ae2cb: lbpm_color_simulator Database::getData(std::string const&) Database.cpp:83
> [1] 0x000000556696: lbpm_color_simulator StackTrace::Utilities::abort(std::string const&, std::string const&, int) stl_vector.h:108
> [1] 0x00000055cc51: lbpm_color_simulator StackTrace::backtrace()
> [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [2] 0x1545c9238dc3: libc.so.6 clone
> [2] 0x1545c9db814a: libpthread.so.0 pthread_create.c
> [1] 0x1545c8870c94: libopen-pal.so.40 epoll.c:409
> | [1] 0x1545c92390f7: libc.so.6 epoll_wait
> | [1] 0x1545c9dc2b20: libpthread.so.0 sigaction.c
> | [1] 0x00000055a144: lbpm_color_simulator <artificial>
> | [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [1] 0x1545c88301fe: libopen-pal.so.40 opal_progress_threads.c:104
> [1] 0x1545c887d53d: libopen-pal.so.40 poll.c:167
> [1] 0x1545c922da41: libc.so.6 __poll
> [1] 0x1545c9dc2b20: libpthread.so.0 sigaction.c
> [1] 0x00000055a144: lbpm_color_simulator <artificial>
> [1] 0x00000055a103: lbpm_color_simulator <artificial>
> Program abort called in file '/apps/ku/build/lbpm/lbpm-2020/common/Database.cpp' at line 83:
> Variable FlowAdaptor was not found in database
> Bytes used = 271527168
> Stack Trace:
> [1] 0x00000046f56e: lbpm_color_simulator _start
> [1] 0x00000046eb40: lbpm_color_simulator main lbpm_color_simulator.cpp:112
> [1] 0x00000054ba0f: lbpm_color_simulator ScaLBL_ColorModel::Run(int) basic_string.h:222
> [1] 0x0000005aed7f: lbpm_color_simulator Database::getDatabase(std::string const&) shared_ptr.h:510
> [1] 0x0000005ae2cb: lbpm_color_simulator Database::getData(std::string const&) Database.cpp:83
> [1] 0x000000556696: lbpm_color_simulator StackTrace::Utilities::abort(std::string const&, std::string const&, int) stl_vector.h:108
> [1] 0x00000055cc51: lbpm_color_simulator StackTrace::backtrace()
> [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [2] 0x14b183224dc3: libc.so.6 clone
> [2] 0x14b183da414a: libpthread.so.0 pthread_create.c
> [1] 0x14b18285cc94: libopen-pal.so.40 epoll.c:409
> | [1] 0x14b1832250f7: libc.so.6 epoll_wait
> | [1] 0x14b183daeb20: libpthread.so.0 sigaction.c
> | [1] 0x00000055a144: lbpm_color_simulator <artificial>
> | [1] 0x00000055a103: lbpm_color_simulator <artificial>
> [1] 0x14b18281c1fe: libopen-pal.so.40 opal_progress_threads.c:104
> [1] 0x14b18286953d: libopen-pal.so.40 poll.c:167
> [1] 0x14b183219a41: libc.so.6 __poll
> [1] 0x14b183daeb20: libpthread.so.0 sigaction.c
> [1] 0x00000055a144: lbpm_color_simulator <artificial>
> [1] 0x00000055a103: lbpm_color_simulator <artificial>
> --------------------------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun noticed that process rank 5 with PID 846076 on node cn-02-52 exited on signal 6 (Aborted).
> --------------------------------------------------------------------------
>
Regarding the Openmpi, we installed it with OpenHPC package, version is mpirun (Open MPI) 4.0.5 compiled with gcc-9.3
from lbpm.
JamesEMcClure
commented on August 20, 2024
Add the following to your input database
FlowAdaptor {
}
from lbpm.
ahmedsrizk95
commented on August 20, 2024
Noted and worked. Thanks.
But why this did not happen with me before. I was able to run the lbpm_color_simulator without this FlowAdaptor?
from lbpm.
JamesEMcClure
commented on August 20, 2024
We added new functionality that requires a new section in the input database. There are keys that can be populated within this section to control the behavior.
Basically the FlowAdaptor provides a way to dynamically adapt the fluid geometry so that you can more easily change the fluid saturation during steady-state flow.
from lbpm.
ahmedsrizk95
commented on August 20, 2024
Thank you very much. The issue is now solved, I will close it. Thank you again.
from lbpm.
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