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Finite area method (fac::div) fails in parallel |
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October 24, 2012, 09:01 |
Finite area method (fac::div) fails in parallel
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#1 |
New Member
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Hi everyone,
I am a new foam user and working on a modified version of pimpleDyMFoam utilized with a k-omega model in 1.6-ext. The problem is the code works fine for serial runs but stops working in parallel when it comes to line-3: Code:
1- var0.boundaryField()[PAtchID] = U.boundaryField()[PAtchID]; 2- var1.internalField() = vsm.mapToSurface(var0.boundaryField()); 3- areaScalarField var2 = - fac::div(var1); The error message in parallel (where export FOAM_ABORT=1 mpirun --mca orte_base_help_aggregate 0 -d -np 4 pimpleDyMFoam -parallel > log ) is given below: Code:
[n-62-24-13:13854] *** An error occurred in MPI_Recv [n-62-24-13:13854] *** on communicator MPI_COMM_WORLD [n-62-24-13:13854] *** MPI_ERR_TRUNCATE: message truncated [n-62-24-13:13854] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) [n-62-24-13:13854] sess_dir_finalize: proc session dir not empty - leaving [n-62-24-13:13853] sess_dir_finalize: proc session dir not empty - leaving -------------------------------------------------------------------------- mpirun has exited due to process rank 0 with PID 13854 on node n-62-24-13 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- [n-62-24-13:13853] sess_dir_finalize: job session dir not empty - leaving [n-62-24-13:13853] sess_dir_finalize: proc session dir not empty - leaving orterun: exiting with status 15 In the meantime, I have tried different div schemes (in faSchemes file) changing the line Code:
default Gauss linear; What might be the problem? How can I debug more and find the error? Any comments and advices ? Thanks in advance |
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October 25, 2012, 12:25 |
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#2 |
Senior Member
Kyle Mooney
Join Date: Jul 2009
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Have you tried compiling and running in debug? I've had pretty good luck with mpirunDebug when it comes to parallel debugging.
I use the finite area library in parallel but unfortunately I do not use that operator. |
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October 25, 2012, 12:32 |
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#3 |
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Thanks for the reply
I thought that adding "-d" in the mpirun would be enough to debug, but apparently did help at all. Should I compile the program first in a way that it can be debugged in parallel ? and how can I do that? |
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October 25, 2012, 12:46 |
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#4 | |
Senior Member
Kyle Mooney
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Quote:
Yep, recompile with the debug compiler option set. Set this option by running this in the shell: Code:
export WM_COMPILE_OPTION=Debug You might need to install mpirunDebug from your linux software repository. I don't think it comes with the standard MPI package. |
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October 25, 2012, 12:58 |
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#5 |
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Thanks for the replies, I will be working on that
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October 29, 2012, 10:09 |
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#6 |
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I have re-compiled my code entering the "export WM_COMPILE_OPTION=Debug" to the terminal first. It gave me the below given message.
-------------------------- g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O0 -fdefault-inline -ggdb3 -DFULLDEBUG -DNoRepository -ftemplate-depth-40 -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/dynamicMesh/dynamicFvMesh/lnInclude -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/dynamicMesh/dynamicMesh/lnInclude -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/meshTools/lnInclude -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/turbulenceModels -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/transportModels -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/transportModels/incompressible/singlePhaseTransportModel -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/finiteArea/lnInclude -DFACE_DECOMP -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/tetDecompositionFiniteElement/lnInclude -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/tetDecompositionMotionSolver/lnInclude -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/finiteVolume/lnInclude -IlnInclude -I. -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/OpenFOAM/lnInclude -I/appl/OpenFOAM/OpenFOAM-1.6-ext/src/OSspecific/POSIX/lnInclude -fPIC -Xlinker --add-needed Make/linux64GccDPOpt/pimpleDyMFoam.o -L/appl/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt \ -ldynamicFvMesh -ltopoChangerFvMesh -ldynamicMesh -lmeshTools -lincompressibleTransportModels -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteArea -lfiniteVolume -llduSolvers -lOpenFOAM -liberty -ldl -ggdb3 -DFULLDEBUG -lm -o /zhome/83/d/74221/OpenFOAM/cuba-1.6-ext/applications/bin/linux64GccDPOpt/pimpleDyMFoam ------------------------------- later I decomposed my domain and entered mpirunDebug -np 4 pimpleDyMFoam -parallel later I have selected Choose running method: 0)normal 1)gdb+xterm 2)gdb 3)log 4)log+xterm 5)xterm+valgrind 6)nemiver: 1 Run all processes local or distributed? 1)local 2)remote: 2 It produced gdbCommands, mpirun.schema, processor0.sh, processor1.sh, processor2.sh and processor3.sh files. How can I start the runs per each processor? If I just type processor0.sh to the terminal, I get the following in the processor0.log file and terminal. ----------------------- GNU gdb (GDB) Red Hat Enterprise Linux (7.2-48.el6) Copyright (C) 2010 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-redhat-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... Reading symbols from /zhome/83/d/74221/OpenFOAM/cuba-1.6-ext/applications/bin/linux64GccDPOpt/pimpleDyMFoam...(no debugging symbols found)...done. [Thread debugging using libthread_db enabled] Detaching after fork from child process 22079. [New Thread 0x7fffee345700 (LWP 22083)] [Thread 0x7fffee345700 (LWP 22083) exited] --> FOAM FATAL ERROR: bool Pstream::init(int& argc, char**& argv) : attempt to run parallel on 1 processor From function Pstream::init(int& argc, char**& argv) in file Pstream.C at line 74. FOAM aborting Program received signal SIGABRT, Aborted. 0x00000030f8232885 in raise () from /lib64/libc.so.6 #0 0x00000030f8232885 in raise () from /lib64/libc.so.6 #1 0x00000030f8234065 in abort () from /lib64/libc.so.6 #2 0x00007ffff448d28b in Foam::error::abort() () from /appl/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt/libOpenFOAM.so #3 0x00007ffff3b781da in Foam::Pstream::init(int&, char**&) () from /appl/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt/openmpi-system/libPstream.so #4 0x00007ffff449a655 in Foam::argList::argList(int&, char**&, bool, bool) () from /appl/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt/libOpenFOAM.so #5 0x00000000004252b3 in main () Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.47.el6_2.5.x86_64 libgcc-4.4.5-6.el6.x86_64 libibverbs-1.1.4-2.el6.x86_64 librdmacm-1.0.10-2.el6.x86_64 libstdc++-4.4.5-6.el6.x86_64 zlib-1.2.3-25.el6.x86_64 [?1034h(gdb) -------------------------------- Could anyone give me more information on how to use mpirunDebug? |
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November 1, 2012, 04:40 |
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#7 |
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Hi everyone,
I could not make a progress on mpirun debugging yet but I have another question. How can I make the processors synchronized before evaluating the line ? Code:
3- areaScalarField var2 = - fac::div(var1); |
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November 8, 2012, 11:14 |
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#8 |
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Anyone knows how to make the processors wait for each other before evaluating some piece of code as above ?
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November 10, 2012, 05:36 |
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#9 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
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Greetings Cuba,
In reply to your last post and PM you sent me:
Bruno
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November 15, 2012, 08:03 |
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#10 |
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Thanks for the reply wyldckat
It did help me to have a better understanding about Pstream commands. I finally solved (at least I got around it) my problem. My problem was briefly ... one of subdomains was entering the routine while others were not as the condition defined to enter the routine was not true for them. In the mean time, to find the maximum value of a variable defined on a patch over all the subdomains, I have tried both gMax(var) and max(reduce(var, maxOp<scalarField>)) commands. But the one found by the gMax was not the maximum and was actually smaller than the one found by the reduce command. Anyone noticed such a thing before? Thanks again for the replies |
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November 20, 2012, 08:03 |
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#11 | |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
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Hi Cuba,
Quote:
By the way, the maximum reported value, which one was actually correct? Because it's also possible that one of them was actually picking up an outdated value! For example, one of them might be picking up a value that was communicated between processes at the beginning of the iterations, but the maximum value was calculated only after those iterations, and since it was located between processes, the value is no longer up-to-date... Best regards, Bruno
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